Final polish: fix autoboxing, final fields, null-safe getters, lineSeparator

- BondChange: make bondChangeDelta final, remove setter, inline computation
- MCSSolution: null-safe getters (return 0/0.0 instead of null)
- AtomContainerComparatorBy2DCenter: Double.compare() instead of autoboxing
- MinSelection: fix Double.valueOf(int) == double comparison
- BondEnergies: diamond operator
- TestUtility: make DEBUG field final
- Replace System.getProperty("line.separator") with System.lineSeparator()
  across 7 files

All 135 tests pass.

Author: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>

Author: asad

src/main/java/com/bioinceptionlabs/reactionblast/graphics/direct/AtomContainerComparatorBy2DCenter.java

@@ -47,9 +47,9 @@ public int compare(IAtomContainer atCont1, IAtomContainer atCont2) {
             Point2d p2 = get2DCenter(atCont2);
             if (p1 != null && p2 != null) {
                 if (p1.x != p2.x) {
-                    return Double.valueOf(p1.x).compareTo(p2.x);
+                    return Double.compare(p1.x, p2.x);
                 } else {
-                    return Double.valueOf(p1.y).compareTo(p2.y);
+                    return Double.compare(p1.y, p2.y);
                 }
             }
         }

src/main/java/com/bioinceptionlabs/reactionblast/mapping/algorithm/checks/MinSelection.java

@@ -186,7 +186,7 @@ public boolean isSubAndCompleteMatchFlag() {
     }
 
     private boolean isMCSSubgraph(IAtomContainer educt, double mcsSize) throws CDKException {
-        return Double.valueOf(educt.getAtomCount()) == mcsSize;
+        return educt.getAtomCount() == (int) mcsSize;
     }
 
     /**

src/main/java/com/bioinceptionlabs/reactionblast/mapping/graph/MCSSolution.java

@@ -60,10 +60,10 @@ public MCSSolution(int queryPosition, int targetPosition,
     }
 
     /**
-     * @return the stereoScore
+     * @return the stereoScore, or 0 if null
      */
     public Integer getStereoScore() {
-        return stereoScore;
+        return stereoScore != null ? stereoScore : 0;
     }
 
     /**
@@ -74,10 +74,10 @@ public void setStereoScore(Integer stereoScore) {
     }
 
     /**
-     * @return the fragmentSize
+     * @return the fragmentSize, or 0 if null
      */
     public Integer getFragmentSize() {
-        return fragmentSize;
+        return fragmentSize != null ? fragmentSize : 0;
     }
 
     /**
@@ -88,10 +88,10 @@ public void setFragmentSize(Integer fragmentSize) {
     }
 
     /**
-     * @return the energy
+     * @return the energy, or 0.0 if null
      */
     public Double getEnergy() {
-        return energy;
+        return energy != null ? energy : 0.0;
     }
 
     /**

src/main/java/com/bioinceptionlabs/reactionblast/mechanism/BondChangeCalculator.java

@@ -89,7 +89,7 @@
  */
 public class BondChangeCalculator extends AbstractChangeCalculator implements IChangeCalculator {
 
-    private static final String NEW_LINE = System.getProperty("line.separator");
+    private static final String NEW_LINE = System.lineSeparator();
     private static final long serialVersionUID = 98698690880809981L;
     private final static ILoggingTool LOGGER
             = createLoggingTool(BondChangeCalculator.class);

src/main/java/com/bioinceptionlabs/reactionblast/mechanism/MappingSolution.java

@@ -31,7 +31,7 @@
  */
 public class MappingSolution implements Serializable {
 
-    private static final String NEW_LINE = System.getProperty("line.separator");
+    private static final String NEW_LINE = System.lineSeparator();
     private static final long serialVersionUID = 1678787866L;
 
     private final IMappingAlgorithm algorithmID;

src/main/java/com/bioinceptionlabs/reactionblast/mechanism/RMatrix.java

@@ -46,7 +46,7 @@
  */
 public final class RMatrix extends EBIMatrix implements Serializable {
 
