X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=4b1c9ce8782b9badd34c8c33ccda4bbce9be175b;hb=528dcd143968fc270232e4cec64a79b447aa5ec6;hp=465a67271d54098188a07443866c09f2a23cbcb1;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 465a672..4b1c9ce 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,8 @@
  */
 package jalview.javascript;
 
-import java.awt.Color;
 import java.util.ArrayList;
+import java.util.List;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
@@ -30,6 +30,7 @@ import jalview.appletgui.AlignFrame;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolCommands;
+import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
@@ -133,7 +134,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return modelSet;
   }
 
-  @Override
   public void mouseOverStructure(int atomIndex, String strInfo)
   {
 
@@ -144,24 +144,27 @@ public class MouseOverStructureListener extends JSFunctionExec implements
   }
 
   @Override
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
+  public void highlightAtoms(List<AtomSpec> atoms)
   {
-    String[] st = new String[0];
-    try
-    {
-      executeJavascriptFunction(_listenerfn, st = new String[]
-      { "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),
-          "" + atomIndex });
-    } catch (Exception ex)
+    for (AtomSpec atom : atoms)
     {
-      System.err.println("Couldn't execute callback with " + _listenerfn
-              + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
-              + "," + st[3] + "\n");
-      ex.printStackTrace();
-
+      try
+      {
+        // TODO is this right? StructureSelectionManager passes pdbFile as the
+        // field that is interpreted (in 2.8.2) as pdbId?
+        // JBPComment: yep - this is right! the Javascript harness uses the
+        // absolute pdbFile URI to locate the PDB file in the external viewer
+        executeJavascriptFunction(_listenerfn, new String[]
+        { "mouseover", "" + atom.getPdbFile(),
+                    "" + atom.getChain(),
+            "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
+      } catch (Exception ex)
+      {
+        System.err.println("Couldn't execute callback with " + _listenerfn
+                + " for atomSpec: " + atom);
+        ex.printStackTrace();
+      }
     }
-
   }
 
   @Override
@@ -202,7 +205,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
               .getSequenceRenderer();
       FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
-              .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
+              .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
               ((jalview.appletgui.AlignmentPanel) source).av) : null;
       if (fr != null)
       {
@@ -283,13 +286,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
   }
 
   @Override
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    return null;
-  }
-
-  @Override
   public AlignFrame getAlignFrame()
   {
     // associated with all alignframes, always.
@@ -316,4 +312,10 @@ public class MouseOverStructureListener extends JSFunctionExec implements
 
   }
 
+  @Override
+  public boolean isListeningFor(SequenceI seq)
+  {
+    return true;
+  }
+
 }