JAL-3187 hacks to get peptide variant in to Jmol hover tooltip

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 1135478..e85d387 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -50,6 +50,7 @@ import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.StringTokenizer;
 import java.util.Vector;
 
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
@@ -65,6 +66,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
 {
+  private String lastMessage;
+
   boolean allChainsSelected = false;
 
   /*
@@ -89,8 +92,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   String lastCommand;
 
-  String lastMessage;
-
   boolean loadedInline;
 
   StringBuffer resetLastRes = new StringBuffer();
@@ -478,6 +479,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastCommand = command;
   }
 
+  Thread colourby = null;
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -485,15 +487,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   @Override
   protected void colourBySequence(
-          StructureMappingcommandSet[] colourBySequenceCommands)
+          final StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+    if (colourby != null)
+    {
+      colourby.interrupt();
+      colourby = null;
+    }
+    colourby = new Thread(new Runnable()
     {
-      for (String cbyseq : cpdbbyseq.commands)
+      @Override
+      public void run()
       {
-        executeWhenReady(cbyseq);
+        for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+        {
+          for (String cbyseq : cpdbbyseq.commands)
+          {
+            executeWhenReady(cbyseq);
+          }
+        }
       }
-    }
+    });
+    colourby.start();
   }
 
   /**
@@ -808,7 +823,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     viewer.openStringInline(string);
   }
 
-  public void mouseOverStructure(int atomIndex, String strInfo)
+  protected void mouseOverStructure(int atomIndex, final String strInfo)
   {
     int pdbResNum;
     int alocsep = strInfo.indexOf("^");
@@ -862,7 +877,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       try
       {
         // recover PDB filename for the model hovered over.
-        int mnumber = new Integer(mdlId).intValue() - 1;
+        int mnumber = Integer.valueOf(mdlId).intValue() - 1;
         if (_modelFileNameMap != null)
         {
           int _mp = _modelFileNameMap.length - 1;
@@ -889,18 +904,34 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       } catch (Exception e)
       {
       }
-      ;
     }
-    if (lastMessage == null || !lastMessage.equals(strInfo))
+
+    /*
+     * highlight position on alignment(s); if some text is returned, 
+     * show this as a second line on the structure hover tooltip
+     */
+    String label = getSsm().mouseOverStructure(pdbResNum, chainId,
+            pdbfilename);
+    if (label != null)
     {
-      getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+      StringTokenizer toks = new StringTokenizer(strInfo, " ");
+      StringBuilder sb = new StringBuilder();
+      sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
+              .append(chainId).append("/1");
+      sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ")
+              .append(toks.nextToken());
+      sb.append("|").append(label).append("\"");
+      evalStateCommand(sb.toString());
     }
-
-    lastMessage = strInfo;
   }
 
   public void notifyAtomHovered(int atomIndex, String strInfo, String data)
   {
+    if (strInfo.equals(lastMessage))
+    {
+      return;
+    }
+    lastMessage = strInfo;
     if (data != null)
     {
       System.err.println("Ignoring additional hover info: " + data
@@ -1240,7 +1271,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return chainNames;
   }
 
-  protected abstract IProgressIndicator getIProgressIndicator();
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return null;
+  }
 
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
   {