Eliminate 4 interfaces/ subdirectories, flatten into parent packages

Removed reactionblast/interfaces/, fingerprints/interfaces/,
mapping/interfaces/, mechanism/interfaces/ — moved 15 interfaces
to parent packages, deleted 3 unused interfaces (IMolContainer,
IFingerPrintContainer, IStandardizer inlined into StandardizeReaction).

142 → 139 files, 33 → 28 packages. All 135 tests pass.

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

Author: asad

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

@@ -45,7 +45,7 @@
 import org.w3c.dom.Element;
 import com.bioinceptionlabs.reactionblast.fingerprints.PatternFingerprinter;
 import com.bioinceptionlabs.reactionblast.fingerprints.ReactionFingerprinter;
-import com.bioinceptionlabs.reactionblast.fingerprints.interfaces.IPatternFingerprinter;
+import com.bioinceptionlabs.reactionblast.fingerprints.IPatternFingerprinter;
 import com.bioinceptionlabs.reactionblast.mechanism.BondChangeCalculator;
 import com.bioinceptionlabs.reactionblast.mechanism.MappingSolution;
 import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;

src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/Feature.java

@@ -22,7 +22,7 @@
 import java.text.DecimalFormat;
 import java.util.Comparator;
 
-import com.bioinceptionlabs.reactionblast.fingerprints.interfaces.IFeature;
+import com.bioinceptionlabs.reactionblast.fingerprints.IFeature;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/FingerprintGenerator.java

@@ -28,7 +28,7 @@
 import org.openscience.cdk.layout.StructureDiagramGenerator;
 import org.openscience.cdk.tools.ILoggingTool;
 import static org.openscience.cdk.tools.LoggingToolFactory.createLoggingTool;
-import com.bioinceptionlabs.reactionblast.fingerprints.interfaces.IFingerprintGenerator;
+import com.bioinceptionlabs.reactionblast.fingerprints.IFingerprintGenerator;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

…st/fingerprints/interfaces/IFeature.java …reactionblast/fingerprints/IFeature.javasrc/main/java/com/bioinceptionlabs/reactionblast/fingerprints/interfaces/IFeature.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/IFeature.java src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/interfaces/IFeature.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/IFeature.java

@@ -17,7 +17,7 @@
  * MA 02110-1301  USA
  */
 
-package com.bioinceptionlabs.reactionblast.fingerprints.interfaces;
+package com.bioinceptionlabs.reactionblast.fingerprints;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

…ts/interfaces/IFingerprintGenerator.java …/fingerprints/IFingerprintGenerator.javasrc/main/java/com/bioinceptionlabs/reactionblast/fingerprints/interfaces/IFingerprintGenerator.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/IFingerprintGenerator.java src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/interfaces/IFingerprintGenerator.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/IFingerprintGenerator.java

@@ -16,7 +16,7 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
  * MA 02110-1301  USA
  */
-package com.bioinceptionlabs.reactionblast.fingerprints.interfaces;
+package com.bioinceptionlabs.reactionblast.fingerprints;
 
 import java.util.BitSet;
 import org.openscience.cdk.exception.CDKException;

…ts/interfaces/IPatternFingerprinter.java …/fingerprints/IPatternFingerprinter.javasrc/main/java/com/bioinceptionlabs/reactionblast/fingerprints/interfaces/IPatternFingerprinter.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/IPatternFingerprinter.java src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/interfaces/IPatternFingerprinter.java renamed to src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/IPatternFingerprinter.java

@@ -17,7 +17,7 @@
  * MA 02110-1301  USA
  */
 
-package com.bioinceptionlabs.reactionblast.fingerprints.interfaces;
+package com.bioinceptionlabs.reactionblast.fingerprints;
 
 import java.util.BitSet;
 import java.util.Collection;

src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/PatternComparators.java

@@ -26,7 +26,7 @@
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
-import com.bioinceptionlabs.reactionblast.fingerprints.interfaces.IPatternFingerprinter;
+import com.bioinceptionlabs.reactionblast.fingerprints.IPatternFingerprinter;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/PatternFingerprinter.java

@@ -38,8 +38,8 @@
 import org.openscience.cdk.tools.LoggingToolFactory;
 import static com.bioinceptionlabs.reactionblast.fingerprints.FingerprintGenerator.getFingerprinterSize;
 import static com.bioinceptionlabs.reactionblast.fingerprints.PatternComparators.overallComparator;
-import com.bioinceptionlabs.reactionblast.fingerprints.interfaces.IFeature;
-import com.bioinceptionlabs.reactionblast.fingerprints.interfaces.IPatternFingerprinter;
+import com.bioinceptionlabs.reactionblast.fingerprints.IFeature;
+import com.bioinceptionlabs.reactionblast.fingerprints.IPatternFingerprinter;
 
 /**
  * @contact Syed Asad Rahman, BioInception.

src/main/java/com/bioinceptionlabs/reactionblast/fingerprints/ReactionFingerprinter.java

@@ -34,7 +34,7 @@
 import static org.openscience.smsd.MoleculeInitializer.initializeMolecule;
 import static org.openscience.smsd.tools.ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID;
 import static com.bioinceptionlabs.reactionblast.fingerprints.FingerprintGenerator.getFingerprinterSize;
-import com.bioinceptionlabs.reactionblast.fingerprints.interfaces.IPatternFingerprinter;
+import com.bioinceptionlabs.reactionblast.fingerprints.IPatternFingerprinter;
 
 /**
  * @contact Syed Asad Rahman, BioInception.