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Simplified fully qualified names where an existing import is present …
…(PMD Reports).

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
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Mark B Vine authored and johnmay committed Aug 30, 2014
1 parent 49eec3d commit 1273835
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Showing 18 changed files with 74 additions and 74 deletions.
Expand Up @@ -167,7 +167,7 @@ public static int[][] computeFloydAPSP(double costMatrix[][]) {
*/
@TestMethod("testDepthFirstTargetSearch_IAtomContainer_IAtom_IAtom_IAtomContainer")
public static boolean depthFirstTargetSearch(IAtomContainer molecule, IAtom root, IAtom target, IAtomContainer path) {
java.util.List<IBond> bonds = molecule.getConnectedBondsList(root);
List<IBond> bonds = molecule.getConnectedBondsList(root);
IAtom nextAtom;
root.setFlag(CDKConstants.VISITED, true);
for (IBond bond : bonds) {
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22 changes: 11 additions & 11 deletions base/data/src/main/java/org/openscience/cdk/Atom.java
Expand Up @@ -78,16 +78,16 @@ public class Atom extends AtomType implements IAtom, Serializable, Cloneable {
* A 2D point specifying the location of this atom in a 2D coordinate
* space.
*/
protected javax.vecmath.Point2d point2d = (Point2d) CDKConstants.UNSET;
protected Point2d point2d = (Point2d) CDKConstants.UNSET;
/**
* A 3 point specifying the location of this atom in a 3D coordinate
* space.
*/
protected javax.vecmath.Point3d point3d = (Point3d) CDKConstants.UNSET;
protected Point3d point3d = (Point3d) CDKConstants.UNSET;
/**
* A 3 point specifying the location of this atom in a crystal unit cell.
*/
protected javax.vecmath.Point3d fractionalPoint3d = (Point3d) CDKConstants.UNSET;
protected Point3d fractionalPoint3d = (Point3d) CDKConstants.UNSET;
/**
* The number of implicitly bound hydrogen atoms for this atom.
*/
Expand Down Expand Up @@ -127,7 +127,7 @@ public Atom(String elementSymbol) {
* @param elementSymbol The symbol of the atom
* @param point3d The 3D coordinates of the atom
*/
public Atom(String elementSymbol, javax.vecmath.Point3d point3d)
public Atom(String elementSymbol, Point3d point3d)
{
this(elementSymbol);
this.point3d = point3d;
Expand All @@ -139,7 +139,7 @@ public Atom(String elementSymbol, javax.vecmath.Point3d point3d)
* @param elementSymbol The Element
* @param point2d The Point
*/
public Atom(String elementSymbol, javax.vecmath.Point2d point2d)
public Atom(String elementSymbol, Point2d point2d)
{
this(elementSymbol);
this.point2d = point2d;
Expand Down Expand Up @@ -240,7 +240,7 @@ public Integer getImplicitHydrogenCount() {
*
* @see #getPoint2d
*/
public void setPoint2d(javax.vecmath.Point2d point2d) {
public void setPoint2d(Point2d point2d) {
this.point2d = point2d;
notifyChanged();
}
Expand All @@ -253,7 +253,7 @@ public void setPoint2d(javax.vecmath.Point2d point2d) {
*
* @see #getPoint3d
*/
public void setPoint3d(javax.vecmath.Point3d point3d) {
public void setPoint3d(Point3d point3d) {
this.point3d = point3d;
notifyChanged();
}
Expand All @@ -266,7 +266,7 @@ public void setPoint3d(javax.vecmath.Point3d point3d) {
* @see #getFractionalPoint3d
* @see org.openscience.cdk.Crystal
*/
public void setFractionalPoint3d(javax.vecmath.Point3d point3d) {
public void setFractionalPoint3d(Point3d point3d) {
this.fractionalPoint3d = point3d;
notifyChanged();
}
Expand All @@ -291,7 +291,7 @@ public void setStereoParity(Integer stereoParity) {
*
* @see #setPoint2d
*/
public javax.vecmath.Point2d getPoint2d() {
public Point2d getPoint2d() {
return this.point2d;
}
/**
Expand All @@ -302,7 +302,7 @@ public javax.vecmath.Point2d getPoint2d() {
*
* @see #setPoint3d
*/
public javax.vecmath.Point3d getPoint3d() {
public Point3d getPoint3d() {
return this.point3d;
}

