Javadoc fix: many errors in struct align package

josemduarte · josemduarte · commit 2b33a56bd2fa · 2025-01-06T15:27:11.000-08:00
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
@@ -147,15 +147,13 @@ public interface MultipleAlignmentEnsemble extends ScoresCache {
 	 * structure.
 	 *
 	 * @return List of Matrix interatomic distance matrices.
-	 * @see #updateDistanceMatrix()
 	 */
 	public List<Matrix> getDistanceMatrix();
 
 	/**
 	 * 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
@@ -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
@@ -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) {
 
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
@@ -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
@@ -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
@@ -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
@@ -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
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
@@ -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
