Remove ~40 more commented-out debug lines from 15 files

asad · asad · commit 3983909e97aa · 2026-03-24T18:38:16.000Z
Clean ConvexHull (10 lines), StereogenicCenterCalculator (8 lines), BoundsTree, SignatureRootFinder, ValencyCalculator, MolContainer, FingerPrintContainer, filters, graphics, and utility classes. Fix duplicate @SuppressWarnings in EBIArrayList. Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/containers/FingerPrintContainer.java b/src/main/java/com/bioinceptionlabs/reactionblast/containers/FingerPrintContainer.java
@@ -202,9 +202,7 @@ public boolean isKeyPresent(String Key) throws IOException {
     @Override
     public void setValue(String Key, BitSet Value)
             throws IOException {
-//        System.out.println("KEY " + Key + " val: " + Value.cardinality());
         FingerPrintMap.put(Key, Value);
-//        System.out.println("FingerPrintMap " + FingerPrintMap.size() + " val: " + Value.cardinality());
     }
 
     /**
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/containers/MolContainer.java b/src/main/java/com/bioinceptionlabs/reactionblast/containers/MolContainer.java
@@ -207,7 +207,7 @@ public boolean isIdentical(IAtomContainer _queryMol,
     private boolean isSubgraphIdentical(IAtomContainer _mol,
             IAtomContainer _rMol,
             boolean removeHydrogen) throws CDKException, IOException {
-//        System.out.println("Graph matching");
+
 
         IAtomContainer mol1 = _mol;
         IAtomContainer mol2 = _rMol;
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/ConvexHull.java b/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/ConvexHull.java
@@ -144,7 +144,7 @@ public Rectangle getMinimumAreaBoundingRectangleBruteForce() {
                 minArea = area;
                 winnerIndex = index;
             }
-//            System.out.println("rect " + rect);
+
         }
         Vector2d edge = edgeVector(hull[hull.length - 1], hull[0]);
         Rectangle rect = getRectangleBrute(edge, hull.length - 1, 0);
@@ -154,7 +154,6 @@ public Rectangle getMinimumAreaBoundingRectangleBruteForce() {
             minArea = area;
             winnerIndex = hull.length;
         }
-//        System.out.println("winner = " + winnerIndex);
 
         return minRect;
     }
@@ -213,12 +212,7 @@ public Rectangle getMinimumAreaBoundingRectangle() {
                 minArea = area;
                 minRect = rectangle;
             }
-//            System.out.println(
-//                    "rotated angle = " + rotatedAngle
-//                    + " min " + minArea
-//                    + " r = " + rectangle
-//                    + " caliper_a " + caliperA
-//                    + " caliper_b " + caliperB);
+
         }
         return minRect;
     }
@@ -237,11 +231,7 @@ private Rectangle getRectangleBrute(
         double maxAngle = 0;
         Vector2d vN = new Vector2d(vector);
         vN.normalize();
-//        System.out.println("tailIndex " + tailPointIndex 
-//                + " visiting points from " 
-//                + hullIDs[headPointIndex]
-//                + " tailPt" + toString(tailPoint)
-//                + " headPt" + toString(headPoint));
+
         int max = 0;
         while (visited < hull.length) {
             if (index == hull.length) {
@@ -251,7 +241,7 @@ private Rectangle getRectangleBrute(
                 vMax = hull[index];
             } else {
                 double angle = prj(tailPoint, headPoint, hull[index]);
-//                System.out.println(index + " proj " + hullIDs[index] + " " + angle);
+
                 if (angle < minAngle) {
                     min = index;
                     minAngle = angle;
@@ -277,12 +267,12 @@ private Rectangle getRectangleBrute(
         Point2d vMin = hull[min];
         Point2d tailProj = project(tailPoint, headPoint, vMax, true);
         Point2d headProj = project(tailPoint, headPoint, vMin, true);
-//        System.out.println("vMax = " + hullIDs[max] + " vMin = " + hullIDs[min]);
+
         Rectangle r
                 = new Rectangle(thirdPoint, tailProj, headProj, thirdPointDist);
         r.pointY = vMin;
         r.pointZ = vMax;
-//        System.out.println(toString(tailPoint, headPoint, tailProj, headProj, vMin, vMax));
+
         return r;
     }
 
