resolving javadoc problems

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Apr 15, 2013 · 6a4781b · 6a4781b
1 parent 82aba8b
commit 6a4781b
Show file tree

Hide file tree

Showing 37 changed files with 68 additions and 70 deletions.
diff --git a/src/main/org/openscience/cdk/fingerprint/PubchemFingerprinter.java b/src/main/org/openscience/cdk/fingerprint/PubchemFingerprinter.java
@@ -111,7 +111,7 @@ public PubchemFingerprinter(IChemObjectBuilder builder) {
      * @return the fingerprint
      * @throws CDKException if there is an error during substructure 
      * searching or atom typing
-     * @see #getBitFingerprintAsBytes()
+     * @see #getFingerprintAsBytes()
      */
     @TestMethod("testFingerprint")
     public IBitFingerprint getBitFingerprint(IAtomContainer atomContainer) 

diff --git a/src/main/org/openscience/cdk/geometry/volume/VABCVolume.java b/src/main/org/openscience/cdk/geometry/volume/VABCVolume.java
@@ -69,10 +69,10 @@ public class VABCVolume {
     private static AtomTypeFactory atomTypeList = null;
 
     /**
-     * Calculates the volume for the given {@link IMolecule}. This methods assumes
+     * Calculates the volume for the given {@link IAtomContainer}. This methods assumes
      * that atom types have been perceived.
      *
-     * @param  molecule {@link IMolecule} to calculate the volume of.
+     * @param  molecule {@link IAtomContainer} to calculate the volume of.
      * @return          the volume in cubic &Aring;ngstr&ouml;m.
      */
     public static double calculate(IAtomContainer molecule) throws CDKException {

diff --git a/src/main/org/openscience/cdk/group/AbstractDiscretePartitionRefiner.java b/src/main/org/openscience/cdk/group/AbstractDiscretePartitionRefiner.java
@@ -182,7 +182,7 @@ public void applyTo(Permutation p) {
     /**
      * Get the upper-half of the adjacency matrix under the permutation.
      * 
-     * @param p a permutation of the adjacency matrix
+     * @param permutation a permutation of the adjacency matrix
      * @return a string containing the permuted values of half the matrix
      */
     @TestMethod("getHalfMatrixStringTest")

diff --git a/src/main/org/openscience/cdk/group/DisjointSetForest.java b/src/main/org/openscience/cdk/group/DisjointSetForest.java
@@ -34,7 +34,7 @@
  * 
  * @author maclean
  * @cdk.module group
- * @cdk.keywords union-find
+ * @cdk.keyword union-find
  */
 @TestClass("DisjointSetForestTest")
 public class DisjointSetForest {

diff --git a/src/main/org/openscience/cdk/interfaces/ISetting.java b/src/main/org/openscience/cdk/interfaces/ISetting.java
@@ -25,7 +25,7 @@
 
 /**
  * A simple setting that can be managed by the SettingManager. Currently the only
- * required method is {@see getName()} and provides the key with which setting are
+ * required method is {@link #getName()} and provides the key with which setting are
  * added and retrieved with.
  *
  * @author      johnmay

diff --git a/src/main/org/openscience/cdk/io/ChemObjectIO.java b/src/main/org/openscience/cdk/io/ChemObjectIO.java
@@ -35,10 +35,10 @@
 
 /**
  * Provides some basic functionality for readers and writers. This includes
- * managing the {@see IChemObjectIOListener}'s and managing of {@see IOSetting}'s.
- * The IOSettings are managed via the {@see SettingManager} class with most
+ * managing the {@link IChemObjectIOListener}'s and managing of {@link IOSetting}'s.
+ * The IOSettings are managed via the {@link SettingManager} class with most
  * method's wrapped to more descriptive method names (e.g.
- * {@see SettingManger#get(String)} is invoked by {@see getSetting(String)}).
+ * {@link SettingManager#get(String)} is invoked by {@link #getSetting(String)}).
  *
  * @author johnmay
  * @cdk.module io
@@ -149,8 +149,8 @@ public Collection<IOSetting> getSettings() {
     }
 
