Javadoc fix: param fixes

josemduarte · josemduarte · commit 193287b7bff3 · 2025-01-03T11:00:23.000-08:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
@@ -44,6 +44,7 @@
  *
  * @author Mark Chapman
  * @param <C> each element of the {@link Sequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> implements Serializable, AlignedSequence<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java
@@ -34,6 +34,7 @@
  * @author Mark Chapman
  * @author Paolo Pavan
  * @param <C> each element of the {@link Sequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public interface AlignedSequence<S extends Sequence<C>, C extends Compound> extends Sequence<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/MutableAlignedSequence.java
@@ -34,6 +34,7 @@
  * @author Mark Chapman
  * @author Paolo Pavan
  * @param <C> each element of the {@link AlignedSequence} is a {@link Compound} of type C
+ * @param <S> the sequence type
  */
 public interface MutableAlignedSequence<S extends Sequence<C>, C extends Compound> extends AlignedSequence<S, C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java b/biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java
@@ -40,15 +40,16 @@
 /**
  * This class models a search Hsp.
  * You will retrieve a list of this using iterator of a Hit
- *
+ * <p>
  * Designed by Paolo Pavan.
  * You may want to find my contacts on Github and LinkedIn for code info
  * or discuss major changes.
  * https://github.com/paolopavan
  *
  * @author Paolo Pavan
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
-
 public abstract class Hsp <S extends Sequence<C>, C extends Compound> {
 	private static final Logger logger = LoggerFactory.getLogger(Hsp.class);
 	private Integer hspNum;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/FileProxyProteinSequenceCreator.java
@@ -55,7 +55,7 @@ public class FileProxyProteinSequenceCreator implements SequenceCreatorInterface
 
 	/**
 	 * Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read
-	 * @param fastaFile
+	 * @param file
 	 * @param compoundSet
 	 */
 	public FileProxyProteinSequenceCreator(File file, CompoundSet<AminoAcidCompound> compoundSet, SequenceParserInterface sequenceParser ) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
@@ -53,7 +53,8 @@
 /**
  * Use {@link GenbankReaderHelper} as an example of how to use this class where {@link GenbankReaderHelper} should be the
  * primary class used to read Genbank files
- *
+ * @param <S> the sequence type
+ * @param <C> the compound type
  */
 public class GenbankReader<S extends AbstractSequence<C>, C extends Compound> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/FastaHeaderFormatInterface.java
@@ -28,12 +28,15 @@
 /**
  *
  * @author Scooter Willis <willishf at gmail dot com>
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface FastaHeaderFormatInterface<S extends Sequence<?>, C extends Compound> {
+
 	/**
 	 *
 	 * @param sequence
 	 * @return
 	 */
-	public String getHeader(S sequence);
+	String getHeader(S sequence);
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/GenbankHeaderFormatInterface.java
@@ -28,16 +28,18 @@
 
 /**
  * @author mckeee1
- *
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface GenbankHeaderFormatInterface<S extends Sequence<?>, C extends Compound> {
+
+	public static final String UNKNOWN_DNA = "UNK";
+
 	/**
 	 *
 	 * @param sequence
 	 * @return
 	 */
-	public static final String UNKNOWN_DNA = "UNK";
-
-	public String getHeader(S sequence);
+	String getHeader(S sequence);
 
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceCreatorInterface.java
@@ -33,6 +33,7 @@
 /**
  *
  * @author Scooter Willis <willishf at gmail dot com>
+ * @param <C> the compound type
  */
 public interface SequenceCreatorInterface<C extends Compound> {
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/template/SequenceHeaderParserInterface.java
@@ -28,6 +28,8 @@
 /**
  *
  * @author Scooter Willis <willishf at gmail dot com>
+ * @param <C> the compound type
+ * @param <S> the sequence type
  */
 public interface SequenceHeaderParserInterface<S extends Sequence<?>, C extends Compound> {
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
@@ -51,7 +51,7 @@
  *
  *
  * @author Scooter Willis <willishf at gmail dot com>
- * @param <C>
+ * @param <C> the compound type
  */
 public class SequenceFileProxyLoader<C extends Compound> implements ProxySequenceReader<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
@@ -39,9 +39,8 @@
 /**
  * An example of a ProxySequenceReader that is created from a String. Used for testing
  * @author Scooter Willis <willishf at gmail dot com>
- * @param <C>
+ * @param <C> the compound type
  */
-
 public class StringProxySequenceReader<C extends Compound> implements ProxySequenceReader<C> {
 
 	private String sequence;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/ArrayListSequenceReader.java
@@ -39,7 +39,7 @@
 /**
  * Stores a Sequence as a collection of compounds in an ArrayList
  *
- * @param <C>
+ * @param <C> the compound type
  */
 public class ArrayListSequenceReader<C extends Compound> implements SequenceReader<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -47,7 +47,7 @@
 /**
  *
  * The base class for DNA, RNA and Protein sequences.
- * @param <C>
+ * @param <C> the compound type
  */
 public abstract class AbstractSequence<C extends Compound> implements Sequence<C> {
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/SoftHashMap.java
@@ -39,6 +39,8 @@
  * containsKey(), values() etc do not work.
  * <p>
  * This class is therefore best used as a cache simply to put and get items by a known key
+ * @param <K> the key type
+ * @param <V> the value type
  */
 public class SoftHashMap<K, V> extends AbstractMap<K, V> {
 

Original file line number	Diff line number	Diff line change
`@@ -44,6 +44,7 @@`
`44`	`44`	`*`
`45`	`45`	`* @author Mark Chapman`
`46`	`46`	`* @param <C> each element of the {@link Sequence} is a {@link Compound} of type C`
	`47`	`+ * @param <S> the sequence type`
`47`	`48`	`*/`
`48`	`49`	`public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> implements Serializable, AlignedSequence<S, C> {`
`49`	`50`
Original file line number	Diff line number	Diff line change
`@@ -28,12 +28,15 @@`
`28`	`28`	`/**`
`29`	`29`	`*`
`30`	`30`	`* @author Scooter Willis <willishf at gmail dot com>`
	`31`	`+ * @param <C> the compound type`
	`32`	`+ * @param <S> the sequence type`
`31`	`33`	`*/`
`32`	`34`	`public interface FastaHeaderFormatInterface<S extends Sequence<?>, C extends Compound> {`
	`35`	`+`
`33`	`36`	`/**`
`34`	`37`	`*`
`35`	`38`	`* @param sequence`
`36`	`39`	`* @return`
`37`	`40`	`*/`
`38`		`- public String getHeader(S sequence);`
	`41`	`+ String getHeader(S sequence);`
`39`	`42`	`}`
Original file line number	Diff line number	Diff line change
`@@ -33,6 +33,7 @@`
`33`	`33`	`/**`
`34`	`34`	`*`
`35`	`35`	`* @author Scooter Willis <willishf at gmail dot com>`
	`36`	`+ * @param <C> the compound type`
`36`	`37`	`*/`
`37`	`38`	`public interface SequenceCreatorInterface<C extends Compound> {`
`38`	`39`	`/**`
Original file line number	Diff line number	Diff line change
`@@ -28,6 +28,8 @@`
`28`	`28`	`/**`
`29`	`29`	`*`
`30`	`30`	`* @author Scooter Willis <willishf at gmail dot com>`
	`31`	`+ * @param <C> the compound type`
	`32`	`+ * @param <S> the sequence type`
`31`	`33`	`*/`
`32`	`34`	`public interface SequenceHeaderParserInterface<S extends Sequence<?>, C extends Compound> {`
`33`	`35`	`/**`