Javadoc fix: errors in modfinder module

josemduarte · josemduarte · commit bb073294543c · 2025-01-07T14:16:37.000-08:00
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java
@@ -30,7 +30,7 @@
  * contains information about a certain Component.
  * The Component class uses the extensible enum pattern.
  * You can't instantiate Component directly, instead
- * you have to use one of the {@link register} and {@link of} methods.
+ * you have to use one of the register and {@link #of} methods.
  *
  * @author Jianjiong Gao
  * @since 3.0
@@ -109,7 +109,7 @@ public boolean isCTerminal() {
 	/**
 	 * Get a Component that does not have to occur at terminals. If the
 	 * corresponding component has already been registered, return that one.
-	 * @param pdbccIds possible Protein Data Bank ID.
+	 * @param pdbccId possible Protein Data Bank ID.
 	 * @return a component.
 	 * @throws IllegalArgumentException if pdbccId or type is null,
 	 *  or the pdbccId has been registered as a different type.
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ModificationLinkage.java
@@ -54,10 +54,10 @@ public ModificationLinkage(
 	 *
 	 * @param components {@link Component}s involved in a modification.
 	 * @param indexOfComponent1 index of the first component.
-	 * @param labelOfAtomOnComponent1 label of the atom on the first
+	 * @param pdbNameOfAtomsOnComponent1 label of the atom on the first
 	 *  component.
 	 * @param indexOfComponent2 index of the second component.
-	 * @param labelOfAtomOnComponent2 label of the atom on the second
+	 * @param pdbNameOfAtomsOnComponent2 label of the atom on the second
 	 *  component.
 	 */
 	public ModificationLinkage(
@@ -77,10 +77,10 @@ public ModificationLinkage(
 	 *
 	 * @param components {@link Component}s involved in a modification.
 	 * @param indexOfComponent1 index of the first component.
-	 * @param labelOfAtomOnComponent1 label of the atom on the first
+	 * @param pdbNameOfPotentialAtomsOnComponent1 label of the atom on the first
 	 *  component.
 	 * @param indexOfComponent2 index of the second component.
-	 * @param labelOfAtomOnComponent2 label of the atom on the second
+	 * @param pdbNameOfPotentialAtomsOnComponent2 label of the atom on the second
 	 *  component.
 	 */
 	public ModificationLinkage(
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java
@@ -206,7 +206,7 @@ public static void register(final ProteinModification modification) {
 
 	/**
 	 * Remove a modification from registry.
-	 * @param mod
+	 * @param modification
 	 */
 	public static void unregister(ProteinModification modification) {
 		if (modification==null) throw new IllegalArgumentException("modification == null!");
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompound.java
@@ -47,7 +47,7 @@ public interface ModifiedCompound {
 
 	/**
 	 *
-	 * @return {@link ProteinModificationBean} occurred on the residue.
+	 * @return {@link ProteinModification} occurred on the residue.
 	 */
 	public ProteinModification getModification();
 
@@ -73,19 +73,18 @@ public interface ModifiedCompound {
 	/**
 	 *
 	 * @return a set of atom linkages.
-	 * @see #getLinkedGroupPairs
 	 * @see StructureAtomLinkage
 	 */
 	public Set<StructureAtomLinkage> getAtomLinkages();
 
-	/** Set atom linkages
+	/**
+	 * Set atom linkages
 	 *
-	 * @return
 	 */
 	public void setAtomLinkages(Set<StructureAtomLinkage> linkages);
 
 	/**
-	 * Add a linkage. Add new the involved groups first using {@link addGroup}.
+	 * Add a linkage. Add new the involved groups first using addGroup.
 	 * @param linkage an atom linkage.
 	 * @return true if this linkage was not already contained.
 	 * @see StructureAtomLinkage
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ModifiedCompoundImpl.java
@@ -65,7 +65,6 @@ public ModifiedCompoundImpl(){
 	 * Use this constructor for a modified residue.
 	 * @param modification {@link ProteinModification}.
 	 * @param modifiedResidue modified group.
-	 * @return a {@link ModifiedCompound}.
 	 * @throws IllegalArgumentException if either argument is null.
 	 */
 	public ModifiedCompoundImpl (
