X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=607193317fb359e82ed041342c5ee71581e1be88;hb=abf6493d02ec6a018a1602e329f0ba2c64bbd205;hp=4b1c9ce8782b9badd34c8c33ccda4bbce9be175b;hpb=43b415c68805f3dec44a6ddc666d52220483c120;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 4b1c9ce..6071933 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -20,9 +20,6 @@
  */
 package jalview.javascript;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -35,6 +32,10 @@ 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
@@ -69,8 +70,8 @@ import jalview.structure.StructureSelectionManager;
  * @author Jim Procter (jprocter)
  * 
  */
-public class MouseOverStructureListener extends JSFunctionExec implements
-        JsCallBack, StructureListener
+public class MouseOverStructureListener extends JSFunctionExec
+        implements JsCallBack, StructureListener
 {
 
   String _listenerfn;
@@ -87,49 +88,45 @@ 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()
+  public String[] getStructureFiles()
   {
     return modelSet;
   }
@@ -154,10 +151,10 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         // 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() });
+        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
@@ -173,10 +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][];
@@ -205,12 +206,14 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
               .getSequenceRenderer();
       FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
-              .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
-              ((jalview.appletgui.AlignmentPanel) source).av) : null;
+              .isShowSequenceFeatures()
+                      ? new jalview.appletgui.FeatureRenderer(
+                              ((jalview.appletgui.AlignmentPanel) source).av)
+                      : null;
       if (fr != null)
       {
-        ((jalview.appletgui.FeatureRenderer) fr)
-                .transferSettings(((jalview.appletgui.AlignmentPanel) source)
+        ((jalview.appletgui.FeatureRenderer) fr).transferSettings(
+                ((jalview.appletgui.AlignmentPanel) source)
                         .getFeatureRenderer());
       }
       ;
@@ -220,8 +223,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       ArrayList<String[]> ccomands = new ArrayList<String[]>();
       ArrayList<String> pdbfn = new ArrayList<String>();
       StructureMappingcommandSet[] colcommands = JmolCommands
-              .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
-                      ((AlignmentViewPanel) source).getAlignment());
+              .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
+                      (AlignmentViewPanel) source);
       if (colcommands == null)
       {
         return;
@@ -242,28 +245,25 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         System.arraycopy(ccset, 0, ccomandset, sz, ccset.length);
         sz += ccset.length;
       }
-      if (jvlite.isJsMessageSetChanged(
-              mclass = "colourstruct",
+      if (jvlite.isJsMessageSetChanged(mclass = "colourstruct",
               mhandle = ((jalview.appletgui.AlignmentPanel) source).av
-                      .getViewId(), ccomandset))
+                      .getViewId(),
+              ccomandset))
       {
         jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
         // and notify javascript handler
-        String st[] = new String[]
-        {
-            "colourstruct",
+        String st[] = new String[] { "colourstruct",
             "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
-            "" + ccomandset.length,
-            jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
-                    .size()])) };
+            "" + ccomandset.length, jvlite.arrayToSeparatorList(
+                    pdbfn.toArray(new String[pdbfn.size()])) };
         try
         {
           executeJavascriptFunction(true, _listenerfn, st);
         } catch (Exception ex)
         {
-          System.err.println("Couldn't execute callback with "
-                  + _listenerfn + " using args { " + st[0] + ", " + st[1]
-                  + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n");
+          System.err.println("Couldn't execute callback with " + _listenerfn
+                  + " using args { " + st[0] + ", " + st[1] + ", " + st[2]
+                  + "," + st[3] + "}"); // + ","+st[4]+"\n");
           ex.printStackTrace();
 
         }
@@ -298,12 +298,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
-  public void finalise()
-  {
-    jvlite = null;
-    super.finalize();
-  }
-
   @Override
   public void releaseReferences(Object svl)
   {