diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
index d525c6bfe8..cecd981223 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
@@ -30,7 +30,7 @@
 /**
  * This class is used to support the implementation of properties stated in IPeptideProperties.
  * It initializes several values that would be needed for the computation of properties such as
- * <p/>
+ * <p>
  * Molecular weight<br/>
  * Instability index<br/>
  * Hydropathy value<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
index e90e7bd568..5342013b61 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
@@ -35,7 +35,7 @@
 /**
  * An interface to generate some basic physico-chemical properties of protein sequences.<br/>
  * The following properties could be generated:
- * <p/>
+ * <p>
  * Molecular weight<br/>
  * Absorbance<br/>
  * Extinction coefficient<br/>
@@ -258,7 +258,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
 	 * Returns the net charge of sequence at pH 7. The sequence argument must be
 	 * a protein sequence consisting of only non-ambiguous characters.
 	 * The net charge will be computed using the approach stated in
-	 * <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge>here</a>
+	 * <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge">here</a>
 	 *
 	 * pKa values used will be either
 	 * those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539"
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
index 0fab96f94a..7f39fff79e 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
@@ -28,7 +28,7 @@ public interface IProfeatProperties {
 	/**
 	 * Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf<br/>
 	 * An interface class to generate the properties of a protein sequence based on its converted attributes.<br/>
-	 * The seven different attributes are<p/>
+	 * The seven different attributes are<p>
 	 * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
 	 * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
 	 * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
@@ -103,8 +103,8 @@ public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
 	 * Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.<br/>
 	 * Example: "1111122222"<br/>
 	 * For the above example,<br/>
-	 * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
-	 * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
+	 * position of the GROUPING.GROUP1 &amp; DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
+	 * position of the GROUPING.GROUP1 &amp; DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
 	 *
 	 * @param sequence
 	 * 	a protein sequence consisting of non-ambiguous characters only
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
index d8844476f4..dd0d310439 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
@@ -119,8 +119,8 @@ public static Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(String seque
 	 * An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.<br/>
 	 * Example: "1111122222"<br/>
 	 * For the above example,<br/>
-	 * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
-	 * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
+	 * position of the GROUPING.GROUP1 &amp; DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
+	 * position of the GROUPING.GROUP1 &amp; DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
 	 *
 	 * @param sequence
 	 * 	a protein sequence consisting of non-ambiguous characters only
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
index a88d93add3..e298ab2520 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
@@ -28,7 +28,7 @@ public abstract class Convertor {
 	/**
 	 * Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf<br/>
 	 * An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.<br/>
-	 * The seven different attributes are<p/>
+	 * The seven different attributes are<p>
 	 * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
 	 * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
 	 * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
index 22143b53cb..a28076aa41 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
@@ -20,7 +20,7 @@
  */
 /**
  * Set of classes that enable the conversion protein sequences into various attributes.
- * The seven different attributes are<p/>
+ * The seven different attributes are<p>
  * Hydrophobicity (Polar, Neutral, Hydrophobicity)<br/>
  * Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)<br/>
  * Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)<br/>
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
index 6cc2eb3f35..b389504826 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
@@ -122,7 +122,7 @@ private Alignments() { }
 	 * {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param sequences the {@link List} of {@link Sequence}s to align
 	 * @param type chosen type from list of pairwise sequence alignment routines
 	 * @param gapPenalty the gap penalties used during alignment
@@ -203,7 +203,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getMulti
 	 * Factory method which computes a sequence alignment for the given {@link Sequence} pair.
 	 *
 	 * @param <S> each {@link Sequence} of the pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param query the first {@link Sequence}s to align
 	 * @param target the second {@link Sequence}s to align
 	 * @param type chosen type from list of pairwise sequence alignment routines
@@ -223,7 +223,7 @@ public static <S extends Sequence<C>, C extends Compound> SequencePair<S, C> get
 	 * Factory method which sets up a sequence alignment for all {@link Sequence} pairs in the given {@link List}.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param sequences the {@link List} of {@link Sequence}s to align
 	 * @param type chosen type from list of pairwise sequence alignment routines
 	 * @param gapPenalty the gap penalties used during alignment
@@ -309,7 +309,7 @@ static <E> List<E> getListFromFutures(List<Future<E>> futures) {
 	 * Factory method which constructs a pairwise sequence aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param query the first {@link Sequence} to align
 	 * @param target the second {@link Sequence} to align
 	 * @param type chosen type from list of pairwise sequence alignment routines
@@ -399,7 +399,7 @@ static <S extends Sequence<C>, C extends Compound> PairwiseSequenceScorer<S, C>
 	 * Factory method which constructs a profile-profile aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment profile is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -429,7 +429,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 	 * Factory method which constructs a profile-profile aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment profile is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -459,7 +459,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 	 * Factory method which constructs a profile-profile aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment profile is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -489,7 +489,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 	 * Factory method which constructs a profile-profile aligner.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment profile is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -519,7 +519,7 @@ static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> g
 	 * Factory method which computes a profile alignment for the given {@link Profile} pair.
 	 *
 	 * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param profile1 the first {@link Profile} to align
 	 * @param profile2 the second {@link Profile} to align
 	 * @param type chosen type from list of profile-profile alignment routines
@@ -539,7 +539,7 @@ static <S extends Sequence<C>, C extends Compound> ProfilePair<S, C> getProfileP
 	 * of the {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param tree guide tree to follow aligning profiles from leaves to root
 	 * @param type chosen type from list of profile-profile alignment routines
 	 * @param gapPenalty the gap penalties used during alignment
@@ -592,7 +592,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getProgr
 	 * submitting all of the alignment tasks to the shared thread pool of the {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param aligners list of alignments to run
 	 * @return list of {@link SequencePair} results from running alignments
 	 */
@@ -612,7 +612,7 @@ public static <S extends Sequence<C>, C extends Compound> Profile<S, C> getProgr
 	 * all of the scoring tasks to the shared thread pool of the {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of an alignment pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param scorers list of scorers to run
 	 * @return list of score results from running scorers
 	 */
@@ -637,7 +637,7 @@ public static <S extends Sequence<C>, C extends Compound> double[] runPairwiseSc
 	 * submitting all of the alignment tasks to the shared thread pool of the {@link ConcurrencyTools} utility.
 	 *
 	 * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
-	 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+	 * @param <C> each element of a sequence is a {@link Compound} of type C
 	 * @param aligners list of alignments to run
 	 * @return list of {@link ProfilePair} results from running alignments
 	 */
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
index 4b494db779..d66105681d 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalIdentityScorer.java
@@ -34,7 +34,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class FractionalIdentityScorer<S extends Sequence<C>, C extends Compound> extends AbstractScorer
 		implements PairwiseSequenceScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
index 05911367f8..e9581f1f96 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/FractionalSimilarityScorer.java
@@ -34,7 +34,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class FractionalSimilarityScorer<S extends Sequence<C>, C extends Compound> extends AbstractScorer
 		implements PairwiseSequenceScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
index 47fb7976e0..ff94041bb8 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleProfileProfileAligner.java
@@ -41,7 +41,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class SimpleProfileProfileAligner<S extends Sequence<C>, C extends Compound>
 		extends AbstractProfileProfileAligner<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
index f0ca2bfa23..5b7ff9899b 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmFileAnnotation.java
@@ -160,7 +160,7 @@ public void setDbReferences(Set<DatabaseReference> dbReferences) {
 		this.dbReferences = dbReferences;
 	}
 	/**
-	 * @param dbReference the string without the initial annotation identifier ( #=GS DR )
+	 * @param dbReferenceRepresentingString the string without the initial annotation identifier ( #=GS DR )
 	 */
 	public void addDBReference(String dbReferenceRepresentingString) {
 		if (this.dbReferences == null) {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
index d95a2bfa97..a70e751df5 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/io/StockholmStructure.java
@@ -38,7 +38,8 @@
  * In general, Stockholm File contains the alignment mark-up lines.<br>
  * <br>
  *
- * <Table border="1" align="center">
+ * <table>
+ * <caption></caption>
  * <tr>
  * <td><b>Header Section</b></td>
  * </tr>
@@ -56,18 +57,24 @@
  * Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-".<br>
  * Mark-up lines may include any characters except whitespace. Use underscore ("_") instead of space.<br>
  *
- * <Table border="1">
+ * <table>
+ * <caption></caption>
+ * <tr>
  * <th>section field</th>
  * <th>preferred location</th>
+ * </tr>
  * <tr>
  * <td>#=GF &lt;feature&gt; &lt;Generic per-File annotation, free text&gt;</td>
  * <td>Above the alignment</td>
+ * </tr>
  * <tr>
  * <td>#=GC &lt;feature&gt; &lt;Generic per-Column annotation, exactly 1 char per column&gt;</td>
  * <td>Below the alignment</td>
+ * </tr>
  * <tr>
  * <td>#=GS &lt;seqname&gt; &lt;feature&gt; &lt;Generic per-Sequence annotation, free text&gt;</td>
  * <td>Above the alignment or just below the corresponding sequence</td>
+ * </tr>
  * <tr>
  * <td>#=GR &lt;seqname&gt; &lt;feature&gt; &lt;Generic per-Residue annotation, exactly 1 char per residue&gt;</td>
  * <td>Just below the corresponding sequence</td>
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
index 95d5264f1e..8533ecc91e 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java
@@ -42,7 +42,7 @@
  * will connect the query sequence to the target sequence at the <em>anchors</em>.  This class performs such global
  * sequence comparisons efficiently by dynamic programming with a space requirement reduced from quadratic (a multiple
  * of query sequence length times target sequence length) to only linear (a multiple of query sequence length).  The
- * counterpoint to this reduction in space complexity is a modest (a multiple < 2) increase in time.
+ * counterpoint to this reduction in space complexity is a modest (a multiple &lt; 2) increase in time.
  *
  * @author Mark Chapman
  * @author Daniel Cameron
@@ -67,7 +67,6 @@ public AnchoredPairwiseSequenceAligner() {
 	 * @param target the second {@link Sequence} of the pair to align
 	 * @param gapPenalty the gap penalties used during alignment
 	 * @param subMatrix the set of substitution scores used during alignment
-	 * @param cutsPerSection the number of cuts added to each section during each pass
 	 */
 	public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) {
 		this(query, target, gapPenalty, subMatrix, null);
@@ -80,7 +79,6 @@ public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty,
 	 * @param target the second {@link Sequence} of the pair to align
 	 * @param gapPenalty the gap penalties used during alignment
 	 * @param subMatrix the set of substitution scores used during alignment
-	 * @param cutsPerSection the number of cuts added to each section during each pass
 	 * @param anchors the initial list of anchors
 	 */
 	public AnchoredPairwiseSequenceAligner(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix, int[] anchors) {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
index 3ff44d8a8c..7e2d739db9 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/GuanUberbacher.java
@@ -34,7 +34,7 @@
  * {@link Compound} of each {@link Sequence}).  This class performs such global sequence comparisons efficiently by
  * dynamic programming with a space requirement reduced from quadratic (a multiple of query sequence length times
  * target sequence length) to only linear (a multiple of query sequence length).  The counterpoint to this reduction in
- * space complexity is a modest (a multiple < 2) increase in time.
+ * space complexity is a modest (a multiple &lt; 2) increase in time.
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
index 19fcc9c98f..1ea2e0de81 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java
@@ -46,7 +46,7 @@
  * @author Mark Chapman
  * @author Daniel Cameron
  * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public abstract class AbstractMatrixAligner<S extends Sequence<C>, C extends Compound> extends AbstractScorer
 		implements MatrixAligner<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
index 8c86470608..699ff77d36 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java
@@ -37,7 +37,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public abstract class AbstractPairwiseSequenceAligner<S extends Sequence<C>, C extends Compound>
 		extends AbstractMatrixAligner<S, C> implements PairwiseSequenceAligner<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
index 01cba48463..140627de9c 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java
@@ -43,7 +43,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public abstract class AbstractProfileProfileAligner<S extends Sequence<C>, C extends Compound>
 		extends AbstractMatrixAligner<S, C> implements ProfileProfileAligner<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java
index 75ec8b4df8..76e735c031 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/Aligner.java
@@ -32,7 +32,7 @@
  *
  * @author Mark Chapman
  * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface Aligner<S extends Sequence<C>, C extends Compound> extends Scorer {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
index e1c4616620..7201513800 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java
@@ -34,7 +34,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class CallablePairwiseSequenceAligner<S extends Sequence<C>, C extends Compound>
 		implements Callable<SequencePair<S, C>> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
index 063426a91a..042138f144 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/CallableProfileProfileAligner.java
@@ -33,8 +33,8 @@
  * Implements a concurrency wrapper for a {@link ProfileProfileAligner}.
  *
  * @author Mark Chapman
- * @param <S> each {@link Sequence} of the {@link Profile} pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each {@link Sequence} of the profile pair is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public class CallableProfileProfileAligner<S extends Sequence<C>, C extends Compound>
 		implements Callable<ProfilePair<S, C>> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java
index 87f9f504ce..dd8e38ceeb 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/MatrixAligner.java
@@ -30,8 +30,8 @@
  * Defines an {@link Aligner} which builds a score matrix during computation.
  *
  * @author Mark Chapman
- * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each element of the alignment profile is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface MatrixAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C> {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java
index 094a18bead..4166bcfef4 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairInProfileScorer.java
@@ -32,7 +32,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface PairInProfileScorer<S extends Sequence<C>, C extends Compound> extends PairwiseSequenceScorer<S, C> {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java
index 696ff6ecd8..960c3a527b 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PairwiseSequenceAligner.java
@@ -32,7 +32,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} of the alignment pair is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface PairwiseSequenceAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
 		PairwiseSequenceScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java
index 573944b413..124f2ff132 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/PartitionRefiner.java
@@ -28,11 +28,11 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- * Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
+ * Defines an algorithm which computes a new alignment profile by splitting a current alignment and realigning.
  *
  * @author Mark Chapman
- * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each element of the alignment profile is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface PartitionRefiner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
 		ProfileProfileScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java
index 6df23e0909..1e6fe7cccf 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileAligner.java
@@ -28,11 +28,11 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- * Defines an {@link Aligner} for a pair of {@link Profile}s.
+ * Defines an {@link Aligner} for a pair of profiles.
  *
  * @author Mark Chapman
- * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each {@link Sequence} in the pair of alignment profiles is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface ProfileProfileAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
 		ProfileProfileScorer<S, C> {
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java
index 1d114841ee..c525b9c75a 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/ProfileProfileScorer.java
@@ -32,7 +32,7 @@
  *
  * @author Mark Chapman
  * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface ProfileProfileScorer<S extends Sequence<C>, C extends Compound> extends Scorer {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java
index dba02a028c..f93c000380 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/RescoreRefiner.java
@@ -29,12 +29,12 @@
 import org.biojava.nbio.core.sequence.template.Sequence;
 
 /**
- * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
+ * Defines an algorithm which computes a new alignment profile by rescoring all pairs in an alignment and
  * realigning.
  *
  * @author Mark Chapman
- * @param <S> each element of the alignment {@link Profile} is of type S
- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> each element of the alignment profile is of type S
+ * @param <C> each element of a sequence is a {@link Compound} of type C
  */
 public interface RescoreRefiner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C> {
 
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
index dc8ead79a7..9cae7734cb 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/Comparison.java
@@ -38,9 +38,9 @@ public class Comparison {
 	/**
 	 * this is a gapped PID calculation
 	 *
-	 * @param s1
+	 * @param seq1
 	 *            SequenceI
-	 * @param s2
+	 * @param seq2
 	 *            SequenceI
 	 * @return float
 	 */
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
index d0464bae8b..922f301a8c 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/phylo/DistanceMatrixCalculator.java
@@ -54,9 +54,9 @@ private DistanceMatrixCalculator() {}
 	 * that differ between two aligned sequences. The percentage of identity
 	 * (PID) is the fraction of identical sites between two aligned sequences.
 	 *
-	 * <pre>
+	 * <code>
 	 * D = 1 - PID
-	 * </pre>
+	 * </code>
 	 *
 	 * The gapped positons in the alignment are ignored in the calculation. This
 	 * method is a wrapper to the forester implementation of the calculation:
@@ -65,7 +65,7 @@ private DistanceMatrixCalculator() {}
 	 * @param msa
 	 *            MultipleSequenceAlignment
 	 * @return DistanceMatrix
-	 * @throws Exception
+	 * @throws IOException
 	 */
 	public static <C extends Sequence<D>, D extends Compound> DistanceMatrix fractionalDissimilarity(
 			MultipleSequenceAlignment<C, D> msa) throws IOException {
@@ -81,9 +81,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix fractio
 	 * The Poisson (correction) evolutionary distance (d) is a function of the
 	 * fractional dissimilarity (D), given by:
 	 *
-	 * <pre>
+	 * <code>
 	 * d = -log(1 - D)
-	 * </pre>
+	 * </code>
 	 *
 	 * The gapped positons in the alignment are ignored in the calculation. This
 	 * method is a wrapper to the forester implementation of the calculation:
@@ -109,14 +109,14 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix poisson
 	 * dissimilarity (D) specially needed for large evolutionary distances. It
 	 * is given by:
 	 *
-	 * <pre>
+	 * <code>
 	 * d = -log(1 - D - 0.2 * D<sup>2</sup>)
-	 * </pre>
+	 * </code>
 	 *
 	 * The equation is derived by fitting the relationship between the
 	 * evolutionary distance (d) and the fractional dissimilarity (D) according
 	 * to the PAM model of evolution (it is an empirical approximation for the
-	 * method {@link #pamDistance(MultipleSequenceAlignment}). The gapped
+	 * method {@link #pamMLdistance(MultipleSequenceAlignment)}). The gapped
 	 * positons in the alignment are ignored in the calculation. This method is
 	 * a wrapper to the forester implementation of the calculation:
 	 * {@link PairwiseDistanceCalculator#calcKimuraDistances(Msa)}.
@@ -190,9 +190,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix percent
 	 * The fractional dissimilarity score (Ds) is a relative measure of the
 	 * dissimilarity between two aligned sequences. It is calculated as:
 	 *
-	 * <pre>
+	 * <code>
 	 * Ds = sum( max(M) - M<sub>ai,bi</sub> ) / (max(M)-min(M)) ) / L
-	 * </pre>
+	 * </code>
 	 *
 	 * Where the sum through i runs for all the alignment positions, ai and bi
 	 * are the AA at position i in the first and second aligned sequences,
@@ -270,9 +270,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix fractio
 	 * maximum similarity score between self-alignments (each sequence against
 	 * itself). Calculation of the score is as follows:
 	 *
-	 * <pre>
+	 * <code>
 	 * Ds = maxScore - sum<sub>i</sub>(M<sub>ai,bi</sub>)
-	 * </pre>
+	 * </code>
 	 *
 	 * It is recommended to use the method
 	 * {@link #fractionalDissimilarityScore(MultipleSequenceAlignment, SubstitutionMatrix)}
@@ -362,9 +362,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi
 	 * substitution rate of 1% per site. The fractional dissimilarity (D) of two
 	 * aligned sequences is related with the PAM distance (d) by the equation:
 	 *
-	 * <pre>
+	 * <code>
 	 * D = sum(fi * (1 - M<sub>ii</sub><sup>d</sup>))
-	 * </pre>
+	 * </code>
 	 *
 	 * Where the sum is for all 20 AA, fi denotes the natural fraction of the
 	 * given AA and M is the substitution matrix (in this case the PAM1 matrix).
@@ -373,9 +373,9 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix dissimi
 	 * likelihood (ML) approach is used, which consists in finding d that
 	 * maximazies the function:
 	 *
-	 * <pre>
+	 * <code>
 	 * L(d) = product(f<sub>ai</sub> * (1 - M<sub>ai,bi</sub><sup>d</sup>))
-	 * </pre>
+	 * </code>
 	 *
 	 * Where the product is for every position i in the alignment, and ai and bi
 	 * are the AA at position i in the first and second aligned sequences,
@@ -400,11 +400,11 @@ public static <C extends Sequence<D>, D extends Compound> DistanceMatrix pamMLdi
 	 * strutures. It is based on the diffusive model for protein fold evolution
 	 * (Grishin 1995). The structural deviations are captured as RMS deviations.
 	 *
-	 * <pre>
+	 * <code>
 	 * d<sub>Sij</sub> = (rmsd<sub>max</sub><sup>2</sup> / alpha<sup>2</sup>) *
 	 *        ln( (rmsd<sub>max</sub><sup>2</sup> - rmsd<sub>0</sub><sup>2</sup>) /
 	 *        (rmsd<sub>max</sub><sup>2</sup> - (rmsd<sub>ij</sub><sup>2</sup>) )
-	 * </pre>
+	 * </code>
 	 *
 	 * @param rmsdMat
 	 *            RMSD matrix for all structure pairs (symmetric matrix)
diff --git a/biojava-core/src/main/java/demo/UncompressFile.java b/biojava-core/src/main/java/demo/UncompressFile.java
index bd36ee5983..7258d6d18b 100644
--- a/biojava-core/src/main/java/demo/UncompressFile.java
+++ b/biojava-core/src/main/java/demo/UncompressFile.java
@@ -38,7 +38,7 @@ public class UncompressFile {
 	 * Reads a file, uncompresses it, and sends the result to stdout.
 	 * Also writes trivial statistics to stderr.
 	 * @param args An array with one String element, the name of the file to read.
-	 * @throws IOException for any failure
+	 * @throws Exception for any failure
 	 */
 	public static void main(String[] args) throws Exception {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
index 85d0a03c26..331480bbef 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
@@ -44,6 +44,7 @@
  *
  * @author Mark Chapman
  * @param <C> each element of the {@link Sequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> implements Serializable, AlignedSequence<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
index 4b853fcb37..7cfdb7dedc 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java
@@ -159,7 +159,7 @@ protected SimpleProfile(Profile<S, C> query, Profile<S, C> target, List<Step> sx
 	 /**
 	 * Creates a profile for the already aligned sequences.
 	 * @param alignedSequences the already aligned sequences
-	 * @throws IllegalArgument if aligned sequences differ in length or
+	 * @throws IllegalArgumentException if aligned sequences differ in length or
 	 * collection is empty.
 	 */
 	public SimpleProfile(Collection<AlignedSequence<S,C>> alignedSequences) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
index 3f55a3897a..ab737b536e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
@@ -78,7 +78,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getIdentity() {
 	}
 
 	/**
-	 * Returns Blosum 100 matrix by Henikoff & Henikoff
+	 * Returns Blosum 100 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 100 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum100() {
@@ -86,7 +86,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum100() {
 	}
 
 	/**
-	 * Returns Blosum 30 matrix by Henikoff & Henikoff
+	 * Returns Blosum 30 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 30 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum30() {
@@ -94,7 +94,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum30() {
 	}
 
 	/**
-	 * Returns Blosum 35 matrix by Henikoff & Henikoff
+	 * Returns Blosum 35 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 35 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum35() {
@@ -102,7 +102,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum35() {
 	}
 
 	/**
-	 * Returns Blosum 40 matrix by Henikoff & Henikoff
+	 * Returns Blosum 40 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 40 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum40() {
@@ -110,7 +110,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum40() {
 	}
 
 	/**
-	 * Returns Blosum 45 matrix by Henikoff & Henikoff
+	 * Returns Blosum 45 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 45 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum45() {
@@ -118,7 +118,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum45() {
 	}
 
 	/**
-	 * Returns Blosum 50 matrix by Henikoff & Henikoff
+	 * Returns Blosum 50 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 50 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum50() {
@@ -126,7 +126,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum50() {
 	}
 
 	/**
-	 * Returns Blosum 55 matrix by Henikoff & Henikoff
+	 * Returns Blosum 55 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 55 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum55() {
@@ -134,7 +134,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum55() {
 	}
 
 	/**
-	 * Returns Blosum 60 matrix by Henikoff & Henikoff
+	 * Returns Blosum 60 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 60 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum60() {
@@ -142,7 +142,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum60() {
 	}
 
 	/**
-	 * Returns Blosum 62 matrix by Henikoff & Henikoff
+	 * Returns Blosum 62 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 62 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum62() {
@@ -150,7 +150,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum62() {
 	}
 
 	/**
-	 * Returns Blosum 65 matrix by Henikoff & Henikoff
+	 * Returns Blosum 65 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 65 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum65() {
@@ -158,7 +158,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum65() {
 	}
 
 	/**
-	 * Returns Blosum 70 matrix by Henikoff & Henikoff
+	 * Returns Blosum 70 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 70 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum70() {
@@ -166,7 +166,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum70() {
 	}
 
 	/**
-	 * Returns Blosum 75 matrix by Henikoff & Henikoff
+	 * Returns Blosum 75 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 75 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum75() {
@@ -174,7 +174,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum75() {
 	}
 
 	/**
-	 * Returns Blosum 80 matrix by Henikoff & Henikoff
+	 * Returns Blosum 80 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 80 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum80() {
@@ -182,7 +182,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum80() {
 	}
 
 	/**
-	 * Returns Blosum 85 matrix by Henikoff & Henikoff
+	 * Returns Blosum 85 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 85 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum85() {
@@ -190,7 +190,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum85() {
 	}
 
 	/**
-	 * Returns Blosum 90 matrix by Henikoff & Henikoff
+	 * Returns Blosum 90 matrix by Henikoff &amp; Henikoff
 	 * @return Blosum 90 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getBlosum90() {
@@ -198,7 +198,7 @@ public static SubstitutionMatrix<AminoAcidCompound> getBlosum90() {
 	}
 
 	/**
-	 * Returns PAM 250 matrix by Gonnet, Cohen & Benner
+	 * Returns PAM 250 matrix by Gonnet, Cohen &amp; Benner
 	 * @return Gonnet 250 matrix
 	 */
 	public static SubstitutionMatrix<AminoAcidCompound> getGonnet250() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
index bc64496810..cbb959fd25 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
@@ -34,11 +34,12 @@
  * @author Mark Chapman
  * @author Paolo Pavan
  * @param <C> each element of the {@link Sequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public interface AlignedSequence<S extends Sequence<C>, C extends Compound> extends Sequence<C> {
 
 	/**
-	 * Defines an alignment step in order to pass alignment information from an {@link Aligner} to a constructor.
+	 * Defines an alignment step in order to pass alignment information from an Aligner to a constructor.
 	 */
 	enum Step { COMPOUND, GAP }
 
@@ -65,7 +66,7 @@ enum Step { COMPOUND, GAP }
 	 *
 	 * @param sequenceIndex index in the original {@link Sequence}
 	 * @return column index within an alignment
-	 * @throws IndexOutOfBoundsException if sequenceIndex < 1 or sequenceIndex >
+	 * @throws IndexOutOfBoundsException if sequenceIndex &lt; 1 or sequenceIndex >
 	 *         {@link #getOriginalSequence()}.{@link #getLength()}
 	 */
 	int getAlignmentIndexAt(int sequenceIndex);
@@ -130,7 +131,7 @@ enum Step { COMPOUND, GAP }
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return index in the original {@link Sequence}
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int getSequenceIndexAt(int alignmentIndex);
 
