JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / javascript / MouseOverStructureListener.java

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 2ecaf6c..4f833bc 100644 (file)
--- 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.
  * 
@@ -20,9 +20,6 @@
  */
 package jalview.javascript;
 
-import java.awt.Color;
-import java.util.ArrayList;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -30,10 +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 jalview.util.HttpUtils;
+
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Propagate events involving PDB structures associated with sequences to a
@@ -86,54 +88,49 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     {
       for (int i = 0; i < modelSet.length; i++)
       {
-        // resolve a real filename
-        try
-        {
-          if (new java.net.URL(modelSet[i]).openConnection() != null)
-          {
-            continue;
-          }
-        } catch (Exception x)
-        {
-        }
-        ;
-        try
-        {
-          String db = jvlite.getDocumentBase().toString();
-          db = db.substring(0, db.lastIndexOf("/"));
-          if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)
-          {
-            modelSet[i] = db + "/" + modelSet[i];
-            continue;
-          }
-        } catch (Exception x)
-        {
-        }
-        ;
-        try
-        {
-          if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])
-                  .openConnection() != null)
-          {
-            modelSet[i] = jvlite.getCodeBase() + modelSet[i];
-            continue;
-          }
-        } catch (Exception x)
-        {
-        }
-        ;
-
+        modelSet[i] = resolveModelFile(modelSet[i]);
       }
     }
   }
 
+  /**
+   * Returns the first out of: file, file prefixed by document base, or file
+   * prefixed by codebase which can be resolved to a valid URL. If none can,
+   * returns the input parameter value.
+   * 
+   * @param file
+   */
+  public String resolveModelFile(String file)
+  {
+    // TODO reuse JalviewLite.LoadingThread.addProtocol instead
+    if (HttpUtils.isValidUrl(file))
+    {
+      return file;
+    }
+
+    String db = jvlite.getDocumentBase().toString();
+    db = db.substring(0, db.lastIndexOf("/"));
+    String docBaseFile = db + "/" + file;
+    if (HttpUtils.isValidUrl(docBaseFile))
+    {
+      return docBaseFile;
+    }
+
+    String cb = jvlite.getCodeBase() + file;
+    if (HttpUtils.isValidUrl(cb))
+    {
+      return cb;
+    }
+
+    return file;
+  }
+
   @Override
   public String[] getPdbFile()
   {
     return modelSet;
   }
 
-  @Override
   public void mouseOverStructure(int atomIndex, String strInfo)
   {
 
@@ -144,24 +141,27 @@ 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
@@ -170,10 +170,14 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     final Object source = srce;
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(jvlite);
-    // if (jvlite.debug)
-    // {
-    // ssm.reportMapping();
-    // }
+
+    if (JalviewLite.debug)
+    {
+      System.err.println(this.getClass().getName() + " modelSet[0]: "
+              + modelSet[0]);
+      ssm.reportMapping();
+    }
+
     if (source instanceof jalview.api.AlignmentViewPanel)
     {
       SequenceI[][] sequence = new SequenceI[modelSet.length][];
@@ -246,8 +250,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       {
         jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
         // and notify javascript handler
-        String st[] = new String[]
-        {
+        String st[] = new String[] {
             "colourstruct",
             "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
             "" + ccomandset.length,
@@ -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.
@@ -302,7 +298,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
-  public void finalise()
+  public void finalize() throws Throwable
   {
     jvlite = null;
     super.finalize();
@@ -316,4 +312,10 @@ public class MouseOverStructureListener extends JSFunctionExec implements
 
   }
 
+  @Override
+  public boolean isListeningFor(SequenceI seq)
+  {
+    return true;
+  }
+
 }