Expand All @@ -315,7 +315,7 @@ public javax.vecmath.Point3d getPoint3d() {
* @see #setFractionalPoint3d
* @see org.openscience.cdk.CDKConstants for predefined values.
*/
public javax.vecmath.Point3d getFractionalPoint3d() {
public Point3d getFractionalPoint3d() {
return this.fractionalPoint3d;
}

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22 changes: 11 additions & 11 deletions base/silent/src/main/java/org/openscience/cdk/silent/Atom.java
Expand Up @@ -80,16 +80,16 @@ public class Atom extends AtomType implements IAtom, Serializable, Cloneable {
* A 2D point specifying the location of this atom in a 2D coordinate
* space.
*/
protected javax.vecmath.Point2d point2d = (Point2d) CDKConstants.UNSET;
protected Point2d point2d = (Point2d) CDKConstants.UNSET;
/**
* A 3 point specifying the location of this atom in a 3D coordinate
* space.
*/
protected javax.vecmath.Point3d point3d = (Point3d) CDKConstants.UNSET;
protected Point3d point3d = (Point3d) CDKConstants.UNSET;
/**
* A 3 point specifying the location of this atom in a crystal unit cell.
*/
protected javax.vecmath.Point3d fractionalPoint3d = (Point3d) CDKConstants.UNSET;
protected Point3d fractionalPoint3d = (Point3d) CDKConstants.UNSET;
/**
* The number of implicitly bound hydrogen atoms for this atom.
*/
Expand Down Expand Up @@ -129,7 +129,7 @@ public Atom(String elementSymbol) {
* @param elementSymbol The symbol of the atom
* @param point3d The 3D coordinates of the atom
*/
public Atom(String elementSymbol, javax.vecmath.Point3d point3d)
public Atom(String elementSymbol, Point3d point3d)
{
this(elementSymbol);
this.point3d = point3d;
Expand All @@ -141,7 +141,7 @@ public Atom(String elementSymbol, javax.vecmath.Point3d point3d)
* @param elementSymbol The Element
* @param point2d The Point
*/
public Atom(String elementSymbol, javax.vecmath.Point2d point2d)
public Atom(String elementSymbol, Point2d point2d)
{
this(elementSymbol);
this.point2d = point2d;
Expand Down Expand Up @@ -240,7 +240,7 @@ public Integer getImplicitHydrogenCount() {
*
* @see #getPoint2d
*/
public void setPoint2d(javax.vecmath.Point2d point2d) {
public void setPoint2d(Point2d point2d) {
this.point2d = point2d;
}
/**
Expand All @@ -252,7 +252,7 @@ public void setPoint2d(javax.vecmath.Point2d point2d) {
*
* @see #getPoint3d
*/
public void setPoint3d(javax.vecmath.Point3d point3d) {
public void setPoint3d(Point3d point3d) {
this.point3d = point3d;
}
/**
Expand All @@ -264,7 +264,7 @@ public void setPoint3d(javax.vecmath.Point3d point3d) {
* @see #getFractionalPoint3d
* @see org.openscience.cdk.Crystal
*/
public void setFractionalPoint3d(javax.vecmath.Point3d point3d) {
public void setFractionalPoint3d(Point3d point3d) {
this.fractionalPoint3d = point3d;
}
/**
Expand All @@ -287,7 +287,7 @@ public void setStereoParity(Integer stereoParity) {
*
* @see #setPoint2d
*/
public javax.vecmath.Point2d getPoint2d() {
public Point2d getPoint2d() {
return this.point2d;
}
/**
Expand All @@ -298,7 +298,7 @@ public javax.vecmath.Point2d getPoint2d() {
*
* @see #setPoint3d
*/
public javax.vecmath.Point3d getPoint3d() {
public Point3d getPoint3d() {
return this.point3d;
}

Expand All @@ -311,7 +311,7 @@ public javax.vecmath.Point3d getPoint3d() {
* @see #setFractionalPoint3d
* @see org.openscience.cdk.CDKConstants for predefined values.
*/
public javax.vecmath.Point3d getFractionalPoint3d() {
public Point3d getFractionalPoint3d() {
return this.fractionalPoint3d;
}

