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 50aba62..e85d387 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
@@ -49,6 +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;
@@ -64,6 +66,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
 {
+  private String lastMessage;
+
   boolean allChainsSelected = false;
 
   /*
@@ -72,7 +76,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private boolean associateNewStructs = false;
 
-  Vector<String> atomsPicked = new Vector<String>();
+  Vector<String> atomsPicked = new Vector<>();
 
   private List<String> chainNames;
 
@@ -88,8 +92,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   String lastCommand;
 
-  String lastMessage;
-
   boolean loadedInline;
 
   StringBuffer resetLastRes = new StringBuffer();
@@ -477,6 +479,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastCommand = command;
   }
 
+  Thread colourby = null;
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -484,15 +487,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   @Override
   protected void colourBySequence(
-          StructureMappingcommandSet[] colourBySequenceCommands)
+          final StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+    if (colourby != null)
     {
-      for (String cbyseq : cpdbbyseq.commands)
+      colourby.interrupt();
+      colourby = null;
+    }
+    colourby = new Thread(new Runnable()
+    {
+      @Override
+      public void run()
       {
-        executeWhenReady(cbyseq);
+        for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+        {
+          for (String cbyseq : cpdbbyseq.commands)
+          {
+            executeWhenReady(cbyseq);
+          }
+        }
       }
-    }
+    });
+    colourby.start();
   }
 
   /**
@@ -610,7 +626,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     if (modelFileNames == null)
     {
-      List<String> mset = new ArrayList<String>();
+      List<String> mset = new ArrayList<>();
       _modelFileNameMap = new int[viewer.ms.mc];
       String m = viewer.ms.getModelFileName(0);
       if (m != null)
@@ -670,7 +686,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public synchronized String[] getStructureFiles()
   {
-    List<String> mset = new ArrayList<String>();
+    List<String> mset = new ArrayList<>();
     if (viewer == null)
     {
       return new String[0];
@@ -807,7 +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("^");
@@ -861,34 +877,61 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       try
       {
         // recover PDB filename for the model hovered over.
-        int _mp = _modelFileNameMap.length - 1,
-                mnumber = new Integer(mdlId).intValue() - 1;
-        while (mnumber < _modelFileNameMap[_mp])
+        int mnumber = Integer.valueOf(mdlId).intValue() - 1;
+        if (_modelFileNameMap != null)
         {
-          _mp--;
+          int _mp = _modelFileNameMap.length - 1;
+
+          while (mnumber < _modelFileNameMap[_mp])
+          {
+            _mp--;
+          }
+          pdbfilename = modelFileNames[_mp];
         }
-        pdbfilename = modelFileNames[_mp];
-        if (pdbfilename == null)
+        else
         {
-          pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
-                  .getAbsolutePath();
-        }
+          if (mnumber >= 0 && mnumber < modelFileNames.length)
+          {
+            pdbfilename = modelFileNames[mnumber];
+          }
 
+          if (pdbfilename == null)
+          {
+            pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
+                    .getAbsolutePath();
+          }
+        }
       } 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
@@ -1060,8 +1103,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
-    chainNames = new ArrayList<String>();
-    chainFile = new Hashtable<String, String>();
+    chainNames = new ArrayList<>();
+    chainFile = new Hashtable<>();
     boolean notifyLoaded = false;
     String[] modelfilenames = getStructureFiles();
     // first check if we've lost any structures
@@ -1127,7 +1170,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           // see JAL-623 - need method of matching pasted data up
           {
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    pdbfile, DataSourceType.PASTE);
+                    pdbfile, DataSourceType.PASTE,
+                    getIProgressIndicator());
             getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
@@ -1159,7 +1203,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             }
             // Explicitly map to the filename used by Jmol ;
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    fileName, protocol);
+                    fileName, protocol, getIProgressIndicator());
             // pdbentry[pe].getFile(), protocol);
 
           }
@@ -1227,6 +1271,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return chainNames;
   }
 
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return null;
+  }
+
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
   {
     notifyAtomPicked(iatom, strMeasure, null);