Move ImageGenerator + EBIMatrix to legacy package

Profiling showed these are 95%+ dead code during core mapping:
- ImageGenerator: visualization only, not needed for AAM pipeline
- EBIMatrix: 96.4% dead methods, only a few matrix ops used

Moved to com.bioinceptionlabs.reactionblast.legacy/ for future cleanup.
All imports updated. 148/148 tests pass.

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

Author: asad

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

@@ -32,7 +32,7 @@
 import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
-import com.bioinceptionlabs.reactionblast.tools.ImageGenerator;
+import com.bioinceptionlabs.reactionblast.legacy.ImageGenerator;
 import com.bioinceptionlabs.reactionblast.tools.ChemicalFileIO.MDLV2000RXNWriter;
 
 /**

…nlabs/reactionblast/tools/EBIMatrix.java …labs/reactionblast/legacy/EBIMatrix.javasrc/main/java/com/bioinceptionlabs/reactionblast/tools/EBIMatrix.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/legacy/EBIMatrix.java src/main/java/com/bioinceptionlabs/reactionblast/tools/EBIMatrix.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/legacy/EBIMatrix.java

@@ -16,7 +16,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
  * MA 02110-1301  USA
  */
-package com.bioinceptionlabs.reactionblast.tools;
+package com.bioinceptionlabs.reactionblast.legacy;
 
 import java.io.BufferedReader;
 import java.io.PrintWriter;

…/reactionblast/tools/ImageGenerator.java …reactionblast/legacy/ImageGenerator.javasrc/main/java/com/bioinceptionlabs/reactionblast/tools/ImageGenerator.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/legacy/ImageGenerator.java src/main/java/com/bioinceptionlabs/reactionblast/tools/ImageGenerator.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/legacy/ImageGenerator.java

@@ -16,7 +16,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
  * MA 02110-1301  USA
  */
-package com.bioinceptionlabs.reactionblast.tools;
+package com.bioinceptionlabs.reactionblast.legacy;
 
 import java.awt.Image;
 import java.awt.image.BufferedImage;

src/main/java/com/bioinceptionlabs/reactionblast/mapping/Reactor.java

@@ -11,8 +11,8 @@
 import com.bioinceptionlabs.reactionblast.mapping.algorithm.MappingChecks;
 import com.bioinceptionlabs.reactionblast.mapping.algorithm.Holder;
 import com.bioinceptionlabs.reactionblast.tools.CDKSMILES;
-import com.bioinceptionlabs.reactionblast.tools.EBIMatrix;
-import com.bioinceptionlabs.reactionblast.tools.ImageGenerator;
+import com.bioinceptionlabs.reactionblast.legacy.EBIMatrix;
+import com.bioinceptionlabs.reactionblast.legacy.ImageGenerator;
 import com.bioinceptionlabs.reactionblast.tools.MoleculeTools.BasicDebugger;
 import java.io.IOException;
 import java.io.Serializable;

src/main/java/com/bioinceptionlabs/reactionblast/mapping/algorithm/Holder.java

@@ -32,7 +32,7 @@
 import com.bioinceptionlabs.reactionblast.mapping.Reactor.Debugger;
 import com.bioinceptionlabs.reactionblast.mapping.BestMatch;
 import com.bioinceptionlabs.reactionblast.mapping.IMappingAlgorithm;
-import com.bioinceptionlabs.reactionblast.tools.EBIMatrix;
+import com.bioinceptionlabs.reactionblast.legacy.EBIMatrix;
 
 import org.openscience.cdk.tools.ILoggingTool;
 import static org.openscience.cdk.tools.LoggingToolFactory.createLoggingTool;

src/main/java/com/bioinceptionlabs/reactionblast/mapping/algorithm/MappingChecks.java

@@ -50,7 +50,7 @@
 import org.openscience.smsd.AtomBondMatcher.BondMatcher;
 import com.bioinceptionlabs.reactionblast.mapping.ReactionContainer;
 import com.bioinceptionlabs.reactionblast.mapping.IResult;
-import com.bioinceptionlabs.reactionblast.tools.EBIMatrix;
+import com.bioinceptionlabs.reactionblast.legacy.EBIMatrix;
 
 /**
  * Consolidated mapping checks for the algorithm package.

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

@@ -35,7 +35,7 @@
 import static org.openscience.cdk.interfaces.IBond.Stereo.NONE;
 import static org.openscience.cdk.interfaces.IBond.Stereo.UP;
 import static org.openscience.cdk.interfaces.IBond.Stereo.UP_OR_DOWN;
-import com.bioinceptionlabs.reactionblast.tools.EBIMatrix;
+import com.bioinceptionlabs.reactionblast.legacy.EBIMatrix;
 import static org.openscience.smsd.ExtAtomContainerManipulator.aromatizeMolecule;
 import com.bioinceptionlabs.reactionblast.tools.MoleculeTools.ValencyCalculator;
 

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

@@ -33,7 +33,7 @@
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.tools.ILoggingTool;
 import static org.openscience.cdk.tools.LoggingToolFactory.createLoggingTool;
-import com.bioinceptionlabs.reactionblast.tools.EBIMatrix;
+import com.bioinceptionlabs.reactionblast.legacy.EBIMatrix;
 
 /**
  * This class create the RMatrix of a reaction according to the DU-Theory.

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

@@ -46,8 +46,9 @@
 import com.bioinceptionlabs.reactionblast.mechanism.BondChangeCalculator;
 import com.bioinceptionlabs.reactionblast.mechanism.MappingSolution;
 import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
-import static com.bioinceptionlabs.reactionblast.tools.ImageGenerator.LeftToRightReactionCenterImage;
-import static com.bioinceptionlabs.reactionblast.tools.ImageGenerator.TopToBottomReactionLayoutImage;
+import com.bioinceptionlabs.reactionblast.legacy.ImageGenerator;
+import static com.bioinceptionlabs.reactionblast.legacy.ImageGenerator.LeftToRightReactionCenterImage;
+import static com.bioinceptionlabs.reactionblast.legacy.ImageGenerator.TopToBottomReactionLayoutImage;
 import com.bioinceptionlabs.reactionblast.tools.ChemicalFileIO.MDLV2000Reader;
 import com.bioinceptionlabs.reactionblast.tools.MoleculeTools.ExtReactionManipulatorTool;