@@ -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
 	 */
 
@@ -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> {
 
@@ -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> {
 
@@ -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> {
 
@@ -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) {
 
@@ -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>
 
@@ -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) {
 
@@ -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
 
@@ -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> {
 
@@ -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> {
Original file line number	Diff line number	Diff line change
`@@ -34,7 +34,7 @@`
`34`	`34`	`*`
`35`	`35`	`* @author Mark Chapman`
`36`	`36`	`* @param <S> each {@link Sequence} of the alignment pair is of type S`
`37`		`- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C`
	`37`	`+ * @param <C> each element of a sequence is a {@link Compound} of type C`
`38`	`38`	`*/`
`39`	`39`	`public class FractionalIdentityScorer<S extends Sequence<C>, C extends Compound> extends AbstractScorer`
`40`	`40`	`implements PairwiseSequenceScorer<S, C> {`
Original file line number	Diff line number	Diff line change
`@@ -41,7 +41,7 @@`
`41`	`41`	`*`
`42`	`42`	`* @author Mark Chapman`
`43`	`43`	`* @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S`
`44`		`- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C`
	`44`	`+ * @param <C> each element of a sequence is a {@link Compound} of type C`
`45`	`45`	`*/`
`46`	`46`	`public class SimpleProfileProfileAligner<S extends Sequence<C>, C extends Compound>`
`47`	`47`	`extends AbstractProfileProfileAligner<S, C> {`
Original file line number	Diff line number	Diff line change
`@@ -160,7 +160,7 @@ public void setDbReferences(Set<DatabaseReference> dbReferences) {`
`160`	`160`	`this.dbReferences = dbReferences;`
`161`	`161`	`}`
`162`	`162`	`/**`
`163`		`- * @param dbReference the string without the initial annotation identifier ( #=GS DR )`
	`163`	`+ * @param dbReferenceRepresentingString the string without the initial annotation identifier ( #=GS DR )`
`164`	`164`	`*/`
`165`	`165`	`public void addDBReference(String dbReferenceRepresentingString) {`
`166`	`166`	`if (this.dbReferences == null) {`
Original file line number	Diff line number	Diff line change
`@@ -37,7 +37,7 @@`
`37`	`37`	`*`
`38`	`38`	`* @author Mark Chapman`
`39`	`39`	`* @param <S> each {@link Sequence} of the alignment pair is of type S`
`40`		`- * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C`
	`40`	`+ * @param <C> each element of a sequence is a {@link Compound} of type C`
`41`	`41`	`*/`
`42`	`42`	`public abstract class AbstractPairwiseSequenceAligner<S extends Sequence<C>, C extends Compound>`
`43`	`43`	`extends AbstractMatrixAligner<S, C> implements PairwiseSequenceAligner<S, C> {`