3253-omnibus save

[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 fa31fd9..453152e 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -44,12 +44,12 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
-import java.security.AccessControlException;
 import java.util.ArrayList;
 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 +65,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         implements JmolStatusListener, JmolSelectionListener,
         ComponentListener
 {
+  private String lastMessage;
+
   boolean allChainsSelected = false;
 
   /*
@@ -89,8 +91,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   String lastCommand;
 
-  String lastMessage;
-
   boolean loadedInline;
 
   StringBuffer resetLastRes = new StringBuffer();
@@ -619,74 +619,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private int _modelFileNameMap[];
 
-  // ////////////////////////////////
-  // /StructureListener
-  // @Override
-  public synchronized String[] getPdbFilex()
-  {
-    if (viewer == null)
-    {
-      return new String[0];
-    }
-    if (modelFileNames == null)
-    {
-      List<String> mset = new ArrayList<>();
-      _modelFileNameMap = new int[viewer.ms.mc];
-      String m = viewer.ms.getModelFileName(0);
-      if (m != null)
-      {
-        String filePath = m;
-        try
-        {
-          filePath = new File(m).getAbsolutePath();
-        } catch (AccessControlException x)
-        {
-          // usually not allowed to do this in applet
-          System.err.println(
-                  "jmolBinding: Using local file string from Jmol: " + m);
-        }
-        if (filePath.indexOf("/file:") != -1)
-        {
-          // applet path with docroot - discard as format won't match pdbfile
-          filePath = m;
-        }
-        mset.add(filePath);
-        _modelFileNameMap[0] = 0; // filename index for first model is always 0.
-      }
-      int j = 1;
-      for (int i = 1; i < viewer.ms.mc; i++)
-      {
-        m = viewer.ms.getModelFileName(i);
-        String filePath = m;
-        if (m != null)
-        {
-          try
-          {
-            filePath = new File(m).getAbsolutePath();
-          } catch (AccessControlException x)
-          {
-            // usually not allowed to do this in applet, so keep raw handle
-            // System.err.println("jmolBinding: Using local file string from
-            // Jmol: "+m);
-          }
-        }
-
-        /*
-         * add this model unless it is read from a structure file we have
-         * already seen (example: 2MJW is an NMR structure with 10 models)
-         */
-        if (!mset.contains(filePath))
-        {
-          mset.add(filePath);
-          _modelFileNameMap[j] = i; // record the model index for the filename
-          j++;
-        }
-      }
-      modelFileNames = mset.toArray(new String[mset.size()]);
-    }
-    return modelFileNames;
-  }
-
   @Override
   public synchronized String[] getStructureFiles()
   {
@@ -827,7 +759,7 @@ 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("^");
@@ -881,7 +813,7 @@ 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;
@@ -908,18 +840,36 @@ 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);
+      // change comma to pipe separator (newline token for Jmol)
+      label = label.replace(',', '|');
+      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