Remove 1147 lines: 5 dead files + 202 commented-out debug lines across 44 files

Deleted orphan files:
- centres/cdk/CMLLoader.java, centres/io/CytoscapeWriter.java
- smsd/interfaces/IResults.java
- mapping/blocks/BlockReactionCanoniser.java (376 lines)
- mapping/blocks/BlockMapper.java

Removed all remaining commented-out System.out/println/err/printStackTrace
across 44 files including RXNFileManipulator (62 lines), MappingUtility (25),
DirectReactionDrawer (25), ReactionSimilarityTool (20), MappingHandler (18).

345 → 340 Java files. All 135 tests pass.

Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>

Author: asad

src/main/java/com/bioinceptionlabs/aamtool/ReactionDecoder.java

@@ -579,8 +579,6 @@ private void AnnotateTask(CommandLine annotateLine,
                 | ParserConfigurationException
                 | TransformerException
                 | DOMException e) {
-            //System.out.println("Error " + e.getCause());
-            //e.printStackTrace();
             LOGGER.error(SEVERE, null, e);
         }
     }

src/main/java/com/bioinceptionlabs/centres/cdk/CMLLoader.java

@@ -97,8 +97,6 @@ public List<Ligand<A>> getLigands(A atom) {
     @Override
     public void reroot(Ligand<A> ligand) {
 
-//        System.out.println("tails: " + arcs.tails);
-//        System.out.println("heads: " + arcs.heads);
         root = ligand;
         ligand.reset();
 
@@ -272,7 +270,6 @@ class ArcMap {
         private final Map<Ligand<A>, Arc<A>> heads = new HashMap<>();
 
         public void remove(Arc<A> arc) {
-            //System.out.println("\tremoving " + arc.getTail() + ": " + arc + " and " + arc.getHead() + ": " + arc);
             tails.remove(arc.getTail(), arc);
             heads.remove(arc.getHead());
         }

src/main/java/com/bioinceptionlabs/centres/graph/AbstractDigraph.java

@@ -92,7 +92,6 @@ public static float getTanimotoSimilarity(BitSet Molecule1, BitSet Molecule2) th
         float _bitset1_cardinality = bitset1.cardinality();
         float _bitset2_cardinality = bitset2.cardinality();
 
-//        System.out.println("bitset1: "+ bitset1.size() + " " + " bitset2" + bitset2.size());
         if (bitset1.size() != bitset2.size()) {
             throw new Exception("BitSets must have the same bit length");
         }

src/main/java/com/bioinceptionlabs/centres/io/CytoscapeWriter.java

@@ -440,9 +440,6 @@ public Rectangle2D drawAtomID(IAtom atom, IAtomContainer container, Graphics2D g
             pos = suggestedPosition;
         }
 
-        //        System.out.println("Alignment for atom " + atomID + " " + pos
-        //                + " given annotations at "
-        //                + labelManager.getAnnotationPositionsAsString(atom));
 
         double aW2 = atomSymbolBounds.getWidth() / 2;
         double bW2 = bounds.getWidth() / 2;
@@ -488,7 +485,6 @@ public Rectangle2D drawAtomID(IAtom atom, IAtomContainer container, Graphics2D g
         if (pos != null) {
             labelManager.setUsedPosition(atom, pos);
         } else {
-//            System.err.println("position null for ID " + atomID);
         }
 
         Point2f tp = getTextPoint(g, atomID, pID.x, pID.y);

src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/tools/Similarity.java

@@ -181,7 +181,6 @@ public Rectangle2D drawRBlastReaction(RBlastReaction rBlastReaction, int w, int
         }
 
         if (params.drawLabelPanel) {
-//            System.out.println("drawing labels");
             g.setTransform(originalTransform);
             g.translate((w / 2), (h / 2));
             g.setFont(new Font(params.labelPanelFont, PLAIN, params.labelPanelFontSize));
@@ -208,11 +207,6 @@ public Rectangle2D drawRBlastReaction(RBlastReaction rBlastReaction, int w, int
             int cropY = max(0, (int) dY / 2);
             int cropW = (int) min(finalWidth, w);
             int cropH = (int) min(finalHeight, w);
-//            System.out.println("CROPPING totalBounds " 
-//                    + BoundsPrinter.toString(totalBoundingBox));
-//            System.out.println("zoom " + zoom + " dX " + dX + " dY " + dY 
-//                            + " crop " + cropX + " " + cropY + " " 
-//                                       + cropW + " " + cropH);
             if ((cropX + cropW > w) || (cropY + cropH > h)) {
                 LOGGER.debug("Not cropping to ["
                         + cropX + ", " + cropY + "] "

