X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=239d0f3f1c3c80a9d971c07d843d98169c4ad9d6;hb=a5e22141bc3185284588761a69f023d527e7f18e;hp=88fba0284f1ecfd91c8d575bd27f80ad7c41142c;hpb=6f2610ec4d7a79dde17f9b3d02225c62aa52cfd8;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 88fba02..239d0f3 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -22,7 +22,7 @@ package jalview.javascript;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
+import jalview.api.SequenceRendererI;
 import jalview.appletgui.AlignFrame;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.SequenceI;
@@ -32,10 +32,8 @@ import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -72,8 +70,8 @@ import java.util.List;
  * @author Jim Procter (jprocter)
  * 
  */
-public class MouseOverStructureListener extends JSFunctionExec implements
-        JsCallBack, StructureListener
+public class MouseOverStructureListener extends JSFunctionExec
+        implements JsCallBack, StructureListener
 {
 
   String _listenerfn;
@@ -96,15 +94,16 @@ public class MouseOverStructureListener extends JSFunctionExec implements
   }
 
   /**
-   * Returns the first of file, file prefixed by document base, file prefixed by
-   * codebase which can be resolved to a valid URL. If none can, returns the
-   * input parameter value.
+   * 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)
   {
-    if (isValidUrl(file))
+    // TODO reuse JalviewLite.LoadingThread.addProtocol instead
+    if (HttpUtils.isValidUrl(file))
     {
       return file;
     }
@@ -112,13 +111,13 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     String db = jvlite.getDocumentBase().toString();
     db = db.substring(0, db.lastIndexOf("/"));
     String docBaseFile = db + "/" + file;
-    if (isValidUrl(docBaseFile))
+    if (HttpUtils.isValidUrl(docBaseFile))
     {
       return docBaseFile;
     }
 
     String cb = jvlite.getCodeBase() + file;
-    if (isValidUrl(cb))
+    if (HttpUtils.isValidUrl(cb))
     {
       return cb;
     }
@@ -126,45 +125,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return file;
   }
 
-  /**
-   * Returns true if it is possible to open an input stream at the given URL,
-   * else false. The input stream is closed.
-   * 
-   * @param file
-   * @return
-   */
-  private boolean isValidUrl(String file)
-  {
-    InputStream is = null;
-    try
-    {
-      is = new URL(file).openStream();
-      if (is != null)
-      {
-        return true;
-      }
-    } catch (IOException x)
-    {
-      // MalformedURLException, FileNotFoundException
-      return false;
-    } finally
-    {
-      if (is != null)
-      {
-        try
-        {
-          is.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
-    }
-    return false;
-  }
-
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return modelSet;
   }
@@ -190,9 +152,9 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         // 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() });
+                new String[]
+                { "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(),
+                    "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() });
       } catch (Exception ex)
       {
         System.err.println("Couldn't execute callback with " + _listenerfn
@@ -211,8 +173,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements
 
     if (JalviewLite.debug)
     {
-      System.err.println(this.getClass().getName() + " modelSet[0]: "
-              + modelSet[0]);
+      System.err.println(
+              this.getClass().getName() + " modelSet[0]: " + modelSet[0]);
       ssm.reportMapping();
     }
 
@@ -241,15 +203,17 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         // }
       }
 
-      SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
+      SequenceRendererI 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());
       }
       ;
@@ -259,8 +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, true);
       if (colcommands == null)
       {
         return;
@@ -281,27 +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();
 
         }
@@ -336,12 +298,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
-  public void finalise()
-  {
-    jvlite = null;
-    super.finalize();
-  }
-
   @Override
   public void releaseReferences(Object svl)
   {