Merge branch 'features/JAL-2320_closeChimeraAction' into releases/Release_2_10_Branch

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 501e345..327d787 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -41,6 +41,7 @@ import jalview.util.MessageManager;
 import java.awt.Color;
 import java.net.BindException;
 import java.util.ArrayList;
+import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -64,6 +65,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private static final String ALPHACARBON = "CA";
 
+  private List<String> chainNames = new ArrayList<String>();
+
+  private Hashtable<String, String> chainFile = new Hashtable<String, String>();
+
   /*
    * Object through which we talk to Chimera
    */
@@ -194,10 +199,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param protocol
    */
   public JalviewChimeraBinding(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     viewer = new ChimeraManager(new StructureManager(true));
   }
 
@@ -277,11 +281,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     boolean first = true;
     for (String chain : toshow)
     {
+      int modelNumber = getModelNoForChain(chain);
+      String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
+              + chain.split(":")[1];
       if (!first)
       {
         cmd.append(",");
       }
-      cmd.append(":.").append(chain);
+      cmd.append(showChainCmd);
       first = false;
     }
 
@@ -290,7 +297,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * window, but it looks more helpful not to (easier to relate chains to the
      * whole)
      */
-    final String command = "~display #*; ~ribbon #*; ribbon "
+    final String command = "~display #*; ~ribbon #*; ribbon :"
             + cmd.toString();
     sendChimeraCommand(command, false);
   }
@@ -801,18 +808,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     {
       return new String[0];
     }
-    // if (modelFileNames == null)
-    // {
-    // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
-    // _modelFileNameMap = new int[chimodels.size()];
-    // int j = 0;
-    // for (ChimeraModel chimodel : chimodels)
-    // {
-    // String mdlName = chimodel.getModelName();
-    // }
-    // modelFileNames = new String[j];
-    // // System.arraycopy(mset, 0, modelFileNames, 0, j);
-    // }
 
     return chimeraMaps.keySet().toArray(
             modelFileNames = new String[chimeraMaps.size()]);
@@ -1105,35 +1100,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Returns a list of chains mapped in this viewer. Note this list is not
-   * currently scoped per structure.
-   * 
-   * @return
-   */
-  public List<String> getChainNames()
-  {
-    List<String> names = new ArrayList<String>();
-    String[][] allNames = getChains();
-    if (allNames != null)
-    {
-      for (String[] chainsForPdb : allNames)
-      {
-        if (chainsForPdb != null)
-        {
-          for (String chain : chainsForPdb)
-          {
-            if (chain != null && !names.contains(chain))
-            {
-              names.add(chain);
-            }
-          }
-        }
-      }
-    }
-    return names;
-  }
-
-  /**
    * Send a 'focus' command to Chimera to recentre the visible display
    */
   public void focusView()
@@ -1168,4 +1134,30 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       sm.highlightStructure(this, seq, positions);
     }
   }
+
+  @Override
+  public List<String> getChainNames()
+  {
+    return chainNames;
+  }
+
+  public Hashtable<String, String> getChainFile()
+  {
+    return chainFile;
+  }
+
+  public List<ChimeraModel> getChimeraModelByChain(String chain)
+  {
+    return chimeraMaps.get(chainFile.get(chain));
+  }
+
+  public int getModelNoForChain(String chain)
+  {
+    List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
+    if (foundModels != null && !foundModels.isEmpty())
+    {
+      return foundModels.get(0).getModelNumber();
+    }
+    return -1;
+  }
 }