Organize symmetry packages and classes

lafita · lafita · commit 4e1a3597f0c1 · 2016-06-17T18:03:57.000+02:00
Split core package into axis, cluster and core. Axis contains the
classes that calculate axes properties, cluster contains the classes
related to clustering chains into subunits, and core contains the
algorithms and classes to detect symmetry
diff --git a/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java b/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java
@@ -27,7 +27,7 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry;
-import org.biojava.nbio.structure.symmetry.core.AxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.AxisAligner;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/analysis/CalcBioAssemblySymmetry.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/analysis/CalcBioAssemblySymmetry.java
@@ -27,6 +27,8 @@
 
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.align.util.ResourceManager;
+import org.biojava.nbio.structure.cluster.Subunits;
+import org.biojava.nbio.structure.symmetry.axis.AxisAligner;
 import org.biojava.nbio.structure.symmetry.core.*;
 import org.biojava.nbio.structure.symmetry.jmolScript.JmolSymmetryScriptGenerator;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java
@@ -24,6 +24,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
+
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
@@ -38,7 +39,7 @@
 import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.util.RotationAxis;
-import org.biojava.nbio.structure.symmetry.core.AxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.AxisAligner;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
 import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
 import org.biojava.nbio.structure.symmetry.internal.SymmetryAxes;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGenerator.java
@@ -20,9 +20,9 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.symmetry.core.AxisAligner;
-import org.biojava.nbio.structure.symmetry.core.HelixAxisAligner;
-import org.biojava.nbio.structure.symmetry.core.RotationAxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.AxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 
 import javax.vecmath.Color4f;
 import javax.vecmath.Matrix4d;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorC1.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorC1.java
@@ -23,7 +23,7 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.symmetry.core.RotationAxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.geometry.RectangularPrism;
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorCn.java
@@ -23,7 +23,7 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.symmetry.core.RotationAxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.geometry.Prism;
 import org.biojava.nbio.structure.symmetry.geometry.RectangularPrism;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorDn.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorDn.java
@@ -23,7 +23,7 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.symmetry.core.RotationAxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.geometry.Prism;
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorH.java
@@ -23,8 +23,8 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.symmetry.core.HelixAxisAligner;
-import org.biojava.nbio.structure.symmetry.core.Subunits;
+import org.biojava.nbio.structure.cluster.Subunits;
+import org.biojava.nbio.structure.symmetry.axis.HelixAxisAligner;
 import org.jcolorbrewer.ColorBrewer;
 
 import javax.vecmath.*;
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorI.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorI.java
@@ -23,7 +23,7 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.symmetry.core.RotationAxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.geometry.Icosahedron;
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorO.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorO.java
@@ -23,7 +23,7 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.symmetry.core.RotationAxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.geometry.Octahedron;
 
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorPointGroup.java
@@ -23,10 +23,10 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
+import org.biojava.nbio.structure.cluster.Subunits;
+import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.core.Rotation;
-import org.biojava.nbio.structure.symmetry.core.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.core.RotationGroup;
-import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.Polyhedron;
 import org.jcolorbrewer.ColorBrewer;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorT.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/jmolScript/JmolSymmetryScriptGeneratorT.java
@@ -23,7 +23,7 @@
  */
 package org.biojava.nbio.structure.symmetry.jmolScript;
 
-import org.biojava.nbio.structure.symmetry.core.RotationAxisAligner;
+import org.biojava.nbio.structure.symmetry.axis.RotationAxisAligner;
 import org.biojava.nbio.structure.symmetry.geometry.Tetrahedron;
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ChainClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ChainClusterer.java
@@ -18,11 +18,13 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster;
 
 import javax.vecmath.Point3d;
+
 import java.util.*;
 
 /**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ClusterMerger.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ClusterMerger.java
@@ -18,10 +18,13 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import java.util.*;
 
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
+import org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster;
+
 /**
  * Merges clusters based on their sequence identity. This class does the actual
  * agglomerative clustering calculation, while {@link SequenceAlignmentCluster}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ClusterProteinChains.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ClusterProteinChains.java
@@ -18,9 +18,11 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
+import org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster;
 
 import java.util.Collections;
 import java.util.List;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/PairwiseAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/PairwiseAlignment.java
@@ -18,10 +18,12 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import java.util.Arrays;
 