@@ -371,7 +361,7 @@ private Rectangle getRectangle(
                 increasing = false;
             }
         }
-//        System.out.println(toString(tailPoint, headPoint, remainExPoint, tailExPt, projTail, headExPt, projHead)); 
+
 
         return new Rectangle(remainExPoint, projTail, projHead,
                 pointLineDistance(tailPoint, headPoint, remainExPoint));
@@ -412,7 +402,7 @@ private Point2d project(Point2d p1, Point2d p2, Point2d p3, boolean outSeg) {
             } else {
                 p = new Point2d(p1.x + (t * dx), p1.y + (t * dy));
             }
-//            if (outSeg) System.out.println("projecting t = " + t + " " + toString(p1, p2, p3, p));
+
             return p;
         }
     }
@@ -632,9 +622,7 @@ public Rectangle(Point2d pointOnAB, Point2d cornerC, Point2d cornerD, double dis
                 cdVecNormalized.normalize();
             }
             Vector2d perp = new Vector2d(cdVecNormalized.y, -cdVecNormalized.x);
-//            System.out.println(
-//                    pointOnAB + " " +  cornerC + " " +  cornerD + " " +  distToCD
-//                    + " " +  cdVec + " " +  perp);
+
             cornerA = new Point2d(cornerD);
             cornerA.scaleAdd(distToCD, perp, cornerA);
             cornerB = new Point2d(cornerC);
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/MoleculeLabelDrawer.java b/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/MoleculeLabelDrawer.java
@@ -60,7 +60,7 @@ public void draw(Map<String, String> labelMap, BoundsTree labelBounds, Graphics2
             double x = bounds.getCenterX();
             double y = bounds.getCenterY();
             Point2f p = super.getTextPoint(g, label, x, y);
-//            System.out.println("drawing string at " + x + " " + y);
+
             g.drawString(label, p.x, p.y);
         }
     }
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/SignatureRootFinder.java b/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/SignatureRootFinder.java
@@ -177,7 +177,7 @@ public static List<RootSystem> findRootSystems(
 
             }
         }
-//        System.out.println("RS for " + atomContainer.getID() + " = " + rootSystems);
+
 
         // now, join together any root systems that are adjacent
         boolean merging = true;
@@ -193,7 +193,7 @@ public static List<RootSystem> findRootSystems(
                 if (adjacent(rootSystem, otherRootSystem, atomContainer)) {
                     mergedRootSystems.add(rootSystem.merge(otherRootSystem));
                     hasMerged = true;
-//                    System.out.println("merge " + rootSystem + " and " + otherRootSystem);
+
                 } else {
                     mergedRootSystems.add(otherRootSystem);
                 }
@@ -217,7 +217,7 @@ public static List<RootSystem> findRootSystems(
             });
         }
 
-//        System.out.println("RS for " + atomContainer.getID() + " = " + rootSystems + " after merging ");
+
         return rootSystems;
     }
 
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/layout/AbstractDirectLayout.java b/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/layout/AbstractDirectLayout.java
@@ -120,9 +120,9 @@ public void translateTo(IAtomContainer ac, double x, double y, Rectangle2D bound
             atom.getPoint2d().y += dy;
         }
 //        bounds.setFrameFromCenter(x, y, bounds.getMinX() + dx, bounds.getMinY() + dy);
-//        System.out.print(ac.getID() + " ADL Before : " + BoundsPrinter.toString(bounds));
+
         bounds.setRect(bounds.getMinX() + dx, bounds.getMinY() + dy, bounds.getWidth(), bounds.getHeight());
-//        System.out.println(" After: " + BoundsPrinter.toString(bounds) + " " + dx + " " + dy);
+
     }
     
     /**
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/layout/BoundsTree.java b/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/layout/BoundsTree.java
@@ -125,7 +125,7 @@ public void add(String label, Rectangle2D bounds) {
             root.add(bounds);
         }
         if (root != null) {
-//            System.out.println("root " + BoundsPrinter.toString(root) + " added " + BoundsPrinter.toString(bounds) + " " + label);
+
         }
     }
 
