Javadoc fix: errors in ontology module

josemduarte · josemduarte · commit b55dc80cfba0 · 2025-01-07T15:07:47.000-08:00
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Ontology.java
@@ -40,7 +40,6 @@
  * @author Matthew Pocock
  *
  * @since 1.4
- * @see org.biojavax.ontology.ComparableOntology
  */
 
 public interface Ontology  {
@@ -129,7 +128,6 @@ public interface Ontology  {
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name)
@@ -148,7 +146,6 @@ public Term createTerm(String name)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name, String description)
@@ -168,7 +165,6 @@ public Term createTerm(String name, String description)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Term createTerm(String name, String description, Object[] synonyms)
@@ -187,7 +183,6 @@ public Term createTerm(String name, String description, Object[] synonyms)
 	 *         some other constraint of this implementation.
 	 * @throws AlreadyExistsException if a term of this name already exists
 	 * @return The newly created term.
-	 * @throws ChangeVetoException
 	 */
 
 	public Variable createVariable(String name, String description)
@@ -208,7 +203,6 @@ public Variable createVariable(String name, String description)
 	 * @param t  the Term to import
 	 * @param localName  the local name to import it under, optionally null
 	 * @return a Term
-	 * @throws ChangeVetoException
 	 * @throws IllegalArgumentException
 	 */
 
@@ -228,7 +222,6 @@ public Term importTerm(Term t, String localName)
 	 * @return  a new Triple over these three terms
 	 * @throws AlreadyExistsException if a triple already exists with the same
 	 *      subject, object and predicate, regardless of the name and description
-	 * @throws ChangeVetoException
 	 * @throws NullPointerException if subject, object or predicate are null
 	 * @throws IllegalArgumentException if subject, object or predicate are not all
 	 *      from the same ontology
@@ -251,7 +244,6 @@ public Triple createTriple(Term subject, Term object, Term predicate, String nam
 	/**
 	 * Remove a term from an ontology, together with all triples which refer to it.
 	 * @param t
-	 * @throws ChangeVetoException
 	 */
 
 	public void deleteTerm(Term t) ;
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Term.java
@@ -32,7 +32,7 @@
 
 
 /**
- * A term in an ontology.  This has an {@link org.biojava.nbio.Annotation Annotation}
+ * A term in an ontology.  This has an {@link Annotation Annotation}
  * which can be used for storing additional human-displayable information.  It
  * is strongly recommended that the Annotation is not used for any machine-readable
  * data -- this should be represented by relations in the ontology instead.
@@ -51,9 +51,7 @@
  * @author Thomas Down
  * @author Matthew Pocock
  * @since 1.4
- * @see org.biojavax.ontology.ComparableTerm
  */
-
 public interface Term extends Annotatable {
 	/**
 	 * ChangeType which indicates that this term's ontology has been
@@ -113,7 +111,6 @@ public interface Term extends Annotatable {
 
 	/**
 	 * Simple in-memory implementation of an ontology term.
-	 * @see org.biojavax.ontology.SimpleComparableTerm
 	 * This can be used to implement Ontology.createTerm
 	 */
 
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/Triple.java
@@ -41,7 +41,6 @@
  * @author Thomas Down
  * @author Matthew Pocock
  * @since 1.4
- * @see org.biojavax.ontology.ComparableTriple
  */
 
 public interface Triple
@@ -79,7 +78,6 @@ public interface Triple
 	 * If you do not implement hashcode in this way then you have no guarantee
 	 * that your Triple objects will be found in an ontology and that they will
 	 * not be duplicated.
-	 * </p>
 	 */
 	@Override
 	public int hashCode();
@@ -90,19 +88,18 @@ public interface Triple
 	 * <p>
 	 * Two triples are equivalent if they have the same subject, object and
 	 * predicate fields.
-	 * <pre>
+	 * <pre>{@code
 	 * if (! (o instanceof Triple)) {
 	 *     return false;
 	 * }
 	 * Triple to = (Triple) o;
 	 * return to.getSubject() == getSubject() &&
 	 *        to.getObject() == getObject() &&
 	 *        to.getPredicate() == getPredicate();
-	 * </pre>
+	 * }</pre>
 	 * If you do not implement equals in this way then you have no guarantee
 	 * that your Triple objects will be found in an ontology and that they will
 	 * not be duplicated.
-	 * </p>
 	 */
 	@Override
 	public boolean equals(Object obj);
@@ -111,9 +108,7 @@ public interface Triple
 	 * Basic in-memory implementation of a Triple in an ontology
 	 *
 	 * This can be used to implement Ontology.createTriple
-	 * @see org.biojavax.ontology.SimpleComparableTriple
 	 */
-
 	public static final class Impl
 
 	implements Triple, java.io.Serializable {
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/io/TabDelimParser.java
@@ -54,15 +54,15 @@
  * the core ontology.
  * </p>
  *
- * <code><pre>
+ * <pre>
  * ...
  * triple	is-a	any
  * triple	has-a	source
  * triple	has-a	target
  * triple	has-a	predicate
  * (triple,has-a,any)	size	3
  * ...
- * </pre></code>
+ * </pre>
  *
  * <p>
  * The first four lines just associate triple with some type with a predicate
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileParser.java
@@ -33,12 +33,13 @@
 import java.util.*;
 
