X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=bfec5b274ae824ceb7cedeaaf60417453737e8af;hb=ec1c914a99011e20634fbff19df71e2627766dfd;hp=a6a72e0f75040e1daa1cbfb40280609c8cb8db8e;hpb=6bf5604d306cbcd55289639967411ddbafcac682;p=jalview.git
diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index a6a72e0..bfec5b2 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -23,25 +23,21 @@ package jalview.ext.rbvi.chimera;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.gui.Desktop;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.ColorUtils;
-import jalview.util.Comparison;
-import jalview.util.IntRangeComparator;
+import jalview.util.StructureCommands;
import java.awt.Color;
import java.util.ArrayList;
-import java.util.Collections;
import java.util.HashMap;
-import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@@ -52,7 +48,7 @@ import java.util.Map;
* @author JimP
*
*/
-public class ChimeraCommands
+public class ChimeraCommands extends StructureCommands
{
public static final String NAMESPACE_PREFIX = "jv_";
@@ -121,156 +117,6 @@ public class ChimeraCommands
}
/**
- * Build a data structure which records contiguous subsequences for each colour.
- * From this we can easily generate the Chimera command for colour by sequence.
- *
- *
- * Color
- * Model number
- * Chain
- * list of start/end ranges
- *
- *
- * Ordering is by order of addition (for colours and positions), natural
- * ordering (for models and chains)
- *
- * @param ssm
- * @param files
- * @param sequence
- * @param sr
- * @param hideHiddenRegions
- * @param viewPanel
- * @return
- */
- protected static Map