Replace IBond ref compares.

cdk · May 17, 2017 · cd54e43 · cd54e43
1 parent 76d03d7
commit cd54e43
Show file tree

Hide file tree

Showing 12 changed files with 18 additions and 18 deletions.
diff --git a/base/data/src/main/java/org/openscience/cdk/AtomContainer.java b/base/data/src/main/java/org/openscience/cdk/AtomContainer.java
@@ -491,7 +491,7 @@ public int indexOf(IAtom atom) {
     @Override
     public int indexOf(IBond bond) {
         for (int i = 0; i < bondCount; i++) {
-            if (bonds[i] == bond) return i;
+            if (bonds[i].equals(bond)) return i;
         }
         return -1;
     }
@@ -1217,7 +1217,7 @@ public boolean contains(IAtom atom) {
     @Override
     public boolean contains(IBond bond) {
         for (int i = 0; i < getBondCount(); i++) {
-            if (bond == bonds[i]) return true;
+            if (bonds[i].equals(bond)) return true;
         }
         return false;
     }

diff --git a/base/data/src/main/java/org/openscience/cdk/Ring.java b/base/data/src/main/java/org/openscience/cdk/Ring.java
@@ -116,7 +116,7 @@ public IBond getNextBond(IBond bond, IAtom atom) {
         IBond tempBond;
         for (int f = 0; f < getBondCount(); f++) {
             tempBond = getBond(f);
-            if (tempBond.contains(atom) && bond != tempBond) return tempBond;
+            if (tempBond.contains(atom) && !tempBond.equals(bond)) return tempBond;
         }
         return null;
     }

diff --git a/...somorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java b/...somorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
@@ -636,7 +636,7 @@ public int indexOf(IAtom atom) {
     @Override
     public int indexOf(IBond bond) {
         for (int i = 0; i < bondCount; i++) {
-            if (bonds[i] == bond) return i;
+            if (bonds[i].equals(bond)) return i;
         }
         return -1;
     }
@@ -1439,7 +1439,7 @@ public boolean contains(IAtom atom) {
     @Override
     public boolean contains(IBond bond) {
         for (int i = 0; i < getBondCount(); i++) {
-            if (bond == bonds[i]) return true;
+            if (bonds[i].equals(bond)) return true;
         }
         return false;
     }

diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java b/base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java
@@ -470,7 +470,7 @@ public int indexOf(IAtom atom) {
     @Override
     public int indexOf(IBond bond) {
         for (int i = 0; i < bondCount; i++) {
-            if (bonds[i] == bond) return i;
+            if (bonds[i].equals(bond)) return i;
         }
         return -1;
     }
@@ -1152,7 +1152,7 @@ public boolean contains(IAtom atom) {
     @Override
     public boolean contains(IBond bond) {
         for (int i = 0; i < getBondCount(); i++) {
-            if (bond == bonds[i]) return true;
+            if (bonds[i].equals(bond)) return true;
         }
         return false;
     }

diff --git a/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java b/base/silent/src/main/java/org/openscience/cdk/silent/Ring.java
@@ -116,7 +116,7 @@ public IBond getNextBond(IBond bond, IAtom atom) {
         IBond tempBond;
         for (int f = 0; f < getBondCount(); f++) {
             tempBond = getBond(f);
-            if (tempBond.contains(atom) && bond != tempBond) return tempBond;
+            if (tempBond.contains(atom) && !tempBond.equals(bond)) return tempBond;
         }
         return null;
     }

diff --git a/base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java b/base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java
@@ -338,7 +338,7 @@ private void traversePaths(State state, IAtom beg, IBond prev) throws CDKExcepti
             throw new CDKException("Too many paths! Structure is likely a cage, reduce path length or increase path limit");
         if (state.apath.size() < state.maxDepth) {
             for (IBond bond : state.getBonds(beg)) {
-                if (bond == prev)
+                if (bond.equals(prev))
                     continue;
                 final IAtom nbr = bond.getOther(beg);
                 if (state.visit(nbr)) {

diff --git a/base/standard/src/main/java/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java b/base/standard/src/main/java/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
@@ -686,7 +686,7 @@ public static List<RMap> makeAtomsMapOfBondsMap(List<RMap> l, IAtomContainer g1,
             for (int j = 0; j < 2; j++) {
                 List<IBond> bondsConnectedToAtom1j = g1.getConnectedBondsList(atom1[j]);
                 for (int k = 0; k < bondsConnectedToAtom1j.size(); k++) {
-                    if (bondsConnectedToAtom1j.get(k) != bond1) {
+                    if (!bondsConnectedToAtom1j.get(k).equals(bond1)) {
                         IBond testBond = (IBond) bondsConnectedToAtom1j.get(k);
                         for (int m = 0; m < l.size(); m++) {
                             IBond testBond2;

