pir format ambiguity and todo regarding 'format override' parameter

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 9226dc4..7329a6f 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -258,6 +258,7 @@ public class JalviewLite extends Applet
   public AlignFrame loadAlignment(String text, String title)
   {
     Alignment al = null;
+    
     String format = new IdentifyFile().Identify(text,
             AppletFormatAdapter.PASTE);
     try
@@ -599,7 +600,7 @@ public class JalviewLite extends Applet
      * State variable: format of file source
      */
     String format;
-
+    String _file;
     JalviewLite applet;
     private void dbgMsg(String msg)
     {
@@ -635,14 +636,10 @@ public class JalviewLite extends Applet
       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);
-      dbgMsg("File identified as '" + format + "'");
+      this._file=_file;
       applet = _applet;
     }
 
@@ -660,6 +657,12 @@ public class JalviewLite extends Applet
 
     private void startLoading()
     {
+      AlignFrame newAlignFrame;
+      dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+      file = setProtocolState(_file);
+
+      format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      dbgMsg("File identified as '" + format + "'");
       dbgMsg("Loading started.");
       Alignment al = null;
       try
@@ -673,16 +676,20 @@ public class JalviewLite extends Applet
       if ((al != null) && (al.getHeight() > 0))
       {
         dbgMsg("Successfully loaded file.");
-        initialAlignFrame = new AlignFrame(al, applet, file, embedded);
+        newAlignFrame = new AlignFrame(al, applet, file, embedded);
+        if (initialAlignFrame==null)
+        {
+          initialAlignFrame = newAlignFrame;
+        }
         // update the focus.
-        currentAlignFrame = initialAlignFrame;
+        currentAlignFrame = newAlignFrame;
 
         if (protocol == jalview.io.AppletFormatAdapter.PASTE)
         {
-          currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
+          newAlignFrame.setTitle("Sequences from " + getDocumentBase());
         }
 
-        currentAlignFrame.statusBar.setText("Successfully loaded file "
+        newAlignFrame.statusBar.setText("Successfully loaded file "
                 + file);
 
         String treeFile = applet.getParameter("tree");
@@ -708,7 +715,7 @@ public class JalviewLite extends Applet
 
             if (fin.getTree() != null)
             {
-              currentAlignFrame.loadTree(fin, treeFile);
+              newAlignFrame.loadTree(fin, treeFile);
               dbgMsg("Successfuly imported tree.");
             }
             else
@@ -726,14 +733,14 @@ public class JalviewLite extends Applet
         {
           param = setProtocolState(param);
 
-          currentAlignFrame.parseFeaturesFile(param, protocol);
+          newAlignFrame.parseFeaturesFile(param, protocol);
         }
 
         param = getParameter("showFeatureSettings");
         if (param != null && param.equalsIgnoreCase("true"))
         {
-          currentAlignFrame.viewport.showSequenceFeatures(true);
-          new FeatureSettings(currentAlignFrame.alignPanel);
+          newAlignFrame.viewport.showSequenceFeatures(true);
+          new FeatureSettings(newAlignFrame.alignPanel);
         }
 
         param = getParameter("annotations");
@@ -742,11 +749,11 @@ public class JalviewLite extends Applet
           param = setProtocolState(param);
 
           if (new AnnotationFile().readAnnotationFile(
-                  currentAlignFrame.viewport.getAlignment(), param,
+                  newAlignFrame.viewport.getAlignment(), param,
                   protocol))
           {
-            currentAlignFrame.alignPanel.fontChanged();
-            currentAlignFrame.alignPanel.setScrollValues(0, 0);
+            newAlignFrame.alignPanel.fontChanged();
+            newAlignFrame.alignPanel.setScrollValues(0, 0);
           }
           else
           {
@@ -766,7 +773,7 @@ public class JalviewLite extends Applet
             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
                     param, protocol);
             JnetAnnotationMaker.add_annotation(predictions,
-                    currentAlignFrame.viewport.getAlignment(), 0, false); // false==do
+                    newAlignFrame.viewport.getAlignment(), 0, false); // false==do
             // not
             // add
             // sequence
@@ -774,8 +781,8 @@ public class JalviewLite extends Applet
             // from
             // concise
             // output
-            currentAlignFrame.alignPanel.fontChanged();
-            currentAlignFrame.alignPanel.setScrollValues(0, 0);
+            newAlignFrame.alignPanel.fontChanged();
+            newAlignFrame.alignPanel.setScrollValues(0, 0);
           } catch (Exception ex)
           {
             ex.printStackTrace();
@@ -814,7 +821,7 @@ public class JalviewLite extends Applet
               String sequence = applet.getParameter("PDBSEQ");
               if (sequence != null)
                 seqs = new SequenceI[]
-                { (Sequence) currentAlignFrame.getAlignViewport()
+                { (Sequence) newAlignFrame.getAlignViewport()
                         .getAlignment().findName(sequence) };
 
             }
@@ -834,7 +841,7 @@ public class JalviewLite extends Applet
                   tmp2.addElement(st2.nextToken());
                   seqstring = st2.nextToken();
                 }
-                tmp.addElement((Sequence) currentAlignFrame
+                tmp.addElement((Sequence) newAlignFrame
                         .getAlignViewport().getAlignment().findName(
                                 seqstring));
               }
@@ -888,13 +895,13 @@ public class JalviewLite extends Applet
               if (jmolAvailable)
               {
                 new jalview.appletgui.AppletJmol(pdb, seqs, chains,
-                        currentAlignFrame.alignPanel, protocol);
+                        newAlignFrame.alignPanel, protocol);
                 lastFrameX += 40;
                 lastFrameY += 40;
               }
               else
                 new MCview.AppletPDBViewer(pdb, seqs, chains,
-                        currentAlignFrame.alignPanel, protocol);
+                        newAlignFrame.alignPanel, protocol);
             }
           }
 
@@ -908,13 +915,13 @@ public class JalviewLite extends Applet
         param = getParameter("hidefeaturegroups");
         if (param != null)
         {
-          applet.setFeatureGroupState(param, false);
+          applet.setFeatureGroupStateOn(newAlignFrame,param, false);
         }
         // show specific groups
         param = getParameter("showfeaturegroups");
         if (param != null)
         {
-          applet.setFeatureGroupState(param, true);
+          applet.setFeatureGroupStateOn(newAlignFrame,param, true);
         }
       }
       else