@@ -213,10 +213,10 @@ public List<String> getBoundLabels() {
      */
     public void shift(double dx, double dy) {
         childMap.keySet().stream().map(key -> childMap.get(key)).forEachOrdered(bounds -> {
-            //            System.out.print(key + " Before : " + BoundsPrinter.toString(bounds));
+
             bounds.setRect(bounds.getMinX() + dx, bounds.getMinY() + dy,
                     bounds.getWidth(), bounds.getHeight());
-//            System.out.println(" After: " + BoundsPrinter.toString(bounds) + " " + dx + " " + dy);
+
         });
     }
 
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/layout/ZoomToFitLayout.java b/src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/layout/ZoomToFitLayout.java
@@ -88,7 +88,7 @@ public void layout(IAtomContainer mol, Dimension cellCanvas, Graphics2D g) {
     private double calculateZoom(IAtomContainer ac, double w, double h) {
         double borderX = drawer.getParams().borderX;
         double borderY = drawer.getParams().borderY;
-//        System.out.println("border " + borderX + " " + borderY);
+
         double canvasWidth = w;
         double canvasHeight = h;
         double scaleFactor
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/mechanism/StereogenicCenterCalculator.java b/src/main/java/com/bioinceptionlabs/reactionblast/mechanism/StereogenicCenterCalculator.java
@@ -167,11 +167,6 @@ public List<StereoChange> compare(IReaction reaction, Map<IAtom, IStereoAndConfo
                 IStereoAndConformation pAtom2DCDKStereo = chirality2DCDK.get(atomT);
                 IStereoAndConformation rAtom2DStereo = chirality2DChemaxon.get(atomQ);
                 IStereoAndConformation pAtom2DStereo = chirality2DChemaxon.get(atomT);
-                //                    System.out.println("atomQ " + atomQ.getID() + " S: " + atomQ.getSymbol());
-//                    System.out.println("atomT " + atomT.getID() + " S: " + atomT.getSymbol());
-//
-//                    System.out.println("atomQ " + chirality2DCDK.containsKey(atomQ));
-//                    System.out.println("atomT " + chirality2DCDK.containsKey(atomT));
                 if (isStereogenicChange(rAtom2DStereo, pAtom2DStereo)) {
                     StereoChange sc = new StereoChange(rAtom2DStereo, pAtom2DStereo, atomQ, atomT);
                     stereoChangeList.add(sc);
@@ -210,11 +205,6 @@ public List<StereoChange> compare(IReaction reaction, Map<IAtom, IStereoAndConfo
             targetAtoms.stream().filter((atomT) -> (atomQ.getID().equals(atomT.getID()) && !atomQ.getSymbol().equalsIgnoreCase("H"))).forEachOrdered((atomT) -> {
                 IStereoAndConformation rAtom2DCDKStereo = chirality2DCDK.get(atomQ);
                 IStereoAndConformation pAtom2DCDKStereo = chirality2DCDK.get(atomT);
-//                    System.out.println("atomQ " + atomQ.getID() + " S: " + atomQ.getSymbol());
-//                    System.out.println("atomT " + atomT.getID() + " S: " + atomT.getSymbol());
-//
-//                    System.out.println("atomQ " + chirality2DCDK.containsKey(atomQ));
-//                    System.out.println("atomT " + chirality2DCDK.containsKey(atomT));
                 if (isStereogenicChange(rAtom2DCDKStereo, pAtom2DCDKStereo)) {
                     StereoChange sc = new StereoChange(rAtom2DCDKStereo, pAtom2DCDKStereo, atomQ, atomT);
                     stereoChangeList.add(sc);
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/signature/RBlastMoleculeSignature.java b/src/main/java/com/bioinceptionlabs/reactionblast/signature/RBlastMoleculeSignature.java
@@ -198,9 +198,6 @@ public String getSmilesForAtomSignature(int atomIndex, int height, ICanonicalMol
         builder.makeFromColoredTree(tree);
         IAtomContainer fragment = builder.getAtomContainer();
         fragment = permute(labeller.getCanonicalPermutation(fragment), fragment);
-//        System.out.println(new AtomContainerPrinter().toString(fragment));
-//        System.out.println(Arrays.toString(labeller.getCanonicalPermutation(fragment)));
-//        return "";
         RBlastSmilesGenerator smilesGenerator
                 = new RBlastSmilesGenerator(false, labeller);
         try {
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/tools/CreateDirectory.java b/src/main/java/com/bioinceptionlabs/reactionblast/tools/CreateDirectory.java
@@ -79,7 +79,7 @@ private void createDir() throws IOException {
                 throw new IOException(msg);
             }
 
