X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=cd702910762ff63e34c1ef8e1b31625e6a99bd1c;hb=15f308b25f41681924975f6e4c7d564ebe31263e;hp=766393e61944111111084049eaddc012cd304c60;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 766393e..cd70291 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,26 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.javascript;
 
-import java.awt.Color;
-import java.util.ArrayList;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -28,11 +27,15 @@ 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;
 import jalview.structure.StructureSelectionManager;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Propagate events involving PDB structures associated with sequences to a
  * javascript function. Generally, the javascript handler is called with a
@@ -131,7 +134,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return modelSet;
   }
 
-  @Override
   public void mouseOverStructure(int atomIndex, String strInfo)
   {
 
@@ -142,24 +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
@@ -200,7 +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)
       {
@@ -281,13 +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.