X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=725a702da877fce68aab0c669e68abaa7f32be87;hb=67fe33692d163752fd467468b18ace4a9b4eac7d;hp=a21aabe7c25ca3a54071fba19ce810cf97ca2949;hpb=affd24332b831acf0ffe4697dc1efafe8e414b31;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a21aabe..725a702 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -32,18 +32,12 @@ public class AlignFrame extends GAlignFrame
   final AlignViewport viewport;
   public static final int NEW_WINDOW_WIDTH = 700;
   public static final int NEW_WINDOW_HEIGHT = 500;
+  public String currentFileFormat = "Jalview";
 
   public AlignFrame(AlignmentI al)
   {
-    try{
-      String ip = java.net.InetAddress.getLocalHost().getHostAddress();
-      if( !ip.startsWith("10."))
-        webService.setVisible(false);
-    }
-    catch(java.net.UnknownHostException e){}
     viewport = new AlignViewport(al);
 
-
     alignPanel = new AlignmentPanel(this, viewport);
     alignPanel.annotationPanel.adjustPanelHeight();
     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
@@ -67,34 +61,36 @@ public class AlignFrame extends GAlignFrame
 
   }
 
-  protected void saveAs_actionPerformed(ActionEvent e)
+  public void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
-    String suffix [] = null;
-    if(e.getActionCommand().equals("FASTA"))
-      suffix = new String[]{"fa", "fasta"};
-    else if(e.getActionCommand().equals("MSF"))
-      suffix = new String[]{"msf"};
-    else if(e.getActionCommand().equals("CLUSTAL"))
-      suffix = new String[]{"aln"};
-    else if(e.getActionCommand().equals("BLC"))
-      suffix = new String[]{"blc"};
-    else if(e.getActionCommand().equals("PIR"))
-      suffix = new String[]{"pir"};
-    else if(e.getActionCommand().equals("PFAM"))
-      suffix = new String[]{"pfam"};
-
-
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
-        , suffix, e.getActionCommand()+" file");
+        ,  new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},
+          new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"},
+          currentFileFormat);
+
+    chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
+    chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
     if(value == JalviewFileChooser.APPROVE_OPTION)
     {
+      currentFileFormat  = chooser.getSelectedFormat();
+
+      if (currentFileFormat.equals("Jalview"))
+      {
+        String shortName = title.replace('/', '_');
+        title = title.replace('\\', '_');
+        String choice = chooser.getSelectedFile().getPath();
+        Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,
+                              choice);
+        // USE Jalview2XML to save this file
+        return;
+      }
+
       String choice =  chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
+      String output = FormatAdapter.formatSequences(currentFileFormat, viewport.getAlignment().getSequences());
       try{
         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
         out.println(output);
@@ -112,7 +108,7 @@ public class AlignFrame extends GAlignFrame
      cap.formatForOutput();
      frame.setContentPane(cap);
      Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
-     cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
+     cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
   }
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
@@ -205,6 +201,7 @@ public class AlignFrame extends GAlignFrame
   {
     // must make sure we add new sequence objects her, not refs to the existing sequences
     redoList.clear();
+
     SequenceI[] seq = new SequenceI[viewport.getAlignment().getHeight()];
     for(int i=0; i<viewport.getAlignment().getHeight(); i++)
     {
@@ -212,6 +209,7 @@ public class AlignFrame extends GAlignFrame
                              viewport.getAlignment().getSequenceAt(i).getSequence());
     }
 
+
     historyList.add(0, new Object[]{type,  seq} );
     updateEditMenuBar();
   }
@@ -232,9 +230,14 @@ public class AlignFrame extends GAlignFrame
     redoList.add(0, new Object[] {history[0], seq});
 
       seq = (SequenceI[]) history[1];
+      AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
       viewport.setAlignment( new Alignment(seq) );
+      viewport.alignment.setGapCharacter( Preferences.gapSymbol );
       updateEditMenuBar();
+      for(int i=0; i<old.length; i++)
+        viewport.alignment.addAnnotation(old[i]);
       viewport.updateConsensus();
+      viewport.updateConservation();
       alignPanel.repaint();
   }
 
@@ -284,21 +287,42 @@ public class AlignFrame extends GAlignFrame
 
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getSelectionGroup()==null)
-     return;
+     if(viewport.getSelectionGroup()==null)
+       return;
 
-   SequenceGroup sg = viewport.getSelectionGroup();
+     SequenceGroup sg = viewport.getSelectionGroup();
 
      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
      StringBuffer buffer= new StringBuffer();
 