@@ -154,7 +155,7 @@ enum Step { COMPOUND, GAP }
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return true if this column has a gap
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	boolean isGap(int alignmentIndex);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
index cfe85f7d33..edef1d54b7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
@@ -34,6 +34,7 @@
  * @author Mark Chapman
  * @author Paolo Pavan
  * @param <C> each element of the {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public interface MutableAlignedSequence<S extends Sequence<C>, C extends Compound> extends AlignedSequence<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java
index 811de73b31..62575a1bf2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/Profile.java
@@ -58,7 +58,7 @@ enum StringFormat {
 	 *
 	 * @param listIndex index of sequence in profile
 	 * @return desired sequence
-	 * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
+	 * @throws IndexOutOfBoundsException if listIndex &lt; 1 or listIndex &gt; number of sequences
 	 */
 	AlignedSequence<S, C> getAlignedSequence(int listIndex);
 
@@ -101,8 +101,8 @@ enum StringFormat {
 	 * @param listIndex index of sequence in profile
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence element
-	 * @throws IndexOutOfBoundsException if listIndex < 1, listIndex > number of sequences, alignmentIndex < 1, or
-	 *     alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if listIndex &lt; 1, listIndex &gt; number of sequences, alignmentIndex &lt; 1, or
+	 *     alignmentIndex &gt; {@link #getLength()}
 	 */
 	C getCompoundAt(int listIndex, int alignmentIndex);
 
@@ -113,7 +113,7 @@ enum StringFormat {
 	 * @param sequence either an {@link AlignedSequence} or an original {@link Sequence}
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence element
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	C getCompoundAt(S sequence, int alignmentIndex);
 
@@ -122,7 +122,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return list of counts
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int[] getCompoundCountsAt(int alignmentIndex);
 
@@ -132,7 +132,7 @@ enum StringFormat {
 	 * @param alignmentIndex column index within an alignment
 	 * @param compounds list of compounds to count
 	 * @return corresponding list of counts
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds);
 
@@ -141,7 +141,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence elements
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	List<C> getCompoundsAt(int alignmentIndex);
 
@@ -157,7 +157,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return list of fractional weights
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	float[] getCompoundWeightsAt(int alignmentIndex);
 
@@ -167,7 +167,7 @@ enum StringFormat {
 	 * @param alignmentIndex column index within an alignment
 	 * @param compounds list of compounds to count
 	 * @return corresponding list of fractional weights
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	float[] getCompoundWeightsAt(int alignmentIndex, List<C> compounds);
 
@@ -177,7 +177,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence indices
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int[] getIndicesAt(int alignmentIndex);
 
@@ -236,7 +236,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return true if any {@link AlignedSequence} has a gap at the given index
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	boolean hasGap(int alignmentIndex);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java
index 24f2315e00..1367fb6be9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SequencePair.java
@@ -41,7 +41,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param alignmentIndex column index in alignment
 	 * @return the query sequence element
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	C getCompoundInQueryAt(int alignmentIndex);
 
@@ -50,7 +50,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param alignmentIndex column index in alignment
 	 * @return the target sequence element
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	C getCompoundInTargetAt(int alignmentIndex);
 
@@ -59,7 +59,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param alignmentIndex column index in alignment
 	 * @return index in query {@link Sequence}
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int getIndexInQueryAt(int alignmentIndex);
 
@@ -68,7 +68,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param targetIndex index in target {@link Sequence}
 	 * @return index in query {@link Sequence}
-	 * @throws IndexOutOfBoundsException if targetIndex < 1 or targetIndex > {@link #getTarget()}.getLength()
+	 * @throws IndexOutOfBoundsException if targetIndex &lt; 1 or targetIndex &gt; {@link #getTarget()}.getLength()
 	 */
 	int getIndexInQueryForTargetAt(int targetIndex);
 
@@ -77,7 +77,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param alignmentIndex column index in alignment
 	 * @return index in target {@link Sequence}
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	int getIndexInTargetAt(int alignmentIndex);
 
@@ -86,7 +86,7 @@ public interface SequencePair<S extends Sequence<C>, C extends Compound> extends
 	 *
 	 * @param queryIndex index in query {@link Sequence}
 	 * @return index in target {@link Sequence}
-	 * @throws IndexOutOfBoundsException if queryIndex < 1 or queryIndex > {@link #getQuery()}.getLength()
+	 * @throws IndexOutOfBoundsException if queryIndex &lt; 1 or queryIndex &gt; {@link #getQuery()}.getLength()
 	 */
 	int getIndexInTargetForQueryAt(int queryIndex);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java
index 22a8de5f5c..436fc7a44b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/SubstitutionMatrix.java
@@ -103,7 +103,7 @@ public interface SubstitutionMatrix<C extends Compound> {
 	 * Rescales the matrix so that to {@link #getMaxValue()} - {@link #getMinValue()} = scale.
 	 *
 	 * @param scale new normalization scale of this matrix
-	 * @throws IllegalArgumentException if scale < 1
+	 * @throws IllegalArgumentException if scale &lt; 1
 	 */
 	SubstitutionMatrix<C> normalizeMatrix(short scale);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/ParserException.java b/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/ParserException.java
index acd8cc47fb..5afaa7c412 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/ParserException.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/exceptions/ParserException.java
@@ -23,7 +23,7 @@
  */
 /**
  * General abstraction of different parsing errors
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ParserException extends RuntimeException {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
index 7a27828feb..832997bb2b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
@@ -40,15 +40,16 @@
 /**
  * This class models a search Hsp.
  * You will retrieve a list of this using iterator of a Hit
- *
+ * <p>
  * Designed by Paolo Pavan.
  * You may want to find my contacts on Github and LinkedIn for code info
  * or discuss major changes.
  * https://github.com/paolopavan
  *
  * @author Paolo Pavan
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
-
 public abstract class Hsp <S extends Sequence<C>, C extends Compound> {
 	private static final Logger logger = LoggerFactory.getLogger(Hsp.class);
 	private Integer hspNum;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
index 479df1ac4d..d9279b8cce 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/ResultFactory.java
@@ -34,7 +34,6 @@
  *
  * @author Paolo Pavan
  */
-
 public interface ResultFactory {
 	/**
 	 * returns a list of file extensions associated to this ResultFactory
@@ -49,7 +48,8 @@ public interface ResultFactory {
 	 *
 	 * @param maxEScore
 	 * @return
-	 * @throws Exception
+	 * @throws IOException
+	 * @throws ParseException
 	 */
 	List<Result> createObjects(double maxEScore) throws IOException, ParseException;
 	/**
@@ -57,7 +57,8 @@ public interface ResultFactory {
 	 * to a file in the same format that it is able to read.
 	 *
 	 * @param results
-	 * @throws Exception
+	 * @throws IOException
+	 * @throws ParseException
 	 */
 	void storeObjects(List<Result> results) throws IOException, ParseException;
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
index 95ffb9fcfc..e864068afd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/SearchIO.java
@@ -64,7 +64,6 @@ public class SearchIO implements Iterable<Result>{
 	 * file extension.
 	 *
 	 * @param f
-	 * @throws Exception
 	 */
 	public SearchIO (File f)  throws IOException, ParseException{
 		factory = guessFactory(f);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
index 73932d9147..5ccd89f459 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java
@@ -43,7 +43,7 @@
 
 /**
  * Re-designed by Paolo Pavan on the footprint of:
- * org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis <willishf at gmail dot com>
+ * org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis 
  *
  * You may want to find my contacts on Github and LinkedIn for code info
  * or discuss major changes.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java
index 8acb7a7e83..0342ec7a46 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java
@@ -18,7 +18,7 @@
  *      http://www.biojava.org/
  *
  * Created on 3/1/2010
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 
 package org.biojava.nbio.core.sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
index f897622f3c..2fbd638b82 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSSequence.java
@@ -32,7 +32,7 @@
  * Represents a exon or coding sequence in a gene. It has a parent {@link TranscriptSequence}
  * where a TranscriptSequence is the child of a GeneSequence
  * Not important for protein construction but the phase is used if outputting the gene
- * to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
+ * to a gff3 file. <a href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a>
  * @author Scooter Willis
  */
 public class CDSSequence extends DNASequence {
@@ -90,8 +90,8 @@ public Strand getStrand() {
 	 * A CDS sequence if negative stranded needs to be reverse complement
 	 * to represent the actual coding sequence. When getting a ProteinSequence
 	 * from a TranscriptSequence this method is callled for each CDSSequence
-	 * {@link http://www.sequenceontology.org/gff3.shtml}
-	 * {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
+	 * <a href="http://www.sequenceontology.org/gff3.shtml">http://www.sequenceontology.org/gff3.shtml</a>
+	 * <a href="http://biowiki.org/~yam/bioe131/GFF.ppt">http://biowiki.org/~yam/bioe131/GFF.ppt</a>
 	 * @return coding sequence
 	 */
 	public String getCodingSequence() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
index 000adce936..9086382155 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/DataSource.java
@@ -35,8 +35,8 @@
  * General database identifier       gnl|database|identifier
  * NCBI Reference Sequence           ref|accession|locus
  * Local Sequence identifier         lcl|identifier
- * </pr>
- * @author Scooter Willis <willishf at gmail dot com>
+ * </pre>
+ * @author Scooter Willis 
  */
 
 public enum DataSource {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java
index 64495b251f..43389f433c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java
@@ -30,7 +30,7 @@
 /**
  * Sort Exon where it is a little confusing if exons should always be ordered left to right
  * where a negative stranded gene should go the other direction. Need to think about this?
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ExonComparator implements Comparator<ExonSequence>, Serializable{
 	private static final long serialVersionUID = 1;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
index a3e706716b..318df7cf9f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/RNASequence.java
@@ -39,7 +39,7 @@
 
 /**
  * RNASequence where RNACompoundSet are the allowed values
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 
 public class RNASequence extends AbstractSequence<NucleotideCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java
index 066aa930de..742b47bfce 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java
@@ -29,7 +29,7 @@
 
 /**
  * Used to sort sequences in ascending order of  bioBegin property.
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SequenceComparator implements Comparator<AbstractSequence<?>>, Serializable{
 	private static final long serialVersionUID = 1;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
index edf891c4f7..e0d06eb0c7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/edits/Edit.java
@@ -114,7 +114,7 @@ protected void setSequence(Sequence<C> sequence) {
 		 * @param editingSequence Asked for in-case we need to do String to
 		 * Sequence conversion so we need a CompoundSet which is given
 		 * by the Sequence we are editing
-		 * @return The Sequence<C> object we wish to insert
+		 * @return The {@link Sequence<C>} object we wish to insert
 		 */
 		public Sequence<C> getTargetSequence(Sequence<C> editingSequence) {
 			if (sequence == null && stringSequence != null) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
index 16e894697c..5f0ed8043f 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/AbstractFeature.java
@@ -36,7 +36,7 @@
  * A feature is currently any descriptive item that can be associated with a sequence position(s)
  * A feature has a type and a source which is currently a string to allow flexibility for the user
  * Ideally well defined features should have a class to describe attributes of that feature
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public abstract class AbstractFeature<S extends AbstractSequence<C>, C extends Compound>
 		implements FeatureInterface<S, C> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
index 7598f77f33..3cc8b8897a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DBReferenceInfo.java
@@ -34,7 +34,7 @@
  * Currently implement when the {@link UniprotProxySequenceReader} is used
  * to load a protein sequence
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Paolo Pavan
  */
 public class DBReferenceInfo extends Qualifier {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
index 20c00034dd..a302d08857 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
@@ -30,7 +30,7 @@
 /**
  * If a SequenceProxyReader implements this interface then that external source
  * has a list of cross reference id(s)
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface DatabaseReferenceInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
index 3b49341d22..68b518b051 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureDbReferenceInfo.java
@@ -11,7 +11,7 @@
  * Copyright for this code is held jointly by the individual
  * authors.  These should be listed in @author doc comments.
  *
- * @author Jacek Grzebyta <github:jgrzebyta>
+ * @author Jacek Grzebyta &lt;github:jgrzebyta&gt;
  *
  * For more information on the BioJava project and its aims,
  * or to join the biojava-l mailing list, visit the home page
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
index 47564bcefa..8976953fd0 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureInterface.java
@@ -33,11 +33,11 @@
  * the surface of a protein where different sequence positions make up that feature. Ligand binding pocket is another example.
  * The location in its current form knows the start and stop position in a sequence and thus should contain knowledge about the
  * actual sequence.
- *
+ * <p>
  * A feature can contain features to handle cases where a domain is a feature and the secondary structures covered by that domain
  * and other requirements for grouping.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Paolo Pavan
  */
 public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compound> {
@@ -46,32 +46,26 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * Get the short description that can be used to describe the feature
 	 * @return
 	 */
-
-	public String getShortDescription();
+	String getShortDescription();
 
 	/**
 	 * Set the short description that can be used to describe the feature
 	 * @param shortDescription
 	 */
+	void setShortDescription(String shortDescription);
 
-	public void setShortDescription(String shortDescription);
-
-	  /**
+	 /**
 	 * Get the description that can be used to describe the feature
 	 * @return
 	 */
+	String getDescription();
 
-	public String getDescription();
-
-
-	  /**
+	 /**
 	 * Set the description that can be used to describe the feature
-	 * @return
 	 */
+	void setDescription(String description);
 
-	public void setDescription(String description);
-
-		/**
+	/**
 	 * The location(s) of this feature where the location should contain a reference to parent and sequence etc.
 	 * <p>
 	 * The location may be complicated, or simply a range.
@@ -80,7 +74,7 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 *
 	 * @return a Location anchoring this feature
 	 */
-	public AbstractLocation getLocations();
+	AbstractLocation getLocations();
 
 		/**
 	 * The new location for this feature.
@@ -93,14 +87,14 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param loc the new Location for this feature
 	 *
 	 */
-	public void setLocation(AbstractLocation loc);
+	void setLocation(AbstractLocation loc);
 
-		/**
+	/**
 	 * The type of the feature.
 	 *
 	 * @return the type of this sequence
 	 */
-	public String getType();
+	String getType();
 
 	/**
 	 * Change the type of this feature.
@@ -108,15 +102,15 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param type  new type String
 	 *
 	 */
-	public void setType(String type);
+	void setType(String type);
 
 
-		/**
+	/**
 	 * The source of the feature. This may be a program or process.
 	 *
 	 * @return the source, or generator
 	 */
-	public String getSource();
+	String getSource();
 
 	/**
 	 * Change the source of the FeatureInterface.
@@ -124,66 +118,60 @@ public interface FeatureInterface<S extends AbstractSequence<C>, C extends Compo
 	 * @param source the new source String
 	 *
 	 */
-	public void setSource(String source);
+	void setSource(String source);
 
 	/**
 	 * Set the parent feature
 	 * @param feature
 	 */
-
-	public void setParentFeature(FeatureInterface<S, C> feature);
+	void setParentFeature(FeatureInterface<S, C> feature);
 
 	/**
 	 * Get the parent feature
 	 * @return
 	 */
-
-	public FeatureInterface<S, C> getParentFeature();
+	FeatureInterface<S, C> getParentFeature();
 
 	/**
 	 * Get the features contained by this feature
 	 * @return
 	 */
-
-	public List<FeatureInterface<S, C>> getChildrenFeatures();
+	List<FeatureInterface<S, C>> getChildrenFeatures();
 
 	/**
 	 * Set the children features
 	 * @param features
 	 */
+	void setChildrenFeatures(List<FeatureInterface<S, C>> features);
 
-	public void setChildrenFeatures(List<FeatureInterface<S, C>> features);
 
-
-		/**
+	/**
 	 * @return the userObject
 	 */
-	public Object getUserObject();
+	Object getUserObject();
 
 	/**
 	 * @param userObject the userObject to set
 	 */
-	public void setUserObject(Object userObject);
-
+	void setUserObject(Object userObject);
 
 	/**
 	 * Get the qualifiers for this feature
 	 * @return
 	 */
 
-	public Map<String, List<Qualifier>> getQualifiers();
+	Map<String, List<Qualifier>> getQualifiers();
 
 	/**
 	 * Set the qualifiers
 	 * @param qualifiers
 	 */
+	void setQualifiers(Map<String, List<Qualifier>> qualifiers);
 
-	public void setQualifiers(Map<String, List<Qualifier>> qualifiers);
 	/**
 	 * Add a qualifier
 	 * @param qualifier
 	 */
-
-	public void addQualifier(String key, Qualifier qualifier);
+	void addQualifier(String key, Qualifier qualifier);
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
index 1b1acd994e..e7bef35d6c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
@@ -28,7 +28,7 @@
  * Models the keywords that are annotated for a protein sequence at Uniprot. If a ProxySequenceReader
  * implements this interface then the sequence will call this method
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface FeaturesKeyWordInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
index 524bdfdaa3..3e6304c5c6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/QuantityFeature.java
@@ -31,7 +31,7 @@
  * It is common to have a numerical value or values associated with a feature. This can then
  * be used in heat maps or other visual indicators when viewing a sequence. Multiple quantities
  * could represent a time corse study and display a color gradient
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class QuantityFeature<S extends AbstractSequence<C>, C extends Compound> extends AbstractFeature<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/TextFeature.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/TextFeature.java
index 2b8cf26b59..5634e065a9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/TextFeature.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/TextFeature.java
@@ -26,7 +26,7 @@
 
 /**
  * A implmentation of AbstractFeature
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class TextFeature<S extends AbstractSequence<C>, C extends Compound> extends AbstractFeature<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
index ea6f9abe1c..9561e21660 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java
@@ -171,9 +171,9 @@ public int[] getQcalls() {
 	}
 
 	/**
-	 * Returns the original programmatically determined (unedited) sequence as a <code>AbstractSequence<NucleotideCompound></code>.
+	 * Returns the original programmatically determined (unedited) sequence as a {@link AbstractSequence<NucleotideCompound>}.
 	 *
-	 * @return AbstractSequence<NucleotideCompound> sequence
+	 * @return sequence
 	 */
 	public AbstractSequence<NucleotideCompound> getSequence() throws CompoundNotFoundException {
 		DNASequenceCreator creator = new DNASequenceCreator(ABITracerCompoundSet.getABITracerCompoundSet());
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
index 998bbada13..30aa52c5d7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/BufferedReaderBytesRead.java
@@ -174,7 +174,7 @@ private void fill() throws IOException {
 	 * Reads a single character.
 	 *
 	 * @return The character read, as an integer in the range
-	 *         0 to 65535 (<tt>0x00-0xffff</tt>), or -1 if the
+	 *         0 to 65535 (<code>0x00-0xffff</code>), or -1 if the
 	 *         end of the stream has been reached
 	 * @exception  IOException  If an I/O error occurs
 	 */
@@ -521,7 +521,7 @@ public boolean markSupported() {
 	 *                         whose size is no smaller than limit.
 	 *                         Therefore large values should be used with care.
 	 *
-	 * @exception  IllegalArgumentException  If readAheadLimit is < 0
+	 * @exception  IllegalArgumentException  If readAheadLimit is &lt; 0
 	 * @exception  IOException  If an I/O error occurs
 	 */
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
index 94b2a6d918..0fb731ab10 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java
@@ -41,14 +41,15 @@
  * <p>The user collection will be the same length as the resulting ProteinSequence.
  * Each object can be cast to a Boolean. If true, the corresponding position in
  * the input file was uppercase.
- *
- * <h3>Example</h3>
- * <code><pre>CasePreservingProteinSequenceCreator creator =
+ * <p>
+ * Example
+ * <code>
+ *    CasePreservingProteinSequenceCreator creator =
  *    new CasePreservingProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet());
- *AbstractSequence<AminoAcidCompound> seq = creator.getSequence("aaAA",0);
- *System.out.println(seq.getSequenceAsString()); //"AAAA"
- *System.out.println(seq.getUserCollection()); //"[false, false, true, true]"
- *</code></pre>
+ *    AbstractSequence&lt;AminoAcidCompound&gt; seq = creator.getSequence("aaAA",0);
+ *    System.out.println(seq.getSequenceAsString()); //"AAAA"
+ *    System.out.println(seq.getUserCollection()); //"[false, false, true, true]"
+ * </code>
  */
 public class CasePreservingProteinSequenceCreator extends ProteinSequenceCreator {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
index 78a5dd4832..64a9467f3e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/DNASequenceCreator.java
@@ -37,7 +37,7 @@
  * A helper class that allows different ways to read a string and create a DNA sequence. Used in FastaReaderHelper
  * and probably a layer that isn't needed
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class DNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
index 2297e5e070..065bfff79a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaGeneWriter.java
@@ -35,7 +35,7 @@
  * A Gene sequence has a Positive or Negative Strand where we want to write out to a stream the 5 to 3 prime version.
  * It is also an option to write out the gene sequence where the exon regions are upper case
  * 6/22/2010 FastaWriter needs to be sequence aware to handle writing out a GeneSequence which is negative Strand with the proper sequence
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaGeneWriter {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
index 4493766202..973a2813c6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaReaderHelper.java
@@ -39,7 +39,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaReaderHelper {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaSequenceParser.java
index 35043c93bc..7140c094c5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaSequenceParser.java
@@ -28,7 +28,7 @@
 
 /**
  * Used to parse a stream of a fasta file to get the sequence
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaSequenceParser implements SequenceParserInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
index ff425bde49..f0fc191ff2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriter.java
@@ -44,7 +44,7 @@
  * and that is used when writing to the stream. This behavior can be overwritten by implementing
  * a custom FastaHeaderFormatInterface.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaWriter<S extends Sequence<?>, C extends Compound> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
index dfeae8a642..364260d9a2 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FastaWriterHelper.java
@@ -39,7 +39,7 @@
 
 /**
  * The class that should be used to write out fasta file of a sequence collection
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaWriterHelper {
 
@@ -96,7 +96,7 @@ public static void writeGeneSequence(File file, Collection<GeneSequence> geneSeq
 	/**
 	 * Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
 	 * @param outputStream
-	 * @param dnaSequences
+	 * @param geneSequences
 	 * @throws Exception
 	 */
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
index 21b0699ab6..96317cecdd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyDNASequenceCreator.java
@@ -45,7 +45,7 @@
  * Same approach can be used for genome sequence data stored in a local fasta file, in a database or via http
  * interface to a remote server
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FileProxyDNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
@@ -56,8 +56,9 @@ public class FileProxyDNASequenceCreator implements
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
-	 * @param fastaFile
+	 * @param file
 	 * @param compoundSet
+	 * @param sequenceParser
 	 */
 	public FileProxyDNASequenceCreator(File file,
 			CompoundSet<NucleotideCompound> compoundSet,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
index e45907a2ed..f7e1cc7ab6 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
@@ -55,7 +55,7 @@ public class FileProxyProteinSequenceCreator implements SequenceCreatorInterface
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
-	 * @param fastaFile
+	 * @param file
 	 * @param compoundSet
 	 */
 	public FileProxyProteinSequenceCreator(File file, CompoundSet<AminoAcidCompound> compoundSet, SequenceParserInterface sequenceParser ) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
index 58fe3f98d7..53de88bb06 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyRNASequenceCreator.java
@@ -45,7 +45,7 @@
  * Same approach can be used for genome sequence data stored in a local fasta file, in a database or via http
  * interface to a remote server
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FileProxyRNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
@@ -56,7 +56,7 @@ public class FileProxyRNASequenceCreator implements
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
-	 * @param fastaFile
+	 * @param file
 	 * @param compoundSet
 	 */
 	public FileProxyRNASequenceCreator(File file,
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
index e2f4e8bf25..7f67918377 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
@@ -12,7 +12,7 @@
  * authors.  These should be listed in @author doc comments.
  *
  * @author Scooter Willis ;lt;willishf at gmail dot com&gt;
- * @author Karl Nicholas <github:karlnicholas>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
  * @author Paolo Pavan
  *
  * For more information on the BioJava project and its aims,
@@ -53,7 +53,8 @@
 /**
  * Use {@link GenbankReaderHelper} as an example of how to use this class where {@link GenbankReaderHelper} should be the
  * primary class used to read Genbank files
- *
+ * @param <S> the sequence type
+ * @param <C> the compound type
  */
 public class GenbankReader<S extends AbstractSequence<C>, C extends Compound> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
index 5146310591..7d382ce6b9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java
@@ -41,7 +41,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenbankReaderHelper {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
index 90653612e7..7b7f0e1450 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -17,7 +17,7 @@
  * @author Bubba Puryear
  * @author George Waldon
  * @author Deepak Sheoran
- * @author Karl Nicholas <github:karlnicholas>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
  * @author Jacek Grzebyta
  * @author Paolo Pavan
  *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
index c99a9c23fd..9d47db3bbd 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankWriter.java
@@ -69,7 +69,6 @@ public GenbankWriter(OutputStream os, Collection<S> sequences,
 	 * @param headerFormat
 	 * @param lineLength
 	 */
-
 	public GenbankWriter(OutputStream os, Collection<S> sequences,
 			GenbankHeaderFormatInterface<S, C> headerFormat, int lineLength) {
 		this.os = os;
@@ -82,9 +81,7 @@ public GenbankWriter(OutputStream os, Collection<S> sequences,
 	 * Allow an override of operating system line separator for programs that
 	 * needs a specific CRLF or CR or LF option
 	 *
-	 * @param lineSeparator
 	 */
-
 	public void process() throws Exception {
 		// Loosely based on code from Howard Salis
 		// TODO - Force lower case?
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.java
index a007af0a61..c26b8362da 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderFormat.java
@@ -32,7 +32,7 @@
  * use the accession id. This allows the implementation by the user to write out complex header
  * with id notes etc without rewriting the fasta writer
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenericFastaHeaderFormat<S extends AbstractSequence<?>, C extends Compound> implements FastaHeaderFormatInterface<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
index 1556bf838e..f4c8ea3416 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java
@@ -59,7 +59,7 @@
  * NCBI Reference Sequence           ref|accession|locus
  * Local Sequence identifier         lcl|identifier
  *</pre>
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenericFastaHeaderParser<S extends AbstractSequence<C>, C extends Compound> implements SequenceHeaderParserInterface<S,C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
index 7b1dc0524d..4fd6354110 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericGenbankHeaderParser.java
@@ -11,7 +11,7 @@
  * Copyright for this code is held jointly by the individual
  * authors.  These should be listed in @author doc comments.
  *
- * @author Karl Nicholas <github:karlnicholas>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
  *
  * For more information on the BioJava project and its aims,
  * or to join the biojava-l mailing list, visit the home page
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
index 0f9b3ca950..65e9d96830 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/IUPACParser.java
@@ -266,7 +266,7 @@ public boolean isStart(AminoAcidCompound compound) {
 		 * @param aminoAcids The target amino acid compounds objects
 		 */
 				@Override
-		public List<Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides,
+		public List<Codon> getCodons(CompoundSet<NucleotideCompound> nucleotides,
 				CompoundSet<AminoAcidCompound> aminoAcids) {
 
 			if (this.codons.isEmpty()) {
@@ -277,9 +277,9 @@ public List<Codon> getCodons(CompoundSet<NucleotideCompound> nucelotides,
 				for (int i = 0; i < aminoAcidStrings.size(); i++) {
 
