bug fix for Features/Annotations file parameter parsing in JalviewLite reported and...

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 1202c68..82a5911 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -163,12 +163,34 @@ public class AppletJmol extends EmbmenuFrame
 
     if(pdbentry.getFile()!=null)
     {
+      // import structure data from pdbentry.getFile based on given protocol
       if (protocol.equals(AppletFormatAdapter.PASTE))
+      { 
         loadInline(pdbentry.getFile());
-      else
+      } else
+      if (protocol.equals(AppletFormatAdapter.FILE) || protocol.equals(AppletFormatAdapter.URL)){
           viewer.openFile(pdbentry.getFile());
+      }
+      else
+        {
+        // probably CLASSLOADER based datasource..
+        // Try and get a reader on the datasource, and pass that to Jmol
+        try {
+          FileParse fparser = new jalview.io.FileParse(protocol, pdbentry.getFile());
+          if (!fparser.isValid())
+          {
+            throw new Exception("Invalid datasource. "+fparser.getWarningMessage());
+          }
+          viewer.openReader(pdbentry.getFile(), pdbentry.getId(), fparser.getReader());
+        } catch (Exception e)
+        {
+          // give up!
+          System.err.println("Couldn't access pdbentry id="+pdbentry.getId()+" and file="+pdbentry.getFile()+" using protocol="+protocol);
+          e.printStackTrace();
+        }
+        }
     }
-
+    
     jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400);
   }
 

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 4d45f8c..4945ec0 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -436,19 +436,34 @@ public class JalviewLite
   class LoadingThread
       extends Thread
   {
-    String file;
+    /**
+     * State variable: File source 
+     */
+    String file; 
+    /**
+     * State variable: protocol for access to file source
+     */
     String protocol;
+    /**
+     * State variable: format of file source
+     */
     String format;
     JalviewLite applet;
-
-    public LoadingThread(String _file,
-                         JalviewLite _applet)
+    private void dbgMsg(String msg)
     {
       if (applet.debug)
       {
-        System.err.println("Loading thread started with:\n>>file\n"+_file+">>endfile");
+        System.err.println(msg);
       }
-      file = _file;
+    }
+    /**
+     * update the protocol state variable for accessing the datasource
+     * located by file. 
+     * @param file
+     * @return possibly updated datasource string
+     */
+    public String setProtocolState(String file)
+    {
       if (file.startsWith("PASTE"))
       {
         file = file.substring(5);
@@ -463,15 +478,17 @@ public class JalviewLite
         file = addProtocol(file);
         protocol = AppletFormatAdapter.URL;
       }
-      if (applet.debug)
-      {
-        System.err.println("Protocol identified as '"+protocol+"'");
-      }
+      dbgMsg("Protocol identified as '"+protocol+"'");
+      return file;
+    }
+    public LoadingThread(String _file,
+                         JalviewLite _applet)
+    {
+      dbgMsg("Loading thread started with:\n>>file\n"+_file+">>endfile");
+      file = setProtocolState(_file);
+      
       format = new jalview.io.IdentifyFile().Identify(file, protocol);
-      if (applet.debug)
-      {
-        System.err.println("File identified as '"+format+"'");
-      }
+      dbgMsg("File identified as '"+format+"'");
       applet = _applet;
     }
 
@@ -482,6 +499,7 @@ public class JalviewLite
 
     private void startLoading()
     {
+      dbgMsg("Loading started.");
       Alignment al = null;
       try
       {
@@ -490,10 +508,12 @@ public class JalviewLite
       }
       catch (java.io.IOException ex)
       {
+        dbgMsg("File load exception.");
         ex.printStackTrace();
       }
       if ( (al != null) && (al.getHeight() > 0))
       {
+        dbgMsg("Successfully loaded file.");
         initialAlignFrame =  new AlignFrame(al,
                                            applet,
                                            file,
@@ -518,7 +538,8 @@ public class JalviewLite
         {
           try
           {
-            if (inArchive(treeFile))
+            treeFile = setProtocolState(treeFile);
+            /*if (inArchive(treeFile))
             {
               protocol = AppletFormatAdapter.CLASSLOADER;
             }
@@ -527,7 +548,7 @@ public class JalviewLite
               protocol = AppletFormatAdapter.URL;
               treeFile = addProtocol(treeFile);
             }
-
+             */
             jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
                 protocol);
 