     /**
-     * Fires {@see IChemObjectIOListener#processIOSettingQuestion()} for all
-     * managed listeners.
+     * Fires {@link IChemObjectIOListener#processIOSettingQuestion(org.openscience.cdk.io.setting.IOSetting)}
+     * for all managed listeners.
      *
      * @param setting the setting to process
      */

diff --git a/src/main/org/openscience/cdk/io/IChemObjectIO.java b/src/main/org/openscience/cdk/io/IChemObjectIO.java
@@ -96,8 +96,8 @@ public interface IChemObjectIO extends Closeable {
     /**
      * Access all the listeners for this ChemObject Reader or Writer. This will
      * returned an unmodifiable list of listeners. Listeners should be added to and
-     * removed from the reader/writer using {@see addListener(IChemObjectIOListener)} and
-     * {@see removeListener(IChemObjectIOListener)}
+     * removed from the reader/writer using {@link #addChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener)} and
+     * {@link #removeChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener)}
      *
      * @return all listeners managed by this IO object
      */
@@ -127,7 +127,7 @@ public interface IChemObjectIO extends Closeable {
     public <S extends IOSetting> S addSetting(IOSetting setting);
 
     /**
-     * Adds a collection of {@see IOSetting}s to the reader/writer. This
+     * Adds a collection of {@link IOSetting}s to the reader/writer. This
      * is useful for transferring/propagating settings between different
      * reader/writer.
      *
@@ -194,7 +194,7 @@ public interface IChemObjectIO extends Closeable {
     public <S extends IOSetting> S getSetting(String name, Class<S> c);
 
     /**
-     * Access a collection of {@see IOSetting}s for this reader/writer.
+     * Access a collection of {@link IOSetting}s for this reader/writer.
      * @return collection of IOSetting's
      * @see #addSettings(java.util.Collection)
      */

diff --git a/src/main/org/openscience/cdk/io/MoSSOutputReader.java b/src/main/org/openscience/cdk/io/MoSSOutputReader.java
@@ -132,10 +132,10 @@ public boolean accepts(Class testClass) {
     }
 
     /**
-     * Read a {@link IMoleculeSet} from the input source.
+     * Read a {@link IAtomContainerSet} from the input source.
      *
-     * @param  object an {@link IMoleculeSet} into which the data is stored.
-     * @return        the content in a {@link IMoleculeSet} object
+     * @param  object an {@link IAtomContainerSet} into which the data is stored.
+     * @return        the content in a {@link IAtomContainerSet} object
      */
     public <T extends IChemObject> T read(T object) throws CDKException {
         if (object instanceof IAtomContainerSet) {
@@ -166,7 +166,7 @@ public <T extends IChemObject> T read(T object) throws CDKException {
     }
 
     /**
-     * Read the file content into a {@link IMoleculeSet}.
+     * Read the file content into a {@link IAtomContainerSet}.
      * @param molSet an {@link IAtomContainerSet} to store the structures
      * @return the {@link IAtomContainerSet} containing the molecules read in
      * @throws java.io.IOException if there is an error during reading

diff --git a/src/main/org/openscience/cdk/io/Mopac7Reader.java b/src/main/org/openscience/cdk/io/Mopac7Reader.java
@@ -96,7 +96,7 @@ public Mopac7Reader(Reader input) {
     /**
      * Constructs a new Mopac7reader that can read a molecule from a given {@link InputStream}.
      *
-     * @param  in  The {@link InputStream} to read from
+     * @param  input  The {@link InputStream} to read from
      */
     public Mopac7Reader(InputStream input) {
         this(new InputStreamReader(input));

diff --git a/src/main/org/openscience/cdk/io/RssWriter.java b/src/main/org/openscience/cdk/io/RssWriter.java
@@ -41,7 +41,7 @@
 import org.openscience.cdk.libio.cml.Convertor;
 
 /**
- * Generates an RSS feed. It the object is a {@link IMoleculeSet}, the molecules
+ * Generates an RSS feed. It the object is a {@link IAtomContainerSet}, the molecules
  * are put in separately. All other objects are made CML and put in.
  *
  * @cdk.module       libiocml

diff --git a/src/main/org/openscience/cdk/io/SDFWriter.java b/src/main/org/openscience/cdk/io/SDFWriter.java
@@ -147,7 +147,7 @@ public boolean accepts(Class classObject) {
     /**
      * Writes a IChemObject to the MDL SD file formated output. It can only
      * output IChemObjects of type {@link IChemFile}, {@link IAtomContainerSet}
-     * and {@link IMoleculeSet}.
+     * and {@link IAtomContainerSet}.
      *
      * @param object an acceptable {@link IChemObject} 
      *

diff --git a/src/main/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java b/src/main/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java
@@ -16,7 +16,7 @@
  * Iterate over conformers of a collection of molecules stored in SDF format.
  * <p/>
  * This class is analogous to the {@link org.openscience.cdk.io.iterator.IteratingSDFReader} except that
- * rather than return a single {@link org.openscience.cdk.interfaces.IMolecule} at each iteration this
+ * rather than return a single {@link org.openscience.cdk.interfaces.IAtomContainer} at each iteration this
  * class will return all the conformers for a given molecule at each iteration.
  * <p/>
  * The class assumes that the molecules are stored in SDF format and that all conformers for a given

