Javadoc fix: remaining errors in structure module. Mostly obsolete references

josemduarte · josemduarte · commit 2bbc82438cc8 · 2025-01-07T13:52:17.000-08:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/scop/ScopDescriptionTest.java
@@ -30,7 +30,7 @@
 
 
 /**
- * @author Spencer Bliven <sbliven@ucsd.edu>
+ * @author Spencer Bliven sbliven@ucsd.edu
  *
  */
 public class ScopDescriptionTest {
diff --git a/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java b/biojava-structure/src/main/java/demo/DemoChangeChemCompProvider.java
@@ -34,9 +34,8 @@
 
 /**
  *  This demo shows how to use an alternative ChemCompProvider. The default mechanism in BioJava is to access chemical
- *  componentsby using the {@link DownloadChemCompProvider}. It fetches and locally caches chemical component
- *  definitions as they are encountered during file parsing. It can be enabled by using the
- *  {@link FileParsingParameters#setLoadChemCompInfo(boolean)} method.
+ *  components by using the {@link DownloadChemCompProvider}. It fetches and locally caches chemical component
+ *  definitions as they are encountered during file parsing.
  * <p>
  * The {@link AllChemCompProvider} downloads and unpacks all chemcomps. It is slower and requires more memory than the
  * default {@link DownloadChemCompProvider}, but it avoids network access to the FTP site, if a new chemcomp is
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java
@@ -1312,7 +1312,7 @@ public void setSequentialAlignment(boolean sequentialAlignment) {
 	 * up to the alignment algorithm.
 	 *
 	 * <p>Note:
-	 * A {@link org.biojava.nbio.structure.gui.JMatrixPanel}, which is used in
+	 * The org.biojava.nbio.structure.gui.JMatrixPanel, used in
 	 * the structure-gui package to display distance matrices, will display the
 	 * transpose of this matrix. Be sure to take that into account when debugging
 	 * visually.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AlignmentTools.java
@@ -239,8 +239,6 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 			}
 		}
 
-
-
 		Map<S, T> imageMap = new HashMap<>(alignmentMap.size());
 