-            //System.out.println("Created dir: " + dir.getAbsolutePath());
+
             // path=dir.getAbsolutePath();
         }
     }
diff --git a/src/main/java/com/bioinceptionlabs/reactionblast/tools/ValencyCalculator.java b/src/main/java/com/bioinceptionlabs/reactionblast/tools/ValencyCalculator.java
@@ -90,7 +90,7 @@ private static void initialize() {
             } else {
                 valencElectronMap.put(symbol, 99);
             }
-//            System.out.println("Atom " + symbol + " grp: " + PeriodicTable.getGroup(symbol) + " P " + PeriodicTable.getPeriod(symbol));
+
         }
         /* 
          * Metal
@@ -113,7 +113,7 @@ private static void initialize() {
         valencElectronMap.put("A", 1);
         valencElectronMap.put("X", 8);
         valencElectronMap.put("PsH", 1);
-//        System.out.println("valencElectronMap Size " + valencElectronMap.size());
+
         isInitialized = true;
     }
 
diff --git a/src/main/java/org/openscience/smsd/filters/EnergyFilter.java b/src/main/java/org/openscience/smsd/filters/EnergyFilter.java
@@ -100,7 +100,7 @@ public void fillMap(Map<Integer, Double> energySelectionMap) {
 
     private Double getMappedMoleculeEnergies(AtomAtomMapping mcsAtomSolution) throws CDKException {
 
-//        System.out.println("\nSort By Energies");
+
         double totalBondEnergy = -9999.0;
 
         IAtomContainer educt = SilentChemObjectBuilder.getInstance().newInstance(IAtomContainer.class, chemfilter.getQuery());
diff --git a/src/main/java/org/openscience/smsd/filters/StereoFilter.java b/src/main/java/org/openscience/smsd/filters/StereoFilter.java
@@ -111,7 +111,7 @@ private boolean getStereoBondChargeMatch(Map<Integer, Double> stereoScoreMap,
         for (Integer Key : allStereoAtomMCS.keySet()) {
             try {
                 double score = 0.0;
-                //            System.out.println("\nStart score " + score);
+
                 AtomAtomMapping atomMapMCS = allStereoAtomMCS.get(Key);
                 double atomScore = getAtomScore(score, atomMapMCS, chemfilter.getQuery(), chemfilter.getTarget());
                 Map<IBond, IBond> bondMaps = makeBondMapsOfAtomMaps(chemfilter.getQuery(), chemfilter.getTarget(), atomMapMCS);
@@ -154,7 +154,7 @@ private Map<IBond, IBond> makeBondMapsOfAtomMaps(IAtomContainer ac1, IAtomContai
                 }
             });
         });
-//        System.out.println("Mol Map size:" + bondbondMappingMap.size());
+
         return bondbondMappingMap;
     }
 
diff --git a/src/main/java/org/openscience/smsd/tools/Utility.java b/src/main/java/org/openscience/smsd/tools/Utility.java
@@ -128,7 +128,7 @@ public static List<Integer> getBubbleSort(List<Integer> unSortedVector) {
                 }
             }
         }
-//        System.out.println("Bubble Sort: " + sortedVector);
+
         return sortedVector;
     }
 