diff --git a/src/main/org/openscience/cdk/io/iterator/IteratingSMILESReader.java b/src/main/org/openscience/cdk/io/iterator/IteratingSMILESReader.java
@@ -79,7 +79,7 @@ public class IteratingSMILESReader
      * @param  in  The Reader to read from
      * @param builder The builder to use
      * @see org.openscience.cdk.DefaultChemObjectBuilder
-     * @see org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder
+     * @see org.openscience.cdk.silent.SilentChemObjectBuilder
      */
     @TestMethod("testSMILESFileWithNames")
     public IteratingSMILESReader(Reader in, IChemObjectBuilder builder) {

diff --git a/src/main/org/openscience/cdk/io/setting/SettingManager.java b/src/main/org/openscience/cdk/io/setting/SettingManager.java
@@ -35,9 +35,9 @@
 
 /**
  * Provides dynamic management of settings. This
- * was created with the intention of managing {@see IOSetting}'s for {@see IChemObjectIO}
+ * was created with the intention of managing {@link IOSetting}'s for {@link org.openscience.cdk.io.IChemObjectIO}
  * however it could be recycled for other purposes where dynamic settings are required.
- * Settings are stored in a {@see Map} using the name of the setting as the key. The name is
+ * Settings are stored in a {@link Map} using the name of the setting as the key. The name is
  * normalised (lowercase and whitespace removal) to allow 'fuzzy' setting access. This means
  * that character case differences do not affect the retrieval of objects.
  * <p/>
@@ -98,7 +98,7 @@ private static String key(String name) {
 
     /**
      * Generate a simple key for the given setting. This method is a convenience
-     * method for {@see key(String)}
+     * method for {@link #key(String)}
      *
      * @param setting the setting to which a key will be generated for
      *
@@ -152,9 +152,9 @@ public T add(T setting) {
 
     /**
      * Access the setting stored for given name. If not setting is found the provided
-     * name an {@see InvalidParameterException} will be thrown. The method is generic
+     * name an {@link InvalidParameterException} will be thrown. The method is generic
      * to allow simplified access to settings. This however means that if the incorrect
-     * type is provided a {@see ClassCastException} may be thrown.
+     * type is provided a {@link ClassCastException} may be thrown.
      * <p/>
      * <pre>{@code
      * SettingManager manager = ...;
@@ -233,8 +233,8 @@ public Collection<T> getSettings() {
 
     /**
      * Compatibility method generates an array of ISetting objects. This method
-     * wraps a call to {@see Collection#toArray(T[])} and so is used the same way.
-     * Note: it is preferable to use the collection's accessor {@see getSettings()}
+     * wraps a call to {@link Collection#toArray(Object[])}} and so is used the same way.
+     * Note: it is preferable to use the collection's accessor {@link #getSettings()}
      * <p/>
      * Usage: <pre>{@code
      * IOSetting[] settings = manager.toArray(new IOSetting[0]);

diff --git a/src/main/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java b/src/main/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
@@ -1450,7 +1450,7 @@ public boolean contains(IElectronContainer electronContainer)
      * Clones this AtomContainer object and its content.
      *
      * @return    The cloned object
-     * @see       #shallowCopy
+     * @see       #QueryAtomContainer(org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.IChemObjectBuilder)
      */
     public IQueryAtomContainer clone() throws CloneNotSupportedException {
         IAtom[] newAtoms;

diff --git a/src/main/org/openscience/cdk/isomorphism/matchers/QueryBond.java b/src/main/org/openscience/cdk/isomorphism/matchers/QueryBond.java
@@ -411,7 +411,7 @@ public boolean compare(Object object) {
      * Checks whether a query bond is connected to another one.
      * This can only be true if the query bonds have an Atom in common.
      *
-     * @param query bond The query bond which is checked to be connect with this one
+     * @param bond bond The query bond which is checked to be connect with this one
      * @return true if the query bonds share an atom, otherwise false
      */
     public boolean isConnectedTo(IBond bond) {

diff --git a/src/main/org/openscience/cdk/isomorphism/matchers/RGroupQuery.java b/src/main/org/openscience/cdk/isomorphism/matchers/RGroupQuery.java
@@ -62,7 +62,7 @@
  * including a root plus a bunch of substituents, which are all atom containers.
  * So that would be a lot of sample code here. <br>
  * The best way to get a feel for the way the RGroup objects are populated is to
- * run the {@link org.openscience.cdk.io.RGroupQueryReaderTest} and look at the sample
+ * run the RGroupQueryReaderTest and look at the sample
  * input RGroup query files contained in the CDK and how they translate into
  * RGroupXX objects. The JChempaint application can visualize the input files for you. 
  *

diff --git a/src/main/org/openscience/cdk/libio/jena/Convertor.java b/src/main/org/openscience/cdk/libio/jena/Convertor.java
@@ -62,10 +62,10 @@
 public class Convertor {
 
