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Merge branch 'jdoc' into cdk-1.4.x
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rajarshi committed Mar 20, 2012
2 parents 055646a + c6ec88f commit 3f2c646
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Showing 12 changed files with 23 additions and 37 deletions.
4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/controller/IMouseEventRelay.java
Expand Up @@ -52,15 +52,15 @@ public interface IMouseEventRelay {
* @param screenCoordX the x part of the screen coordinate where the event happened.
* @param screenCoordY the y part of the screen coordinate where the event happened.
*/
public abstract void mouseClickedDownRight(int x, int y);
public abstract void mouseClickedDownRight(int screenCoordX, int screenCoordY);

/**
* Event to signal that the right mouse button has been released.
*
* @param screenCoordX the x part of the screen coordinate where the event happened.
* @param screenCoordY the y part of the screen coordinate where the event happened.
*/
public abstract void mouseClickedUpRight(int x, int y);
public abstract void mouseClickedUpRight(int screenCoordX, int screenCoordY);

/**
* Event to signal that a mouse button has been double clicked.
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Expand Up @@ -149,7 +149,7 @@ public IteratingMDLReader(InputStream in, IChemObjectBuilder builder) {
* skip is set to true then the reader will keep trying to read more molecules
* until the end of the file is reached.
*
* @param in the {@see InputStream} to read from
* @param in the {@link InputStream} to read from
* @param builder builder to use
* @param skip whether to skip null molecules
*/
Expand All @@ -165,7 +165,7 @@ public IteratingMDLReader(InputStream in, IChemObjectBuilder builder, boolean sk
* skip is set to true then the reader will keep trying to read more molecules
* until the end of the file is reached.
*
* @param in the {@see Reader} to read from
* @param in the {@link Reader} to read from
* @param builder builder to use
* @param skip whether to skip null molecules
*/
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Expand Up @@ -169,10 +169,6 @@ private int countImplicitHydrogens(IAtom atom) {
}

/** {@inheritDoc}
*
* @param targetContainer
* @param targetAtom
* @return
*/
public boolean matches(IAtomContainer targetContainer, IAtom targetAtom) {
if (smartQueryAtom != null && qAtom == null) {
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Expand Up @@ -115,10 +115,6 @@ public DefaultRGraphAtomMatcher(IAtomContainer queryContainer, IAtom template, i
}

/** {@inheritDoc}
*
* @param targetContainer
* @param targetAtom
* @return
*/
public boolean matches(IAtomContainer targetContainer, IAtom targetAtom) {
if (qAtom instanceof IQueryAtom) {
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Expand Up @@ -170,10 +170,6 @@ private int countImplicitHydrogens(IAtom atom) {
}

/** {@inheritDoc}
*
* @param targetContainer
* @param targetAtom
* @return
*/
public boolean matches(TargetProperties targetContainer, IAtom targetAtom) {
if (smartQueryAtom != null && qAtom == null) {
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Expand Up @@ -43,7 +43,6 @@ public class ExactMapping {
* Extract atom mapping from the cliques and stores it in a List
* @param comp_graph_nodes
* @param clique_List_org
* @return
*/
private static List<Integer> extractCliqueMapping(List<Integer> comp_graph_nodes, List<Integer> clique_List_org) {

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Expand Up @@ -43,8 +43,7 @@
import org.openscience.cdk.smsd.tools.MolHandler;

/**
* This class acts as a handler class for CDKMCS algorithm
* {@link org.openscience.cdk.smsd.algorithm.cdk.CDKMCS}.
* This class acts as a handler class for {@link CDKMCS} algorithm.
*
* @cdk.module smsd
* @cdk.githash
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Expand Up @@ -43,8 +43,7 @@
import org.openscience.cdk.smsd.tools.MolHandler;

/**
* This class acts as a handler class for CDKMCS algorithm
* {@link org.openscience.cdk.smsd.algorithm.cdk.CDKMCS}.
* This class acts as a handler class for {@link CDKMCS} algorithm.
*
* @cdk.module smsd
* @cdk.githash
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17 changes: 9 additions & 8 deletions src/main/org/openscience/cdk/smsd/filters/ChemicalFilters.java
Expand Up @@ -867,9 +867,10 @@ private int getFragmentCount(IAtomContainer molecule) {
}

/**
* Get bond order value as IBond order
* @param srcOrder
* @return
* Get bond order value as {@link Order}.
*
* @param srcOrder numerical bond order
* @return the bond order type for the given numerical bond order
*/
public static IBond.Order convertOrder(double srcOrder) {
if (srcOrder > 3.5) {
Expand All @@ -888,9 +889,11 @@ public static IBond.Order convertOrder(double srcOrder) {
}

/**
*Get bond order value as integer
* @param bond
* @return
* Get bond order value as {@code int} value.
*
* @param bond The {@link IBond} for which the order is returned.
* @return 1 for a single bond, 2 for a double bond, 3 for a triple bond, 4 for a quadruple bond,
* and 0 for any other bond type.
*/
public static int convertBondOrder(IBond bond) {
int value = 0;
Expand All @@ -916,7 +919,6 @@ public static int convertBondOrder(IBond bond) {
/**
* Get stereo value as integer
* @param bond
* @return
*/
public static int convertBondStereo(IBond bond) {
int value = 0;
Expand Down Expand Up @@ -951,7 +953,6 @@ public static int convertBondStereo(IBond bond) {
/**
* Get stereo value as Stereo enum
* @param stereoValue
* @return
*/
public static IBond.Stereo convertStereo(int stereoValue) {
IBond.Stereo stereo = IBond.Stereo.NONE;
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Expand Up @@ -3,18 +3,17 @@
import org.openscience.cdk.interfaces.IReaction;

/**
* @cdk.module smsd
* @cdk.module smsd
* @cdk.githash
*/

public interface ICanonicalReactionLabeller {

/**
* Convert a reaction into a canonical form by canonizing each of the
* structures in the reaction in turn.
*
* @param reaction
* @return
* @param reaction the {@link IReaction} to be processed
* @return the canonical {@link IReaction}
*/
public IReaction getCanonicalReaction(IReaction reaction);

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7 changes: 4 additions & 3 deletions src/main/org/openscience/cdk/smsd/ring/HanserRingFinder.java
Expand Up @@ -87,9 +87,10 @@ public HanserRingFinder() {
}

/**
* Returns collection of rings
* @param molecule
* @return
* Returns a collection of rings.
*
* @param molecule
* @return a {@link Collection} of {@link List}s containing one ring each
* @see org.openscience.cdk.smsd.ring.RingFinder#findRings(org.openscience.cdk.interfaces.IAtomContainer)
*/
public Collection<List<IAtom>> findRings(IAtomContainer molecule) {
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Expand Up @@ -731,7 +731,7 @@ public static double getDBE(IMolecularFormula formula) throws CDKException{
*
* @param atomContainer IAtomContainer object
* @return a molecular formula object
* @see getMolecularFormula(IAtomContainer,IMolecularFormula)
* @see #getMolecularFormula(IAtomContainer,IMolecularFormula)
*/
@TestMethod("testGetMolecularFormula_IAtomContainer")
public static IMolecularFormula getMolecularFormula(IAtomContainer atomContainer) {
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