@@ -536,6 +557,9 @@ public class JalviewLite
             if (fin.getTree() != null)
             {
               currentAlignFrame.loadTree(fin, treeFile);
+              dbgMsg("Successfuly imported tree.");
+            } else {
+              dbgMsg("Tree parameter did not resolve to a valid tree.");
             }
           }
           catch (Exception ex)
@@ -547,11 +571,8 @@ public class JalviewLite
         String param = getParameter("features");
         if (param != null)
         {
-          if (!inArchive(param))
-          {
-            param = addProtocol(param);
-          }
-
+          param = setProtocolState(param);
+          
           currentAlignFrame.parseFeaturesFile(param, protocol);
         }
 
@@ -564,19 +585,19 @@ public class JalviewLite
 
         param = getParameter("annotations");
         if (param != null)
-        {
-          if (!inArchive(param))
-          {
-            param = addProtocol(param);
-          }
-
-          new AnnotationFile().readAnnotationFile(
+        { 
+          param = setProtocolState(param);
+          
+          if (new AnnotationFile().readAnnotationFile(
               currentAlignFrame.viewport.getAlignment(),
               param,
-              protocol);
-
-          currentAlignFrame.alignPanel.fontChanged();
-          currentAlignFrame.alignPanel.setScrollValues(0, 0);
+              protocol))
+          {
+            currentAlignFrame.alignPanel.fontChanged();
+            currentAlignFrame.alignPanel.setScrollValues(0, 0);
+          } else {
+            System.err.println("Annotations were not added from annotation file '"+param+"'");
+          }
 
         }
 
@@ -585,21 +606,12 @@ public class JalviewLite
         {
           try
           {
-            if (inArchive(param))
-            {
-              protocol = AppletFormatAdapter.CLASSLOADER;
-            }
-            else
-            {
-              protocol = AppletFormatAdapter.URL;
-              param = addProtocol(param);
-            }
-
+            param = setProtocolState(param);
             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
                 param, protocol);
-            new JnetAnnotationMaker().add_annotation(predictions,
+            JnetAnnotationMaker.add_annotation(predictions,
                 currentAlignFrame.viewport.getAlignment(),
-                0, false); // do not add sequence profile from concise output
+                0, false); // false==do not add sequence profile from concise output
             currentAlignFrame.alignPanel.fontChanged();
             currentAlignFrame.alignPanel.setScrollValues(0, 0);
           }
@@ -675,15 +687,14 @@ public class JalviewLite
                 tmp2.copyInto(chains);
               }
             }
-
-            if (inArchive(param) && !jmolAvailable)
-            {
-              protocol = AppletFormatAdapter.CLASSLOADER;
-            }
-            else
+            param = setProtocolState(param);
+            
+            if (!jmolAvailable && protocol==AppletFormatAdapter.CLASSLOADER)
             {
-              protocol = AppletFormatAdapter.URL;
-              param = addProtocol(param);
+              // TODO: pass PDB file in classloader on to Jmol
+              // This exception preserves the current behaviour where, even if the local pdb file was identified in the class loader
+              protocol = AppletFormatAdapter.URL; // this is probably NOT CORRECT!
+              param = addProtocol(param); // 
             }
 
             pdb.setFile(param);
@@ -753,7 +764,11 @@ public class JalviewLite
       //Netscape Communicator for instance.
       try
       {
-        return (getClass().getResourceAsStream("/" + file) != null);
+        boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
+        if (debug)
+        {  System.err.println("Resource '"+file+"' was "+(rtn ? "" : "not") +" located by classloader.");
+        }
+        return rtn;
       }
       catch (Exception ex)
       {
@@ -767,6 +782,10 @@ public class JalviewLite
       if (file.indexOf("://") == -1)
       {
         file = getCodeBase() + file;
+        if (debug)
+        {
+          System.err.println("Prepended codebase for resource: '"+file+"'");
+        }
       }
 
       return file;

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 4c69ce0..04a673c 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -287,4 +287,13 @@ public class FileParse
       return "From Paste + ("+index+")";
     }
   }
+  
+  public Reader getReader() throws IOException
+  {
+    if (dataIn!=null && dataIn.ready())
+    {
+      return dataIn;
+    }
+    return null;
+  }
 }