X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=dfe5c4fb4bedaed2744210f27dddb668aa75c59d;hb=63e93122d1722a69e997a9ac64502ef74c4a7a17;hp=2ecaf6c040bef02a3fec21a3182b1d513bfa1071;hpb=648f0d7f48b5865bd43b5edbe71f5e483f0cc455;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 2ecaf6c..dfe5c4f 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.
  * 
@@ -20,21 +20,23 @@
  */
 package jalview.javascript;
 
-import java.awt.Color;
-import java.util.ArrayList;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AlignmentPanel;
 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
@@ -133,7 +135,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return modelSet;
   }
 
-  @Override
   public void mouseOverStructure(int atomIndex, String strInfo)
   {
 
@@ -144,24 +145,27 @@ 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
+    for (AtomSpec atom : atoms)
     {
-      executeJavascriptFunction(_listenerfn, st = new String[]
-      { "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),
-          "" + atomIndex });
-    } catch (Exception ex)
-    {
-      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
@@ -174,7 +178,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     // {
     // ssm.reportMapping();
     // }
-    if (source instanceof jalview.api.AlignmentViewPanel)
+    if (source instanceof AlignmentViewPanel)
     {
       SequenceI[][] sequence = new SequenceI[modelSet.length][];
       for (int m = 0; m < modelSet.length; m++)
@@ -199,15 +203,15 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         // }
       }
 
-      SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
+      SequenceRenderer sr = ((AlignmentPanel) source)
               .getSequenceRenderer();
-      FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
+      FeatureRenderer fr = ((AlignmentPanel) source).av
               .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
-              ((jalview.appletgui.AlignmentPanel) source).av) : null;
+              ((AlignmentPanel) source).av) : null;
       if (fr != null)
       {
         ((jalview.appletgui.FeatureRenderer) fr)
-                .transferSettings(((jalview.appletgui.AlignmentPanel) source)
+                .transferSettings(((AlignmentPanel) source)
                         .getFeatureRenderer());
       }
       ;
@@ -224,7 +228,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         return;
       }
       int sz = 0;
-      for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      for (StructureMappingcommandSet ccset : colcommands)
       {
         sz += ccset.commands.length;
         ccomands.add(ccset.commands);
@@ -241,7 +245,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       }
       if (jvlite.isJsMessageSetChanged(
               mclass = "colourstruct",
-              mhandle = ((jalview.appletgui.AlignmentPanel) source).av
+              mhandle = ((AlignmentPanel) source).av
                       .getViewId(), ccomandset))
       {
         jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
@@ -249,7 +253,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         String st[] = new String[]
         {
             "colourstruct",
-            "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
+            "" + ((AlignmentPanel) source).av.getViewId(),
             "" + ccomandset.length,
             jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
                     .size()])) };
@@ -283,13 +287,6 @@ 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 +313,10 @@ public class MouseOverStructureListener extends JSFunctionExec implements
 
   }
 
+  @Override
+  public boolean isListeningFor(SequenceI seq)
+  {
+    return true;
+  }
+
 }