-    private static final String NEW_LINE = System.getProperty("line.separator");
+    private static final String NEW_LINE = System.lineSeparator();
     private static final long serialVersionUID = 7057060562283378684L;
     private static final ILoggingTool LOGGER = createLoggingTool(RMatrix.class);
 

src/main/java/com/bioinceptionlabs/reactionblast/mechanism/helper/AtomAtomMappingContainer.java

@@ -44,7 +44,7 @@ public class AtomAtomMappingContainer extends Object implements Serializable {
     private static final ILoggingTool LOGGER
             = LoggingToolFactory.createLoggingTool(AtomAtomMappingContainer.class);
 
-    private static final String NEW_LINE = System.getProperty("line.separator");
+    private static final String NEW_LINE = System.lineSeparator();
     private static final long serialVersionUID = 17879096958755L;
 
     private List<IAtom> reactantAtomArray = new ArrayList<>();

src/main/java/com/bioinceptionlabs/reactionblast/mechanism/helper/BondChange.java

@@ -19,7 +19,6 @@
 package com.bioinceptionlabs.reactionblast.mechanism.helper;
 
 import java.io.Serializable;
-import static java.lang.System.getProperty;
 
 import org.openscience.cdk.interfaces.IBond;
 
@@ -30,7 +29,7 @@
  */
 public class BondChange implements Serializable {
 
-    private static final String NEW_LINE = System.getProperty("line.separator");
+    private static final String NEW_LINE = System.lineSeparator();
     private static final long serialVersionUID = 9890766688070991L;
 
     /**
@@ -94,28 +93,24 @@ public static int convertBondStereo(IBond bond) {
 
     private final IBond reactantBond;
     private final IBond productBond;
-    private float bondChangeDelta;
+    private final float bondChangeDelta;
 
     /**
      *
      * @param reactantBond
      * @param productBond
      */
     public BondChange(IBond reactantBond, IBond productBond) {
-        this.bondChangeDelta = 0;
         this.reactantBond = reactantBond;
         this.productBond = productBond;
         if (this.reactantBond != null && this.productBond != null) {
-            float change = convertBondOrder(this.productBond) - convertBondOrder(this.reactantBond);
-            if (change != 0) {
-                setBondChangeInformation(change);
-            } else if (change == 0) {
-                setBondChangeInformation(0);
-            }
+            this.bondChangeDelta = convertBondOrder(this.productBond) - convertBondOrder(this.reactantBond);
         } else if (this.reactantBond == null && this.productBond != null) {
-            setBondChangeInformation(convertBondOrder(this.productBond));
+            this.bondChangeDelta = convertBondOrder(this.productBond);
         } else if (this.reactantBond != null && this.productBond == null) {
-            setBondChangeInformation(convertBondOrder(this.reactantBond));
+            this.bondChangeDelta = convertBondOrder(this.reactantBond);
+        } else {
+            this.bondChangeDelta = 0;
         }
     }
 
@@ -140,13 +135,6 @@ public float getBondChangeDelta() {
         return bondChangeDelta;
     }
 
-    /**
-     * @param bondChangeDelta the bondChangeDelta to set
-     */
-    private void setBondChangeInformation(float bondChangeInformation) {
-        this.bondChangeDelta = bondChangeInformation;
-    }
-
     @Override
     public String toString() {
         StringBuilder result = new StringBuilder();

src/main/java/com/bioinceptionlabs/reactionblast/tools/TestUtility.java

@@ -55,7 +55,7 @@ public class TestUtility {
     public static final String MACIE_RXN = "rxn/macie/";
     private final static ILoggingTool LOGGER
             = createLoggingTool(TestUtility.class);
-    private static boolean DEBUG = false;
+    private static final boolean DEBUG = false;
 
     /**
      *

src/main/java/com/bioinceptionlabs/reactionblast/tools/rxnfile/MDLV2000Reader.java

@@ -122,7 +122,7 @@
  */
 public class MDLV2000Reader extends DefaultChemObjectReader {
 
-    private static final String NEW_LINE = System.getProperty("line.separator");
+    private static final String NEW_LINE = System.lineSeparator();
     BufferedReader input = null;
     private static ILoggingTool LOGGER = LoggingToolFactory.createLoggingTool(MDLV2000Reader.class);