src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/DirectAtomDrawer.java

@@ -299,11 +299,6 @@ public Image drawReaction(IReaction reaction, int w, int h, boolean invert) {
             int cropY = max(0, (int) dY / 2);
             int cropW = (int) min(finalWidth, w);
             int cropH = (int) min(finalHeight, w);
-//            System.out.println("CROPPING totalBounds " 
-//                    + BoundsPrinter.toString(totalBoundingBox));
-//            System.out.println("zoom " + zoom + " dX " + dX + " dY " + dY 
-//                            + " crop " + cropX + " " + cropY + " " 
-//                                       + cropW + " " + cropH);
             if ((cropX + cropW > w) || (cropY + cropH > h)) {
                 LOGGER.debug("Not cropping " + (cropX + cropW) + " " + w + " "
                         + (cropY + cropH) + " " + h);
@@ -449,7 +444,6 @@ private void drawReaction(IReaction reaction,
                 = reaction.getReactants().getAtomContainer(index);
         String reactantsID = reaction.getReactants().getID();
         String boundsID = reactionID + "_" + reactantsID + "_" + lastReactant.getID() + ":" + index;
-//        System.out.println("looking up bounds " + boundsID);
         Rectangle2D lastRBound = boundsTree.get(boundsID);
         double xPos;
         double yPos;
@@ -462,7 +456,6 @@ private void drawReaction(IReaction reaction,
         }
         arrowCenter = new Point2d(xPos, yPos);
 
-//        System.out.println("arrow center @ " + arrowCenter);
         if (params.arrowType == FORWARD) {
             arrowDrawer.drawArrow(g, arrowCenter, reactionAxis);
         } else if (params.arrowType == BACKWARD) {
@@ -543,7 +536,6 @@ public BoundsTree centerOn(IReaction reaction, double cx, double cy, BoundsTree
         double boundsY = boundsTree.getRoot().getCenterY();
         double dx = cx - boundsX;
         double dy = cy - boundsY;
-//        System.out.println("shifting (" + boundsX + ", " + boundsY + ") by "+ dx + " " + dy);
         return shift(reaction, boundsTree, dx, dy);
     }
 
@@ -588,9 +580,6 @@ public BoundsTree shift(
             }
         }
 
-//        Rectangle2D rBB = boundsTree.get(reaction.getID());
-//        System.out.println("reaction center " + rBB.getCenterX() + " " + rBB.getCenterY());
-//        System.out.println("arrow center " + reactionLayout.getArrowCenter());
         return boundsTree;
     }
 
@@ -604,18 +593,12 @@ private BoundsTree shift(IAtomContainerSet reactants, String rootLabel,
         for (IAtomContainer atomContainer : reactants.atomContainers()) {
             String fullLabel = rootLabel + "_" + label + "_" + atomContainer.getID() + ":" + counter;
             String subLabel = label + "_" + atomContainer.getID() + ":" + counter;
-//            System.out.println(fullLabel);
-
-//            System.out.println("Atoms From" + BoundsPrinter.toString(GeometryTools.getRectangle2D(atomContainer)));
             translate2D(atomContainer, dx, dy);
             Rectangle2D uBounds = unshiftedMolSetTree.get(fullLabel);
             Rectangle2D sBounds = new Rectangle2D.Double(uBounds.getMinX() + dx,
                     uBounds.getMinY() + dy,
                     uBounds.getWidth(),
                     uBounds.getHeight());
-//            System.out.println("From " + BoundsPrinter.toString(uBounds));
-//            System.out.println("To   " + BoundsPrinter.toString(sBounds));
-//            System.out.println("Atoms To" + BoundsPrinter.toString(GeometryTools.getRectangle2D(atomContainer)));
             boundsTree.add(subLabel, sBounds);
             counter++;
         }
@@ -624,9 +607,6 @@ private BoundsTree shift(IAtomContainerSet reactants, String rootLabel,
 
     private Axis getAxisOfExpansion(
             int targetWidth, int targetHeight, double zoomedWidth, double zoomedHeight) {
-//        int borderX = params.borderX;
-//        int borderY = params.borderY;
-//        int border2 = borderX * 2;
         double widthRatio = targetWidth / zoomedWidth;
         double heightRatio = targetHeight / zoomedHeight;
         if (widthRatio < heightRatio) {
@@ -799,7 +779,6 @@ public void drawMoleculeSet(IAtomContainerSet reactants, String reactionID, doub
             if (i > 0) {
                 IAtomContainer previous = reactants.getAtomContainer(i - 1);
                 String previousLabel = reactionID + "_" + reactants.getID() + "_" + previous.getID() + ":" + (i - 1);
-//                System.out.println("getting " + previousLabel);
                 drawPlus(previous, previousLabel, yAxis, boundsTree, g);
                 moleculeDrawer.drawMolecule(current, g);
             } else {
@@ -823,10 +802,7 @@ public void drawPlus(IAtomContainer ac, String acLabel, double yAxis, BoundsTree
         if (boundsTree == null) {
             bounds = getRectangle2D(ac);
         } else {
-//            System.out.print("looking up " + acLabel);
             bounds = boundsTree.get(acLabel);
-//            System.out.println(" found " + BoundsPrinter.toString(bounds));
-//            System.out.println(boundsTree);
         }
 
         Rectangle2D textBounds = getTextBounds(g, "+");
@@ -844,7 +820,6 @@ public void drawPlus(IAtomContainer ac, String acLabel, double yAxis, BoundsTree
                 posAlongAxis - halfWidth, yAxis - halfHeight, tbW, tbH));
         g.setColor(BLACK);
         g.setFont(new Font("ARIAL", PLAIN, params.plusFontSize));
-//        System.out.println("drawing plus at " + p);
         g.drawString("+", p.x, p.y);
     }