X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraBinding.java;h=b954677ffeb53d3500fe8e344c14e3fefdc98b18;hb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;hp=9a570fc46ed1d195904c8a73b831768c07c521bc;hpb=799c26111d6936a2e70cb5f1fd7d7312311e6db9;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 9a570fc..b954677 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -20,14 +20,12 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResultsI;
@@ -174,13 +172,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       if (getSsm() != null)
       {
         getSsm().addStructureViewerListener(this);
-        // ssm.addSelectionListener(this);
-        FeatureRenderer fr = getFeatureRenderer(null);
-        if (fr != null)
-        {
-          fr.featuresAdded();
-        }
-        refreshGUI();
       }
       return true;
     } catch (Exception q)
@@ -298,7 +289,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   public void closeViewer(boolean closeChimera)
   {
-    getSsm().removeStructureViewerListener(this, this.getPdbFile());
+    getSsm().removeStructureViewerListener(this, this.getStructureFiles());
     if (closeChimera)
     {
       viewer.exitChimera();
@@ -346,10 +337,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   @Override
   public String superposeStructures(AlignmentI[] _alignment,
-          int[] _refStructure, ColumnSelection[] _hiddenCols)
+          int[] _refStructure, HiddenColumns[] _hiddenCols)
   {
     StringBuilder allComs = new StringBuilder(128);
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
 
     if (!waitForFileLoad(files))
     {
@@ -362,7 +353,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     {
       int refStructure = _refStructure[a];
       AlignmentI alignment = _alignment[a];
-      ColumnSelection hiddenCols = _hiddenCols[a];
+      HiddenColumns hiddenCols = _hiddenCols[a];
 
       if (refStructure >= files.length)
       {
@@ -586,7 +577,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * to the Chimera command 'list models type molecule', see
      * ChimeraManager.getModelList().
      */
-    List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
+    List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
     boolean hasSubModels = maps != null && maps.size() > 1;
     return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
   }
@@ -699,17 +690,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /**
    * @param files
    * @param sr
-   * @param fr
-   * @param viewport
+   * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignViewportI viewport)
+          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
   {
     return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, fr, viewport);
+            getSequence(), sr, viewPanel);
   }
 
   /**
@@ -756,7 +745,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public synchronized String[] getPdbFile()
+  public synchronized String[] getStructureFiles()
   {
     if (viewer == null)
     {
@@ -1110,17 +1099,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   {
     // TODO refactor as required to pull up to an interface
     AlignmentI alignment = avp.getAlignment();
-    FeatureRenderer fr = getFeatureRenderer(avp);
-
-    /*
-     * fr is null if feature display is turned off
-     */
-    if (fr == null)
-    {
-      return 0;
-    }
 
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return 0;
@@ -1128,7 +1108,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
     StructureMappingcommandSet commandSet = ChimeraCommands
             .getSetAttributeCommandsForFeatures(getSsm(), files,
-                    getSequence(), fr, alignment);
+                    getSequence(), avp);
     String[] commands = commandSet.commands;
     if (commands.length > 10)
     {