biojava · josemduarte · Jan 7, 2025 · Jan 3, 2025 · Jan 3, 2025 · Jan 3, 2025
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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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/...a-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java b/...a-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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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/...nt/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java b/...nt/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
@@ -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/...va-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java b/...va-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/...nt/src/main/java/org/biojava/nbio/alignment/template/AbstractPairwiseSequenceAligner.java b/...nt/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/...ment/src/main/java/org/biojava/nbio/alignment/template/AbstractProfileProfileAligner.java b/...ment/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
@@ -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/...nt/src/main/java/org/biojava/nbio/alignment/template/CallablePairwiseSequenceAligner.java b/...nt/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>> {