 
-/** A class to parse the content of an OBO file. It delegates handling of the
+/**
+ * A class to parse the content of an OBO file. It delegates handling of the
  * content to the OBOFileEventListener implementation.
  *
  * This file contains parts of the OBO-Edit file OBOParseEngine, (particularly the encoding and decoding part)
  *
- * http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup
+ * See <a href="http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup">link</a>
  * Thanks to the OboEdit developers for giving permission to release this in BioJava.
  *
  *
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
@@ -75,7 +75,6 @@
  * @author  Matthew Pocock
  * @author <a href="mailto:kdj@sanger.ac.uk">Keith James</a> (docs).
  * @author  Kalle N&auml;slund (docs)
- * @see org.biojavax.RichAnnotatable
  * @since 1.0
  */
 public interface Annotatable  {
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotation.java
@@ -53,7 +53,6 @@
  *
  * @author Matthew Pocock
  * @author Thomas Down
- * @see org.biojavax.RichAnnotation
  *
  *
  * @since 1.0
@@ -96,8 +95,6 @@ public interface Annotation  {
 	 * @param value the new value for this key
 	 * @throws IllegalArgumentException if the property <code>key</code> is not
 	 *         legal
-	 * @throws ChangeVetoException if this annotation object can't be changed, or
-	 *         if the change was vetoed.
 	 */
 	void setProperty(Object key, Object value)
 	;
@@ -108,7 +105,6 @@ void setProperty(Object key, Object value)
 	 *
 	 * @param key the key object
 	 * @throws NoSuchElementException if the property doesn't exist
-	 * @throws ChangeVetoException if the change is vetoed
 	 * @since 1.3
 	 *
 	 */
@@ -147,7 +143,7 @@ public void removeProperty(Object key)
 	 * A really useful empty and immutable annotation object.
 	 * </p>
 	 *
-	 * Be careful when stooring Annotation arguments to
+	 * Be careful when storing Annotation arguments to
 	 *  constructors. It is possible that you have been passed EMPTY_ANNOTATION but
 	 * that code later on will access this object believing it to be
 	 * mutable. For example, the SeqIO factory code clones some
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/EmptyAnnotation.java
@@ -35,7 +35,6 @@
  *
  * @since 1.0 as part of Annotation
  * @since 1.4 as top-level class
- * @see org.biojavax.EmptyRichAnnotation
  */
 class EmptyAnnotation
 

Original file line number	Diff line number	Diff line change
`@@ -33,12 +33,13 @@`
`33`	`33`	`import java.util.*;`
`34`	`34`
`35`	`35`
`36`		`-/** A class to parse the content of an OBO file. It delegates handling of the`
	`36`	`+/**`
	`37`	`+ * A class to parse the content of an OBO file. It delegates handling of the`
`37`	`38`	`* content to the OBOFileEventListener implementation.`
`38`	`39`	`*`
`39`	`40`	`* This file contains parts of the OBO-Edit file OBOParseEngine, (particularly the encoding and decoding part)`
`40`	`41`	`*`
`41`		`- * http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup`
	`42`	`+ * See <a href="http://geneontology.cvs.sourceforge.net/geneontology/go-dev/java/oboedit/sources/org/geneontology/oboedit/dataadapter/OBOParseEngine.java?revision=1.10&view=markup">link</a>`
`42`	`43`	`* Thanks to the OboEdit developers for giving permission to release this in BioJava.`
`43`	`44`	`*`
`44`	`45`	`*`
Original file line number	Diff line number	Diff line change
`@@ -53,7 +53,6 @@`
`53`	`53`	`*`
`54`	`54`	`* @author Matthew Pocock`
`55`	`55`	`* @author Thomas Down`
`56`		`- * @see org.biojavax.RichAnnotation`
`57`	`56`	`*`
`58`	`57`	`*`
`59`	`58`	`* @since 1.0`
`@@ -96,8 +95,6 @@ public interface Annotation {`
`96`	`95`	`* @param value the new value for this key`
`97`	`96`	`* @throws IllegalArgumentException if the property <code>key</code> is not`
`98`	`97`	`* legal`
`99`		`- * @throws ChangeVetoException if this annotation object can't be changed, or`
`100`		`- * if the change was vetoed.`
`101`	`98`	`*/`
`102`	`99`	`void setProperty(Object key, Object value)`
`103`	`100`	`;`
`@@ -108,7 +105,6 @@ void setProperty(Object key, Object value)`
`108`	`105`	`*`
`109`	`106`	`* @param key the key object`
`110`	`107`	`* @throws NoSuchElementException if the property doesn't exist`
`111`		`- * @throws ChangeVetoException if the change is vetoed`
`112`	`108`	`* @since 1.3`
`113`	`109`	`*`
`114`	`110`	`*/`
`@@ -147,7 +143,7 @@ public void removeProperty(Object key)`
`147`	`143`	`* A really useful empty and immutable annotation object.`
`148`	`144`	`* </p>`
`149`	`145`	`*`
`150`		`- * Be careful when stooring Annotation arguments to`
	`146`	`+ * Be careful when storing Annotation arguments to`
`151`	`147`	`* constructors. It is possible that you have been passed EMPTY_ANNOTATION but`
`152`	`148`	`* that code later on will access this object believing it to be`
`153`	`149`	`* mutable. For example, the SeqIO factory code clones some`
Original file line number	Diff line number	Diff line change
`@@ -35,7 +35,6 @@`
`35`	`35`	`*`
`36`	`36`	`* @since 1.0 as part of Annotation`
`37`	`37`	`* @since 1.4 as top-level class`
`38`		`- * @see org.biojavax.EmptyRichAnnotation`
`39`	`38`	`*/`
`40`	`39`	`class EmptyAnnotation`
`41`	`40`