 					List<String> codonString    = codonStrings.get(i);
-					NucleotideCompound one      = getCompound(codonString, 0, nucelotides);
-					NucleotideCompound two      = getCompound(codonString, 1, nucelotides);
-					NucleotideCompound three    = getCompound(codonString, 2, nucelotides);
+					NucleotideCompound one      = getCompound(codonString, 0, nucleotides);
+					NucleotideCompound two      = getCompound(codonString, 1, nucleotides);
+					NucleotideCompound three    = getCompound(codonString, 2, nucleotides);
 					boolean start               = ("M".equals(startCodonStrings.get(i)));
 					boolean stop                = ("*".equals(aminoAcidStrings.get(i)));
 					AminoAcidCompound aminoAcid = aminoAcids
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
index 1efebed609..6f4e839ca7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ProteinSequenceCreator.java
@@ -37,7 +37,7 @@
  * Used to create a ProteinSequence from a String to allow for details
  * about the location of the sequence etc.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ProteinSequenceCreator implements
 		SequenceCreatorInterface<AminoAcidCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
index 0a691f1afa..16f69cbf74 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/RNASequenceCreator.java
@@ -35,7 +35,7 @@
 /**
  * Used to create a RNA sequence
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class RNASequenceCreator implements
 		SequenceCreatorInterface<NucleotideCompound> {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblRecord.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblRecord.java
index 1e84382b54..46497b5a0d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblRecord.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblRecord.java
@@ -64,7 +64,7 @@ public class EmblRecord {
 	 * 6. Taxonomic division
 	 * 7. Sequence length
 	 *
-	 * @return EmblId
+	 * @return
 	 */
 	public EmblId getEmblId() {
 		return emblId;
@@ -80,7 +80,7 @@ public void setEmblId(EmblId emblId) {
 	 * The citations provide access to the papers from which the data has been
 	 * abstracted.
 	 *
-	 * @return EmblReference
+	 * @return
 	 */
 	public List<EmblReference> getEmblReference() {
 		return emblReference;
@@ -94,7 +94,7 @@ public void setEmblReference(List<EmblReference> emblReference) {
 	 * The AC (Accession number) line lists the accession numbers associated with
 	 * the entry.
 	 *
-	 * @return List<String>
+	 * @return
 	 */
 	public List<String> getAccessionNumber() {
 		return accessionNumber;
@@ -119,7 +119,7 @@ public void setProjectIdentifier(String projectIdentifier) {
 	 * The OG (OrGanelle) linetype indicates the sub-cellular location of non-nuclear
 	 * sequences.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getOrGanelle() {
 		return orGanelle;
@@ -132,7 +132,7 @@ public void setOrGanelle(String orGanelle) {
 	/**
 	 * The DT  line shows when an entry first appeared in the database
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getCreatedDate() {
 		return createdDate;
@@ -146,7 +146,7 @@ public void setCreatedDate(String createdDate) {
 	 * The FH (Feature Header) lines are present only to improve readability of
 	 * an entry when it is printed or displayed on a terminal screen.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getFeatureHeader() {
 		return featureHeader;
@@ -161,7 +161,7 @@ public void setFeatureHeader(String featureHeader) {
 	 * sequence data. Regions or sites in the sequence which are of interest are
 	 * listed in the table.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getFeatureTable() {
 		return featureTable;
@@ -190,7 +190,7 @@ public void setLastUpdatedDate(String lastUpdatedDate) {
 	 * sequence codes, the region of the genome from which it is derived, or other
 	 * information which helps to identify the sequence.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getSequenceDescription() {
 		return sequenceDescription;
@@ -205,7 +205,7 @@ public void setSequenceDescription(String sequenceDescription) {
 	 * cross-reference indexes of the sequence entries based on functional,
 	 * structural, or other categories deemed important.
 	 *
-	 * @return List<String>
+	 * @return
 	 */
 	public List<String> getKeyword() {
 		return keyword;
@@ -235,7 +235,7 @@ public void setOrganismSpecies(String organismSpecies) {
 	 * The OC (Organism Classification) lines contain the taxonomic classification
 	 * Of the source organism
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getOrganismClassification() {
 		return organismClassification;
@@ -249,7 +249,7 @@ public void setOrganismClassification(String organismClassification) {
 	 * The DR (Database Cross-reference) line cross-references other databases which
 	 * contain information related to the entry in which the DR line appears.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getDatabaseCrossReference() {
 		return databaseCrossReference;
@@ -262,7 +262,7 @@ public void setDatabaseCrossReference(String databaseCrossReference) {
 	/**
 	 * The AH (Assembly Header) line provides column headings for the assembly information.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getAssemblyHeader() {
 		return assemblyHeader;
@@ -290,7 +290,7 @@ public void setAssemblyInformation(String assemblyInformation) {
 	 * Con(structed) sequences in the CON data classes represent complete
 	 * chromosomes, genomes and other long sequences constructed from segment entries.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getConstructedSequence() {
 		return constructedSequence;
@@ -304,7 +304,7 @@ public void setConstructedSequence(String constructedSequence) {
 	 * The SQ (SeQuence header) line marks the beginning of the sequence data and
 	 * Gives a summary of its content.
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getSequenceHeader() {
 		return sequenceHeader;
@@ -317,7 +317,7 @@ public void setSequenceHeader(String sequenceHeader) {
 	/**
 	 * The Sequence Data Line
 	 *
-	 * @return String
+	 * @return
 	 */
 	public String getSequence() {
 		return sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
index a0bb6af6d3..bfd3092357 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
@@ -27,13 +27,16 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface FastaHeaderFormatInterface<S extends Sequence<?>, C extends Compound> {
+
 	/**
 	 *
 	 * @param sequence
 	 * @return
 	 */
-	public String getHeader(S sequence);
+	String getHeader(S sequence);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
index 5e08a424bf..0dff2d40eb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
@@ -28,16 +28,18 @@
 
 /**
  * @author mckeee1
- *
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface GenbankHeaderFormatInterface<S extends Sequence<?>, C extends Compound> {
+
+	public static final String UNKNOWN_DNA = "UNK";
+
 	/**
 	 *
 	 * @param sequence
 	 * @return
 	 */
-	public static final String UNKNOWN_DNA = "UNK";
-
-	public String getHeader(S sequence);
+	String getHeader(S sequence);
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
index 9ec26dc225..c03900055b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
@@ -32,7 +32,8 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
+ * @param <C> the compound type
  */
 public interface SequenceCreatorInterface<C extends Compound> {
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
index dba9d7ca3d..a49e27c754 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
@@ -27,7 +27,9 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface SequenceHeaderParserInterface<S extends Sequence<?>, C extends Compound> {
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
index fd536e2802..82b2cab38b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceParserInterface.java
@@ -27,15 +27,15 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface SequenceParserInterface {
 	/**
 	 *
-	 * @param dataInput
+	 * @param bufferedReader
 	 * @param sequenceLength
 	 * @return
-	 * @throws Exception
+	 * @throws IOException
 	 */
-	public String getSequence(BufferedReader bufferedReader,int sequenceLength) throws IOException;
+	String getSequence(BufferedReader bufferedReader,int sequenceLength) throws IOException;
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
index b60bc9eb00..fe3dfcd42a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/util/IOUtils.java
@@ -157,7 +157,7 @@ public static List<String> getList(File file) throws IOException {
 	 *
 	 * @param file File which may or may not be GZipped
 	 * @return The final stream
-	 * @throws IOExceptio n
+	 * @throws IOException
 	 */
 	public static InputStream openFile(File file) throws IOException {
 		final InputStream is;
@@ -178,7 +178,7 @@ public static InputStream openFile(File file) throws IOException {
 
 	/**
 	 * Closure interface used when working with
-	 * {@link IOUtils#processReader(String)}. Each time a line is encountered
+	 * {@link IOUtils#processReader(BufferedReader, ReaderProcessor)}. Each time a line is encountered
 	 * the object that implements this interface will be invoked.
 	 *
 	 * @author ayates
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
index d3e6c52661..f443472aad 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -11,7 +11,7 @@
  * Copyright for this code is held jointly by the individual
  * authors.  These should be listed in @author doc comments.
  *
- * @author Karl Nicholas <github:karlnicholas>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
  *
  * For more information on the BioJava project and its aims,
  * or to join the biojava-l mailing list, visit the home page
@@ -42,8 +42,8 @@
 import java.util.Map;
 
 /**
- * @author Karl Nicholas <github:karlnicholas>
- * @author Jacek Grzebyta <github:jgrzebyta>
+ * @author Karl Nicholas &lt;github:karlnicholas&gt;
+ * @author Jacek Grzebyta &lt;github:jgrzebyta&gt;
  */
 public class GenbankProxySequenceReader<C extends Compound> extends StringProxySequenceReader<C> implements FeaturesKeyWordInterface, DatabaseReferenceInterface, FeatureRetriever {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
index 61df84f46d..ef4bf016cb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
@@ -50,8 +50,8 @@
  * data was loaded and then after X amount of time clear the contents to free up memory.
  *
  *
- * @author Scooter Willis <willishf at gmail dot com>
- * @param <C>
+ * @author Scooter Willis 
+ * @param <C> the compound type
  */
 public class SequenceFileProxyLoader<C extends Compound> implements ProxySequenceReader<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
index b97ad43bb9..86323d1289 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
@@ -38,10 +38,9 @@
 
 /**
  * An example of a ProxySequenceReader that is created from a String. Used for testing
- * @author Scooter Willis <willishf at gmail dot com>
- * @param <C>
+ * @author Scooter Willis 
+ * @param <C> the compound type
  */
-
 public class StringProxySequenceReader<C extends Compound> implements ProxySequenceReader<C> {
 
 	private String sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
index f1cd7a7471..38feabdbf5 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -120,7 +120,6 @@ public UniprotProxySequenceReader(Document document, CompoundSet<C> compoundSet)
 	 * @param xml
 	 * @param compoundSet
 	 * @return UniprotProxySequenceReader
-	 * @throws Exception
 	 */
 	public static <C extends Compound> UniprotProxySequenceReader<C> parseUniprotXMLString(String xml, CompoundSet<C> compoundSet) {
 		try {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
index d36d882c98..38f96d7d08 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/LocationHelper.java
@@ -113,7 +113,7 @@ public static Location location(int start, int end, Strand strand, int length) {
 	 * other location builder this allows you to express your input
 	 * location on the reverse strand
 	 *
-	 * @param location The location which currently expresses the outer
+	 * @param start The location which currently expresses the outer
 	 * bounds of a circular location.
 	 * @param length The length of the circular genomic unit
 	 * @return The circular location; can optionally return a normal non
@@ -307,7 +307,7 @@ public static Strand detectStrand(List<Location> subLocations) {
 	}
 
 	/**
-	 * Assumes that the first element is the start & clones it
+	 * Assumes that the first element is the start &amp; clones it
 	 */
 	public static Point detectStart(List<Location> subLocations) {
 		return subLocations.get(0).getStart().clonePoint();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SequenceLocation.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SequenceLocation.java
index 443f7d9f06..beb03e3be7 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SequenceLocation.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SequenceLocation.java
@@ -31,7 +31,7 @@
 import java.util.List;
 /**
  * A location in a sequence that keeps a reference to its parent sequence
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Paolo Pavan
  */
 public class SequenceLocation<S extends AbstractSequence<C>, C extends Compound> extends SimpleLocation {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
index b0887bf706..266f9a6f1b 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/Location.java
@@ -71,7 +71,7 @@ public interface Location extends Iterable<Location>, Accessioned {
 	/**
 	 * Gives access to the sub locations for this location. However this does
 	 * not return sub-locations of sub-locations. For that functionality use
-	 * {@link #getAllSubLocations()}.
+	 * {@link #getRelevantSubLocations()}.
 	 *
 	 * @return A list of a single level of sub-locations
 	 */
@@ -107,7 +107,7 @@ public interface Location extends Iterable<Location>, Accessioned {
 	 * Will return a SequenceReader object which represents the outer bounds
 	 * of this Location
 	 *
-	 * @param &lt;C&gt; The type of compound to use
+	 * @param <C> The type of compound to use
 	 * @param sequence The sequence object to work with
 	 * @return The sequence
 	 */
@@ -118,7 +118,7 @@ public interface Location extends Iterable<Location>, Accessioned {
 	 * locations i.e. those locations which are not complex and define the
 	 * true Sequence represented
 	 *
-	 * @param &lt;C&gt; The type of compound to use
+	 * @param <C> The type of compound to use
 	 * @param sequence The sequence object to work with
 	 * @return The full assembled sequence
 	 */
@@ -166,7 +166,7 @@ public static Location location(int start, int end, Strand strand, int length) {
 		 * other location builder this allows you to express your input
 		 * location on the reverse strand
 		 *
-		 * @param location The location which currently expresses the outer
+		 * @param start The location which currently expresses the outer
 		 * bounds of a circular location.
 		 * @param length The length of the circular genomic unit
 		 * @return The circular location; can optionally return a normal non
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/AbstractReference.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/AbstractReference.java
index 64c9792a0b..3c9958cb5c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/AbstractReference.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/AbstractReference.java
@@ -22,7 +22,7 @@
 
 /**
  * @since 5.0.0
- * @Author Jim Tang
+ * @author Jim Tang
  */
 public abstract class AbstractReference implements ReferenceInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/GenbankReference.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/GenbankReference.java
index 9e67dcb0fa..ff8db13727 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/GenbankReference.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/GenbankReference.java
@@ -24,7 +24,7 @@
  * For Genbank format file only.
  *
  * @since 5.0.0
- * @Author Jim Tang
+ * @author Jim Tang
  */
 public class GenbankReference extends AbstractReference {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/ReferenceInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/ReferenceInterface.java
index 2c3b8fa457..6c86cca96d 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/ReferenceInterface.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/reference/ReferenceInterface.java
@@ -22,7 +22,7 @@
 
 /**
  * @since 5.0.0
- * @Author Jim Tang
+ * @author Jim Tang
  */
 public interface ReferenceInterface {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
index 5e499261c1..1cfc068fbb 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
@@ -39,7 +39,7 @@
 /**
  * Stores a Sequence as a collection of compounds in an ArrayList
  *
- * @param <C>
+ * @param <C> the compound type
  */
 public class ArrayListSequenceReader<C extends Compound> implements SequenceReader<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
index 4c1f064ea6..8ca85aeec3 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/BitSequenceReader.java
@@ -64,7 +64,7 @@ public BitSequenceReader(BitArrayWorker<C> worker, AccessionID accession) {
 	}
 
 	/**
-	 * Class is immutable & so this is unsupported
+	 * Class is immutable, so this is unsupported
 	 */
 	@Override
 	public void setCompoundSet(CompoundSet<C> compoundSet) {
@@ -72,7 +72,7 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 	}
 
 	/**
-	 * Class is immutable & so this is unsupported
+	 * Class is immutable, so this is unsupported
 	 */
 	@Override
 	public void setContents(String sequence) throws CompoundNotFoundException {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
index 46a0501b8a..ae1471b52c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
@@ -56,7 +56,7 @@ public class JoiningSequenceReader<C extends Compound> implements ProxySequenceR
 	private int[] minSequenceIndex;
 
 	/**
-	 * Allows creation of the store from Vargs Sequence<C> objects. CompoundSet
+	 * Allows creation of the store from Vargs {@link Sequence<C>} objects. CompoundSet
 	 * defaults to the first element of the array (assuming there are elements
 	 * available during construction otherwise we will throw an illegal
 	 * state exception).
@@ -66,7 +66,7 @@ public JoiningSequenceReader(Sequence<C>... sequences) {
 	}
 
 	/**
-	 * Allows creation of the store from List<Sequence<C>>. CompoundSet
+	 * Allows creation of the store from {@link List<Sequence<C>>}. CompoundSet
 	 * defaults to the first element of the List (assuming there are elements
 	 * available during construction otherwise we will throw an illegal
 	 * state exception).
@@ -217,7 +217,7 @@ else if (midMinPosition > position && midMaxPosition > position) {
 
 	/**
 	 * Iterator implementation which attempts to move through the 2D structure
-	 * attempting to skip onto the next sequence as & when it is asked to
+	 * attempting to skip onto the next sequence as &amp; when it is asked to
 	 */
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
index 995a358ef0..c2b02debee 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SequenceAsStringHelper.java
@@ -29,7 +29,7 @@
 /**
  * This is a common method that can be used across multiple storage/proxy implementations to
  * handle Negative strand and other interesting elements of sequence data.
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SequenceAsStringHelper<C extends Compound> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
index b02c1e0c77..fd492f1bf9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/SingleCompoundSequenceReader.java
@@ -168,7 +168,7 @@ public AccessionID getAccession() {
 	}
 
 	/**
-	 * Delegates to {@link SequenceMixin#countCompounds(org.biojava.nbio.core.sequence.template.Sequence, C[]) }
+	 * Delegates to {@link SequenceMixin#countCompounds}
 	 */
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
index b5b2d29740..38cf55d09c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -47,7 +47,7 @@
 /**
  *
  * The base class for DNA, RNA and Protein sequences.
- * @param <C>
+ * @param <C> the compound type
  */
 public abstract class AbstractSequence<C extends Compound> implements Sequence<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
index 6dbeda2208..aa04cb8c8a 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Compound.java
@@ -28,21 +28,23 @@
 
 public interface Compound {
 
-	public boolean equalsIgnoreCase(Compound compound);
+	boolean equalsIgnoreCase(Compound compound);
 
-	public String getDescription();
+	String getDescription();
 
-	public void setDescription(String description);
+	void setDescription(String description);
 
-	public String getShortName();
+	String getShortName();
 
-	public void setShortName(String shortName);
+	void setShortName(String shortName);
 
-	public String getLongName();
+	String getLongName();
 
-	public void setLongName(String longName);
+	void setLongName(String longName);
 
-	public Float getMolecularWeight();
+	Float getMolecularWeight();
 
-	public void setMolecularWeight(Float molecularWeight);
+	void setMolecularWeight(Float molecularWeight);
+
+	String toString();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java
index e6f632224b..033fa84e85 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/LightweightProfile.java
@@ -52,7 +52,7 @@ enum StringFormat {
 	 *
 	 * @param listIndex index of sequence in profile
 	 * @return desired sequence
-	 * @throws IndexOutOfBoundsException if listIndex < 1 or listIndex > number of sequences
+	 * @throws IndexOutOfBoundsException if listIndex &lt; 1 or listIndex &gt; number of sequences
 	 */
 	S getAlignedSequence(int listIndex);
 
@@ -68,7 +68,7 @@ enum StringFormat {
 	 *
 	 * @param alignmentIndex column index within an alignment
 	 * @return the sequence elements
-	 * @throws IndexOutOfBoundsException if alignmentIndex < 1 or alignmentIndex > {@link #getLength()}
+	 * @throws IndexOutOfBoundsException if alignmentIndex &lt; 1 or alignmentIndex &gt; {@link #getLength()}
 	 */
 	List<C> getCompoundsAt(int alignmentIndex);
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
index c3dec3d0bd..a71c9ba6f8 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceMixin.java
@@ -150,7 +150,7 @@ public static <C extends Compound> Map<C, Integer> getComposition(Sequence<C> se
 	 * converting to a full length String and then writing the data out
 	 *
 	 * @param <C> Type of compound
-	 * @param writer The writer to send data to
+	 * @param appendable The writer to send data to
 	 * @param sequence The sequence to write out
 	 * @throws IOException Thrown if we encounter a problem
 	 */
@@ -244,7 +244,7 @@ public static <C extends Compound> SequenceView<C> createSubSequence(
 	 * Implements sequence shuffling by first materializing the given
 	 * {@link Sequence} into a {@link List}, applying
 	 * {@link Collections#shuffle(List)} and then returning the shuffled
-	 * elements in a new instance of {@link SequenceBackingStore} which behaves
+	 * elements in a new instance of {@link Sequence} which behaves
 	 * as a {@link Sequence}.
 	 */
 	public static <C extends Compound> Sequence<C> shuffle(Sequence<C> sequence) {
@@ -285,7 +285,7 @@ public static <C extends Compound> List<SequenceView<C>> nonOverlappingKmers(Seq
 
 	/**
 	 * Used to generate overlapping k-mers such i.e. ATGTA will give rise to
-	 * ATG, TGT & GTA
+	 * ATG, TGT &amp; GTA
 	 *
 	 * @param <C> Compound to use
 	 * @param sequence Sequence to build from
@@ -343,7 +343,7 @@ public static <C extends Compound> SequenceView<C> inverse(Sequence<C> sequence)
 	/**
 	 * A case-insensitive manner of comparing two sequence objects together.
 	 * We will throw out any compounds which fail to match on their sequence
-	 * length & compound sets used. The code will also bail out the moment
+	 * length &amp; compound sets used. The code will also bail out the moment
 	 * we find something is wrong with a Sequence. Cost to run is linear to
 	 * the length of the Sequence.
 	 *
@@ -359,7 +359,7 @@ public static <C extends Compound> boolean sequenceEqualityIgnoreCase(Sequence<C
 	/**
 	 * A case-sensitive manner of comparing two sequence objects together.
 	 * We will throw out any compounds which fail to match on their sequence
-	 * length & compound sets used. The code will also bail out the moment
+	 * length &amp; compound sets used. The code will also bail out the moment
 	 * we find something is wrong with a Sequence. Cost to run is linear to
 	 * the length of the Sequence.
 	 *
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
index 7d75a10d6a..bb86de83c9 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/Table.java
@@ -57,8 +57,8 @@ CompoundSet<Codon> getCodonCompoundSet(
 	/**
 	 * Instance of a Codon which is 3 {@link NucleotideCompound}s, its
 	 * corresponding {@link AminoAcidCompound} and if it is a start or stop codon.
-	 * The object implements hashCode & equals but according to the nucleotide
-	 * compounds & not to the designation of it being a start, stop & amino
+	 * The object implements hashCode &amp; equals but according to the nucleotide
+	 * compounds &amp; not to the designation of it being a start, stop &amp; amino
 	 * acid compound
 	 *
 	 * @author ayates
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
index 162d760f05..f79bd0465e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java
@@ -39,7 +39,7 @@
  * Protein sequence.
  *
  * In order to build one look at @ TranscriptionEngine.Builder} which provides
- * intelligent defaults & allows you to build an engine which is nearly the same
+ * intelligent defaults and allows you to build an engine which is nearly the same
  * as the default one but with a few changes. All of the engine is customisable.
  *
  * By default the code will attempt to:
@@ -48,7 +48,7 @@
  * <li>Trim Stops</li>
  * <li>Convert initiating codons to M</li>
  * <li>Allow for the fuzzy translation of Codons i.e. if it contains an N that
- * produces a {@link Sequence}&lt;{@link{AminoAcidCompound}&gt; with an X at
+ * produces a {@link Sequence<AminoAcidCompound>} with an X at
  * that position
  * </ul>
  *
@@ -170,7 +170,7 @@ public CompoundSet<AminoAcidCompound> getAminoAcidCompounds() {
 	}
 
 	/**
-	 * This class is the way to create a {@link TranslationEngine}.
+	 * This class is the way to create a {@link TranscriptionEngine}.
 	 */
 	public static class Builder {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
index 3259676ef0..0b132b180e 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java
@@ -336,8 +336,8 @@ public static boolean ping(String url, int timeout) {
 	 * </code>
 	 * <p>
 	 *
-	 * <bold>NB. User should execute connect() method before getting input
-	 * stream.</bold>
+	 * <strong>NB. User should execute connect() method before getting input
+	 * stream.</strong>
 	 * @return
 	 * @throws IOException
 	 * @author Jacek Grzebyta
@@ -350,7 +350,7 @@ public static URLConnection prepareURLConnection(String url, int timeout) throws
 	}
 
 	/**
-	 * Recursively delete a folder & contents
+	 * Recursively delete a folder &amp; contents
 	 *
 	 * @param dir directory to delete
 	 */
@@ -375,7 +375,7 @@ public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOExce
 	    });
 	}
 	/**
-	 * Recursively delete a folder & contents
+	 * Recursively delete a folder &amp; contents
 	 *
 	 * @param dir directory to delete
 	 */
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
index 09f8a6760d..5df00ea661 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/FlatFileCache.java
@@ -58,7 +58,7 @@ private FlatFileCache(){
 
 	/**
 	 * The file is read and the bytes stored immediately.
-	 * <p/> 
+	 * <p> 
 	 * Once added, {@code fileToCache} can be modified or deleted and the cached values will not change.
 	 * @param key
 	 * @param fileToCache A readable file, of Integer.MAX bytes length or less.
@@ -123,7 +123,7 @@ public  static InputStream getInputStream(String key){
 
 	/**
 	 * Returns the number of items in the cache.
-	 * If the cache is {@}, returns -1
+	 * If the cache is empty, returns -1
 	 * @return
 	 */
 	public static int size() {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
index f3bcef0468..2c10948b55 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
@@ -31,13 +31,16 @@
 import org.slf4j.LoggerFactory;
 