diff --git a/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingSetManipulator.java b/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingSetManipulator.java
@@ -249,7 +249,7 @@ public static boolean ringAlreadyInSet(IRing newRing, IRingSet ringSet) {
             if (ring.getBondCount() == newRing.getBondCount()) {
                 for (IBond newBond : newRing.bonds()) {
                     for (IBond bond : ring.bonds()) {
-                        if (newBond == bond) {
+                        if (newBond.equals(bond)) {
                             equals = true;
                             equalCount++;
                             break;

diff --git a/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCS.java b/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCS.java
@@ -728,7 +728,7 @@ public static List<CDKRMap> makeAtomsMapOfBondsMap(List<CDKRMap> list, IAtomCont
             for (int j = 0; j < 2; j++) {
                 List<IBond> bondsConnectedToAtom1j = sourceGraph.getConnectedBondsList(atom1[j]);
                 for (int k = 0; k < bondsConnectedToAtom1j.size(); k++) {
-                    if (bondsConnectedToAtom1j.get(k) != bond1) {
+                    if (!bondsConnectedToAtom1j.get(k).equals(bond1)) {
                         IBond testBond = bondsConnectedToAtom1j.get(k);
                         for (int m = 0; m < list.size(); m++) {
                             IBond testBond2;

diff --git a/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java b/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java
@@ -350,7 +350,7 @@ private static List<List<CDKRMap>> makeAtomsMapOfBondsMap(List<CDKRMap> rMapList
                 for (int j = 0; j < 2; j++) {
                     List<IBond> bondsConnectedToAtom1j = graph1.getConnectedBondsList(qAtoms[j]);
                     for (int k = 0; k < bondsConnectedToAtom1j.size(); k++) {
-                        if (bondsConnectedToAtom1j.get(k) != qBond) {
+                        if (!bondsConnectedToAtom1j.get(k).equals(qBond)) {
                             IBond testBond = bondsConnectedToAtom1j.get(k);
                             for (int m = 0; m < rMapList.size(); m++) {
                                 IBond testBond2;

diff --git a/legacy/src/main/java/org/openscience/cdk/tools/DeAromatizationTool.java b/legacy/src/main/java/org/openscience/cdk/tools/DeAromatizationTool.java
@@ -125,7 +125,7 @@ private static boolean deAromatizePyrolle(IRing ring) {
     private static IBond getNextBond(IAtom atom, IBond bond, IRing ring) {
         List<IBond> bonds = ring.getConnectedBondsList(atom);
         for (int i = 0; i < bonds.size(); i++)
-            if (bonds.get(i) != bond) return (IBond) bonds.get(i);
+            if (!bonds.get(i).equals(bond)) return (IBond) bonds.get(i);
         return null;
     }
 
@@ -556,7 +556,7 @@ private static void DearomatizeRing(IAtomContainer ring, IAtom startAtom, IBond
             List<IBond> bonds = ring.getConnectedBondsList(curAtom);
             for (IBond bond : bonds)
             {
-                if (bond!=curBond)
+                if (!bond.equals(curBond))
                 {
                     curBond = bond;
                     break;

diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
@@ -719,8 +719,8 @@ private List<IBond> findUnspecifiedDoubleBonds(int[][] adjList) {
                 continue;
 
             // stereo bond, ignore it depiction is correct
-            if ((doubleBondElements[beg] != null && doubleBondElements[beg].getStereoBond() == bond) ||
-                    (doubleBondElements[end] != null && doubleBondElements[end].getStereoBond() == bond))
+            if ((doubleBondElements[beg] != null && doubleBondElements[beg].getStereoBond().equals(bond)) ||
+                    (doubleBondElements[end] != null && doubleBondElements[end].getStereoBond().equals(bond)))
                 continue;
 
             // is actually a tetrahedral centre
@@ -839,7 +839,7 @@ private boolean hasOnlyPlainBonds(int v, IBond allowedDoubleBond) {
             IBond adjBond = edgeToBond.get(v, neighbor);
             // non single bonds
             if (adjBond.getOrder().numeric() > 1) {
-                if (allowedDoubleBond != adjBond) {
+                if (!allowedDoubleBond.equals(adjBond)) {
                     return false;
                 }
             }