Expand Down
Expand Up @@ -305,7 +305,7 @@ public static int isTetrahedral(IAtomContainer container, IAtom atom, boolean st
{
return (0);
}
java.util.List<IBond> bonds = container.getConnectedBondsList(atom);
List<IBond> bonds = container.getConnectedBondsList(atom);
int up = 0;
int down = 0;
for (IBond bond : bonds) {
Expand Down
Expand Up @@ -40,7 +40,7 @@ public class RandomNumbersTool extends Random {

private static final long serialVersionUID = -8238833473383641882L;

private static java.util.Random random;
private static Random random;
private static long randomSeed;

static {
Expand All @@ -55,7 +55,7 @@ public class RandomNumbersTool extends Random {
* @param base_random a <code>java.util.Random</code> subclass.
*/
@TestMethod("testSetRandom")
public static void setRandom(java.util.Random base_random) {
public static void setRandom(Random base_random) {
random = base_random;
}

Expand Down
Expand Up @@ -149,7 +149,7 @@ public final class Stereocenters {
* @return the stereocenters
*/
public static Stereocenters of(IAtomContainer container) {
GraphUtil.EdgeToBondMap bondMap = GraphUtil.EdgeToBondMap.withSpaceFor(container);
EdgeToBondMap bondMap = EdgeToBondMap.withSpaceFor(container);
int[][] g = GraphUtil.toAdjList(container, bondMap);
return new Stereocenters(container, g, bondMap);
}
Expand Down
Expand Up @@ -1138,7 +1138,7 @@ public static IAtom[] getAtomArray(IAtomContainer container) {
* @return The array of Atom objects.
*/
@TestMethod("testGetAtomArray_List")
public static IAtom[] getAtomArray(java.util.List<IAtom> list) {
public static IAtom[] getAtomArray(List<IAtom> list) {
IAtom[] ret = new IAtom[list.size()];
for (int i = 0; i < ret.length; ++i) ret[i] = list.get(i);
return ret;
Expand All @@ -1162,7 +1162,7 @@ public static IBond[] getBondArray(IAtomContainer container) {
* @return The array of Atom objects.
*/
@TestMethod("testGetBondArray_List")
public static IBond[] getBondArray(java.util.List<IBond> list) {
public static IBond[] getBondArray(List<IBond> list) {
IBond[] ret = new IBond[list.size()];
for (int i = 0; i < ret.length; ++i) ret[i] = list.get(i);
return ret;
Expand All @@ -1184,7 +1184,7 @@ public static IElectronContainer[] getElectronContainerArray(IAtomContainer cont
* @param list The original List.
* @return The array of Atom objects.
*/
public static IElectronContainer[] getElectronContainerArray(java.util.List<IElectronContainer> list) {
public static IElectronContainer[] getElectronContainerArray(List<IElectronContainer> list) {
IElectronContainer[] ret = new IElectronContainer[list.size()];
for (int i = 0; i < ret.length; ++i) ret[i] = list.get(i);
return ret;
Expand Down
Expand Up @@ -173,8 +173,8 @@ public DescriptorValue calculate(IAtom first, IAtom second, IAtomContainer atomC
}
java.util.Iterator<IAtomContainer> detected = acSet.atomContainers().iterator();

java.util.List<IAtom> neighboorsFirst = mol.getConnectedAtomsList(clonedFirst);
java.util.List<IAtom> neighboorsSecond = mol.getConnectedAtomsList(clonedSecond);
List<IAtom> neighboorsFirst = mol.getConnectedAtomsList(clonedFirst);
List<IAtom> neighboorsSecond = mol.getConnectedAtomsList(clonedSecond);

while (detected.hasNext()) {
IAtomContainer detectedAC = detected.next();
Expand Down
Expand Up @@ -277,7 +277,7 @@ else if (connectedBond.getOrder() == CDKConstants.BONDORDER_TRIPLE)
tripleBondCount++;
}
int formalCharge = atom.getFormalCharge();
java.util.List connectedAtoms = ac.getConnectedAtomsList(atom);
List connectedAtoms = ac.getConnectedAtomsList(atom);
int numberOfNeighbours = connectedAtoms.size();

// EXPLICIT hydrogens: count the number of hydrogen atoms
Expand Down

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