 		//TODO handle nulls consistently.
@@ -282,7 +280,7 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide
 	 */
 	public static int getSymmetryOrder(Map<Integer, Integer> alignment,
 									   final int maxSymmetry, final float minimumMetricChange) {
-		return getSymmetryOrder(alignment, new IdentityMap<Integer>(), maxSymmetry, minimumMetricChange);
+		return getSymmetryOrder(alignment, new IdentityMap<>(), maxSymmetry, minimumMetricChange);
 	}
 	/**
 	 * Tries to detect symmetry in an alignment.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -464,8 +464,7 @@ public String getPath() {
 	 * <li>If only a PDB code is provided, the whole structure will be return including ligands, but the first model
 	 * only (for NMR).
 	 * <li>Chain IDs are case sensitive, PDB ids are not. To specify a particular chain write as: 4hhb.A or 4HHB.A</li>
-	 * <li>To specify a SCOP domain write a scopId e.g. d2bq6a1. Some flexibility can be allowed in SCOP domain names,
-	 * see {@link #setStrictSCOP(boolean)}</li>
+	 * <li>To specify a SCOP domain write a scopId e.g. d2bq6a1. </li>
 	 * <li>URLs are accepted as well</li>
 	 * </ul>
 	 *
@@ -672,7 +671,7 @@ public void setFileParsingParams(FileParsingParameters params) {
 	 *
 	 * <p>This setting may be silently ignored by implementations which do not have
 	 * access to the server to determine whether an entry is obsolete, such as
-	 * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
+	 * certain {@link FetchBehavior}s. Note that an obsolete entry may still be
 	 * returned even this is FETCH_CURRENT if the entry is found locally.
 	 *
 	 * @param behavior Whether to fetch obsolete records
@@ -685,7 +684,7 @@ public void setObsoleteBehavior(ObsoleteBehavior behavior) {
 	/**
 	 * Returns how this instance deals with obsolete entries. Note that this
 	 * setting may be ignored by some implementations or in some situations,
-	 * such as when {@link #isAutoFetch()} is false.
+	 * such as certain {@link FetchBehavior}s.
 	 *
 	 * <p>For most implementations, the default value is
 	 * {@link ObsoleteBehavior#THROW_EXCEPTION THROW_EXCEPTION}.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -262,7 +262,7 @@ public FileParsingParameters getFileParsingParameters(){
 	 * </ul>
 	 * <p>This setting may be silently ignored by implementations which do not have
 	 * access to the server to determine whether an entry is obsolete, such as
-	 * if {@link #isAutoFetch()} is false. Note that an obsolete entry may still be
+	 * certain {@link FetchBehavior}s. Note that an obsolete entry may still be
 	 * returned even this is FETCH_CURRENT if the entry is found locally.
 	 *
 	 * @param behavior Whether to fetch obsolete records
@@ -276,7 +276,7 @@ public void setObsoleteBehavior(ObsoleteBehavior behavior) {
 	/**
 	 * Returns how this instance deals with obsolete entries. Note that this
 	 * setting may be ignored by some implementations or in some situations,
-	 * such as when {@link #isAutoFetch()} is false.
+	 * such as certain {@link FetchBehavior}s.
 	 *
 	 * <p>For most implementations, the default value is
 	 * {@link ObsoleteBehavior#THROW_EXCEPTION THROW_EXCEPTION}.
@@ -295,10 +295,9 @@ public ObsoleteBehavior getObsoleteBehavior() {
 	public FetchBehavior getFetchBehavior() {
 		return fetchBehavior;
 	}
+
 	/**
 	 * Set the behavior for fetching files from the server.
-	 * This replaces the {@link #setAutoFetch(boolean)} method with a more
-	 * extensive set of options.
 	 * @param fetchBehavior
 	 */
 	public void setFetchBehavior(FetchBehavior fetchBehavior) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileReader.java
@@ -35,10 +35,7 @@
  * <p>
  *  Several flags can be set for this class
  * <ul>
- *
- * <li> {@link #setAutoFetch(boolean)} - if the PDB file can not be found locally, should it be fetched
- *  from the PDB ftp servers? (default:false)</li>
- * <li> Other parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
+ * <li> Parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}</li>
  * </ul>
  *
  *<h2>Example</h2>
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java
@@ -61,12 +61,12 @@ public MultipleAlignment refine(AFPChain selfAlignment, Atom[] atoms,
 
 	/**
 	 * Refines a CE-Symm alignment so that it is perfectly symmetric.
-	 *
+	 * <p>
 	 * The resulting alignment will have a one-to-one correspondance between
 	 * aligned residues of each symmetric part.
 	 *
 	 * @param afpChain Input alignment from CE-Symm
-	 * @param k Symmetry order. This can be guessed by {@link CeSymm#getSymmetryOrder(AFPChain)}
+	 * @param k Symmetry order. This can be guessed by {@link AlignmentTools#getSymmetryOrder(Map, Map, int, float)}
 	 * @return The refined alignment
 	 * @throws StructureException
 	 * @throws RefinerFailedException
@@ -97,11 +97,11 @@ public static AFPChain refineSymmetry(AFPChain afpChain, Atom[] ca1, Atom[] ca2,
 
 	/**
 	 * Refines a CE-Symm alignment so that it is perfectly symmetric.
-	 *
+	 * <p>
 	 * The resulting alignment will have a one-to-one correspondance between
 	 * aligned residues of each symmetric part.
 	 * @param alignment The input alignment, as a map. This will be modified.
-	 * @param k Symmetry order. This can be guessed by {@link CeSymm#getSymmetryOrder(AFPChain)}
+	 * @param k Symmetry order. This can be guessed by {@link AlignmentTools#getSymmetryOrder(Map, Map, int, float)}
 	 * @return A modified map with the refined alignment
 	 * @throws StructureException
 	 */
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/HetatomImplTest.java
@@ -29,7 +29,7 @@
 
 /**
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class HetatomImplTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/PDBStatusTest.java
@@ -27,7 +27,7 @@
 import java.io.IOException;
 