 
-/** A in memory cache using soft references. (can be garbage collected)
+/**
+ * An in memory cache using soft references. (can be garbage collected)
  * This code is based on: http://java-interview-faqs.blogspot.com/2008/09/building-faster-and-efficient-cache.html
- * <p/>
+ * <p>
  * Note that entrySet() is not implemented and therefore many methods such as keySet(),
  * containsKey(), values() etc do not work.
- * <p/>
+ * <p>
  * This class is therefore best used as a cache simply to put and get items by a known key
+ * @param <K> the key type
+ * @param <V> the value type
  */
 public class SoftHashMap<K, V> extends AbstractMap<K, V> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
index 1fe985d0ba..1ddadf695c 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/StringManipulationHelper.java
@@ -77,7 +77,7 @@ private StringManipulationHelper() {
 	 * <li> Any IOException reading the stream is 'squashed' and not made
 	 *   available to caller
 	 * <li> An additional newline is appended at the end of the string.
-	 * <ul>
+	 * </ul>
 	 * @author andreas
 	 * @param stream
 	 * @return a possibly empty but non-null String
@@ -202,9 +202,9 @@ public static boolean equalsToXml(String expected, String actual) {
 	/**
 	 * Adds padding to left of supplied string
 	 * @param s The String to pad
-	 * @param n an integer >= 1
+	 * @param n an integer &gt;= 1
 	 * @return The left-padded string. 
-	 * @throws IllegalArgumentException if n <= 0
+	 * @throws IllegalArgumentException if n &lt;= 0
 	 */
 	public static String padLeft(String s, int n) {
 		validatePadding(n);
@@ -214,9 +214,9 @@ public static String padLeft(String s, int n) {
 	/**
 	 * Adds padding to right of supplied string
 	 * @param s The String to pad
-	 * @param n an integer >= 1
+	 * @param n an integer &gt;= 1
 	 * @return The right-padded string. 
-	 * @throws IllegalArgumentException if n <= 0
+	 * @throws IllegalArgumentException if n &lt;= 0
 	 */
 	public static String padRight(String s, int n) {
 		validatePadding(n);
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
index 64aee3849a..9b895ef492 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLHelper.java
@@ -164,7 +164,7 @@ public static Element selectParentElement(Element element, String parentName) {
 	/**
 	 * If {@code}xpathExpression{@code} is a plain string with no '/' characterr, this is 
 	 * interpreted as a child element name to search for. 
-	 * <b/>
+	 * <p>
 	 * If {@code}xpathExpression{@code} is an XPath expression, this is evaluated and is assumed
 	 * to identify a single element.
 	 * @param element
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
index 141ddba640..7b799818df 100644
--- a/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
+++ b/biojava-core/src/main/java/org/biojava/nbio/core/util/XMLWriter.java
@@ -113,7 +113,7 @@ public interface XMLWriter {
 	 * avoid namespaces that are used only in leaf-nodes of a tree being re-defined
 	 * every time they are used. The XMLWriter will generally try to use the
 	 * suggested prefix for this namespace, but there is no guarantee of this.
-	 * <p/>
+	 * <p>
 	 * 
 	 * In particular, if the namespace is already in use, the current prefix will still
 	 * be used. Similarly if the suggested prefix has already been used for another
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
index 7981d8e6e3..466cabaa94 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaReaderTest.java
@@ -35,7 +35,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FastaReaderTest {
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
index 132a36d816..06459579a7 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
@@ -37,7 +37,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenbankCookbookTest {
 
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
index e813f863a8..0a03c85586 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
@@ -43,7 +43,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Jacek Grzebyta
  * @author Philippe Soares
  */
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
index 4d8ae7e8bd..b5e5598722 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParserTest.java
@@ -32,7 +32,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GenericFastaHeaderParserTest {
 
@@ -52,7 +52,7 @@ public class GenericFastaHeaderParserTest {
 	 * NCBI Reference Sequence           ref|accession|locus
 	 * Local Sequence identifier         lcl|identifier
 	 *
-	 * @author Scooter Willis <willishf at gmail dot com>
+	 * @author Scooter Willis 
 	 */
 	@Test
 	public void testParseHeader() throws CompoundNotFoundException {
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
index 4150e90ffc..072e25a1e4 100644
--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/SimpleGenbankProxySequenceReaderTest.java
@@ -34,7 +34,6 @@
  *
  * @author Jacek Grzebyta
  * @author Paolo Pavan
- * @see InfoTask
  */
 public class SimpleGenbankProxySequenceReaderTest {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
index 0090ce7786..c9786b3ad0 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java
@@ -36,7 +36,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GeneFeatureHelper {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
index 0d40fe835c..9fb2ebce48 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/BlastHomologyHits.java
@@ -28,7 +28,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class BlastHomologyHits {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
index bc6893d19d..67e22bd992 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/homology/GFF3FromUniprotBlastHits.java
@@ -46,7 +46,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  * @author Mark Chapman
  */
 public class GFF3FromUniprotBlastHits {
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
index b68074e080..dc6a97e702 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/geneid/GeneIDXMLReader.java
@@ -37,7 +37,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GeneIDXMLReader {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
index bcdc0bc32b..f18c14a098 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureHelper.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class FeatureHelper {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GCStats.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GCStats.java
index 2974a13c9c..8ee0881551 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GCStats.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GCStats.java
@@ -26,7 +26,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GCStats {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
index 7432729d97..88af970928 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/GFF3Writer.java
@@ -31,7 +31,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GFF3Writer {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
index d0b2fc8f97..4163be2b56 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/Location.java
@@ -409,9 +409,9 @@ public LocIterator iterator( int windowSize, int increment )
 	 * The part of this location before the specified position. If position is negative,
 	 * count backwards from the end.
 	 * <br><br>
-	 * For position >= 0, return Location( start, start + position ).
+	 * For position &gt;= 0, return Location( start, start + position ).
 	 * <br>
-	 * For position < 0, return Location( start, end + position ).
+	 * For position &lt; 0, return Location( start, end + position ).
 	 * <br>
 	 * @return New location from start of this location to directly before position.
 	 * @param position Where the prefix ends.
@@ -451,9 +451,9 @@ public Location prefix( int position )
 	 * The part of this location after the specified position. If position is negative, count backwards
 	 * from the end.
 	 * <br><br>
-	 * For position >= 0, return Location( start + position, end ).
+	 * For position &gt;= 0, return Location( start + position, end ).
 	 * <br>
-	 * For position < 0, return Location( end - position, end ).
+	 * For position &lt; 0, return Location( end - position, end ).
 	 * <br>
 	 * @return New location from position to end of this location.
 	 * @param position Where the suffix starts.
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
index 06d65933a9..98f36dd22f 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/BlastXMLQuery.java
@@ -33,7 +33,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class BlastXMLQuery {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/OutputHitsGFF.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/OutputHitsGFF.java
index f7ac399455..5ab5e8f13a 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/query/OutputHitsGFF.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/query/OutputHitsGFF.java
@@ -33,7 +33,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class OutputHitsGFF {
 
diff --git a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
index 374dd378a1..a618443d0f 100644
--- a/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
+++ b/biojava-genome/src/main/java/org/biojava/nbio/genome/util/SplitFasta.java
@@ -35,7 +35,7 @@
 
 /**
  * Utility to write each Fasta entry to a unique file
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SplitFasta {
 
diff --git a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
index e5e1a8379d..3c81c50916 100644
--- a/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
+++ b/biojava-genome/src/test/java/org/biojava/nbio/genome/GeneFeatureHelperTest.java
@@ -43,7 +43,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GeneFeatureHelperTest {
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java
index 39f1fdacf2..5976d635c9 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java
@@ -30,7 +30,7 @@
 
 
 /**
- * @author Spencer Bliven <sbliven@ucsd.edu>
+ * @author Spencer Bliven sbliven@ucsd.edu
  *
  */
 public class ScopDescriptionTest {
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/util/StringManipulationTestsHelper.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/util/StringManipulationTestsHelper.java
index 578816efb9..23664c68a3 100644
--- a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/util/StringManipulationTestsHelper.java
+++ b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/util/StringManipulationTestsHelper.java
@@ -42,7 +42,7 @@ public static void assertEqualsIgnoreEndline(String expected, String actual) {
 
 	/**
 	 * Asserts that two XML-representing strings are equal, by recursively
-	 * comparing each node's set of properties & children nodes. This method
+	 * comparing each node's set of properties and children nodes. This method
 	 * should be used when two XMLs are considered identical when all nodes are
 	 * identical regardless to their order
 	 *
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
index 4a35ff5218..08dafb0626 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
@@ -30,7 +30,7 @@
  * contains information about a certain Component.
  * The Component class uses the extensible enum pattern.
  * You can't instantiate Component directly, instead
- * you have to use one of the {@link register} and {@link of} methods.
+ * you have to use one of the register and {@link #of} methods.
  *
  * @author Jianjiong Gao
  * @since 3.0
@@ -109,7 +109,7 @@ public boolean isCTerminal() {
 	/**
 	 * Get a Component that does not have to occur at terminals. If the
 	 * corresponding component has already been registered, return that one.
-	 * @param pdbccIds possible Protein Data Bank ID.
+	 * @param pdbccId possible Protein Data Bank ID.
 	 * @return a component.
 	 * @throws IllegalArgumentException if pdbccId or type is null,
 	 *  or the pdbccId has been registered as a different type.
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java
index 75ddb4c807..8bbccacce3 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java
@@ -54,10 +54,10 @@ public ModificationLinkage(
 	 *
 	 * @param components {@link Component}s involved in a modification.
 	 * @param indexOfComponent1 index of the first component.
-	 * @param labelOfAtomOnComponent1 label of the atom on the first
+	 * @param pdbNameOfAtomsOnComponent1 label of the atom on the first
 	 *  component.
 	 * @param indexOfComponent2 index of the second component.
-	 * @param labelOfAtomOnComponent2 label of the atom on the second
+	 * @param pdbNameOfAtomsOnComponent2 label of the atom on the second
 	 *  component.
 	 */
 	public ModificationLinkage(
@@ -77,10 +77,10 @@ public ModificationLinkage(
 	 *
 	 * @param components {@link Component}s involved in a modification.
 	 * @param indexOfComponent1 index of the first component.
-	 * @param labelOfAtomOnComponent1 label of the atom on the first
+	 * @param pdbNameOfPotentialAtomsOnComponent1 label of the atom on the first
 	 *  component.
 	 * @param indexOfComponent2 index of the second component.
-	 * @param labelOfAtomOnComponent2 label of the atom on the second
+	 * @param pdbNameOfPotentialAtomsOnComponent2 label of the atom on the second
 	 *  component.
 	 */
 	public ModificationLinkage(
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
index 043aa3d779..383560ab01 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
@@ -206,7 +206,7 @@ public static void register(final ProteinModification modification) {
 
 	/**
 	 * Remove a modification from registry.
-	 * @param mod
+	 * @param modification
 	 */
 	public static void unregister(ProteinModification modification) {
 		if (modification==null) throw new IllegalArgumentException("modification == null!");
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
index 164c3d86d9..1a65fcdfbc 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
@@ -47,7 +47,7 @@ public interface ModifiedCompound {
 
 	/**
 	 *
-	 * @return {@link ProteinModificationBean} occurred on the residue.
+	 * @return {@link ProteinModification} occurred on the residue.
 	 */
 	public ProteinModification getModification();
 
@@ -73,19 +73,18 @@ public interface ModifiedCompound {
 	/**
 	 *
 	 * @return a set of atom linkages.
-	 * @see #getLinkedGroupPairs
 	 * @see StructureAtomLinkage
 	 */
 	public Set<StructureAtomLinkage> getAtomLinkages();
 
-	/** Set atom linkages
+	/**
+	 * Set atom linkages
 	 *
-	 * @return
 	 */
 	public void setAtomLinkages(Set<StructureAtomLinkage> linkages);
 
 	/**
-	 * Add a linkage. Add new the involved groups first using {@link addGroup}.
+	 * Add a linkage. Add new the involved groups first using addGroup.
 	 * @param linkage an atom linkage.
 	 * @return true if this linkage was not already contained.
 	 * @see StructureAtomLinkage
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
index 889d3948b2..435772defd 100644
--- a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
@@ -65,7 +65,6 @@ public ModifiedCompoundImpl(){
 	 * Use this constructor for a modified residue.
 	 * @param modification {@link ProteinModification}.
 	 * @param modifiedResidue modified group.
-	 * @return a {@link ModifiedCompound}.
 	 * @throws IllegalArgumentException if either argument is null.
 	 */
 	public ModifiedCompoundImpl (
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
index b921fdd243..5463d3ccee 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
@@ -40,7 +40,6 @@
  * @author Matthew Pocock
  *
  * @since 1.4
- * @see org.biojavax.ontology.ComparableOntology
  */
 
 public interface Ontology  {
@@ -129,7 +128,6 @@ public interface Ontology  {
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name)
@@ -148,7 +146,6 @@ public Term createTerm(String name)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name, String description)
@@ -168,7 +165,6 @@ public Term createTerm(String name, String description)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name, String description, Object[] synonyms)
@@ -187,7 +183,6 @@ public Term createTerm(String name, String description, Object[] synonyms)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Variable createVariable(String name, String description)
@@ -208,7 +203,6 @@ public Variable createVariable(String name, String description)
 	 * @param t  the Term to import
 	 * @param localName  the local name to import it under, optionally null
 	 * @return a Term
-	 * @throws ChangeVetoException
 	 * @throws IllegalArgumentException
 	 */
 
@@ -228,7 +222,6 @@ public Term importTerm(Term t, String localName)
 	 * @return  a new Triple over these three terms
 	 * @throws AlreadyExistsException if a triple already exists with the same
 	 *      subject, object and predicate, regardless of the name and description
-	 * @throws ChangeVetoException
 	 * @throws NullPointerException if subject, object or predicate are null
 	 * @throws IllegalArgumentException if subject, object or predicate are not all
 	 *      from the same ontology
@@ -251,7 +244,6 @@ public Triple createTriple(Term subject, Term object, Term predicate, String nam
 	/**
 	 * Remove a term from an ontology, together with all triples which refer to it.
 	 * @param t
-	 * @throws ChangeVetoException
 	 */
 
 	public void deleteTerm(Term t) ;
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
index 209c76414f..df26dcbcba 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
@@ -32,7 +32,7 @@
 
 
 /**
- * A term in an ontology.  This has an {@link org.biojava.nbio.Annotation Annotation}
+ * A term in an ontology.  This has an {@link Annotation Annotation}
  * which can be used for storing additional human-displayable information.  It
  * is strongly recommended that the Annotation is not used for any machine-readable
  * data -- this should be represented by relations in the ontology instead.
@@ -51,9 +51,7 @@
  * @author Thomas Down
  * @author Matthew Pocock
  * @since 1.4
- * @see org.biojavax.ontology.ComparableTerm
  */
-
 public interface Term extends Annotatable {
 	/**
 	 * ChangeType which indicates that this term's ontology has been
@@ -113,7 +111,6 @@ public interface Term extends Annotatable {
 
 	/**
 	 * Simple in-memory implementation of an ontology term.
-	 * @see org.biojavax.ontology.SimpleComparableTerm
 	 * This can be used to implement Ontology.createTerm
 	 */
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
index a265f2ff56..368bfea36e 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
@@ -41,7 +41,6 @@
  * @author Thomas Down
  * @author Matthew Pocock
  * @since 1.4
- * @see org.biojavax.ontology.ComparableTriple
  */
 
 public interface Triple
@@ -79,7 +78,6 @@ public interface Triple
 	 * If you do not implement hashcode in this way then you have no guarantee
 	 * that your Triple objects will be found in an ontology and that they will
 	 * not be duplicated.
-	 * </p>
 	 */
 	@Override
 	public int hashCode();
@@ -90,7 +88,7 @@ public interface Triple
 	 * <p>
 	 * Two triples are equivalent if they have the same subject, object and
 	 * predicate fields.
-	 * <pre>
+	 * <pre>{@code
 	 * if (! (o instanceof Triple)) {
 	 *     return false;
 	 * }
@@ -98,11 +96,10 @@ public interface Triple
 	 * return to.getSubject() == getSubject() &&
 	 *        to.getObject() == getObject() &&
 	 *        to.getPredicate() == getPredicate();
-	 * </pre>
+	 * }</pre>
 	 * If you do not implement equals in this way then you have no guarantee
 	 * that your Triple objects will be found in an ontology and that they will
 	 * not be duplicated.
-	 * </p>
 	 */
 	@Override
 	public boolean equals(Object obj);
@@ -111,9 +108,7 @@ public interface Triple
 	 * Basic in-memory implementation of a Triple in an ontology
 	 *
 	 * This can be used to implement Ontology.createTriple
-	 * @see org.biojavax.ontology.SimpleComparableTriple
 	 */
-
 	public static final class Impl
 
 	implements Triple, java.io.Serializable {
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
index 2c0ed0a3ae..77259b0e5b 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
@@ -54,7 +54,7 @@
  * the core ontology.
  * </p>
  *
- * <code><pre>
+ * <pre>
  * ...
  * triple	is-a	any
  * triple	has-a	source
@@ -62,7 +62,7 @@
  * triple	has-a	predicate
  * (triple,has-a,any)	size	3
  * ...
- * </pre></code>
+ * </pre>
  *
  * <p>
  * The first four lines just associate triple with some type with a predicate
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java
index b6aed42304..43c5d532bc 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/package-info.java
@@ -19,10 +19,8 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * Tools for loading and saving ontologies.
  * </P>
- * </BODY>
  */
 package org.biojava.nbio.ontology.io;
\ No newline at end of file
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
index 96474a5385..8e8a16d174 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
@@ -33,12 +33,13 @@
 import java.util.*;
 
 
-/** A class to parse the content of an OBO file. It delegates handling of the
+/**
+ * A class to parse the content of an OBO file. It delegates handling of the
  * content to the OBOFileEventListener implementation.
  *
  * This file contains parts of the OBO-Edit file OBOParseEngine, (particularly the encoding and decoding part)
  *
- * http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup
+ * See <a href="http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup">link</a>
  * Thanks to the OboEdit developers for giving permission to release this in BioJava.
  *
  *
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
index 4018aa0655..c1be7a3c99 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
@@ -75,7 +75,6 @@
  * @author  Matthew Pocock
  * @author <a href="mailto:kdj@sanger.ac.uk">Keith James</a> (docs).
  * @author  Kalle Näslund (docs)
- * @see org.biojavax.RichAnnotatable
  * @since 1.0
  */
 public interface Annotatable  {
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
index a0cf3ce65a..e0ade9cc6b 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
@@ -53,7 +53,6 @@
  *
  * @author Matthew Pocock
  * @author Thomas Down
- * @see org.biojavax.RichAnnotation
  *
  *
  * @since 1.0
@@ -96,8 +95,6 @@ public interface Annotation  {
 	 * @param value the new value for this key
 	 * @throws IllegalArgumentException if the property <code>key</code> is not
 	 *         legal
-	 * @throws ChangeVetoException if this annotation object can't be changed, or
-	 *         if the change was vetoed.
 	 */
 	void setProperty(Object key, Object value)
 	;
@@ -108,7 +105,6 @@ void setProperty(Object key, Object value)
 	 *
 	 * @param key the key object
 	 * @throws NoSuchElementException if the property doesn't exist
-	 * @throws ChangeVetoException if the change is vetoed
 	 * @since 1.3
 	 *
 	 */
@@ -147,7 +143,7 @@ public void removeProperty(Object key)
 	 * A really useful empty and immutable annotation object.
 	 * </p>
 	 *
-	 * Be careful when stooring Annotation arguments to
+	 * Be careful when storing Annotation arguments to
 	 *  constructors. It is possible that you have been passed EMPTY_ANNOTATION but
 	 * that code later on will access this object believing it to be
 	 * mutable. For example, the SeqIO factory code clones some
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java
index 99a48861ea..985d55e911 100644
--- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java
+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java
@@ -35,7 +35,6 @@
  *
  * @since 1.0 as part of Annotation
  * @since 1.4 as top-level class
- * @see org.biojavax.EmptyRichAnnotation
  */
 class EmptyAnnotation
 
diff --git a/biojava-ontology/src/main/java/package-info.java b/biojava-ontology/src/main/java/package-info.java
index 56cc7e5eba..7cafa32539 100644
--- a/biojava-ontology/src/main/java/package-info.java
+++ b/biojava-ontology/src/main/java/package-info.java
@@ -19,7 +19,6 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * A general-purpose API for ontologies.
  * These are directed graphs consisting of <code>Term</code> obects.  Each
@@ -30,5 +29,4 @@
  * <P>Some interfaces and implementations from this package are extended in
  * {@link org.biojavax.ontology biojavax} to better facilitate their persistence to
  * biosql.</P>
- * </BODY>
  */
\ No newline at end of file
diff --git a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
index ccb85292b8..91862f0e36 100644
--- a/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
+++ b/biojava-protein-disorder/src/main/java/org/biojava/nbio/ronn/Jronn.java
@@ -270,7 +270,6 @@ public static Map<FastaSequence,Range[]> getDisorder(List<FastaSequence> sequenc
 	 * @throws FileNotFoundException if the input file cannot be found
 	 * @throws IOException of the system cannot access or read from the input file
 	 * @see #getDisorder(FastaSequence)
-	 * @see #Jronn.Range
 	 */
 	public static Map<FastaSequence,Range[]> getDisorder(String fastaFile) throws IOException {
 		final List<FastaSequence> sequences = SequenceUtil.readFasta(new FileInputStream(fastaFile));
diff --git a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
index 97f32828be..5d91f22aa8 100644
--- a/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
+++ b/biojava-structure-gui/src/main/java/demo/AFPFromFasta.java
@@ -41,10 +41,9 @@
 
 /**
  * Demo displaying a structural alignment from a FASTA file using {@link FastaAFPChainConverter}.
- *
- * @author dmyerstu
- * @see {@link DemoAlignmentFromFasta} Also demonstrates the display of {@link StructureAlignment StructureAlignments} from FASTA sequences, but does so using the more general
+ * See {@link DemoAlignmentFromFasta} Also demonstrates the display of {@link StructureAlignment StructureAlignments} from FASTA sequences, but does so using the more general
  *      {@link FastaStructureParser}
+ * @author dmyerstu
  */
 public class AFPFromFasta {
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
index 98ed76f7a4..af2f8f9d91 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
@@ -35,13 +35,13 @@
 import org.slf4j.LoggerFactory;
 
 
-/** A class that obtains two structures via DAS and aligns them
+/**
+ * A class that obtains two structures via DAS and aligns them
  *  This is done in a separate thread.
  *  It is possible to register Event listeners to get notification of when the download has finished.
  *
  * @author Andreas Prlic
  * @since 1.7
- * @version %I% %G%
  */
 public class AlignmentCalc implements AlignmentCalculationRunnable {
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
index 0532d91498..b96b10a066 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DotPlotPanel.java
@@ -56,7 +56,6 @@ public class DotPlotPanel extends ScaleableMatrixPanel {
 	/**
 	 *
 	 * @param alignment The alignment to plot
-	 * @param background [Optional]A matrix of 'background colors' over which to draw the alignment.
 	 *
 	 *	Originally designed as a matrix of RMSD values between AFPs, so it is colorized
 	 *	accordingly from red (0) to black (>10).
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
index 91ca7571b4..3c60ab3275 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MemoryMonitor.java
@@ -51,7 +51,7 @@
 
 
 /**
- * Tracks Memory allocated & used, displayed in graph form.
+ * Tracks Memory allocated and used, displayed in graph form.
  */
 public class MemoryMonitor extends JPanel {
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
index 240246bb88..41eaf80b1e 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/SelectPDBPanel.java
@@ -43,7 +43,8 @@
 import org.biojava.nbio.structure.gui.util.StructurePairSelector;
 
 
-/** A Panel that allows user to specify PDB & chain ID, as well as sub-ranges
+/**
+ * A Panel that allows user to specify PDB and chain ID, as well as sub-ranges
  *
  * @author Andreas
  *
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
index 483df6f2df..3614907b5b 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAligPanel.java
@@ -154,8 +154,8 @@ public MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 	/**
 	 * Constructor using a MultipleAlignment.
 	 *
-	 * @param multAln
-	 * @param colors
+	 * @param msa
+	 * @param jm
 	 */
 	public MultipleAligPanel(MultipleAlignment msa, AbstractAlignmentJmol jm) {
 		this();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
index 4663505797..535ad182fe 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java
@@ -196,7 +196,7 @@ public Structure getStructure(){
 
 	/**
 	 * Set the title of the AlignmentJmol window.
-	 * @param label
+	 * @param title
 	 */
 	public void setTitle(String title){
 		frame.setTitle(title);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java
index 138365c88a..001686e4f6 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/events/package-info.java
@@ -19,12 +19,10 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * Some event classes for the protein structure GUIs.
  * Possible start classes are one level higher at
  * org.biojava.nbio.structure.gui.BiojavaJmol, and org.biojava.nbio.structure.gui.AlignmentGui.
  * </P>
- * </BODY>
  */
 package org.biojava.nbio.structure.gui.events;
\ No newline at end of file
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java
index 1a4bc6d6af..ed9ae12804 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/package-info.java
@@ -19,13 +19,11 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * A few convenience classes to view protein structures with Jmol (if it is on the classpath),
  * to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
  * Possible start classes are BiojavaJmol, AlignmentGui.
  * Also MVC interface for structure-gui
  * </P>
- * </BODY>
  */
 package org.biojava.nbio.structure.gui;
\ No newline at end of file
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
index 5cd010b356..d691a5237d 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/ContinuousColorMapperTransform.java
@@ -60,7 +60,7 @@ public Color getColor(double value) {
 
 	/**
 	 * An arbitrary transform over reals
-	 * @param the input value
+	 * @param value the input value
 	 * @return the transformed value
 	 */
 	public abstract double transform(double value);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java
index 4aafce9f1e..31e3919ae5 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/HSVColorSpace.java
@@ -79,9 +79,8 @@ public static void main(String[] args) {
 
 
 	}
+
 	/**
-	 * @param type
-	 * @param numcomponents
 	 */
 	public HSVColorSpace() {
 		super(ColorSpace.TYPE_HSV, 3);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
index 9522ec7a15..2e6d1fc4e4 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LinearColorInterpolator.java
@@ -142,7 +142,7 @@ public Color interpolate(Color a, Color b, float mixing) {
 	 * InterpolationDirections.
 	 *
 	 * @param colorSpace The color space for interpolation
-	 * @param interpDirection An array of size colorSpace.getNumComponents()
+	 * @param dir An array of size colorSpace.getNumComponents()
 	 * 		giving the interpolation direction for each component.
 	 */
 	public void setColorSpace(ColorSpace colorSpace, InterpolationDirection[] dir) {
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/package-info.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/package-info.java
index 2c59281a2c..c820470c62 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/package-info.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/package-info.java
@@ -19,12 +19,10 @@
  *
  */
 /**
- * <BODY>
  * <P>
  * Some utility classes for the protein structure GUIs.
  * Possible start classes are one level higher at
  * org.biojava.nbio.structure.ngui.BiojavaJmol, and org.biojava.nbio.structure.gui.AlignmentGui.
  * </P>
- * </BODY>
  */
 package org.biojava.nbio.structure.gui.util;
\ No newline at end of file
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
index 52df113942..ea558927a3 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
@@ -104,7 +104,7 @@ public static MultipleAlignmentJmol displayFull(CeSymmResult symm)
 	 * Displays a single structure in a cartoon representation with each
 	 * symmetric repeat colored differently.
 	 *
-	 * @param msa
+	 * @param symmResult
 	 *            the symmetry multiple alignment obtained from CeSymm
 	 * @throws StructureException
 	 */
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
index 8a5764e1bb..507d4c727e 100644
--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
@@ -38,7 +38,7 @@ public abstract class JmolSymmetryScriptGenerator {
 	/**
 	 * Returns an instance of a JmolSymmetryScriptGenerator, based on the symmetry of a structure (factory method)
 	 * @param axisAligner
-	 * @param rotationGroup
+	 * @param name
 	 * @return instance of JmolSymmetryScriptGenerator
 	 */
 	public static JmolSymmetryScriptGenerator getInstance(AxisAligner axisAligner, String name) {
diff --git a/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java b/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
index b198aeb46a..b3c292c92d 100644
--- a/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
+++ b/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
@@ -34,20 +34,20 @@
 
