fix CruiseControl javadoc warnings

markchapman · markchapman · commit 9870db517637 · 2010-11-19T04:52:27.000Z
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@8436 7c6358e6-4a41-0410-a743-a5b2a554c398
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/Alignments.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/Alignments.java
@@ -58,7 +58,7 @@ public static enum PairInProfileScorerType {
      */
     public static enum PairwiseSequenceAlignerType {
         GLOBAL,              // Needleman-Wunsch/Gotoh
-        GLOBAL_LINEAR_SPACE, // Myers-Miller/Thompson
+        GLOBAL_LINEAR_SPACE, // Guan-Uberbacher
         LOCAL,               // Smith-Waterman/Gotoh
         LOCAL_LINEAR_SPACE   // Smith-Waterman/Gotoh with smart traceback at each maximum
     }
@@ -131,7 +131,6 @@ public static <S extends Sequence<C>, C extends Compound> List<SequencePair<S, C
      * @param <S> each {@link Sequence} of the {@link List} is of type S
      * @param <C> each element of a {@link 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 multiple sequence alignment routines
      * @param settings optional settings that adjust the alignment
      * @return multiple sequence alignment {@link Profile}
      */
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/routines/AlignerHelper.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/routines/AlignerHelper.java
@@ -192,7 +192,6 @@ public static Cut[] getCuts(int k, int[] subproblem, int[] dim, boolean anchor0)
      * next subproblem and this method returns {@code null}.
      *
      * @param anchors current list of anchors
-     * @param targetLength length of the target sequence
      * @return the coordinates for the next subproblem
      */
     public static int[] getNextSubproblem(int[] anchors) {
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/template/GuideTreeNode.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/template/GuideTreeNode.java
@@ -93,7 +93,7 @@ public interface GuideTreeNode<S extends Sequence<C>, C extends Compound> extend
     /**
      * Stores the given profile future.  This allows concurrent execution of alignment tasks.
      *
-     * @param profile new profile to be calculated and then stored at this node
+     * @param profileFuture new profile to be calculated and then stored at this node
      */
     void setProfileFuture(Future<ProfilePair<S, C>> profileFuture);
 
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableProfile.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/template/MutableProfile.java
@@ -38,7 +38,7 @@
 public interface MutableProfile<S extends Sequence<C>, C extends Compound> extends Profile<S, C> {
 
     /**
-     * Sets entirely new set of {@link AlignedSequences}.
+     * Sets entirely new set of {@link AlignedSequence}s.
      *
      * @param sequences new set of sequences
      * @throws IllegalArgumentException if sequences have different lengths

Original file line number	Diff line number	Diff line change
`@@ -192,7 +192,6 @@ public static Cut[] getCuts(int k, int[] subproblem, int[] dim, boolean anchor0)`
`192`	`192`	`* next subproblem and this method returns {@code null}.`
`193`	`193`	`*`
`194`	`194`	`* @param anchors current list of anchors`
`195`		`- * @param targetLength length of the target sequence`
`196`	`195`	`* @return the coordinates for the next subproblem`
`197`	`196`	`*/`
`198`	`197`	`public static int[] getNextSubproblem(int[] anchors) {`
Original file line number	Diff line number	Diff line change
`@@ -93,7 +93,7 @@ public interface GuideTreeNode<S extends Sequence<C>, C extends Compound> extend`
`93`	`93`	`/**`
`94`	`94`	`* Stores the given profile future. This allows concurrent execution of alignment tasks.`
`95`	`95`	`*`
`96`		`- * @param profile new profile to be calculated and then stored at this node`
	`96`	`+ * @param profileFuture new profile to be calculated and then stored at this node`
`97`	`97`	`*/`
`98`	`98`	`void setProfileFuture(Future<ProfilePair<S, C>> profileFuture);`
`99`	`99`
Original file line number	Diff line number	Diff line change
`@@ -38,7 +38,7 @@`
`38`	`38`	`public interface MutableProfile<S extends Sequence<C>, C extends Compound> extends Profile<S, C> {`
`39`	`39`
`40`	`40`	`/**`
`41`		`- * Sets entirely new set of {@link AlignedSequences}.`
	`41`	`+ * Sets entirely new set of {@link AlignedSequence}s.`
`42`	`42`	`*`
`43`	`43`	`* @param sequences new set of sequences`
`44`	`44`	`* @throws IllegalArgumentException if sequences have different lengths`