     /**
-     * Converts a {@link IMolecule} into a {@link Model} representation using the CDK OWL.
+     * Converts a {@link IAtomContainer} into a {@link Model} representation using the CDK OWL.
      *
-     * @param molecule {@link IMolecule} to serialize into a RDF graph.
-     * @return the RDF graph representing the {@link IMolecule}.
+     * @param molecule {@link IAtomContainer} to serialize into a RDF graph.
+     * @return the RDF graph representing the {@link IAtomContainer}.
      */
     public static Model molecule2Model(IAtomContainer molecule) {
         Model model = createCDKModel();
@@ -338,11 +338,11 @@ private static void deserializeElectronContainerFields(
     }
 
     /**
-     * Converts a {@link Model} into an {@link IMolecule} using the given {@link IChemObjectBuilder}.
+     * Converts a {@link Model} into an {@link IAtomContainer} using the given {@link IChemObjectBuilder}.
      *
-     * @param model RDF graph to deserialize into an {@link IMolecule}.
+     * @param model RDF graph to deserialize into an {@link IAtomContainer}.
      * @param builder {@link IChemObjectBuilder} used to create new {@link IChemObject}s.
-     * @return a {@link IMolecule} deserialized from the RDF graph.
+     * @return a {@link IAtomContainer} deserialized from the RDF graph.
      */
     public static IAtomContainer model2Molecule(Model model,
         IChemObjectBuilder builder) {

diff --git a/src/main/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java b/src/main/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java
@@ -82,7 +82,6 @@ public void initilize(Map parameterSet) {
 	 *
 	 * @param  molecule the reference molecule for searching the chain 
 	 * @param  chain  chain to be searched
-	 * @param  molecule  the chain container (reference) molecule
 	 * @return        the atom number of the first heavy atom the number of heavy atoms in the chain
 	 */
 	public int[] findHeavyAtomsInChain(IAtomContainer molecule, IAtomContainer chain) {

diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/FragmentComplexityDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/FragmentComplexityDescriptor.java
@@ -114,9 +114,9 @@ public String[] getDescriptorNames() {
     }    
 
     /**
-     * Calculate the complexity in the supplied {@link AtomContainer}.
+     * Calculate the complexity in the supplied {@link IAtomContainer}.
      * 
-     *@param  container  The {@link AtomContainer} for which this descriptor is to be calculated
+     *@param  container  The {@link IAtomContainer} for which this descriptor is to be calculated
      *@return                   the complexity
      *@see #setParameters
      */

diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
@@ -169,7 +169,7 @@ private DescriptorValue getDummyDescriptorValue(Exception e) {
      * <p/>
      * <p>Same for checkRingSystem, if true the CDKConstant.ISINRING will be set
      *
-     * @param atomContainer The {@link AtomContainer} for which this descriptor is to be calculated
+     * @param atomContainer The {@link IAtomContainer} for which this descriptor is to be calculated
      * @return the number of atoms in the largest chain of this AtomContainer
      * @see #setParameters
      */

diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java
@@ -149,7 +149,7 @@ private DescriptorValue getDummyDescriptorValue(Exception e) {
 
 
     /**
-     * Calculate the count of atoms of the largest pi system in the supplied {@link AtomContainer}.
+     * Calculate the count of atoms of the largest pi system in the supplied {@link IAtomContainer}.
      * <p/>
      * <p>The method require one parameter:
      * <ol>

diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/LongestAliphaticChainDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/LongestAliphaticChainDescriptor.java
@@ -150,12 +150,12 @@ private DescriptorValue getDummyDescriptorValue(Exception e) {
     }
 