 /**
  *  This demo shows how to use an alternative ChemCompProvider. The default mechanism in BioJava is to access chemical
- *  componentsby using the {@link DownloadChemCompProvider}. It fetches and locally caches chemical component
- *  definitions as they are encountered during file parsing. It can be enabled by using the
- *  {@link FileParsingParameters#setLoadChemCompInfo(boolean)} method.
- *
+ *  components by using the {@link DownloadChemCompProvider}. It fetches and locally caches chemical component
+ *  definitions as they are encountered during file parsing.
+ * <p>
  * The {@link AllChemCompProvider} downloads and unpacks all chemcomps. It is slower and requires more memory than the
  * default {@link DownloadChemCompProvider}, but it avoids network access to the FTP site, if a new chemcomp is
  * detected, that has not been downloaded yet.
- *
+ * <p>
  * Since all chemcomps will be kept in memory, the standard memory that is available to a JVM will not be sufficient
  * in order to run this demo. Please start with -Xmx200M
  *
  * @author Andreas Prlic
  */
 public class DemoChangeChemCompProvider {
+
 	public static void main(String[] args){
 		String pdbId = "1O1G";
 		boolean loadChemComp = true;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
index 2e19acb29a..df38b06205 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
@@ -48,7 +48,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @param s  a trimmed String specifying the name value
 	 * @see #getName
 	 */
-	public void   setName(String s);
+	void   setName(String s);
 
 	/**
 	 * Get atom name, e.g. "CA".
@@ -57,42 +57,42 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return a trimmed String representing the name value
 	 * @see #setName
 	 */
-	public String getName();
+	String getName();
 
 	/**
 	 * Set element of the atom name, e.g. {@link Element#Fe}
 	 * @param e  an Element enumeration
 	 * @see #getElement
 	 */
-	public void   setElement(Element e);
+	void   setElement(Element e);
 
 	/**
 	 * Get element of the atom, e.g. {@link Element#Ca}
 	 * @return an Element enumeration
 	 * @see #setElement
 	 */
-	public Element getElement();
+	Element getElement();
 
 	/**
 	 * Set PDB atom number.
 	 * @param i  an int specifying the PDBserial value
 	 * @see #getPDBserial
 	 */
-	public void setPDBserial(int i) ;
+	void setPDBserial(int i) ;
 
 	/**
 	 * Get PDB atom number.
 	 * @return an int representing the PDBserial value
 	 * @see #setPDBserial
 	 */
-	public int  getPDBserial() ;
+	int  getPDBserial() ;
 
 	/**
 	 * Set the coordinates.
 	 * @param c  an array of doubles specifying the coords value
 	 * @see #getCoords
 	 */
-	public void    setCoords(double[] c);
+	void    setCoords(double[] c);
 
 	/**
 	 * Get the coordinates.
@@ -100,7 +100,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @see #setCoords
 	 * @see #getCoordsAsPoint3d()
 	 */
-	public double[] getCoords() ;
+	double[] getCoords() ;
 
 	/**
 	 * Get the coordinates.
@@ -110,56 +110,56 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return a reference to the Point3d coordinates
 	 * @see #getCoords()
 	 */
-	public Point3d getCoordsAsPoint3d();
+	Point3d getCoordsAsPoint3d();
 
 	/**
 	 * Set the X coordinate.
 	 * @param x  a double
 	 * @see #getX()
 	 */
-	public void setX(double x);
+	void setX(double x);
 
 	/**
 	 * Set the Y coordinate.
 	 * @param y  a double
 	 * @see #getY()
 	 */
-	public void setY(double y);
+	void setY(double y);
 
 	/**
 	 * Set the Z coordinate.
 	 * @param z  a double
 	 * @see #getZ()
 	 */
-	public void setZ(double z);
+	void setZ(double z);
 
 	/**
 	 * Get coordinate X.
 	 * @return a double
 	 * @see #setX(double)
 	 */
-	public double getX() ;
+	double getX() ;
 
 	/**
 	 * Get coordinate Y.
 	 * @return a double
 	 * @see #setY(double)
 	 */
-	public double getY() ;
+	double getY() ;
 
 	/**
 	 * Get coordinate Z.
 	 * @return a double
 	 * @see #setZ(double)
 	 */
-	public double getZ() ;
+	double getZ() ;
 
 	/**
 	 * Set alternate Location.
 	 * @param c  a Character object specifying the alt loc value
 	 * @see #getAltLoc
 	 */
-	public void setAltLoc(Character c);
+	void setAltLoc(Character c);
 
 	/**
 	 * Get alternate Location.
@@ -167,41 +167,41 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * is represented by ' ' (space character, ascii 32).
 	 * @see #setAltLoc
 	 */
-	public Character getAltLoc();
+	Character getAltLoc();
 
 	/**
 	 * Set occupancy.
 	 * @param occupancy  a float specifying the occupancy value
 	 * @see #getOccupancy
 	 */
-	public void setOccupancy(float occupancy) ;
+	void setOccupancy(float occupancy) ;
 
 	/**
 	 * Get occupancy.
 	 * @return a float representing the occupancy value
 	 * @see #setOccupancy
 	 */
-	public float getOccupancy();
+	float getOccupancy();
 
 	/**
 	 * Set temp factor .
 	 * @param temp  a float specifying the temp factor value
 	 * @see #getTempFactor
 	 */
-	public void   setTempFactor(float temp) ;
+	void   setTempFactor(float temp) ;
 
 	/**
 	 * Get temp factor.
 	 * @return a float representing the temp factor value
 	 * @see #setTempFactor
 	 */
-	public float getTempFactor() ;
+	float getTempFactor() ;
 
 	/**
 	 * Return an identical copy of this  object .
 	 * @return  an identical copy of this  object
 	 */
-	public Object clone();
+	Object clone();
 
 	/**
 	 * Set the back-reference to its parent Group.
@@ -209,7 +209,7 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @see #getGroup()
 	 */
 
-	public void setGroup(Group parent);
+	void setGroup(Group parent);
 
 	/**
 	 * Return the parent Group of the Atom.
@@ -217,28 +217,27 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @return Group the parent Group of the Atom, or null
 	 * @see #setGroup(Group)
 	 */
-	public Group getGroup();
+	Group getGroup();
 
 	/**
 	 * Add a bond
 	 * @param bond to be added
 	 * @see #getBonds()
 	 */
-	public void addBond(Bond bond);
+	void addBond(Bond bond);
 
 	/**
 	 * Get all {@link Bond}s this atom is part of.
 	 *
 	 * @return a list of {@link Bond}s or null if no bonds exist for this Atom
 	 */
-	public List<Bond> getBonds();
+	List<Bond> getBonds();
 
 	/**
 	 * Sets the bonds
 	 * @param bonds
 	 */
-	public void setBonds(List<Bond> bonds);
-
+	void setBonds(List<Bond> bonds);
 
 	/**
 	 * Test if another atom has a bond to this atom
@@ -246,19 +245,18 @@ public interface Atom extends Cloneable, PDBRecord {
 	 * @param other
 	 * @return
 	 */
-	public boolean hasBond(Atom other);
+	boolean hasBond(Atom other);
 
 	/**
 	 * Get the charge of this atom
 	 *
 	 * @return a the integer charge.
 	 */
-	public short getCharge();
+	short getCharge();
 
 	/**
 	 * Set the charge of this atom
 	 *
-	 * @return void.
 	 */
-	public void setCharge(short charge);
+	void setCharge(short charge);
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
index 194368d763..eef6de2457 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BioAssemblyIdentifier.java
@@ -58,7 +58,7 @@ public BioAssemblyIdentifier(String pdbCode, int biolNr) {
 	}
 
 	/**
-	 * @param pdbCode
+	 * @param pdbId
 	 * @param biolNr
 	 */
 	public BioAssemblyIdentifier(PdbId pdbId, int biolNr) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
index 7af10c23e0..ae4c97f74e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
@@ -26,7 +26,7 @@
  * A simple bond -- it stores information about two atoms as well as information
  * about its bond order.
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  * @author Ulysse Carion
  */
 public interface Bond extends Serializable {
@@ -39,7 +39,7 @@ public interface Bond extends Serializable {
 	 * @see #getAtomB()
 	 * @return one of the two atoms in this bond
 	 */
-	public Atom getAtomA();
+	Atom getAtomA();
 
 	/**
 	 * Gets atom 'B' of this bond. There is no meaning to which atom is 'A' and
@@ -49,7 +49,7 @@ public interface Bond extends Serializable {
 	 * @see #getAtomA()
 	 * @return one of the two atoms in this bond
 	 */
-	public Atom getAtomB();
+	Atom getAtomB();
 
 	/**
 	 * A utility method to get the other atom in a bond, given one of its atoms.
@@ -66,7 +66,7 @@ public interface Bond extends Serializable {
 	 *             if the passed atom is not in this bond
 	 * @return the atom in this bond that was not passed as an argument
 	 */
-	public Atom getOther(Atom exclude);
+	Atom getOther(Atom exclude);
 
 	/**
 	 * Gets the bond order of this bond. A return value of '1' corresponds to a
@@ -74,7 +74,7 @@ public interface Bond extends Serializable {
 	 *
 	 * @return this bond's bond order
 	 */
-	public int getBondOrder();
+	int getBondOrder();
 
 	/**
 	 * Gets the distance between the two atoms of this bond.
@@ -85,5 +85,5 @@ public interface Bond extends Serializable {
 	 *
 	 * @return the distance between the two atoms of this bond.
 	 */
-	public double getLength();
+	double getLength();
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
index 3c5fd7af68..4deac44faa 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
@@ -27,7 +27,7 @@
  * A simple bond -- it stores information about two atoms as well as information
  * about its bond order.
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  * @author Ulysse Carion
  */
 public class BondImpl implements Bond {
@@ -44,7 +44,7 @@ public class BondImpl implements Bond {
 	 * Note that by forming a bond between atoms 'A' and 'B' with this
 	 * constructor, atoms 'A' and 'B' will be updated to have this bond in their
 	 * list of bonds. If you do not want this automatic updating, instead use
-	 * {@link #Bond(Atom, Atom, int, boolean)} with the
+	 * {@link #BondImpl(Atom, Atom, int, boolean)} with the
 	 * <code>addSelfToAtoms</code> flag set to <code>false</code>.
 	 *
 	 * @param atomA one of the atoms in this bond
@@ -83,7 +83,7 @@ public BondImpl(Atom atomA, Atom atomB, int bondOrder, boolean addSelfToAtoms) {
 	 * include this bond.
 	 * <p>
 	 * If you created your Bond with the constructor
-	 * {@link #Bond(Atom, Atom, int)}, this method has already been called for
+	 * {@link #BondImpl(Atom, Atom, int)}, this method has already been called for
 	 * you and should not be called again.
 	 */
 	// TODO first check if those bonds haven't been made already
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
index 9b3f752092..5a8569f396 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondType.java
@@ -23,7 +23,7 @@
 
 /**
  * Work in progress - NOT final!
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public enum BondType {
 	UNDEFINED, COVALENT, IONIC, HBOND, VANDERWAALS, HYDROPHOBIC, METAL, PLANAR, ATOM_PLANE;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index b6fde44843..8c92f876f0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -327,9 +327,9 @@ public static final double getPsi(AminoAcid a, AminoAcid b)
 	}
 
 	/**
-	 * Test if two amino acids are connected, i.e. if the distance from C to N <
+	 * Test if two amino acids are connected, i.e. if the distance from C to N &lt;
 	 * 2.5 Angstrom.
-	 *
+	 * <p>
 	 * If one of the AminoAcids has an atom missing, returns false.
 	 *
 	 * @param a
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
index 6ceba9fd61..0d067373ca 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
@@ -199,7 +199,7 @@ public interface Chain extends Serializable {
 	 * @return the length
 	 * @see #getAtomGroup(int)
 	 * @see #getAtomGroups()
-	 * @see #getSeqResLength())
+	 * @see #getSeqResLength()
 	 */
 	int getAtomLength();
 
@@ -346,18 +346,20 @@ public interface Chain extends Serializable {
 
 	/**
 	 * Get the predominant {@link GroupType} for a given Chain, following these
-	 * rules: <li>if the ratio of number of residues of a certain
+	 * rules:
+	 * <ul>
+	 * <li>if the ratio of number of residues of a certain
 	 * {@link GroupType} to total non-water residues is above the threshold
 	 * {@value org.biojava.nbio.structure.StructureTools#RATIO_RESIDUES_TO_TOTAL}, then that {@link GroupType} is
 	 * returned</li> <li>if there is no {@link GroupType} that is above the
 	 * threshold then the {@link GroupType} with most members is chosen, logging
 	 * it</li>
+	 * </ul>
 	 * <p>
 	 * See also {@link ChemComp#getPolymerType()} and
 	 * {@link ChemComp#getResidueType()} which follow the PDB chemical component
 	 * dictionary and provide a much more accurate description of groups and
 	 * their linking.
-	 * </p>
 	 *
 	 * @return the predominant group type
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
index 8b7b5cb809..1ea0d1633e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
@@ -346,7 +346,7 @@ public interface Group extends Serializable {
 	 * The main group (this group) will contain the first altloc (be it the default '.' or 'A' or a mix of '.' and 'A').
 	 * <p>
 	 * This method will return the altloc groups that are not the main group, e.g.:
-	 *
+	 * <ul>
 	 * <li> if '.' (default), 'A' and 'B' altlocs are present in file, the main group will contain
 	 * the default '.' and this method will return 2 altloc groups
 	 * </li>
@@ -354,7 +354,7 @@ public interface Group extends Serializable {
 	 * <li> if 'A' and 'B' are present in file without a default '.' group, then the main group will contain the 'A'
 	 * location whilst this method will return only 1 altloc group with the 'B' location
 	 * </li>
-	 *
+	 * </ul>
 	 * <p>
 	 * Note that atoms with the default altloc (.) are included in all groups. Atoms with other altlocs (typically A, B, etc)
 	 * will be sorted into groups by altloc.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
index 5a31f407e2..51d69234c7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
@@ -31,9 +31,8 @@
 
 
 /**
- *
  * Interface for a structure object. Provides access to the data of a PDB file.
- *
+ * <p>
  * A structure object allows to access the PDB header information as well
  * as to the data from the ATOM records. The header information is
  * currently available through the following objects:
@@ -61,50 +60,33 @@
  *
  * <p>
  *  The tutorial for the BioJava structure modules can be found at <a href="https://github.com/biojava/biojava3-tutorial/tree/master/structure">github</a>.
- * </p>
- *
- *
  * <hr/>
- * </hr>
  * <p>
  * Q: How can I get a Structure object from a PDB file?
- * </p>
  * <p>
  * A:
- * </p>
  * <pre>
- *  {@link Structure} loadStructure(String pathToPDBFile){
- * 		{@link PDBFileReader} pdbreader = new {@link PDBFileReader}();
- *
- * 		{@link Structure} structure = null;
- * 		try{
- * 			structure = pdbreader.getStructure(pathToPDBFile);
- * 			System.out.println(structure);
- * 		} catch (IOException e) {
- * 			e.printStackTrace();
- * 		}
+ *  Structure loadStructure(String pathToPDBFile) {
+ * 		PDBFileReader pdbreader = new PDBFileReader();
+ * 		Structure structure = pdbreader.getStructure(pathToPDBFile);
+ * 		System.out.println(structure);
  * 		return structure;
  * 	}
  *  </pre>
  *
  * <hr>
- * </hr>
  * <p>
  * Q: How can I calculate Phi and Psi angles of AminoAcids?
- * </p>
  * <p>
  * A:
- * </p>
- * <pre>
- *  void calcPhiPsi({@link Structure} structure){
- *
+ * <pre>{@code
+ *  void calcPhiPsi(Structure structure) {
  *
  * 		// get the first chain from the structure
- *
- * 		{@link Chain} chain  = structure.getChain(0);
+ * 		Chain chain  = structure.getChain(0);
  *
  * 		// A protein chain consists of a number of groups. These can be either
- * 		// {@link AminoAcid}, {@link HetatomImpl Hetatom} or {@link NucleotideImpl Nucleotide} groups.
+ * 		// AminoAcid, HetatomImpl or NucleotideImpl groups.
  * 		//
  * 		// Note: BioJava provides access to both the ATOM and SEQRES data in a PDB file.
  * 		// since we are interested in doing calculations here, we only request the groups
@@ -113,58 +95,35 @@
  * 		//  get the Groups of the chain that are AminoAcids.
  * 		List<Group> groups = chain.getAtomGroups(GroupType.AMINOACID);
  *
- * 		{@link AminoAcid} a;
- * 		{@link AminoAcid} b;
- * 		{@link AminoAcid} c ;
- *
- * 		for ( int i=0; i < groups.size(); i++){
- *
+ * 		AminoAcid a;
+ * 		AminoAcid b;
+ * 		AminoAcid c;
+ * 		for (int i=0; i < groups.size(); i++) {
  * 			// since we requested only groups of type AMINOACID they will always be amino acids
  * 			// Nucleotide and Hetatom groups will not be present in the groups list.
- *
- * 			b = ({@link AminoAcid})groups.get(i);
- *
- * 			double phi =360.0;
- * 			double psi =360.0;
- *
- * 			if ( i > 0) {
- * 				a = ({@link AminoAcid})groups.get(i-1) ;
- * 				try {
- *
- * 					// the Calc class provides utility methods for various calculations on
- * 					// structures, groups and atoms
- *
- * 					phi = {@link Calc}.getPhi(a,b);
- * 				} catch ({@link StructureException} e){
- * 					e.printStackTrace();
- * 					phi = 360.0 ;
- * 				}
+ * 			b = (AminoAcid)groups.get(i);
+ * 			double phi = 360.0;
+ * 			double psi = 360.0;
+ *
+ * 			if (i > 0) {
+ * 				a = (AminoAcid)groups.get(i-1) ;
+ * 				// the Calc class provides utility methods for various calculations on
+ * 				// structures, groups and atoms
+ * 				phi = Calc.getPhi(a,b);
  * 			}
- * 			if ( i < groups.size()-1) {
- * 				c = ({@link AminoAcid})groups.get(i+1) ;
- * 				try {
- * 					psi = {@link Calc}.getPsi(b,c);
- * 				}catch ({@link StructureException} e){
- * 					e.printStackTrace();
- * 					psi = 360.0 ;
- * 				}
+ * 			if (i < groups.size()-1) {
+ * 				c = (AminoAcid)groups.get(i+1) ;
+ * 				psi = Calc.getPsi(b, c);
  * 			}
- *
  * 			System.out.print(b.getPDBCode() + " " + b.getPDBName() + ":"  );
- *
  * 			System.out.println(String.format("\tphi: %+7.2f psi: %+7.2f", phi, psi));
- *
  * 		}
- * </pre>
+ * 	}
+ * }</pre>
  * <hr>
- * </hr>
- *
- *
- *
  *
  * @author Andreas Prlic
  * @since 1.4
- * @version %I% %G%
  */
 public interface Structure extends Cloneable, Serializable {
 
@@ -782,13 +741,11 @@ public interface Structure extends Cloneable, Serializable {
 	 *
 	 * @param pdb_id  a String specifying the PDBCode
 	 * @see #getPDBCode
-	 * @deprecated use {@link #setPDBCode(PdbId)}
+	 * @deprecated use {@link #setPdbId(PdbId)}
 	 */
 	@Deprecated
 	void setPDBCode (String pdb_id);
 
-
-
 	/**
 	 * Returns the PDB identifier associated with this StructureIdentifier.
 	 * @return the {@link PdbId} object
@@ -796,7 +753,6 @@ public interface Structure extends Cloneable, Serializable {
 	 */
 	PdbId getPdbId();
 	
-	
 	/**Sets the {@link PdbId} identifier associated with this structure.
 	 * @param pdbId the {@link PdbId} identifier object to set
 	 * @since 6.0.0
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
index 9b96705c91..0b802787dd 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -81,7 +81,7 @@ public class StructureIO {
 	 *  <ul>
 	 *  <li>If only a PDB code is provided, the whole structure will be return including ligands, but the first model only (for NMR).
 	 *	<li>Chain IDs are case sensitive, PDB ids are not. To specify a particular chain write as: 4hhb.A or 4HHB.A </li>
-	 *  <li>To specify a SCOP domain write a scopId e.g. d2bq6a1. Some flexibility can be allowed in SCOP domain names, see {@link #setStrictSCOP(boolean)}</li>
+	 *  <li>To specify a SCOP domain write a scopId e.g. d2bq6a1</li>
 	 *  <li>URLs are accepted as well</li>
 	 *  </ul>
 	 *
@@ -116,6 +116,7 @@ public static AtomCache getAtomCache() {
 	 * Returns the first biological assembly that is available for the given PDB id.
 	 * <p>
 	 * The output Structure will be different depending on the multiModel parameter:
+	 * <ul>
 	 * <li>
 	 * the symmetry-expanded chains are added as new models, one per transformId. All original models but
 	 * the first one are discarded.
@@ -124,9 +125,10 @@ public static AtomCache getAtomCache() {
 	 * as original with symmetry-expanded chains added with renamed chain ids and names (in the form
 	 * originalAsymId_transformId and originalAuthId_transformId)
 	 * </li>
+	 * </ul>
 	 * <p>
 	 * For more documentation on quaternary structures see:
-	 * {@link http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies}
+	 * <a href="http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies">http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies</a>
 	 *
 	 *
 	 * @param pdbId
@@ -147,7 +149,7 @@ public static Structure getBiologicalAssembly(String pdbId, boolean multiModel)
 	 * using multiModel={@value AtomCache#DEFAULT_BIOASSEMBLY_STYLE}
 	 * <p>
 	 * For more documentation on quaternary structures see:
-	 * {@link http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies}
+	 * <a href="http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies">http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies</a>
 	 *
 	 *
 	 * @param pdbId
@@ -163,6 +165,7 @@ public static Structure getBiologicalAssembly(String pdbId) throws IOException,
 	 * Returns the biological assembly for the given PDB id and bioassembly identifier.
 	 * <p>
 	 * The output Structure will be different depending on the multiModel parameter:
+	 * <ul>
 	 * <li>
 	 * the symmetry-expanded chains are added as new models, one per transformId. All original models but
 	 * the first one are discarded.
@@ -171,6 +174,7 @@ public static Structure getBiologicalAssembly(String pdbId) throws IOException,
 	 * as original with symmetry-expanded chains added with renamed chain ids and names (in the form
 	 * originalAsymId_transformId and originalAuthId_transformId)
 	 * </li>
+	 * </ul>
 	 * @param pdbId
 	 * @param biolAssemblyNr - the ith biological assembly that is available for a PDB ID (we start counting at 1, 0 represents the asym unit).
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
@@ -202,6 +206,7 @@ public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr)
 	 * Returns all biological assemblies for the given PDB id.
 	 * <p>
 	 * The output Structure will be different depending on the multiModel parameter:
+	 * <ul>
 	 * <li>
 	 * the symmetry-expanded chains are added as new models, one per transformId. All original models but
 	 * the first one are discarded.
@@ -210,6 +215,7 @@ public static Structure getBiologicalAssembly(String pdbId, int biolAssemblyNr)
 	 * as original with symmetry-expanded chains added with renamed chain ids and names (in the form
 	 * originalAsymId_transformId and originalAuthId_transformId)
 	 * </li>
+	 * </ul>
 	 * If only one biological assembly is required use {@link #getBiologicalAssembly(String)} or {@link #getBiologicalAssembly(String, int)} instead.
 	 * @param pdbId
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
index cc7d8109b2..ba8de5d870 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
@@ -33,12 +33,12 @@
  * An identifier that <em>uniquely</em> identifies a whole {@link Structure} or
  * arbitrary substructure. Common examples would be reducing a structure to a
  * single chain, domain, or residue range.
- *
+ * <p>
  * StructureIdentifiers are represented by unique strings. The getId() and fromId()
  * methods convert to and from the string representation.
- *
+ * <p>
  * Implementations should provide a constructor which takes a String. A static
- * <tt>fromId(String)</tt> method is also recommended.
+ * <code>fromId(String)</code> method is also recommended.
  *
  * @author dmyersturnbull
  * @author Spencer Bliven
@@ -48,7 +48,7 @@ public interface StructureIdentifier extends Serializable {
 	/**
 	 * Get the String form of this identifier.
 	 *
-	 * It is recommended that the {@link #toString()} method also return the
+	 * It is recommended that the toString() method also return the
 	 * identifier, for consistency during serialization.
 	 * @return The String form of this identifier
 	 */
@@ -59,11 +59,11 @@ public interface StructureIdentifier extends Serializable {
 	 * Loads a structure encompassing the structure identified.
 	 * The Structure returned should be suitable for passing as
 	 * the input to {@link #reduce(Structure)}.
-	 *
+	 * <p>
 	 * It is recommended that the most complete structure available be returned
 	 * (e.g. the full PDB) to allow processing of unselected portions where
 	 * appropriate.
-	 * @param AtomCache A potential sources of structures
+	 * @param cache A potential sources of structures
 	 * @return A Structure containing at least the atoms identified by this,
 	 *  or null if Structures are not applicable.
 	 * @throws StructureException For errors loading and parsing the structure
@@ -92,7 +92,6 @@ public interface StructureIdentifier extends Serializable {
 	 * ID should match that returned by getPdbId(), if applicable.
 	 * @return
 	 * @throws StructureException
-	 * @see StructureTools#getReducedStructure(Structure, String)
 	 */
 	Structure reduce(Structure input) throws StructureException;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
index 4fce5b853e..ae00c8f7f3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -1015,7 +1015,7 @@ public String  getPDBCode () {
 	}
 	
 	/** {@inheritDoc} 
-	 * @deprecated use {@link #setPDBCode(PdbId)}
+	 * @deprecated use {@link #setPdbId(PdbId)}
 	 * */
 	@Deprecated
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
index 796362809f..3505deaf02 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -42,15 +42,15 @@
 
