X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=079f31515fc7c43e013036c8b6e33dca64731f5c;hb=3e63bb86ad0e6f4bc86197053f921cb67b341567;hp=42094550da539211cfc9eaf91002ff01d5cb9977;hpb=798a8f1eda50a57b71e21df22e015da1364ffd1c;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4209455..079f315 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -33,7 +33,7 @@ public class AlignFrame extends GAlignFrame
   public AlignFrame(AlignmentI al)
   {
     super();
-    viewport = new AlignViewport(al,true,true,true,false);
+    viewport = new AlignViewport(al,true,true,false);
 
     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
     String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");
@@ -63,11 +63,27 @@ public class AlignFrame extends GAlignFrame
 
   protected void saveAs_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    String suffix = "";
+    if(e.getActionCommand().equals("FASTA"))
+      suffix = "fa";
+    else if(e.getActionCommand().equals("MSF"))
+      suffix = "msf";
+    else if(e.getActionCommand().equals("CLUSTAL"))
+      suffix = "aln";
+    else if(e.getActionCommand().equals("BLC"))
+      suffix = "blc";
+    else if(e.getActionCommand().equals("PIR"))
+      suffix = "pir";
+    else if(e.getActionCommand().equals("PFAM"))
+      suffix = "pfam";
+
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
+        , new String[]{suffix}, e.getActionCommand()+" file");
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
     chooser.setToolTipText("Save");
     int value = chooser.showSaveDialog(this);
-    if(value == JFileChooser.APPROVE_OPTION)
+    if(value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice =  chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
@@ -98,12 +114,24 @@ public class AlignFrame extends GAlignFrame
     htmlOutput = null;
   }
 
-  protected void createJPG_actionPerformed(ActionEvent e)
+  protected void createPNG_actionPerformed(ActionEvent e)
   {
-
     int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
     int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
 
+    if(!viewport.getWrapAlignment())
+    {
+      height = viewport.alignment.getHeight() * viewport.charHeight;
+      width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
+    }
+
+    alignPanel.makePNG( width, height);
+  }
+
+  protected void epsFile_actionPerformed(ActionEvent e)
+  {
+    int height = (viewport.alignment.getWidth() / viewport.getChunkWidth() +1) * viewport.chunkHeight;
+    int width = alignPanel.seqPanel.getWidth() + alignPanel.idPanel.getWidth();
 
     if(!viewport.getWrapAlignment())
     {
@@ -111,7 +139,8 @@ public class AlignFrame extends GAlignFrame
       width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
     }
 
-    alignPanel.makeJPG( width, height);
+    alignPanel.makeEPS( width, height);
+
   }
 
 
@@ -222,7 +251,7 @@ public class AlignFrame extends GAlignFrame
 
   public void moveSelectedSequences(boolean up)
   {
-    SequenceGroup sg = viewport.getRubberbandGroup();
+    SequenceGroup sg = viewport.getSelectionGroup();
     if (sg == null)
       return;
 
@@ -266,10 +295,10 @@ public class AlignFrame extends GAlignFrame
 
   protected void copy_actionPerformed(ActionEvent e)
   {
-   if(viewport.getRubberbandGroup()==null)
+   if(viewport.getSelectionGroup()==null)
      return;
 
-   SequenceGroup sg = viewport.getRubberbandGroup();
+   SequenceGroup sg = viewport.getSelectionGroup();
 
      Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
      StringBuffer buffer= new StringBuffer();
@@ -352,10 +381,10 @@ public class AlignFrame extends GAlignFrame
   protected void delete_actionPerformed(ActionEvent e)
   {
     addHistoryItem("Delete");
-    if (viewport.getRubberbandGroup() == null)
+    if (viewport.getSelectionGroup() == null)
       return;
 
-     SequenceGroup sg = viewport.getRubberbandGroup();
+     SequenceGroup sg = viewport.getSelectionGroup();
      for (int i=0;i < sg.sequences.size(); i++)
      {
        SequenceI seq = sg.getSequenceAt(i);
@@ -368,7 +397,7 @@ public class AlignFrame extends GAlignFrame
           viewport.getAlignment().getSequences().setElementAt(seq, index);
      }
 
-     viewport.setRubberbandGroup(null);
+     viewport.setSelectionGroup(null);
      viewport.alignment.deleteGroup(sg);
      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
      if(viewport.getAlignment().getHeight()<1)
@@ -404,7 +433,7 @@ public class AlignFrame extends GAlignFrame
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
 
     alignPanel.RefreshPanels();
   }
@@ -413,29 +442,26 @@ public class AlignFrame extends GAlignFrame
 
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
+    SequenceGroup sg = new SequenceGroup();
     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-      sel.addElement( viewport.getAlignment().getSequenceAt(i));
+      sg.addSequence( viewport.getAlignment().getSequenceAt(i));
+    sg.setEndRes(viewport.alignment.getWidth());
+    viewport.setSelectionGroup(sg);
     PaintRefresher.Refresh(null);
   }
 
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setRubberbandGroup(null);
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(null);
   }
 
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    Selection sel = viewport.getSelection();
+    SequenceGroup sg = viewport.getSelectionGroup();
     for (int i=0; i<viewport.getAlignment().getSequences().size(); i++)
-    {
-      if (sel.contains(viewport.getAlignment().getSequenceAt(i)))
-        sel.removeElement(viewport.getAlignment().getSequenceAt(i));
-      else
-        sel.addElement(viewport.getAlignment().getSequenceAt(i));
-    }
+      sg.addOrRemove (viewport.getAlignment().getSequenceAt(i));
+
     PaintRefresher.Refresh(null);
   }
 
@@ -535,6 +561,14 @@ public class AlignFrame extends GAlignFrame
     Desktop.addInternalFrame(frame, "Change Font", 480,100);
   }
 
+  protected void fullSeqId_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowFullId( fullSeqId.isSelected() );
+
+    alignPanel.idPanel.idCanvas.setPreferredSize( alignPanel.calculateIdWidth() );
+    alignPanel.RefreshPanels();
+  }
+
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
       viewport.setColourText( colourTextMenuItem.isSelected() );
@@ -870,7 +904,7 @@ if ( viewport.getConservationSelected() )
 
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelection().size()<2)
+    if(viewport.getSelectionGroup().getSize()<2)
       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
     else
     {
@@ -882,7 +916,8 @@ if ( viewport.getConservationSelected() )
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
-    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
+
+    if( (viewport.getSelectionGroup()!=null && viewport.getSelectionGroup().getSize()<4 && viewport.getSelectionGroup().getSize()>0)
        || viewport.getAlignment().getHeight()<4)
     {
       JOptionPane.showInternalMessageDialog(this, "Principal component analysis must take\n"
@@ -938,9 +973,9 @@ if ( viewport.getConservationSelected() )
     }
 
     TreePanel tp=null;
-   if (viewport.getSelection() != null && viewport.getSelection().size() > 3)
+   if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() > 3)
    {
-     tp = new TreePanel(viewport, viewport.getSelection().asVector(),type, pwType,
+     tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences,type, pwType,
                          0, viewport.alignment.getWidth());
    }
    else