Original file line number	Diff line number	Diff line change
`@@ -202,9 +202,7 @@ public boolean isKeyPresent(String Key) throws IOException {`
`202`	`202`	`@Override`
`203`	`203`	`public void setValue(String Key, BitSet Value)`
`204`	`204`	`throws IOException {`
`205`		`-// System.out.println("KEY " + Key + " val: " + Value.cardinality());`
`206`	`205`	`FingerPrintMap.put(Key, Value);`
`207`		`-// System.out.println("FingerPrintMap " + FingerPrintMap.size() + " val: " + Value.cardinality());`
`208`	`206`	`}`
`209`	`207`
`210`	`208`	`/**`
Original file line number	Diff line number	Diff line change
`@@ -60,7 +60,7 @@ public void draw(Map<String, String> labelMap, BoundsTree labelBounds, Graphics2`
`60`	`60`	`double x = bounds.getCenterX();`
`61`	`61`	`double y = bounds.getCenterY();`
`62`	`62`	`Point2f p = super.getTextPoint(g, label, x, y);`
`63`		`-// System.out.println("drawing string at " + x + " " + y);`
	`63`	`+`
`64`	`64`	`g.drawString(label, p.x, p.y);`
`65`	`65`	`}`
`66`	`66`	`}`
Original file line number	Diff line number	Diff line change
`@@ -177,7 +177,7 @@ public static List<RootSystem> findRootSystems(`
`177`	`177`
`178`	`178`	`}`
`179`	`179`	`}`
`180`		`-// System.out.println("RS for " + atomContainer.getID() + " = " + rootSystems);`
	`180`	`+`
`181`	`181`
`182`	`182`	`// now, join together any root systems that are adjacent`
`183`	`183`	`boolean merging = true;`
`@@ -193,7 +193,7 @@ public static List<RootSystem> findRootSystems(`
`193`	`193`	`if (adjacent(rootSystem, otherRootSystem, atomContainer)) {`
`194`	`194`	`mergedRootSystems.add(rootSystem.merge(otherRootSystem));`
`195`	`195`	`hasMerged = true;`
`196`		`-// System.out.println("merge " + rootSystem + " and " + otherRootSystem);`
	`196`	`+`
`197`	`197`	`} else {`
`198`	`198`	`mergedRootSystems.add(otherRootSystem);`
`199`	`199`	`}`
`@@ -217,7 +217,7 @@ public static List<RootSystem> findRootSystems(`
`217`	`217`	`});`
`218`	`218`	`}`
`219`	`219`
`220`		`-// System.out.println("RS for " + atomContainer.getID() + " = " + rootSystems + " after merging ");`
	`220`	`+`
`221`	`221`	`return rootSystems;`
`222`	`222`	`}`
`223`	`223`
Original file line number	Diff line number	Diff line change
`@@ -120,9 +120,9 @@ public void translateTo(IAtomContainer ac, double x, double y, Rectangle2D bound`
`120`	`120`	`atom.getPoint2d().y += dy;`
`121`	`121`	`}`
`122`	`122`	`// bounds.setFrameFromCenter(x, y, bounds.getMinX() + dx, bounds.getMinY() + dy);`
`123`		`-// System.out.print(ac.getID() + " ADL Before : " + BoundsPrinter.toString(bounds));`
	`123`	`+`
`124`	`124`	`bounds.setRect(bounds.getMinX() + dx, bounds.getMinY() + dy, bounds.getWidth(), bounds.getHeight());`
`125`		`-// System.out.println(" After: " + BoundsPrinter.toString(bounds) + " " + dx + " " + dy);`
	`125`	`+`
`126`	`126`	`}`
`127`	`127`
`128`	`128`	`/**`
Original file line number	Diff line number	Diff line change
`@@ -125,7 +125,7 @@ public void add(String label, Rectangle2D bounds) {`
`125`	`125`	`root.add(bounds);`
`126`	`126`	`}`
`127`	`127`	`if (root != null) {`
`128`		`-// System.out.println("root " + BoundsPrinter.toString(root) + " added " + BoundsPrinter.toString(bounds) + " " + label);`
	`128`	`+`
`129`	`129`	`}`
`130`	`130`	`}`
`131`	`131`
`@@ -213,10 +213,10 @@ public List<String> getBoundLabels() {`
`213`	`213`	`*/`
`214`	`214`	`public void shift(double dx, double dy) {`
`215`	`215`	`childMap.keySet().stream().map(key -> childMap.get(key)).forEachOrdered(bounds -> {`
`216`		`- // System.out.print(key + " Before : " + BoundsPrinter.toString(bounds));`
	`216`	`+`
`217`	`217`	`bounds.setRect(bounds.getMinX() + dx, bounds.getMinY() + dy,`
`218`	`218`	`bounds.getWidth(), bounds.getHeight());`
`219`		`-// System.out.println(" After: " + BoundsPrinter.toString(bounds) + " " + dx + " " + dy);`
	`219`	`+`
`220`	`220`	`});`
`221`	`221`	`}`
`222`	`222`