 /**
  * Represents a structure loaded from a URL (including a file URL)
- *
+ * <p>
  * A few custom query parameters are supported:
  *
  * <ul>
- * <li><tt>format=[pdb|cif]</tt> Specify the file format (will otherwise be
+ * <li><code>format=[pdb|cif]</code> Specify the file format (will otherwise be
  *     guessed from the extension)
- * <li><tt>pdbId=[String]</tt> Specify the PDB ID (also guessed from the filename)
- * <li><tt>chainID=[String]</tt> A single chain from the structure
- * <li><tt>residues=[String]</tt> Residue ranges, in a form understood by
+ * <li><code>pdbId=[String]</code> Specify the PDB ID (also guessed from the filename)
+ * <li><code>chainID=[String]</code> A single chain from the structure
+ * <li><code>residues=[String]</code> Residue ranges, in a form understood by
  *     {@link SubstructureIdentifier}
  * </ul>
  * @author Spencer Bliven
@@ -75,7 +75,7 @@ public class URLIdentifier implements StructureIdentifier {
 	//TODO: should this get renamed to chainname or asymid?
 	public static final String CHAINID_PARAM = "chainid";
 	/**
-	 * URL parameter specifying residue ranges to include, e.g. <tt>residues=A:1-70</tt>
+	 * URL parameter specifying residue ranges to include, e.g. <code>residues=A:1-70</code>
 	 * @see SubstructureIdentifier
 	 */
 	public static final String RESIDUES_PARAM = "residues";
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
index 881fc224b4..e40bdce47c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCPMain.java
@@ -61,7 +61,7 @@ public class CeCPMain extends CeMain {
 	/**
 	 *  version history:
 	 *  1.5 - Added more parameters to the command line, including -maxOptRMSD
-	 *  1.4 - Added DuplicationHint parameter & default to duplicating the shorter chain
+	 *  1.4 - Added DuplicationHint parameter and default to duplicating the shorter chain
 	 *  1.3 - Short CPs are now discarded
 	 *  1.2 - now supports check AlignmentTools.isSequentialAlignment. XML protocol
 	 *  1.1 - skipped, (trying to avoid confusion with jfatcat in all vs. all comparisons)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
index 70f4acb64f..e35e88fce8 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
@@ -39,7 +39,7 @@
  * The original CE paper is available from here: <a href="http://peds.oxfordjournals.org/cgi/content/short/11/9/739">http://peds.oxfordjournals.org/cgi/content/short/11/9/739</a>
  *
  * For a demo of how to use this algorithm, visit the BioJava web site:
- * <a href="">CE usage example</a>.
+ * <a href="https://github.com/biojava/biojava-tutorial/blob/master/structure/alignment.md">CE usage example</a>.
  *
  * The BioJava CE version is based on CE version 2.3 (2003 or 2004).
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
index 106aa08090..b2e7177244 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeParameters.java
@@ -342,7 +342,8 @@ public void setDistanceIncrement(Double distanceIncrement)
 
 
 
-	/** Get the Original RMSD threshold from which the alignment optimization is started
+	/**
+	 * Get the Original RMSD threshold from which the alignment optimization is started
 	 *
 	 * @return oRMSDThreshold
 	 */
@@ -353,7 +354,8 @@ public Double getORmsdThr()
 
 
 
-	/** Set the Original RMSD threshold from which the alignment optimization is started
+	/**
+	 * Set the Original RMSD threshold from which the alignment optimization is started
 	 *
 	 * @param oRmsdThr the threshold
 	 */
@@ -363,16 +365,17 @@ public void setORmsdThr(Double oRmsdThr)
 	}
 
 
-	/** Get the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
+	/**
+	 * Get the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
 	 *
-	 * @param maxNrIterationsForOptimization
 	 */
 	public int getMaxNrIterationsForOptimization() {
 		return maxNrIterationsForOptimization;
 	}
 
 
-	/** Set the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
+	/**
+	 * Set the maximum nr of times the (slow) optimiziation of alignment should iterate. Default: unlimited
 	 *
 	 * @param maxNrIterationsForOptimization
 	 */
@@ -381,7 +384,8 @@ public void setMaxNrIterationsForOptimization(int maxNrIterationsForOptimization
 	}
 
 
-	/** Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
+	/**
+	 * Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
 	 *  By default this is set to 0, meaning no contribution of the sequence alignment score.
 	 *
 	 * @return seqWeight the weight factor (default 0)
@@ -392,7 +396,8 @@ public double getSeqWeight() {
 	}
 
 
-	/** Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
+	/**
+	 * Should sequence conservation be considered as part of the alignment? If yes, this weight factor allows to determine how much.
 	 *  By default this is set to 0, meaning no contribution of the sequence alignment score.
 	 *
 	 * @param seqWeight the weight factor (default 0)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
index 7fa9c4cf28..0f3e4d1283 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
@@ -300,7 +300,7 @@ private static Matrix permuteMatrix(Matrix mat, int cpRows, int cpCols) {
 	/**
 	 * Modifies the {@link AFPChain#setOptAln(int[][][]) optAln} of an AFPChain
 	 * by permuting the second protein.
-	 *
+	 * <p>
 	 * Sets residue numbers in the second protein to <i>(i-cp)%len</i>
 	 *
 	 * @param afpChain
@@ -425,7 +425,7 @@ private static void assignOptAln(AFPChain afpChain, List<List<List<Integer>>> bl
 	/**
 	 * Finds the optimal alignment between two proteins allowing for a circular
 	 * permutation (CP).
-	 *
+	 * <p>
 	 * The precise algorithm is controlled by the
 	 * {@link OptimalCECPParameters parameters}. If the parameter
 	 * {@link OptimalCECPParameters#isTryAllCPs() tryAllCPs} is true, all possible
@@ -456,10 +456,9 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param)
 	/**
 	 * Finds the optimal alignment between two proteins allowing for a circular
 	 * permutation (CP).
-	 *
+	 * <p>
 	 * This algorithm performs a CE alignment for each possible CP site. This is
-	 * quite slow. Use {@link #alignHeuristic(Atom[], Atom[], Object)} for a
-	 * faster algorithm.
+	 * quite slow.
 	 *
 	 * @param ca1 CA atoms of the first protein
 	 * @param ca2 CA atoms of the second protein
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
index 1d1628b51e..1e9e1cf7d7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java
@@ -39,17 +39,17 @@
 
 import javax.vecmath.Matrix4d;
 
-/** a class to chain AFPs to an alignment
+/**
+ * A class to chain AFPs to an alignment
  *
  * @author Andreas Prlic
- *
  */
 public class AFPChainer
 {
 	public static final boolean debug = FatCatAligner.debug;
 	// private static final boolean showAlig = false;
 
-	/**
+	/*
 	// Key function: chain (assembly) the AFPs
 	// a AFP (k) is defined as (i, j, k), with i and j are staring points
 	// AFP extension (eg. AFP(k-1) -> AFP(k) ) requiring
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
index 41cef89031..0c4ee5ec95 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
@@ -973,6 +973,10 @@ public void setOptRmsd(double[] optRmsd)
 		this.optRmsd = optRmsd;
 	}
 
+	/**
+	 * The number of aligned residues in the final alignment.
+	 * @return
+	 */
 	public int getOptLength()
 	{
 		return optLength;
@@ -1023,7 +1027,7 @@ public void setAlnseq2(char[] alnseq2)
 
 	/**
 	 * @return The total length of the alignment, including gaps
-	 * @see #getOptLength(), the number of aligned residues in the final alignment.
+	 * @see #getOptLength()
 	 */
 	public int getAlnLength()
 	{
@@ -1308,7 +1312,7 @@ public void setSequentialAlignment(boolean sequentialAlignment) {
 	 * up to the alignment algorithm.
 	 *
 	 * <p>Note:
-	 * A {@link org.biojava.nbio.structure.gui.JMatrixPanel}, which is used in
+	 * The org.biojava.nbio.structure.gui.JMatrixPanel, used in
 	 * the structure-gui package to display distance matrices, will display the
 	 * transpose of this matrix. Be sure to take that into account when debugging
 	 * visually.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
index c41e31e1c5..802d016c68 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/Block.java
@@ -72,7 +72,7 @@ public interface Block extends ScoresCache {
 	 * alignRes.get(structure).get(residue) = alignRes.get(size).get(length).
 	 *
 	 * @return List a double List of aligned residues for each structure.
-	 * @see #setAlignRes()
+	 * @see #setAlignRes(List)
 	 */
 	public List<List<Integer>> getAlignRes();
 
@@ -89,7 +89,7 @@ public interface Block extends ScoresCache {
 	 * Returns the total number of aligned positions (columns) in the Block.
 	 *
 	 * @return int number of aligned residues.
-	 * @see #getCoreLength();
+	 * @see #getCoreLength()
 	 * @see #size()
 	 */
 	public int length();
@@ -108,7 +108,6 @@ public interface Block extends ScoresCache {
 	 * Block.
 	 *
 	 * @return int number of aligned residues.
-	 * @see #updateCoreLength()
 	 * @see #length()
 	 * @see #size()
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
index becc817e85..e0423b6f8f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockImpl.java
@@ -52,7 +52,6 @@ public class BlockImpl extends AbstractScoresCache implements Serializable,
 	 *
 	 * @param blockSet
 	 *            the parent BlockSet of the BlockImpl instance.
-	 * @return BlockImpl a BlockImpl instance linked to its parent BlockSet.
 	 */
 	public BlockImpl(BlockSet blockSet) {
 
@@ -69,7 +68,6 @@ public BlockImpl(BlockSet blockSet) {
 	 *
 	 * @param b
 	 *            BlockImpl object to be copied.
-	 * @return BlockImpl an identical copy of the input BlockImpl object.
 	 */
 	public BlockImpl(BlockImpl b) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
index 4fdf318c61..ed46d6bbe7 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSet.java
@@ -111,7 +111,7 @@ public interface BlockSet extends ScoresCache {
 	 * This may trigger other properties to update which depend on the
 	 * superposition.
 	 *
-	 * @param matrices
+	 * @param transformations
 	 */
 	public void setTransformations(List<Matrix4d> transformations);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
index 5282f83b31..cbbb3ae895 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/BlockSetImpl.java
@@ -55,7 +55,6 @@ public class BlockSetImpl extends AbstractScoresCache implements Serializable,
 	 *
 	 * @param alignment
 	 *            MultipleAlignment parent of the BlockSet.
-	 * @return BlockSet an instance linked to the parent alignment.
 	 */
 	public BlockSetImpl(MultipleAlignment alignment) {
 
@@ -76,7 +75,6 @@ public BlockSetImpl(MultipleAlignment alignment) {
 	 *
 	 * @param bs
 	 *            BlockSet object to be copied.
-	 * @return BlockSet an identical copy of the input object.
 	 */
 	public BlockSetImpl(BlockSetImpl bs) {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
index d6358a825d..be1c46631c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsemble.java
@@ -147,7 +147,6 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * structure.
 	 *
 	 * @return List of Matrix interatomic distance matrices.
-	 * @see #updateDistanceMatrix()
 	 */
 	public List<Matrix> getDistanceMatrix();
 
@@ -155,7 +154,6 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * Returns the List of MultipleAlignments in the ensemble.
 	 *
 	 * @return List of MultipleAlignment in the ensemble.
-	 * @see #setMultipleAlignments()
 	 */
 	public List<MultipleAlignment> getMultipleAlignments();
 
@@ -165,7 +163,6 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * accessing an index of a List
 	 *
 	 * @return MultipleAlignment at the index in the ensemble.
-	 * @see #setMultipleAlignments()
 	 */
 	public MultipleAlignment getMultipleAlignment(int index);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
index a6df171705..0f0b442a63 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java
@@ -67,7 +67,6 @@ public class MultipleAlignmentEnsembleImpl extends AbstractScoresCache
 	/**
 	 * Default Constructor. Empty ensemble, no structures assigned.
 	 *
-	 * @return MultipleAlignmentEnsemble an empty ensemble instance.
 	 */
 	public MultipleAlignmentEnsembleImpl() {
 
@@ -88,7 +87,6 @@ public MultipleAlignmentEnsembleImpl() {
 	 * @param structureIdentifiers
 	 *            List of Structure names, that can be parsed by
 	 *            {@link AtomCache}.
-	 * @return MultipleAlignmentEnsemble an ensemble with the structures.
 	 */
 	public MultipleAlignmentEnsembleImpl(
 			List<StructureIdentifier> structureIdentifiers) {
@@ -102,7 +100,6 @@ public MultipleAlignmentEnsembleImpl(
 	 *
 	 * @param e
 	 *            MultipleAlignmentEnsemble to copy.
-	 * @return MultipleAlignmentEnsemble identical copy of the input ensemble.
 	 */
 	public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) {
 
@@ -153,7 +150,6 @@ public MultipleAlignmentEnsembleImpl(MultipleAlignmentEnsembleImpl e) {
 	 *            Atoms of the second structure
 	 * @param flexible
 	 *            true if the alignment is flexible (use BlockSets)
-	 * @return MultipleAlignmentEnsemble an ensemble
 	 */
 	public MultipleAlignmentEnsembleImpl(AFPChain afp, Atom[] ca1, Atom[] ca2,
 			boolean flexible) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
index 7f55f1c2f0..738eee30c5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentImpl.java
@@ -53,7 +53,6 @@ public class MultipleAlignmentImpl extends AbstractScoresCache implements
 	/**
 	 * Default Constructor. Empty alignment. No structures assigned.
 	 *
-	 * @return MultipleAlignment an empty MultipleAlignment instance.
 	 */
 	public MultipleAlignmentImpl() {
 		this(new MultipleAlignmentEnsembleImpl()); // assign an empty ensemble.
@@ -65,7 +64,6 @@ public MultipleAlignmentImpl() {
 	 *
 	 * @param ensemble
 	 *            parent MultipleAlignmentEnsemble.
-	 * @return MultipleAlignment an alignment instance part of an ensemble.
 	 */
 	public MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble) {
 
@@ -87,7 +85,6 @@ public MultipleAlignmentImpl(MultipleAlignmentEnsemble ensemble) {
 	 *
 	 * @param ma
 	 *            MultipleAlignmentImpl to copy.
-	 * @return MultipleAlignmentImpl identical copy of the alignment.
 	 */
 	public MultipleAlignmentImpl(MultipleAlignmentImpl ma) {
 
@@ -240,7 +237,6 @@ protected void updateCoreLength() {
 	/**
 	 * Updates all cached properties
 	 *
-	 * @throws StructureException
 	 */
 	protected void updateCache() {
 		updateCoreLength();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
index 702ed1d6a5..e68cbe384e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcMain.java
@@ -91,7 +91,7 @@ public class MultipleMcMain implements MultipleStructureAligner {
 	/**
 	 * Default constructor.
 	 * Default parameters are used.
-	 * @param pairwise the pairwise structure alignment used to generate the
+	 * @param pairwiseAlgo the pairwise structure alignment used to generate the
 	 * 			multiple alignment seed.
 	 */
 	public MultipleMcMain(StructureAlignment pairwiseAlgo){
@@ -177,7 +177,7 @@ private MultipleAlignment generateSeed(List<Atom[]> atomArrays)
 	 * lowest average RMSD against all others.
 	 * The index of this structure is returned.
 	 *
-	 * @param alignments List double containing all-to-all pairwise alignments
+	 * @param afpAlignments List double containing all-to-all pairwise alignments
 	 * @return int reference index
 	 */
 	private static int chooseReferenceRMSD(List<List<AFPChain>> afpAlignments){
@@ -209,7 +209,7 @@ private static int chooseReferenceRMSD(List<List<AFPChain>> afpAlignments){
 	 * It uses the blocks in AFPChain as {@link Block}s in the
 	 * MultipleAlignment, so considers non-topological
 	 * alignments, if the alignment is rigid. If the alignment is flexible,
-	 * it considers the blocks as {@link BlockSets}.
+	 * it considers the blocks as {@link BlockSet}s.
 	 *
 	 * @param afpList the list of pairwise alignments to the reference
 	 * @param atomArrays List of Atoms of the structures
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
index 664f251899..052f147fc6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/mc/MultipleMcOptimizer.java
@@ -108,7 +108,6 @@ public class MultipleMcOptimizer implements Callable<MultipleAlignment> {
 	 *            the parameter beam
 	 * @param reference
 	 *            the index of the most similar structure to all others
-	 * @throws StructureException
 	 */
 	public MultipleMcOptimizer(MultipleAlignment seedAln,
 			MultipleMcParameters params, int reference) {
@@ -235,7 +234,7 @@ private void initialize() throws StructureException {
 	 * <li>Shrink Block: move a block column to the freePool.
 	 * <li>Insert gap: insert a gap in a random position of the alignment.
 	 * </ul>
-	 * </li>
+	 *
 	 */
 	public MultipleAlignment optimize() throws StructureException {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
index 1a9642e251..b17c5ae8f3 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentScorer.java
@@ -304,7 +304,7 @@ public static double getAvgTMScore(List<Atom[]> transformed,
 	 * length.
 	 *
 	 * @param alignment
-	 * @param reference
+	 * @param ref
 	 *            Index of the reference structure
 	 * @return
 	 * @throws StructureException
@@ -427,7 +427,7 @@ public static double getMCScore(MultipleAlignment alignment,
 	 * Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment
 	 * length.
 	 *
-	 * @param transformed
+	 * @param trans
 	 *            List of transformed Atom arrays
 	 * @param d0
 	 *            parameter for the half-score distance
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
index 52f926a5c6..543aaa8405 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -309,7 +309,7 @@ public static List<String> getSequenceAlignment(
 	 * Blocks is indicated by a gap in all positions, meaning that there is a
 	 * possible discontinuity.
 	 *
-	 * @param alignment
+	 * @param msa
 	 *            input MultipleAlignment
 	 * @return String for each row in the alignment, giving the 1-letter code
 	 *         for each aligned residue.
@@ -466,7 +466,7 @@ else if (previousPos[str] + 1 == residue) {
 	 * gap in all positions, meaning that there is something unaligned
 	 * inbetween.
 	 *
-	 * @param alignment
+	 * @param ma
 	 *            input MultipleAlignment
 	 * @return String for each row in the alignment, giving the 1-letter code
 	 *         for each aligned residue.
@@ -479,7 +479,7 @@ public static List<String> getBlockSequenceAlignment(MultipleAlignment ma) {
 	 * Returns the Atom of the specified structure that is aligned in the
 	 * sequence alignment position specified.
 	 *
-	 * @param multAln
+	 * @param msa
 	 *            the MultipleAlignment object from where the sequence alignment
 	 *            has been generated
 	 * @param mapSeqToStruct
@@ -568,7 +568,7 @@ public static int getBlockForSequencePosition(MultipleAlignment multAln,
 	 * Complexity: T(n,l) = O(l*n^2), if n=number of structures and l=alignment
 	 * length.
 	 *
-	 * @param alignment
+	 * @param msa
 	 *            MultipleAlignment
 	 * @return Matrix containing all average residue distances
 	 */
@@ -644,7 +644,7 @@ public static Matrix getAverageResidueDistances(List<Atom[]> transformed) {
 	 * <p>
 	 * For each structure in the alignment, returns an atom for each
 	 * representative atom in the aligned columns, omitting unaligned residues
-	 * (i.e. an array of length <tt>alignment.length()</tt> ).
+	 * (i.e. an array of length <code>alignment.length()</code> ).
 	 * <p>
 	 * All blocks are concatenated together, so Atoms may not appear in the same
 	 * order as in their parent structure. If the alignment blocks contain null
@@ -940,7 +940,6 @@ public static Phylogeny getHSDMTree(MultipleAlignment msta)
 	 * @param msta
 	 *            MultipleAlignment of protein structures
 	 * @return Phylogeny phylogenetic tree
-	 * @throws CompoundNotFoundException
 	 */
 	public static Phylogeny getStructuralTree(MultipleAlignment msta) {
 		double[][] rmsdMat = MultipleAlignmentTools.getRMSDMatrix(msta)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
index 7db5d2e714..771b8b5f68 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentWriter.java
@@ -194,7 +194,7 @@ public static String toAlignedResidues(MultipleAlignment multAln) {
 	 * Converts the transformation Matrices of the alignment into a String
 	 * output.
 	 *
-	 * @param afpChain
+	 * @param alignment
 	 * @return String transformation Matrices
 	 */
 	public static String toTransformMatrices(MultipleAlignment alignment) {
@@ -289,7 +289,7 @@ public static String toXML(MultipleAlignmentEnsemble ensemble)
 	 * ATOM   2004  CA  ARG     4      32.662 -25.111   7.172  132 ARG
 	 * ATOM   2005  CA  GLY     5      29.121 -25.194   8.602  133 ARG
 	 *
-	 * Column 1 -30: Atom & Residue records of query sequence.
+	 * Column 1 -30: Atom and Residue records of query sequence.
 	 * Column 31-54: Coordinates of atoms in query copied from corresponding atoms in template.
 	 * Column 55-59: Corresponding residue number in template based on alignment
 	 * Column 60-64: Corresponding residue name in template
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
index 11f36456ab..8d053a2520 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AFPAlignmentDisplay.java
@@ -168,8 +168,9 @@ public static void getAlign(AFPChain afpChain,Atom[] ca1,Atom[] ca2) {
 	 * <ul>
 	 * <li>{@link AFPChain#getOptAln()} and lengths
 	 * </ul>
-	 *
-	 * <section>Known Bugs</section>
+	 * <p>
+	 * Known Bugs:
+	 * <p>
 	 * Expects the alignment to have linear topology. May give odd results
 	 * for circular permutations and other complicated topologies.
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
index 82d38d010c..c6791f4ed2 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -72,7 +72,7 @@ public class AlignmentTools {
 	 * Since algorithms which create non-sequential alignments split the
 	 * alignment into multiple blocks, some computational time can be saved
 	 * by only checking block boundaries for sequentiality. Setting
-	 * <tt>checkWithinBlocks</tt> to <tt>true</tt> makes this function slower,
+	 * <code>checkWithinBlocks</code> to <code>true</code> makes this function slower,
 	 * but detects AFPChains with non-sequential blocks.
 	 *
 	 * Note that this method should give the same results as
@@ -209,7 +209,7 @@ public static <T> Map<T,T> applyAlignment(Map<T, T> alignmentMap, int k) {
 	 * @param <T>
 	 * @param alignmentMap The input function, as a map (see {@link AlignmentTools#alignmentAsMap(AFPChain)})
 	 * @param identity An identity-like function providing the isomorphism between
-	 *  the codomain of alignmentMap (of type <T>) and the domain (type <S>).
+	 *  the codomain of alignmentMap (of type T) and the domain (type S).
 	 * @param k The number of times to apply the alignment
 	 * @return A new alignment. If the input function is not automorphic
 	 *  (one-to-one), then some inputs may map to null, indicating that the
@@ -239,8 +239,6 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 			}
 		}
 
-
-
 		Map<S, T> imageMap = new HashMap<>(alignmentMap.size());
 
 		//TODO handle nulls consistently.
@@ -282,7 +280,7 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 	 */
 	public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 									   final int maxSymmetry, final float minimumMetricChange) {
-		return getSymmetryOrder(alignment, new IdentityMap<Integer>(), maxSymmetry, minimumMetricChange);
+		return getSymmetryOrder(alignment, new IdentityMap<>(), maxSymmetry, minimumMetricChange);
 	}
 	/**
 	 * Tries to detect symmetry in an alignment.
@@ -303,7 +301,7 @@ public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 	 * identity. If <i>n</i> corresponds to the intrinsic order of the alignment,
 	 * this will be small. This algorithm tries increasing values of <i>n</i>
 	 * and looks for abrupt decreases in the root mean squared offset.
-	 * If none are found at <i>n</i><=maxSymmetry, the alignment is reported as
+	 * If none are found at <i>n</i>&lt;=maxSymmetry, the alignment is reported as
 	 * non-symmetric.
 	 *
 	 * @param alignment The alignment to test for symmetry
@@ -314,7 +312,7 @@ public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 	 *  the calculation time and can lead to overfitting.
 	 * @param minimumMetricChange Percent decrease in root mean squared offsets
 	 *  in order to declare symmetry. 0.4f seems to work well for CeSymm.
-	 * @return The order of symmetry of alignment, or 1 if no order <=
+	 * @return The order of symmetry of alignment, or 1 if no order &lt;=
 	 *  maxSymmetry is found.
 	 *
 	 * @see IdentityMap For a simple identity function
@@ -470,9 +468,10 @@ public static Map<Integer, Integer> guessSequentialAlignment(
 	 * Retrieves the optimum alignment from an AFPChain and returns it as a
 	 * java collection. The result is indexed in the same way as
 	 * {@link AFPChain#getOptAln()}, but has the correct size().
-	 * <pre>
+	 * <pre>{@code
 	 * List<List<List<Integer>>> aln = getOptAlnAsList(AFPChain afpChain);
-	 * aln.get(blockNum).get(structureNum={0,1}).get(pos)</pre>
+	 * aln.get(blockNum).get(structureNum={0,1}).get(pos)
+	 * }</pre>
 	 *
 	 * @param afpChain
 	 * @return
@@ -503,7 +502,7 @@ public static List<List<List<Integer>>> getOptAlnAsList(AFPChain afpChain) {
 
 
 	/**
-	 * A Map<K,V> can be viewed as a function from K to V. This class represents
+	 * A {@code Map<K,V>} can be viewed as a function from K to V. This class represents
 	 * the identity function. Getting a value results in the value itself.
 	 *
 	 * <p>The class is a bit inconsistent when representing its contents. On
@@ -850,7 +849,7 @@ public static AFPChain replaceOptAln(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 	 * @param ca1
 	 * @param ca2 Second set of ca atoms. Will be modified based on the superposition
 	 * @throws StructureException
-	 * @see {@link CECalculator#calc_rmsd(Atom[], Atom[], int, boolean)}
+	 * @see CECalculator#calc_rmsd(Atom[], Atom[], int, boolean)
 	 *  contains much of the same code, but stores results in a CECalculator
 	 *  instance rather than an AFPChain
 	 */
@@ -979,12 +978,13 @@ public static Object resizeArray (Object oldArray, int newSize) {
 	 * <p>Note that more concise representations may be possible.</p>
 	 *
 	 * Examples:
+	 * <ul>
 	 * <li>1>2>3>1</li>
 	 * <li>1>2>3>2 4>3</li>
-	 *
+	 * </ul>
 	 * @param alignment The input function, as a map (see {@link AlignmentTools#alignmentAsMap(AFPChain)})
 	 * @param identity An identity-like function providing the isomorphism between
-	 *  the codomain of alignment (of type <T>) and the domain (type <S>).
+	 *  the codomain of alignment (of type T) and the domain (type S).
 	 * @return
 	 */
 	public static <S,T> String toConciseAlignmentString(Map<S,T> alignment, Map<T,S> identity) {
@@ -1076,9 +1076,9 @@ public static Map<Integer, Integer> fromConciseAlignmentString(String string) {
 
 	/**
 	 * Method that calculates the number of gaps in each subunit block of an optimal AFP alignment.
-	 *
-	 * INPUT: an optimal alignment in the format int[][][].
-	 * OUTPUT: an int[] array of <order> length containing the gaps in each block as int[block].
+	 * @param optAln
+	 * 				an optimal alignment in the format int[][][]
+	 * @return an int[] array of order length containing the gaps in each block as int[block]
 	 */
 	public static int[] calculateBlockGap(int[][][] optAln){
 