+import org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster;
+
 public class PairwiseAlignment {
 	private SequenceAlignmentCluster cluster1 = null;
 	private SequenceAlignmentCluster cluster2 = null;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ProteinChainExtractor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ProteinChainExtractor.java
@@ -18,12 +18,13 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import org.biojava.nbio.structure.*;
 import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
 import org.biojava.nbio.structure.io.mmcif.chem.ResidueType;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ProteinSequenceClusterer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/ProteinSequenceClusterer.java
@@ -18,10 +18,12 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
+import org.biojava.nbio.structure.symmetry.core.SequenceAlignmentCluster;
 
 import java.util.*;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitGraph.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitGraph.java
@@ -18,7 +18,7 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import javax.vecmath.Point3d;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/Subunits.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/Subunits.java
@@ -19,7 +19,7 @@
  *
  */
 
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/UniqueSequenceList.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/UniqueSequenceList.java
@@ -18,7 +18,7 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.cluster;
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.Group;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/analysis/ScanSymmetry.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/analysis/ScanSymmetry.java
@@ -33,14 +33,14 @@
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
 import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.mmcif.AllChemCompProvider;
 import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
 import org.biojava.nbio.structure.rcsb.GetRepresentatives;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryParameters;
 import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
-import org.biojava.nbio.structure.symmetry.core.Subunits;
 import org.biojava.nbio.structure.symmetry.misc.ProteinComplexSignature;
 import org.biojava.nbio.structure.symmetry.utils.BlastClustReader;
 import org.biojava.nbio.structure.xtal.SpaceGroup;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/AxisAligner.java
@@ -18,12 +18,16 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.symmetry.axis;
 
 import javax.vecmath.Matrix3d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
+
+import org.biojava.nbio.structure.cluster.Subunits;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+
 import java.util.List;
 
 public abstract class AxisAligner {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/HelixAxisAligner.java
@@ -18,12 +18,17 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.symmetry.axis;
 
+import org.biojava.nbio.structure.cluster.Subunits;
+import org.biojava.nbio.structure.symmetry.core.Helix;
+import org.biojava.nbio.structure.symmetry.core.HelixLayers;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.*;
+
 import java.util.*;
 
 public class HelixAxisAligner extends AxisAligner {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java
@@ -18,12 +18,17 @@
  *      http://www.biojava.org/
  *
  */
-package org.biojava.nbio.structure.symmetry.core;
+package org.biojava.nbio.structure.symmetry.axis;
 
+import org.biojava.nbio.structure.cluster.Subunits;
+import org.biojava.nbio.structure.symmetry.core.QuatSymmetryResults;
+import org.biojava.nbio.structure.symmetry.core.Rotation;
+import org.biojava.nbio.structure.symmetry.core.RotationGroup;
 import org.biojava.nbio.structure.symmetry.geometry.MomentsOfInertia;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.*;
+
 import java.util.*;
 
 public class RotationAxisAligner extends AxisAligner{
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/C2RotationSolver.java
@@ -21,12 +21,14 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
+import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.AxisAngle4d;
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelicalRepeatUnit.java
@@ -20,9 +20,11 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
+import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.Point3d;
+
 import java.util.*;
 import java.util.Map.Entry;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixExtender.java
@@ -20,10 +20,12 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
+import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
+
 import java.util.ArrayList;
 import java.util.List;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/HelixSolver.java
@@ -20,6 +20,7 @@
  */
 package org.biojava.nbio.structure.symmetry.core;
 
+import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.AxisAngle4d;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
@@ -21,10 +21,12 @@
 
 package org.biojava.nbio.structure.symmetry.core;
 
+import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.geometry.SuperPosition;
 
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
+
 import java.util.List;
 
 /**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryDetector.java
@@ -23,6 +23,10 @@
 package org.biojava.nbio.structure.symmetry.core;
 
 import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.cluster.ChainClusterer;
+import org.biojava.nbio.structure.cluster.ClusterProteinChains;
+import org.biojava.nbio.structure.cluster.SubunitGraph;
+import org.biojava.nbio.structure.cluster.Subunits;
 import org.biojava.nbio.structure.symmetry.utils.CombinationGenerator;
 import org.jgrapht.UndirectedGraph;
 import org.jgrapht.alg.ConnectivityInspector;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryParameters.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSymmetryResults.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/RotationSolver.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SequenceAlignmentCluster.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SequenceAlignmentCluster.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/SystematicSolver.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/IcosahedralSampler.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/utils/SymmetryTools.java
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/core/TestChainClusterer.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/core/TestChainClusterer.java