 /**
- * @author Spencer Bliven <sbliven@ucsd.edu>
+ * @author Spencer Bliven sbliven@ucsd.edu
  *
  */
 public class PDBStatusTest {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/ResidueNumberTest.java
@@ -29,7 +29,7 @@
 
 /**
  *
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class ResidueNumberTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/SiteTest.java
@@ -29,7 +29,7 @@
 
 /**
  * Tests functionality of Site class.
- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
+ * @author Jules Jacobsen jacobsen@ebi.ac.uk
  */
 public class SiteTest {
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
@@ -165,7 +165,7 @@ public void testGetStructureForDomain3() throws IOException, StructureException
 	}
 
 	/**
-	 * Test parsing of chain-less ranges (present in SCOP < 1.73)
+	 * Test parsing of chain-less ranges (present in SCOP &lt; 1.73)
 	 * @throws IOException
 	 * @throws StructureException
 	 */

Original file line number	Diff line number	Diff line change
`@@ -30,7 +30,7 @@`
`30`	`30`
`31`	`31`
`32`	`32`	`/**`
`33`		`- * @author Spencer Bliven <sbliven@ucsd.edu>`
	`33`	`+ * @author Spencer Bliven sbliven@ucsd.edu`
`34`	`34`	`*`
`35`	`35`	`*/`
`36`	`36`	`public class ScopDescriptionTest {`
Original file line number	Diff line number	Diff line change
`@@ -1312,7 +1312,7 @@ public void setSequentialAlignment(boolean sequentialAlignment) {`
`1312`	`1312`	`* up to the alignment algorithm.`
`1313`	`1313`	`*`
`1314`	`1314`	`* <p>Note:`
`1315`		`- * A {@link org.biojava.nbio.structure.gui.JMatrixPanel}, which is used in`
	`1315`	`+ * The org.biojava.nbio.structure.gui.JMatrixPanel, used in`
`1316`	`1316`	`* the structure-gui package to display distance matrices, will display the`
`1317`	`1317`	`* transpose of this matrix. Be sure to take that into account when debugging`
`1318`	`1318`	`* visually.`
Original file line number	Diff line number	Diff line change
`@@ -239,8 +239,6 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide`
`239`	`239`	`}`
`240`	`240`	`}`
`241`	`241`
`242`		`-`
`243`		`-`
`244`	`242`	`Map<S, T> imageMap = new HashMap<>(alignmentMap.size());`
`245`	`243`
`246`	`244`	`//TODO handle nulls consistently.`
`@@ -282,7 +280,7 @@ public static <S,T> Map<S,T> applyAlignment(Map<S, T> alignmentMap, Map<T,S> ide`
`282`	`280`	`*/`
`283`	`281`	`public static int getSymmetryOrder(Map<Integer, Integer> alignment,`
`284`	`282`	`final int maxSymmetry, final float minimumMetricChange) {`
`285`		`- return getSymmetryOrder(alignment, new IdentityMap<Integer>(), maxSymmetry, minimumMetricChange);`
	`283`	`+ return getSymmetryOrder(alignment, new IdentityMap<>(), maxSymmetry, minimumMetricChange);`
`286`	`284`	`}`
`287`	`285`	`/**`
`288`	`286`	`* Tries to detect symmetry in an alignment.`
Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,7 @@`
`29`	`29`
`30`	`30`	`/**`
`31`	`31`	`*`
`32`		`- * @author Jules Jacobsen <jacobsen@ebi.ac.uk>`
	`32`	`+ * @author Jules Jacobsen jacobsen@ebi.ac.uk`
`33`	`33`	`*/`
`34`	`34`	`public class HetatomImplTest {`
`35`	`35`
Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,7 @@`
`27`	`27`	`import java.io.IOException;`
`28`	`28`
`29`	`29`	`/**`
`30`		`- * @author Spencer Bliven <sbliven@ucsd.edu>`
	`30`	`+ * @author Spencer Bliven sbliven@ucsd.edu`
`31`	`31`	`*`
`32`	`32`	`*/`
`33`	`33`	`public class PDBStatusTest {`