@@ -1197,7 +1197,6 @@ public static void alignmentToSIF(Writer out,AFPChain afpChain,
 	 * Does NOT rotate anything.
 	 * @param ca
 	 * @return a list of Chains that is built up from the Atoms in the ca array
-	 * @throws StructureException
 	 */
 	public static final List<Chain> getAlignedModel(Atom[] ca){
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
index 63fc089a97..1435191c2c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -162,7 +162,6 @@ public AtomCache(UserConfiguration config) {
 	 * @return an array of Atoms.
 	 * @throws IOException
 	 * @throws StructureException
-	 * @see
 	 */
 	public Atom[] getAtoms(String name) throws IOException, StructureException {
 		return getAtoms(new StructureName(name));
@@ -189,7 +188,6 @@ public Atom[] getAtoms(StructureIdentifier name) throws IOException, StructureEx
 	 * @return an array of Atoms.
 	 * @throws IOException
 	 * @throws StructureException
-	 * @see
 	 */
 	public Atom[] getRepresentativeAtoms(String name) throws IOException, StructureException {
 		return getRepresentativeAtoms(new StructureName(name));
@@ -223,7 +221,7 @@ public Atom[] getRepresentativeAtoms(StructureIdentifier name) throws IOExceptio
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return a structure object
 	 * @throws IOException
-	 * @throws StructureException if biassemblyId < 0 or other problems while loading structure
+	 * @throws StructureException if biassemblyId &lt; 0 or other problems while loading structure
 	 * @since 3.2
 	 */
 	public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean multiModel)
@@ -247,7 +245,7 @@ public Structure getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
 	 * @return a structure object
 	 * @throws IOException
-	 * @throws StructureException if biassemblyId < 0 or other problems while loading structure
+	 * @throws StructureException if biassemblyId &lt; 0 or other problems while loading structure
 	 * @since 6.0.0
 	 */
 	public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean multiModel)
@@ -305,7 +303,7 @@ public Structure getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean m
 	 * the asymmetric unit will be returned, e.g. for NMR structures.
 	 *
 	 * <p>Biological assemblies can also be accessed using
-	 * <tt>getStructure("BIO:<i>[pdbId]</i>")</tt>
+	 * <code>getStructure("BIO:<i>[pdbId]</i>")</code>
 	 * @param pdbId the PDB id
 	 * @param multiModel if true the output Structure will be a multi-model one with one transformId per model,
 	 * if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).
@@ -466,8 +464,7 @@ public String getPath() {
 	 * <li>If only a PDB code is provided, the whole structure will be return including ligands, but the first model
 	 * only (for NMR).
 	 * <li>Chain IDs are case sensitive, PDB ids are not. To specify a particular chain write as: 4hhb.A or 4HHB.A</li>
-	 * <li>To specify a SCOP domain write a scopId e.g. d2bq6a1. Some flexibility can be allowed in SCOP domain names,
-	 * see {@link #setStrictSCOP(boolean)}</li>
+	 * <li>To specify a SCOP domain write a scopId e.g. d2bq6a1. </li>
 	 * <li>URLs are accepted as well</li>
 	 * </ul>
 	 *
@@ -670,14 +667,14 @@ public void setFileParsingParams(FileParsingParameters params) {
 	 *   Load the requested ID from the PDB's obsolete repository
 	 * <li>{@link ObsoleteBehavior#FETCH_CURRENT FETCH_CURRENT}
 	 *   Load the most recent version of the requested structure
+	 * </ul>
 	 *
 	 * <p>This setting may be silently ignored by implementations which do not have
 	 * access to the server to determine whether an entry is obsolete, such as
-	 * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
+	 * certain {@link FetchBehavior}s. Note that an obsolete entry may still be
 	 * returned even this is FETCH_CURRENT if the entry is found locally.
 	 *
-	 * @param fetchFileEvenIfObsolete Whether to fetch obsolete records
-	 * @see #setFetchCurrent(boolean)
+	 * @param behavior Whether to fetch obsolete records
 	 * @since 4.0.0
 	 */
 	public void setObsoleteBehavior(ObsoleteBehavior behavior) {
@@ -687,7 +684,7 @@ public void setObsoleteBehavior(ObsoleteBehavior behavior) {
 	/**
 	 * Returns how this instance deals with obsolete entries. Note that this
 	 * setting may be ignored by some implementations or in some situations,
-	 * such as when {@link #isAutoFetch()} is false.
+	 * such as certain {@link FetchBehavior}s.
 	 *
 	 * <p>For most implementations, the default value is
 	 * {@link ObsoleteBehavior#THROW_EXCEPTION THROW_EXCEPTION}.
@@ -791,7 +788,7 @@ protected void flagLoadingFinished(PdbId pdbId) {
 
 	/**
 	 * Loads a structure directly by PDB ID
-	 * @param pdbId
+	 * @param id
 	 * @return
 	 * @throws IOException
 	 * @throws StructureException
@@ -806,7 +803,6 @@ public Structure getStructureForPdbId(String id) throws IOException, StructureEx
 	 * @param pdbId
 	 * @return
 	 * @throws IOException
-	 * @throws StructureException
 	 */
 	public Structure getStructureForPdbId(PdbId pdbId) throws IOException {
 		if (pdbId == null)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
index 6e00e1d434..859f944645 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/RotationAxis.java
@@ -374,8 +374,7 @@ private void calculateTranslationalAxis(Matrix rotation, Atom translation) {
 	 * @param atoms Some atoms from the protein, used for determining the bounds
 	 *  	  of the axis.
 	 *
-	 * @return The Jmol script, suitable for calls to
-	 * {@link org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol#evalString() jmol.evalString()}
+	 * @return The Jmol script
 	 */
 	public String getJmolScript(Atom[] atoms){
 		return getJmolScript(atoms, 0);
@@ -442,8 +441,7 @@ public Pair<Atom> getAxisEnds(Atom[] atoms) {
 	 * @param axisID in case of representing more than one axis in the same jmol
 	 * 		  panel, indicate the ID number.
 	 *
-	 * @return The Jmol script, suitable for calls to
-	 * {@link org.biojava.nbio.structure.align.gui.jmol.StructureAlignmentJmol#evalString() jmol.evalString()}
+	 * @return The Jmol script
 	 */
 	public String getJmolScript(Atom[] atoms, int axisID){
 		final double width=.5;// width of JMol object
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
index 70e85acec3..67eba4c966 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/UserConfiguration.java
@@ -306,7 +306,6 @@ public XMLWriter toXML(PrintWriter pw)
 	 * @param xw the XML writer to use
 	 * @return the writer again
 	 * @throws IOException
-	 * @see org.biojava.nbio.structure.align.webstart.ConfigXMLHandler
 	 */
 
 	public XMLWriter toXML(XMLWriter xw)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
index 956bbe90a4..84effc3e44 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/asa/AsaCalculator.java
@@ -618,7 +618,7 @@ private static double getRadiusForNucl(NucleotideImpl nuc, Atom atom) {
 	 *
 	 * If atom is neither part of a nucleotide nor of a standard aminoacid,
 	 * the default vdw radius for the element is returned. If atom is of
-	 * unknown type (element) the vdw radius of {@link Element().N} is returned
+	 * unknown type (element) the vdw radius of {@link Element#N} is returned
 	 *
 	 * @param atom
 	 * @return
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
index 5e0a055a39..9eb9c7c6cf 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/DownloadChemCompProvider.java
@@ -109,11 +109,13 @@ public static void setServerBaseUrl(String serverBaseUrl) {
     /**
      * Set the path to append to the serverBaseUrl (settable in {@link #setServerBaseUrl(String)}).
      * The string can contain placeholders that will be expanded at runtime:
+     * <ul>
      * <li>"{ccd_id}" to be replaced by the chemical component identifier, in capitals</li>
      * <li>"{ccd_id:beginIndex-endIndex}" to be replaced by a substring of the chemical component identifier in capitals,
      * with indices following the same convention as {@link String#substring(int, int)} </li>
      * <li>"{ccd_id:index}" to be replaced by a substring of the chemical component identifier in capitals,
      * with index either a positive or negative integer to substring from left or right of the string respectively.</li>
+     * </ul>
      * If any of the indices are off-bounds, then the full chemical component identifier is replaced
      */
     public static void setChemCompPathUrlTemplate(String chemCompPathUrlTemplate) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/PolymerType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/PolymerType.java
index 78bae77f86..8066044a43 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/PolymerType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/chem/PolymerType.java
@@ -106,22 +106,22 @@ public static PolymerType polymerTypeFromString(String polymerTypeString) {
     }
 
     /**
-     * Convenience <tt>Set</tt> of polymer types classified as protein.  This only contains {@link #peptide}
+     * Convenience <code>Set</code> of polymer types classified as protein.  This only contains {@link #peptide}
      */
     public static final Set<PolymerType> PROTEIN_ONLY;
 
     /**
-     * Convenience <tt>Set</tt> of polymer types classified as DNA.  This only contains {@link #dna}
+     * Convenience <code>Set</code> of polymer types classified as DNA.  This only contains {@link #dna}
      */
     public static final Set<PolymerType> DNA_ONLY;
 
     /**
-     * Convenience <tt>Set</tt> of polymer types classified as RNA.  This only contains {@link #rna}
+     * Convenience <code>Set</code> of polymer types classified as RNA.  This only contains {@link #rna}
      */
     public static final Set<PolymerType> RNA_ONLY;
 
     /**
-     * Convenience <tt>Set</tt> of polymer types classified as DNA.  This contains:
+     * Convenience <code>Set</code> of polymer types classified as DNA.  This contains:
      * <ul>
      * <li>{@link #dna}</li>
      * <li>{@link #rna}</li>
@@ -131,7 +131,7 @@ public static PolymerType polymerTypeFromString(String polymerTypeString) {
     public static final Set<PolymerType> POLYNUCLEOTIDE_ONLY;
 
     /**
-     * Convenience <tt>Set</tt> of all polymer types.
+     * Convenience <code>Set</code> of all polymer types.
      */
     public static final Set<PolymerType> ALL_POLYMER_TYPES;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
index 11e2a59283..6028110eb6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/GridCell.java
@@ -103,9 +103,6 @@ public List<Contact> getContactsWithinCell(){
 	 * within the given cutoff as a list of Contacts containing the indices of the pair and the calculated distance.
 	 *
 	 * @param otherCell
-	 * @param iAtoms the first set of atom coordinates to which the iIndices correspond
-	 * @param jAtoms the second set of atom coordinates to which the jIndices correspond, if null distances are within the iAtoms only
-	 * @param cutoff
 	 * @return
 	 */
 	public List<Contact> getContactsToOtherCell(GridCell otherCell){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
index 5af5a61bc3..60f7c3a91b 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceList.java
@@ -52,7 +52,7 @@ public class StructureInterfaceList implements Serializable, Iterable<StructureI
 	/**
 	 * Default minimum area for a contact between two chains to be considered a
 	 * valid interface.
-	 * @see #removeInterfacesBelowArea(double);
+	 * @see #removeInterfacesBelowArea(double)
 	 */
 	public static final double DEFAULT_MINIMUM_INTERFACE_AREA = 35.0;
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
index 2f9d27997a..f4be5cd4f5 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
@@ -97,7 +97,7 @@ public class EcodInstallation implements EcodDatabase {
 	 * installations at the same path can lead to race conditions when downloading
 	 * files.
 	 * @param cacheLocation Location to save files, typically from the PDB_CACHE_DIR parameter
-	 * @param requestedVersion ECOD requestedVersion to fetch
+	 * @param version ECOD requestedVersion to fetch
 	 */
 	public EcodInstallation(String cacheLocation, String version) {
 		domainsFileLock = new ReentrantReadWriteLock();
@@ -295,7 +295,7 @@ public String getUrl() {
 
 	/**
 	 * Specify a different mirror for the ECOD server.
-	 * @param urlFormat the urlFormat to set
+	 * @param url the urlFormat to set
 	 */
 	public void setUrl(String url) {
 		this.url = url;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
index c1cfeb73e1..b0e440af31 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java
@@ -40,7 +40,7 @@ private CalcPoint() {
 	}
 
 	/**
-	 * Center a cloud of points. This means subtracting the {@lin
+	 * Center a cloud of points. This means subtracting the {@link
 	 * #centroid(Point3d[])} of the cloud to each point.
 	 *
 	 * @param x
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
index bfb029bbe1..c96f2f7125 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionQCP.java
@@ -74,12 +74,12 @@
  * <p>
  * Citations:
  * <p>
- * Liu P, Agrafiotis DK, & Theobald DL (2011) Reply to comment on: "Fast
+ * Liu P, Agrafiotis DK, &amp; Theobald DL (2011) Reply to comment on: "Fast
  * determination of the optimal rotation matrix for macromolecular
  * superpositions." Journal of Computational Chemistry 32(1):185-186.
  * [http://dx.doi.org/10.1002/jcc.21606]
  * <p>
- * Liu P, Agrafiotis DK, & Theobald DL (2010) "Fast determination of the optimal
+ * Liu P, Agrafiotis DK, &amp; Theobald DL (2010) "Fast determination of the optimal
  * rotation matrix for macromolecular superpositions." Journal of Computational
  * Chemistry 31(7):1561-1563. [http://dx.doi.org/10.1002/jcc.21439]
  * <p>
@@ -96,7 +96,7 @@
  * <p>
  * dtheobald@brandeis.edu
  * <p>
- * Pu Liu Johnson & Johnson Pharmaceutical Research and Development, L.L.C. 665
+ * Pu Liu Johnson &amp; Johnson Pharmaceutical Research and Development, L.L.C. 665
  * Stockton Drive Exton, PA 19341 USA
  * <p>
  * pliu24@its.jnj.com
@@ -587,7 +587,7 @@ public Matrix4d superpose(Point3d[] fixed, Point3d[] moved) {
 	 * @param fixed
 	 * @param moved
 	 * @param weight
-	 *            array of weigths for each equivalent point position
+	 *            array of weights for each equivalent point position
 	 * @return weighted RMSD.
 	 */
 	public double getWeightedRmsd(Point3d[] fixed, Point3d[] moved, double[] weight) {
@@ -598,13 +598,11 @@ public double getWeightedRmsd(Point3d[] fixed, Point3d[] moved, double[] weight)
 	/**
 	 * The QCP method can be used as a two-step calculation: first compute the
 	 * RMSD (fast) and then compute the superposition.
-	 *
+	 * <p>
 	 * This method assumes that the RMSD of two arrays of points has been
 	 * already calculated using {@link #getRmsd(Point3d[], Point3d[])} method
 	 * and calculates the transformation of the same two point arrays.
 	 *
-	 * @param fixed
-	 * @param moved
 	 * @return transformation matrix as a Matrix4d to superpose moved onto fixed
 	 *         point arrays
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
index a582f922d2..e6b8548025 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -89,6 +89,7 @@ public BondMaker(Structure structure, FileParsingParameters params) {
 
 	/**
 	 * Creates bond objects and corresponding references in Atom objects:
+	 * <ul>
 	 * <li>
 	 * peptide bonds: inferred from sequence and distances
 	 * </li>
@@ -98,6 +99,7 @@ public BondMaker(Structure structure, FileParsingParameters params) {
 	 * <li>
 	 * intra-group (residue) bonds: read from the chemical component dictionary, via {@link org.biojava.nbio.structure.chem.ChemCompProvider}
 	 * </li>
+	 * </ul>
 	 */
 	public void makeBonds() {
 		logger.debug("Going to start making bonds");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
index 81bf601ab6..1b8278125e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
@@ -51,7 +51,7 @@
 import java.util.*;
 
 /**
- * A collection of static utilities to convert between {@link AFPChain AFPChains} and {@link FastaSequence FastaSequences}.
+ * A collection of static utilities to convert between {@link AFPChain AFPChains} and FastaSequences.
  *
  * @author dmyersturnbull
  * @see StructureSequenceMatcher
@@ -73,7 +73,7 @@ public static AFPChain cpFastaToAfpChain(String first, String second, Structure
 
 	/**
 	 * Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
-	 * {@link cpSite} residues to the right.
+	 * <code>cpSite</code> residues to the right.
 	 *
 	 * @param fastaFile A FASTA file containing exactly 2 sequences, the first unpermuted and the second permuted
 	 * @param cpSite
@@ -97,7 +97,7 @@ public static AFPChain cpFastaToAfpChain(File fastaFile, Structure structure, in
 
 	/**
 	 * Takes a structure and sequence corresponding to an alignment between a structure or sequence and itself (or even a structure with a sequence), where the result has a circular permutation site
-	 * {@link cpSite} residues to the right.
+	 * <code>cpSite</code> residues to the right.
 	 *
 	 * @param first The unpermuted sequence
 	 * @param second The sequence permuted by cpSite
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
index 5297443a34..4ec4577f59 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -259,10 +259,10 @@ public FileParsingParameters getFileParsingParameters(){
 	 *   Load the requested ID from the PDB's obsolete repository
 	 * <li>{@link ObsoleteBehavior#FETCH_CURRENT FETCH_CURRENT}
 	 *   Load the most recent version of the requested structure
-	 *
+	 * </ul>
 	 * <p>This setting may be silently ignored by implementations which do not have
 	 * access to the server to determine whether an entry is obsolete, such as
-	 * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
+	 * certain {@link FetchBehavior}s. Note that an obsolete entry may still be
 	 * returned even this is FETCH_CURRENT if the entry is found locally.
 	 *
 	 * @param behavior Whether to fetch obsolete records
@@ -276,7 +276,7 @@ public void setObsoleteBehavior(ObsoleteBehavior behavior) {
 	/**
 	 * Returns how this instance deals with obsolete entries. Note that this
 	 * setting may be ignored by some implementations or in some situations,
-	 * such as when {@link #isAutoFetch()} is false.
+	 * such as certain {@link FetchBehavior}s.
 	 *
 	 * <p>For most implementations, the default value is
 	 * {@link ObsoleteBehavior#THROW_EXCEPTION THROW_EXCEPTION}.
@@ -295,10 +295,9 @@ public ObsoleteBehavior getObsoleteBehavior() {
 	public FetchBehavior getFetchBehavior() {
 		return fetchBehavior;
 	}
+
 	/**
 	 * Set the behavior for fetching files from the server.
-	 * This replaces the {@link #setAutoFetch(boolean)} method with a more
-	 * extensive set of options.
 	 * @param fetchBehavior
 	 */
 	public void setFetchBehavior(FetchBehavior fetchBehavior) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
index 5591fbdd84..dec97b4f61 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
@@ -30,27 +30,17 @@
 import java.io.InputStream;
 
 /**
- * <p>
  *  The wrapper class for parsing a PDB file.
- *  </p>
- *
  *
- *  <p>
+ * <p>
  *  Several flags can be set for this class
- *  <ul>
- *
- * <li> {@link #setAutoFetch(boolean)} - if the PDB file can not be found locally, should it be fetched
- *  from the PDB ftp servers? (default:false)</li>
- *  <li> Other parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
- *  </ul>
- *  </p>
- *
- *
+ * <ul>
+ * <li> Parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
+ * </ul>
  *
  *<h2>Example</h2>
  * <p>
  * Q: How can I get a Structure object from a PDB file?
- * </p>
  * <p>
  * A:
  * <pre>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
index fd06080118..529526e2e0 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/StructureSequenceMatcher.java
@@ -59,8 +59,7 @@ public class StructureSequenceMatcher {
 	 * @param sequence The input protein sequence
 	 * @param wholeStructure The structure from which to take a substructure
 	 * @return The resulting structure
-	 * @throws StructureException
-	 * @see {@link #matchSequenceToStructure(ProteinSequence, Structure)}
+	 * @see #matchSequenceToStructure(ProteinSequence, Structure)
 	 */
 	public static Structure getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure) {
 		ResidueNumber[] rns = matchSequenceToStructure(sequence, wholeStructure);
@@ -104,8 +103,7 @@ public static Structure getSubstructureMatchingProteinSequence(ProteinSequence s
 	 * @return A ProteinSequence with the full sequence of struct. Chains are
 	 *  concatenated in the same order as the input structures
 	 *
-	 * @see {@link SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which
-	 * 	does the heavy lifting.
+	 * @see SeqRes2AtomAligner#getFullAtomSequence(List, Map, boolean)
 	 *
 	 */
 	public static ProteinSequence getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition ) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
index 00f5d302ec..64c77c3665 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/LUDecomposition.java
@@ -22,10 +22,10 @@
 
 	/** LU Decomposition.
 	<P>
-	For an m-by-n matrix A with m >= n, the LU decomposition is an m-by-n
+	For an m-by-n matrix A with m &gt;= n, the LU decomposition is an m-by-n
 	unit lower triangular matrix L, an n-by-n upper triangular matrix U,
 	and a permutation vector piv of length m so that A(piv,:) = L*U.
-	If m < n, then L is m-by-m and U is m-by-n.
+	If m &lt; n, then L is m-by-m and U is m-by-n.
 	<P>
 	The LU decompostion with pivoting always exists, even if the matrix is
 	singular, so the constructor will never fail.  The primary use of the
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
index 15bd130b99..fab188ce98 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/jama/Matrix.java
@@ -53,7 +53,7 @@
  * 	decomposition classes.  These decompositions are accessed by the Matrix
  * 	class to compute solutions of simultaneous linear equations, determinants,
  * 	inverses and other matrix functions.  The five decompositions are:
- * <P><UL>
+ * <UL>
  * 	<LI>Cholesky Decomposition of symmetric, positive definite matrices.
  * 	<LI>LU Decomposition of rectangular matrices.
  * 	<LI>QR Decomposition of rectangular matrices.
@@ -62,7 +62,7 @@
  * </UL>
  * <DL>
  * <DT><B>Example of use:</B></DT>
- * <P>
+ *
  * <DD>Solve a linear system A x = b and compute the residual norm, ||b - A x||.
  * <P><PRE>
  * 		double[][] vals = {{1.,2.,3},{4.,5.,6.},{7.,8.,10.}};
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
index 0f9066b323..960e18b019 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java
@@ -35,7 +35,7 @@
  *  Does not allow duplicate keys.
  *
  *  This class represents an ordered symbol table. It assumes that
- *  the elements are <tt>Comparable</tt>.
+ *  the elements are <code>Comparable</code>.
  *  It supports the usual <em>put</em>, <em>get</em>, <em>contains</em>,
  *  and <em>delete</em> methods.
  *  It also provides ordered methods for finding the <em>minimum</em>,
@@ -111,9 +111,9 @@ public int size() {
 	}
 
 	/**
-	 * Return an <tt>Iterator</tt> for the keys in the table.
-	 * To iterate over all of the keys in the symbol table <tt>st</tt>, use the
-	 * foreach notation: <tt>for (Key key : st)</tt>.
+	 * Return an <code>Iterator</code> for the keys in the table.
+	 * To iterate over all of the keys in the symbol table <code>st</code>, use the
+	 * foreach notation: <code>for (Key key : st)</code>.
 	 */
 	@Override
 	public Iterator<Key> iterator() {
@@ -121,9 +121,9 @@ public Iterator<Key> iterator() {
 	}
 
 	/**
-	 * Return an <tt>Iterable</tt> for the keys in the table.
-	 * To iterate over all of the keys in the symbol table <tt>st</tt>, use the
-	 * foreach notation: <tt>for (Key key : st.keys())</tt>.
+	 * Return an <code>Iterable</code> for the keys in the table.
+	 * To iterate over all of the keys in the symbol table <code>st</code>, use the
+	 * foreach notation: <code>for (Key key : st.keys())</code>.
 	 */
 	public Iterable<Key> keys() {
 		return st.keySet();
@@ -153,7 +153,7 @@ public Key ceil(Key k) {
 	}
 
 	/**
-	 * Return the largest key in the table <= k.
+	 * Return the largest key in the table &lt;= k.
 	 */
 	public Key floor(Key k) {
 		if (st.containsKey(k)) return k;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/package-info.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/package-info.java
index fecc3afee6..8d5fb81573 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/package-info.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/package-info.java
@@ -19,10 +19,8 @@
  *
  */
 /**
- * <BODY>
- * <P>
  * Interfaces and classes for protein structure (PDB).
- * </P>
+ *
  * <p>
  * See also the <a href="https://github.com/biojava/biojava3-tutorial/blob/master/structure/README.md">BioJava 3 tutorial</a> for more information on the protein structure modules.
  * </p>
@@ -62,8 +60,7 @@
  * For more documentation on how to work with the Structure API please
  * see <a href="http://biojava.org/wiki/BioJava:CookBook#Protein_Structure" target="_top">
  * http://biojava.org/wiki/BioJava:CookBook#Protein_Structure</a>
- * </p>
- * </BODY>
+ *
  * @since 1.5
  */
 package org.biojava.nbio.structure;
\ No newline at end of file
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
index 95bcf1b402..7c359121de 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BioAssemblyTools.java
@@ -262,12 +262,11 @@ public static double getBiologicalMoleculeMaximumExtend( final Structure structu
 
 	/**
 	 * Returns the centroid of the biological molecule.
-	 * @param structure
+	 * @param asymUnit
 	 * @return centroid
 	 * @throws IllegalArgumentException if structure is null
 	 */
-
-	public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit,List<BiologicalAssemblyTransformation> transformations ) {
+	public static double[] getBiologicalMoleculeCentroid( final Structure asymUnit, List<BiologicalAssemblyTransformation> transformations ) {
 		if ( asymUnit == null ) {
 			throw new IllegalArgumentException( "null structure" );
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
index f9597bbb7d..c6ec6bc8ff 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java
@@ -75,6 +75,7 @@ public BiologicalAssemblyBuilder(){
 	 * Builds a Structure object containing the quaternary structure built from given asymUnit and transformations,
 	 * by adding symmetry partners as new models.
 	 * The output Structure will be different depending on the multiModel parameter:
+	 * <ul>
 	 * <li>
 	 * the symmetry-expanded chains are added as new models, one per transformId. All original models but
 	 * the first one are discarded.
@@ -83,6 +84,7 @@ public BiologicalAssemblyBuilder(){
 	 * as original with symmetry-expanded chains added with renamed chain ids and names (in the form
 	 * originalAsymId_transformId and originalAuthId_transformId)
 	 * </li>
+	 * </ul>
 	 * @param asymUnit
 	 * @param transformations
 	 * @param useAsymIds if true use {@link Chain#getId()} to match the ids in the BiologicalAssemblyTransformation (needed if data read from mmCIF),
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
index 04e35fe14d..26b4656767 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/BridgeType.java
@@ -22,7 +22,7 @@
 