-       for(int i=0; i<sg.getSize(); i++)
+     Hashtable orderedSeqs = new Hashtable();
+     for(int i=0; i<sg.getSize(); i++)
+     {
+        SequenceI seq = sg.getSequenceAt(i);
+        int index = viewport.alignment.findIndex(seq);
+        orderedSeqs.put(index+"", seq);
+     }
+
+     int index=0;
+     for(int i=0; i<sg.getSize(); i++)
+     {
+       SequenceI seq = null;
+       while( seq == null )
        {
-         SequenceI seq = sg.getSequenceAt(i);
+         if(orderedSeqs.containsKey(index+""))
+         {
+           seq = (SequenceI) orderedSeqs.get(index + "");
+           index++;
+           break;
+         }
+         else
+           index++;
+       }
+
          buffer.append( seq.getName()+"\t"+seq.findPosition( sg.getStartRes() ) +"\t"
                         +seq.findPosition( sg.getEndRes() )+ "\t"
                         +sg.getSequenceAt(i).getSequence(sg.getStartRes(), sg.getEndRes()+1)+"\n");
-       }
+     }
      c.setContents( new StringSelection( buffer.toString()) , null ) ;
 
   }
@@ -344,7 +368,13 @@ public class AlignFrame extends GAlignFrame
         SequenceI[] newSeqs = new SequenceI[seqs.size()];
         seqs.toArray(newSeqs);
         AlignFrame af = new AlignFrame(new Alignment(newSeqs));
-        Desktop.addInternalFrame(af, "Copied sequences", NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+        String newtitle = new String("Copied sequences");
+        if( title.startsWith("Copied sequences"))
+         newtitle = title;
+       else
+         newtitle = newtitle.concat("- from "+title);
+
+        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
       }
       else
       {
@@ -406,6 +436,7 @@ public class AlignFrame extends GAlignFrame
      Object [] history = (Object[])redoList.remove(0);
      SequenceI[] seq = (SequenceI[]) history[1];
      viewport.setAlignment( new Alignment(seq) );
+     viewport.alignment.setGapCharacter( Preferences.gapSymbol );
      updateEditMenuBar();
      viewport.updateConsensus();
      alignPanel.repaint();
@@ -417,7 +448,6 @@ public class AlignFrame extends GAlignFrame
   {
     viewport.alignment.deleteAllGroups();
     viewport.setSelectionGroup(null);
-
     alignPanel.repaint();
   }
 
@@ -533,18 +563,12 @@ public class AlignFrame extends GAlignFrame
   }
 
 
-  protected void preferences_actionPerformed(ActionEvent e)
-{
-    Preferences pref = new Preferences(viewport);
-}
-
-
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     JInternalFrame frame = new JInternalFrame();
     Finder finder = new Finder(viewport, alignPanel, frame);
     frame.setContentPane(finder);
-    Desktop.addInternalFrame(frame, "Find", 340,110, false);
+    Desktop.addInternalFrame(frame, "Find", 340,110);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 
   }
@@ -623,7 +647,7 @@ public class AlignFrame extends GAlignFrame
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
     if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
     {
-         AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
+         SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
          ((Alignment)viewport.alignment).featuresAdded = true;
     }
     alignPanel.repaint();
@@ -792,16 +816,12 @@ public class AlignFrame extends GAlignFrame
         {
           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
         }
-        else
-          try
-          {
+        else if(cs!=null)
+        {
+          try{
             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
-            sg.cs = cs;
-          }
+          }catch(Exception ex){ex.printStackTrace();}
+        }
 
         if(viewport.getAbovePIDThreshold())
         {
@@ -826,7 +846,7 @@ public class AlignFrame extends GAlignFrame
           ccs.setConsensus( AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
           sg.cs = ccs;
         }
-        else
+        else if(cs!=null)
         {
           // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));
@@ -1201,20 +1221,10 @@ public class AlignFrame extends GAlignFrame
     {
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      TreePanel treepanel = null;
       try
       {
         jalview.io.NewickFile fin = new jalview.io.NewickFile(choice, "File");
-        fin.parse();
-
-        if (fin.getTree() != null)
-        {
-          TreePanel tp = null;
-          tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                             fin, "FromFile", choice);
-          Desktop.addInternalFrame(tp, title, 600, 500);
-          addTreeMenuItem(tp, title);
-        }
+        ShowNewickTree(fin, choice);
       }
       catch (Exception ex)
       {
@@ -1227,4 +1237,21 @@ public class AlignFrame extends GAlignFrame
     }
   }
 
+  public void ShowNewickTree(NewickFile nf, String title)
+  {
+    try{
+      nf.parse();
+      if (nf.getTree() != null)
+      {
+        TreePanel tp = new TreePanel(viewport,
+                                     viewport.getAlignment().getSequences(),
+                                     nf, "FromFile", title);
+        Desktop.addInternalFrame(tp, title, 600, 500);
+        addTreeMenuItem(tp, title);
+        viewport.setCurrentTree(tp.getTree());
+      }
+     }catch(Exception ex){ex.printStackTrace();}
+  }
+
+
 }