Javadoc fix: a few errors from structure module

josemduarte · josemduarte · commit ed7ab8e32d95 · 2025-01-03T15:42:32.000-08:00
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
@@ -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 Bond(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 Bond(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/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
@@ -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/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();
 
@@ -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
@@ -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/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/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/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);
@@ -104,7 +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
+	 * @see SeqRes2AtomAligner#getFullAtomSequence(List, Map, boolean), which
 	 * 	does the heavy lifting.
 	 *
 	 */
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
@@ -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
@@ -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/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

Original file line number	Diff line number	Diff line change
`@@ -327,9 +327,9 @@ public static final double getPsi(AminoAcid a, AminoAcid b)`
`327`	`327`	`}`
`328`	`328`
`329`	`329`	`/**`
`330`		`- * Test if two amino acids are connected, i.e. if the distance from C to N <`
	`330`	`+ * Test if two amino acids are connected, i.e. if the distance from C to N <`
`331`	`331`	`* 2.5 Angstrom.`
`332`		`- *`
	`332`	`+ * <p>`
`333`	`333`	`* If one of the AminoAcids has an atom missing, returns false.`
`334`	`334`	`*`
`335`	`335`	`* @param a`
Original file line number	Diff line number	Diff line change
`@@ -52,7 +52,6 @@ public class BlockImpl extends AbstractScoresCache implements Serializable,`
`52`	`52`	`*`
`53`	`53`	`* @param blockSet`
`54`	`54`	`* the parent BlockSet of the BlockImpl instance.`
`55`		`- * @return BlockImpl a BlockImpl instance linked to its parent BlockSet.`
`56`	`55`	`*/`
`57`	`56`	`public BlockImpl(BlockSet blockSet) {`
`58`	`57`
`@@ -69,7 +68,6 @@ public BlockImpl(BlockSet blockSet) {`
`69`	`68`	`*`
`70`	`69`	`* @param b`
`71`	`70`	`* BlockImpl object to be copied.`
`72`		`- * @return BlockImpl an identical copy of the input BlockImpl object.`
`73`	`71`	`*/`
`74`	`72`	`public BlockImpl(BlockImpl b) {`
`75`	`73`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,6 @@ public class BlockSetImpl extends AbstractScoresCache implements Serializable,`
`55`	`55`	`*`
`56`	`56`	`* @param alignment`
`57`	`57`	`* MultipleAlignment parent of the BlockSet.`
`58`		`- * @return BlockSet an instance linked to the parent alignment.`
`59`	`58`	`*/`
`60`	`59`	`public BlockSetImpl(MultipleAlignment alignment) {`
`61`	`60`
`@@ -76,7 +75,6 @@ public BlockSetImpl(MultipleAlignment alignment) {`
`76`	`75`	`*`
`77`	`76`	`* @param bs`
`78`	`77`	`* BlockSet object to be copied.`
`79`		`- * @return BlockSet an identical copy of the input object.`
`80`	`78`	`*/`
`81`	`79`	`public BlockSetImpl(BlockSetImpl bs) {`
`82`	`80`