 /**
  * A bridge is formed by two non-overlapping stretches of three residues each
- * (i-1,i,i+1) and (j-1,j,j+1), where i<j.
+ * (i-1,i,i+1) and (j-1,j,j+1), where i&lt;j.
  * <p>
  * Depending on two basic patterns, a Bridge can be either of type parallel (H
  * bonds in {(i-1,j) and (j,i+1)} OR {(j-1,i) and (i,j-1)}) or antiparallel (H
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
index 33bdc7c931..6faebae39c 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucState.java
@@ -107,7 +107,7 @@ public char[] getTurn() {
 
 	/**
 	 * Set the turn column corresponding to 3,4 or 5 helix patterns. If starting
-	 * > or ending < was set and the opposite is being set, the value will be
+	 * &gt; or ending &lt; was set and the opposite is being set, the value will be
 	 * converted to X. If a number was set, it will be overwritten by the new
 	 * character.
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
index 4dabe0c0ac..2c399185f1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Helix.java
@@ -101,7 +101,6 @@ public void setRise(double rise) {
 
 	/**
 	 * Returns the pitch angle of the helix
-	 * @param transformation helix transformation
 	 * @return
 	 */
 	public double getAngle() {
@@ -110,7 +109,6 @@ public double getAngle() {
 
 	/**
 	 * Returns the AxisAngle of the helix transformation
-	 * @param transformation helix transformation
 	 * @return
 	 */
 	public AxisAngle4d getAxisAngle() {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
index 5df1278563..1964132a0d 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
@@ -40,7 +40,7 @@ public class QuatSuperpositionScorer {
 	 * TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
 	 * @param subunits subunits to be scored
 	 * @param transformation transformation matrix
-	 * @param permutations permutation that determines which subunits are superposed
+	 * @param permutation permutation that determines which subunits are superposed
 	 * @return
 	 */
 	public static QuatSymmetryScores calcScores(QuatSymmetrySubunits subunits, Matrix4d transformation, List<Integer> permutation) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Rotation.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Rotation.java
index 9f1410abc6..6a9b95c3a6 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Rotation.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Rotation.java
@@ -147,7 +147,7 @@ public int getDirection() {
 	}
 
 	/**
-	 * @param direction the direction to set
+	 * @param axis the direction to set
 	 */
 	public void setDirection(int axis) {
 		this.direction = axis;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
index 9d25a7acbc..70b69afe14 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationGroup.java
@@ -31,7 +31,7 @@
 import java.util.List;
 
 /**
- * @see http://en.wikipedia.org/wiki/Rotation_group_SO(3)
+ * See <a href="http://en.wikipedia.org/wiki/Rotation_group_SO(3)">http://en.wikipedia.org/wiki/Rotation_group_SO(3)</a>
  * @author Peter
  */
 public class RotationGroup implements Iterable<Rotation> {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
index dc6a09053f..697ee41f82 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java
@@ -238,7 +238,7 @@ public int numberOfComponents() {
 	}
 
 	/**
-	 * Make a combined Stoichiometry object of <i>this</> and the <i>other</>.
+	 * Make a combined Stoichiometry object of <i>this</i> and the <i>other</i>.
 	 * The combined list of clusters will be ordered by the number of subunits.
 	 * @return new {@link Stoichiometry} object.
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
index 7de37ee842..5cb5a99458 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Icosahedron.java
@@ -67,7 +67,7 @@ public double getInscribedRadius() {
 	/**
 	 * Sets the radius of an inscribed sphere, that is tangent to each
 	 * of the icosahedron's faces
-	 * @param inscribedRadius the inscribedRadius to set
+	 * @param radius the inscribedRadius to set
 	 */
 	public void setInscribedRadius(double radius) {
 		double side = getSideLengthFromInscribedRadius(radius);
@@ -88,7 +88,7 @@ public double getMidRadius() {
 	/**
 	 * Sets the radius of radius of a sphere, that is tangent to each
 	 * of the icosahedron's edges
-	 * @param midRadius the midRadius to set
+	 * @param radius the midRadius to set
 	 */
 	public void setMidRadius(double radius) {
 		double side = getSideLengthFromMiddleRadius(radius);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
index 6cc5842dda..3165093908 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Octahedron.java
@@ -62,7 +62,7 @@ public double getInscribedRadius() {
 	/**
 	 * Sets the radius of an inscribed sphere, that is tangent to each
 	 * of the octahedron's faces
-	 * @param inscribedRadius the inscribedRadius to set
+	 * @param radius the inscribedRadius to set
 	 */
 	public void setInscribedRadius(double radius) {
 		double side = getSideLengthFromInscribedRadius(radius);
@@ -83,7 +83,7 @@ public double getMidRadius() {
 	/**
 	 * Sets the radius of radius of a sphere, that is tangent to each
 	 * of the octahedron's edges
-	 * @param midRadius the midRadius to set
+	 * @param radius the midRadius to set
 	 */
 	public void setMidRadius(double radius) {
 		double side = getSideLengthFromMiddleRadius(radius);
@@ -92,9 +92,6 @@ public void setMidRadius(double radius) {
 
 	/**
 	 * Returns the vertices of an n-fold polygon of given radius and center
-	 * @param n
-	 * @param radius
-	 * @param center
 	 * @return
 	 */
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
index 770126b601..24166059fc 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Prism.java
@@ -87,7 +87,7 @@ public double getInscribedRadius() {
 	/**
 	 * Sets the radius of an inscribed sphere, that is tangent to each
 	 * of the icosahedron's faces
-	 * @param inscribedRadius the inscribedRadius to set
+	 * @param radius the inscribedRadius to set
 	 */
 	public void setInscribedRadius(double radius) {
 		double side = getSideLengthFromInscribedRadius(radius, n);
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
index 45d32828c3..295c6275e9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/RectangularPrism.java
@@ -82,9 +82,6 @@ public double getCirumscribedRadius() {
 
 	/**
 	 * Returns the vertices of an n-fold polygon of given radius and center
-	 * @param n
-	 * @param radius
-	 * @param center
 	 * @return
 	 */
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
index 7effd81cbe..a402cbef7e 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/Tetrahedron.java
@@ -66,7 +66,7 @@ public double getInscribedRadius() {
 	/**
 	 * Sets the radius of an inscribed sphere, that is tangent to each
 	 * of the tetrahedron's faces
-	 * @param inscribedRadius the inscribedRadius to set
+	 * @param radius the inscribedRadius to set
 	 */
 	public void setInscribedRadius(double radius) {
 		double side = getSideLengthFromInscribedRadius(radius);
@@ -87,7 +87,7 @@ public double getMidRadius() {
 	/**
 	 * Sets the radius of radius of a sphere, that is tangent to each
 	 * of the tetrahedron's edges
-	 * @param midRadius the midRadius to set
+	 * @param radius the midRadius to set
 	 */
 	public void setMidRadius(double radius) {
 		double side = getSideLengthFromMiddleRadius(radius);
@@ -96,9 +96,6 @@ public void setMidRadius(double radius) {
 
 	/**
 	 * Returns the vertices of an n-fold polygon of given radius and center
-	 * @param n
-	 * @param radius
-	 * @param center
 	 * @return
 	 */
 	@Override
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
index 96b41f48e9..345493ce91 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/AngleOrderDetectorPlus.java
@@ -45,7 +45,7 @@ public class AngleOrderDetectorPlus implements OrderDetector {
 	private boolean normalizeError;
 
 	/**
-	 * @param error
+	 * @param angleError
 	 *            maximum angular error, in radians
 	 */
 	public AngleOrderDetectorPlus(double angleError) {
@@ -61,7 +61,7 @@ public AngleOrderDetectorPlus(int maxOrder) {
 	 *
 	 * @param maxOrder
 	 *            maximum order to consider
-	 * @param error
+	 * @param angleError
 	 *            maximum angular error, in radians
 	 */
 	public AngleOrderDetectorPlus(int maxOrder, double angleError) {
@@ -82,7 +82,7 @@ public AngleOrderDetectorPlus(int maxOrder, double angleError) {
 	 *
 	 * @param maxOrder
 	 *            maximum order to consider
-	 * @param error
+	 * @param angleError
 	 *            maximum angular error
 	 * @param normalize
 	 *            indicates whether error should be normalized by the order
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
index 43ee89c234..b8ea01d6a1 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -82,7 +82,6 @@ public class CeSymm {
 	 * <li>2.2 - run multiple symmetry levels recursively to find PG and
 	 * hierarchical symmetries.
 	 * </ul>
-	 * </li>
 	 */
 	public static final String version = "2.2";
 	public static final String algorithmName = "jCE-symm";
@@ -364,7 +363,7 @@ public static CeSymmResult analyze(Atom[] atoms) throws StructureException {
 	 *
 	 * @param atoms
 	 *            representative Atom array of the Structure
-	 * @param param
+	 * @param params
 	 *            CeSymmParameters bean
 	 * @return CeSymmResult
 	 * @throws StructureException
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
index 4527a7fa49..0700e34571 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmIterative.java
@@ -63,7 +63,6 @@
  * <li>Repeat the last two steps until no more significant results are found.
  * <li>Map back all residues in a multiple alignment of the repeats.
  * </ul>
- * </li>
  *
  * @author Aleix Lafita
  * @since 4.1.1
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
index a9e1bcdeb5..79053f55f9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java
@@ -76,7 +76,7 @@ public int order() {
 	 * ResidueGroups {A,B,C}, if A is compatible with B and B is compatible with
 	 * C, then A is not necessarily compatible with C.
 	 *
-	 * @param c2
+	 * @param other
 	 *            second maximally connected component
 	 * @return true if compatible, false otherwise
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
index beeba62df2..a6ad226698 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
@@ -61,12 +61,12 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms,
 
 	/**
 	 * Refines a CE-Symm alignment so that it is perfectly symmetric.
-	 *
+	 * <p>
 	 * The resulting alignment will have a one-to-one correspondance between
 	 * aligned residues of each symmetric part.
 	 *
 	 * @param afpChain Input alignment from CE-Symm
-	 * @param k Symmetry order. This can be guessed by {@link CeSymm#getSymmetryOrder(AFPChain)}
+	 * @param k Symmetry order. This can be guessed by {@link AlignmentTools#getSymmetryOrder(Map, Map, int, float)}
 	 * @return The refined alignment
 	 * @throws StructureException
 	 * @throws RefinerFailedException
@@ -97,11 +97,11 @@ public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 
 	/**
 	 * Refines a CE-Symm alignment so that it is perfectly symmetric.
-	 *
+	 * <p>
 	 * The resulting alignment will have a one-to-one correspondance between
 	 * aligned residues of each symmetric part.
 	 * @param alignment The input alignment, as a map. This will be modified.
-	 * @param k Symmetry order. This can be guessed by {@link CeSymm#getSymmetryOrder(AFPChain)}
+	 * @param k Symmetry order. This can be guessed by {@link AlignmentTools#getSymmetryOrder(Map, Map, int, float)}
 	 * @return A modified map with the refined alignment
 	 * @throws StructureException
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
index 8ea264ba67..d03e90080f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java
@@ -43,7 +43,7 @@
  * Optimizes a symmetry alignment by a Monte Carlo score optimization of the
  * repeat multiple alignment. The superposition of the repeats is not free
  * (felxible), because it is constrained on the symmetry axes found in the
- * structure. This is the main difference to the {@link MultipleMC} algorithm in
+ * structure. This is the main difference to the {@link org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain} algorithm in
  * biojava. Another major difference is that the free Pool is shared for all
  * repeats, so that no residue can appear to more than one repeat at a time.
  * <p>
@@ -107,8 +107,6 @@ public class SymmOptimizer {
 	 *
 	 * @param symmResult
 	 *            CeSymmResult with all the information
-	 * @throws RefinerFailedException
-	 * @throws StructureException
 	 */
 	public SymmOptimizer(CeSymmResult symmResult) {
 
@@ -181,11 +179,12 @@ private void initialize() throws StructureException, RefinerFailedException {
 	 * Optimization method based in a Monte-Carlo approach. Starting from the
 	 * refined alignment uses 4 types of moves:
 	 * <p>
+	 * <ul>
 	 * <li>1- Shift Row: if there are enough freePool residues available.
 	 * <li>2- Expand Block: add another alignment column.
 	 * <li>3- Shrink Block: move a block column to the freePool.
 	 * <li>4- Insert gap: insert a gap in a position of the alignment.
-	 *
+	 * </ul>
 	 * @throws StructureException
 	 * @throws RefinerFailedException
 	 *             if the alignment is not symmetric or too short.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
index 4913ac5cc5..76822af35f 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
@@ -501,7 +501,7 @@ public static Graph<Integer, DefaultEdge> buildSymmetryGraph(
 	 * @param symmetry
 	 *            CeSymmResult
 	 * @throws StructureException
-	 * @result List of structures, by repeat index sequentially
+	 * @return List of structures, by repeat index sequentially
 	 *
 	 */
 	public static List<Structure> divideStructure(CeSymmResult symmetry)
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
index 5d58e019eb..0de5e33bc4 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/SymoplibParser.java
@@ -185,8 +185,8 @@ public static TreeMap<Integer,SpaceGroup> getAllSpaceGroups() {
 	 * A parser for the symop.lib file provided by CCP4. Note: this file is not getting re-distributed by BioJava.
 	 * It can be downloaded from:
 	 *
-	 *  http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup
-	 *
+	 * <a href="http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup">http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&amp;view=markup</a>
+	 * <p>
 	 * Note: this file is not needed by BioJava. BioJava loads equivalent information from the file spacegroups.xml
 	 *
 	 * @param symoplibIS
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
index 74556c2434..8f9d190a71 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
@@ -29,7 +29,7 @@
 
 /**
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class HetatomImplTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
index 82e26bd802..6d97b0889d 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
@@ -27,7 +27,7 @@
 import java.io.IOException;
 
 /**
- * @author Spencer Bliven <sbliven@ucsd.edu>
+ * @author Spencer Bliven sbliven@ucsd.edu
  *
  */
 public class PDBStatusTest {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
index c594f0dd18..c5ebb6c028 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
@@ -29,7 +29,7 @@
 
 /**
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class ResidueNumberTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
index d7a64d0017..5e39000e90 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
@@ -29,7 +29,7 @@
 
 /**
  * Tests functionality of Site class.
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class SiteTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
index ec2763df9a..073a679dbb 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
@@ -165,7 +165,7 @@ public void testGetStructureForDomain3() throws IOException, StructureException
 	}
 
 	/**
-	 * Test parsing of chain-less ranges (present in SCOP < 1.73)
+	 * Test parsing of chain-less ranges (present in SCOP &lt; 1.73)
 	 * @throws IOException
 	 * @throws StructureException
 	 */
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
index a6e4779a44..ccd9d1f238 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCC.java
@@ -30,7 +30,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxCC {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
index a8023284b5..d95f85ca76 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxCoefficient.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxCoefficient {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
index dfc149c54e..4430922993 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxHelper.java
@@ -30,7 +30,7 @@
  * Given the number of options for adjusting the calculations using weighting, strata, clustering etc the helper class can be used to hide
  * the complexity for typical use case.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxHelper {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
index 7bfafba710..c9f4f18056 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java
@@ -32,7 +32,7 @@
 
 /**
  * Holds the results of a cox analysis where calling dump(), toString() will give an output similar to R
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
index d49545efa6..9c54c37618 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMart.java
@@ -44,7 +44,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxMart {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMethod.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMethod.java
index 64cfe1fdde..fe26661fd8 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMethod.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxMethod.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public enum CoxMethod{
 	/**
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
index 943dde980d..d23ded840b 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java
@@ -75,7 +75,7 @@
  *      weights(n)   :case weights
  *      init         :initial estimate for the coefficients
  *      eps          :tolerance for convergence.  Iteration continues until
- *                      the percent change in loglikelihood is <= eps.
+ *                      the percent change in loglikelihood is &lt;= eps.
  *      chol_tol     : tolerance for the Cholesky decompostion
  *      method       : 0=Breslow, 1=Efron
  *      doscale      : 0=don't scale the X matrix, 1=scale the X matrix
@@ -106,7 +106,7 @@
  * <p>
  * the data must be sorted by ascending time within strata
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxR {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
index cc51ec4d3f..3de88ec20a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxScore.java
@@ -24,7 +24,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxScore {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
index 7a99f4db02..6b477cb496 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxVariables.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxVariables {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
index 94baf9dce8..42b34905cc 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/ResidualsCoxph.java
@@ -29,7 +29,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ResidualsCoxph {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java
index 9e050b62da..6a8b9c4316 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/RiskInfo.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class RiskInfo {
 	double weight;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
index 5cf88613ab..8a50d559fb 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/StrataInfo.java
@@ -27,7 +27,7 @@
 /**
  * Information needed to represent a survival curve
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class StrataInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
index c22e6fb9b5..fa3d30f756 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvFitInfo.java
@@ -25,7 +25,7 @@
 /**
  * Contains info for graphing km figures
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvFitInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
index c1ed799293..c60d197682 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfo.java
@@ -29,7 +29,7 @@
  * The code handles figuring out if a variables is continuous or categorical. If categorical will
  * convert to numerical values.
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfo implements Comparable<SurvivalInfo> {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
index 6e292d1633..bf89f51fc8 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoHelper.java
@@ -27,7 +27,7 @@
 
 /**
  * Used to work with SurvivalInfo
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfoHelper {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
index 51c443b0b7..1a87f906f4 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/SurvivalInfoIndex.java
@@ -22,7 +22,7 @@
 
 /**
  * Not used and probably should be deleted
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfoIndex implements Comparable<SurvivalInfoIndex> {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
index fb011e3cf4..b0996e80e6 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTest.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class WaldTest {
 //coxph_wtest, df=as.integer(nvar),as.integer(ntest),as.double(var),tests= as.double(b),solve= double(nvar*ntest),as.double(toler.chol))
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java
index f5f09d8b03..30cdd1e3f3 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/WaldTestInfo.java
@@ -24,7 +24,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class WaldTestInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
index 703936e751..fa012ead4d 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxComparatorInterface.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface CoxComparatorInterface extends Comparator<CoxVariables> {
 	public String getDescription();
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
index 964b1e254f..4ec710d6c1 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesOverallModelFitComparator.java
@@ -28,7 +28,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxVariablesOverallModelFitComparator implements Comparator<CoxVariables>, Serializable {
 	private static final long serialVersionUID = 1;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
index 1c48b2dcf0..3c7e2c16d8 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/CoxVariablesVariableComparator.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CoxVariablesVariableComparator implements CoxComparatorInterface {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
index 5f61766a25..4ac6a3f402 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/MeanModelComparator.java
@@ -28,7 +28,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class MeanModelComparator implements Comparator<CoxVariables>, Serializable {
 	private static final long serialVersionUID = 1;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.java
index f8415af304..899e5e0cb4 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoComparator.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfoComparator implements Comparator<SurvivalInfo>, Serializable {
 	private static final long serialVersionUID = 1;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
index 81098c46cf..f639be0079 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/comparators/SurvivalInfoValueComparator.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvivalInfoValueComparator implements Comparator<SurvivalInfo>, Serializable {
 	private static final long serialVersionUID = 1;
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
index 7760cbe23d..1a3488b1ec 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/AgScore.java
@@ -28,7 +28,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class AgScore {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java
index 4ad714f549..d193e6104b 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/ChiSq.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ChiSq {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Cholesky2.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Cholesky2.java
index 8c4f81af3b..8ce9f73ff5 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Cholesky2.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Cholesky2.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class Cholesky2 {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Chsolve2.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Chsolve2.java
index dad7d06688..8f62db56c3 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Chsolve2.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/stats/Chsolve2.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class Chsolve2 {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
index b5841d9f63..5e734a27ba 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/ChangeValue.java
@@ -23,7 +23,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface ChangeValue {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/CompactCharSequence.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/CompactCharSequence.java
index 68cf58c0a8..eb029560cb 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/CompactCharSequence.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/CompactCharSequence.java
@@ -25,7 +25,7 @@
 
 /**
  *http://www.javamex.com/tutorials/memory/ascii_charsequence.shtml
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class CompactCharSequence implements CharSequence, Serializable {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/HeaderInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/HeaderInfo.java
index 7357eca3a3..71408271db 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/HeaderInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/HeaderInfo.java
@@ -22,7 +22,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class HeaderInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
index 9e4de21fcc..542085942e 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java
@@ -27,7 +27,7 @@
  * Need to handle very large spreadsheets of expression data so keep memory
  * footprint low
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class WorkSheet {
 
@@ -1464,7 +1464,7 @@ static public WorkSheet readCSV(File f, char delimiter) throws Exception {
 	/**
 	 * Read a CSV/Tab delimited file where you pass in the delimiter
 	 *
-	 * @param f
+	 * @param is
 	 * @param delimiter
 	 * @return
 	 * @throws Exception
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
index d8d120aee7..51142aeab0 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/ExpressionFigure.java
@@ -35,7 +35,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ExpressionFigure extends JPanel {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.java
index abdfe810b6..6c2e0b1b90 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/GroupResults.java
@@ -24,7 +24,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class GroupResults {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
index d17d6afa51..c3b9bed262 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KMFigureInfo.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class KMFigureInfo {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
index f1e8877f97..21e68ccdd0 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/KaplanMeierFigure.java
@@ -36,7 +36,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class KaplanMeierFigure extends JPanel {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
index dc3e57994e..c4578f1c8b 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/NumbersAtRiskPanel.java
@@ -31,7 +31,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class NumbersAtRiskPanel extends JPanel {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
index 764c8af76f..0167aa591a 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/figure/SurvFitKM.java
@@ -34,7 +34,7 @@
  * Ported from survfitKM.S When combining multiple entries with same time not
  * sure how the weighting adds up
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class SurvFitKM {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
index 3b1ca8fe15..b507f41f97 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/ClinicalMetaDataOutcome.java
@@ -27,7 +27,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class ClinicalMetaDataOutcome {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
index 5c80054a72..4d48bd71c3 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/DiscreteQuantizerInterface.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public interface DiscreteQuantizerInterface {
 	/**
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
index 964a365cdc..ba64cf1727 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MeanQuantizer.java
@@ -25,7 +25,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class MeanQuantizer implements DiscreteQuantizerInterface {
 
diff --git a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
index bad051b590..75af37ca57 100644
--- a/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
+++ b/biojava-survival/src/main/java/org/biojava/nbio/survival/kaplanmeier/metadata/MetaDataInfo.java
@@ -26,7 +26,7 @@
 
 /**
  *
- * @author Scooter Willis <willishf at gmail dot com>
+ * @author Scooter Willis 
  */
 public class MetaDataInfo {
 
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
index 061475071a..d6389dba98 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastAlignmentParameterEnum.java
@@ -26,7 +26,7 @@
 /**
  * Alignment request parameters accepted by QBlast service.<br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
- * <p/>
+ * <p>
  * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java
index f414fb475d..13be691e5c 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputAlignmentFormatEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available output alignment types.
- * <p/>
+ * <p>
  * Values as used in QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java
index 032d7e800a..3ccb1096e6 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputFormatEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available output formats.
- * <p/>
+ * <p>
  * Values are as used by QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
index dfa144864d..b0ed9354fa 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastOutputParameterEnum.java
@@ -26,7 +26,7 @@
 /**
  * Output parameters accepted by QBlast service. <br/>
  * Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.
- * <p/>
+ * <p>
  * Taken from <a href=https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node9.html>Blast URL API</a>
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java
index 90c0557c78..ee020bc38d 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/BlastProgramEnum.java
@@ -25,7 +25,7 @@
 
 /**
  * Enum representing available blast programs.
- * <p/>
+ * <p>
  * Values are as used by QBlast URL API.
  *
  * @author Gediminas Rimsa
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
index 3fc154d009..7da35cb04b 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/MapToStringTransformer.java
@@ -41,11 +41,11 @@ public class MapToStringTransformer {
 	/**
 	 * Creates {@code MapToStringTransformer} with defaults:
 	 *
-	 * <pre>
+	 * <pre>{@code
 	 * mappingSequence = "=";
 	 * separatorSequence = "&";
 	 * nullValue = "null";
-	 * </pre>
+	 * }</pre>
 	 */
 	public MapToStringTransformer() {
 		this("=", "&", "null");
@@ -76,7 +76,7 @@ public MapToStringTransformer(String mappingSequence, String separatorSequence,
 	 * <p>
 	 * For example, if we have a map with two entries: {@code ("key1", "1")} and
 	 * {@code ("key2", "2")} this method would return {@code "key1=1&key2=2"} if
-	 * {@code mappingSequence} is "=" and separator sequence is "&";
+	 * {@code mappingSequence} is "=" and separator sequence is "&amp;";
 	 *
 	 * @param map map of arguments
 	 * @return String resulting string
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
index 196dc30c90..ccad91b981 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java
@@ -36,7 +36,7 @@
  * This class wraps a QBlast search request parameter {@code Map} by adding several convenient parameter addition
  * methods. Other QBlast URL API parameters should be added using
  * {@link #setAlignmentOption(BlastAlignmentParameterEnum, String)}
- * <p/>
+ * <p>
  * Required parameters are {@code PROGRAM} and {@code DATABASE}, other parameters are optional
  *
  * @author Sylvain Foisy, Diploide BioIT
@@ -137,11 +137,9 @@ public String getBlastDatabase() {
 	/**
 	 * Sets the database to be used with blastall
 	 * <p>
-	 * A list of available databases can be acquired by calling {@link NCBIQBlastService#printRemoteBlastInfo()}
-	 * <p>
 	 * Blastall equivalent: -d
 	 *
-	 * @param db : a valid name to a NCBI blastable database
+	 * @param database a valid name to a NCBI blastable database
 	 */
 	public void setBlastDatabase(String database) {
 		setAlignmentOption(DATABASE, database);
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
index 3c38328ae6..6c4b92eb87 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastOutputProperties.java
@@ -119,7 +119,7 @@ public String getOutputFormat() {
 
 	/**
 	 * Sets the stream output format to get from the QBlast service
-	 * <p/>
+	 * <p>
 	 * If {@code HTML} format is selected, also adds the following parameters (which are removed if another output
 	 * format is chosen):
 	 *
diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
index 42fafb0155..5826949426 100644
--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java
@@ -248,7 +248,7 @@ public boolean isReady(String id) throws Exception {
 
 	/**
 	 * Checks for completion of request.
-	 * <p/>
+	 * <p>
 	 * If expected execution time (RTOE) is available for request, this method will always return false until that time
 	 * passes. This is done to prevent sending unnecessary requests to the server.
 	 *
@@ -307,7 +307,7 @@ public boolean isReady(String id, long present) throws Exception {
 	/**
 	 * Extracts the actual Blast report for given request id according to options provided in {@code outputProperties}
 	 * argument.
-	 * <p/>
+	 * <p>
 	 * If the results are not ready yet, sleeps until they are available. If sleeping is not desired, call this method
 	 * after {@code isReady} returns true
 	 *