     /**
-     * Calculate the count of atoms of the longest aliphatic chain in the supplied {@link AtomContainer}.
+     * Calculate the count of atoms of the longest aliphatic chain in the supplied {@link IAtomContainer}.
      * 
      *  The method require one parameter:
      *  if checkRingSyste is true the CDKConstant.ISINRING will be set
      *
-     *@param  atomContainer  The {@link AtomContainer} for which this descriptor is to be calculated
+     *@param  atomContainer  The {@link IAtomContainer} for which this descriptor is to be calculated
      *@return                   the number of atoms in the longest aliphatic chain of this AtomContainer
      *@see #setParameters
      */

diff --git a/src/main/org/openscience/cdk/reaction/IReactionProcess.java b/src/main/org/openscience/cdk/reaction/IReactionProcess.java
@@ -85,8 +85,8 @@ public interface IReactionProcess {
      * Optionally, parameters may be set which can affect the course of the process.
      *
      *
-     * @param reactants   An {@link org.openscience.cdk.interfaces.IMoleculeSet} for which this process should be initiate.
-     * @param agents      An {@link org.openscience.cdk.interfaces.IMoleculeSet} for which this process should be initiate.
+     * @param reactants   An {@link IAtomContainerSet} for which this process should be initiate.
+     * @param agents      An {@link IAtomContainerSet} for which this process should be initiate.
      * @return the set of reactions.
      * @throws CDKException if an error occurs during the reaction process. See documentation for individual reaction processes
      */

diff --git a/src/main/org/openscience/cdk/renderer/ChemModelRenderer.java b/src/main/org/openscience/cdk/renderer/ChemModelRenderer.java
@@ -46,7 +46,7 @@
 
 /**
  * A general renderer for {@link IChemModel}s, {@link IReaction}s, and
- * {@link IMolecule}s. The chem object
+ * {@link IAtomContainer}s. The chem object
  * is converted into a 'diagram' made up of {@link IRenderingElement}s. It takes
  * an {@link IDrawVisitor} to do the drawing of the generated diagram. Various
  * display properties can be set using the {@link RendererModel}.<p>

diff --git a/src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java b/src/main/org/openscience/cdk/renderer/MoleculeSetRenderer.java
@@ -45,7 +45,7 @@
 
 /**
  * A general renderer for {@link IChemModel}s, {@link IReaction}s, and
- * {@link IMolecule}s. The chem object
+ * {@link IAtomContainer}s. The chem object
  * is converted into a 'diagram' made up of {@link IRenderingElement}s. It takes
  * an {@link IDrawVisitor} to do the drawing of the generated diagram. Various
  * display properties can be set using the {@link RendererModel}.<p>
@@ -136,9 +136,9 @@ public MoleculeSetRenderer(RendererModel rendererModel,List<IGenerator<IAtomCont
     }
 
 	/**
-	 * Setup the transformations necessary to draw this {@link IMoleculeSet}.
+	 * Setup the transformations necessary to draw this {@link IAtomContainerSet}.
 	 *
-	 * @param moleculeSet the {@link IMoleculeSet} for what to set the scale
+	 * @param moleculeSet the {@link IAtomContainerSet} for what to set the scale
 	 * @param screen      the {@link Rectangle} for which to calculate the scale
 	 */
 	public void setup(IAtomContainerSet moleculeSet, Rectangle screen) {
@@ -206,7 +206,7 @@ public Rectangle shift(Rectangle screenBounds, Rectangle diagramBounds) {
      * of the model and calculates the multiplication factor to transform this
      * to the bond length that is set in the RendererModel.
      * 
-     * @param moleculeSet the {@link IMoleculeSet} for what to set the scale
+     * @param moleculeSet the {@link IAtomContainerSet} for what to set the scale
      */
     public void setScale(IAtomContainerSet moleculeSet) {
         double bondLength = AverageBondLengthCalculator.calculateAverageBondLength(moleculeSet);
@@ -233,7 +233,7 @@ public Rectangle paint(IAtomContainerSet moleculeSet, IDrawVisitor drawVisitor)
 	/**
      * Paint a set of molecules.
      *
-     * @param molecules   the {@link IMoleculeSet} to paint
+     * @param molecules   the {@link IAtomContainerSet} to paint
      * @param drawVisitor the visitor that does the drawing
      * @param bounds      the bounds on the screen
      * @param resetCenter

diff --git a/src/main/org/openscience/cdk/renderer/ReactionRenderer.java b/src/main/org/openscience/cdk/renderer/ReactionRenderer.java
@@ -44,7 +44,7 @@
 
 /**
  * A general renderer for {@link IChemModel}s, {@link IReaction}s, and
- * {@link IMolecule}s. The chem object
+ * {@link IAtomContainer}s. The chem object
  * is converted into a 'diagram' made up of {@link IRenderingElement}s. It takes
  * an {@link IDrawVisitor} to do the drawing of the generated diagram. Various
  * display properties can be set using the {@link RendererModel}.<p>