X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=8c7c9bea67d05e9e3f853ecf27ceda78a3f81a84;hb=c59fb56cb143b05c5643a71f5b39996ac1cd2fef;hp=42094550da539211cfc9eaf91002ff01d5cb9977;hpb=798a8f1eda50a57b71e21df22e015da1364ffd1c;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4209455..8c7c9be 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -32,8 +32,7 @@ public class AlignFrame extends GAlignFrame
   final AlignViewport viewport;
   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");
@@ -42,10 +41,18 @@ public class AlignFrame extends GAlignFrame
       viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
 
 
-
     alignPanel = new AlignmentPanel(this, viewport);
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
+    // add conservation graph to alignment
+    viewport.updateConservation();
+    viewport.updateConsensus();
+
+    alignPanel.annotationPanel.adjustPanelHeight();
+    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+
+
     addInternalFrameListener(new InternalFrameAdapter()
    {
      public void internalFrameActivated(InternalFrameEvent evt)
@@ -63,11 +70,27 @@ public class AlignFrame extends GAlignFrame
 
   protected void saveAs_actionPerformed(ActionEvent e)
   {
-    JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    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");
+    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);
@@ -98,20 +121,14 @@ public class AlignFrame extends GAlignFrame
     htmlOutput = null;
   }
 
-  protected void createJPG_actionPerformed(ActionEvent e)
+  protected void createPNG_actionPerformed(ActionEvent e)
   {
+    alignPanel.makePNG();
+  }
 
-    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.makeJPG( width, height);
+  protected void epsFile_actionPerformed(ActionEvent e)
+  {
+    alignPanel.makeEPS();
   }
 
 
@@ -156,6 +173,7 @@ public class AlignFrame extends GAlignFrame
 
   Stack historyList = new Stack();
   Stack redoList = new Stack();
+  JMenuBar jMenuBar1 = new JMenuBar();
 
   void updateEditMenuBar()
   {
@@ -217,12 +235,14 @@ public class AlignFrame extends GAlignFrame
       seq = (SequenceI[]) history[1];
       viewport.setAlignment( new Alignment(seq) );
       updateEditMenuBar();
+      viewport.updateConsensus();
+      alignPanel.RefreshPanels();
       alignPanel.RefreshPanels();
   }
 
   public void moveSelectedSequences(boolean up)
   {
-    SequenceGroup sg = viewport.getRubberbandGroup();
+    SequenceGroup sg = viewport.getSelectionGroup();
     if (sg == null)
       return;
 
@@ -266,10 +286,10 @@ 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();
@@ -329,12 +349,14 @@ public class AlignFrame extends GAlignFrame
         int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;
         if (newHeight > 500)
           newHeight = 500;
-        Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
+        Desktop.addInternalFrame(af, "Copied sequences", 700, 500);
       }
       else
       {
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
+        viewport.updateConservation();
+        viewport.updateConsensus();
         alignPanel.RefreshPanels();
       }
 
@@ -352,10 +374,10 @@ 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 +390,7 @@ 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)
@@ -376,6 +398,8 @@ public class AlignFrame extends GAlignFrame
      {
        this.setClosed(true);
      }catch(Exception ex){}
+   viewport.updateConservation();
+   viewport.updateConsensus();
      alignPanel.RefreshPanels();
 
   }
@@ -388,6 +412,8 @@ public class AlignFrame extends GAlignFrame
      SequenceI[] seq = (SequenceI[]) history[1];
      viewport.setAlignment( new Alignment(seq) );
      updateEditMenuBar();
+     viewport.updateConsensus();
+     alignPanel.RefreshPanels();
      alignPanel.RefreshPanels();
   }
 
@@ -404,7 +430,7 @@ public class AlignFrame extends GAlignFrame
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
     viewport.alignment.deleteAllGroups();
-    viewport.getSelection().clear();
+    viewport.setSelectionGroup(null);
 
     alignPanel.RefreshPanels();
   }
@@ -413,29 +439,26 @@ 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);
   }
 
@@ -455,6 +478,18 @@ public class AlignFrame extends GAlignFrame
       int min = colSel.getMin();
       viewport.getAlignment().trimLeft(min);
       colSel.compensateForEdit(0,min);
+
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveLeft(min);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveLeft(min))
+          viewport.alignment.deleteGroup(sg);
+      }
+
       alignPanel.RefreshPanels();
     }
   }
@@ -466,8 +501,19 @@ public class AlignFrame extends GAlignFrame
     if (colSel.size() > 0)
     {
       int max = colSel.getMax();
-      if(max>1)
-        viewport.getAlignment().trimRight(max);
+      viewport.getAlignment().trimRight(max);
+      if(viewport.getSelectionGroup()!=null)
+        viewport.getSelectionGroup().adjustForRemoveRight(max);
+
+      Vector groups = viewport.alignment.getGroups();
+      for(int i=0; i<groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.get(i);
+        if(!sg.adjustForRemoveRight(max))
+          viewport.alignment.deleteGroup(sg);
+      }
+
+
 
       alignPanel.RefreshPanels();
     }
@@ -478,6 +524,8 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -498,7 +546,8 @@ public class AlignFrame extends GAlignFrame
           jSize--;
         }
     }
-
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -535,6 +584,14 @@ 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() );
@@ -578,9 +635,9 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
+    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
@@ -764,6 +821,10 @@ if ( viewport.getConservationSelected() )
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
+    if(coloursChanging)
+      return;
+
+    coloursChanging = true;
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
@@ -776,11 +837,17 @@ if ( viewport.getConservationSelected() )
      changeColour( ((ConservationColourScheme)cs).cs );
     else
       changeColour( cs );
-  }
 
+    coloursChanging = false;
+  }
 
+  boolean coloursChanging = false;
   public void abovePIDThreshold_actionPerformed(ActionEvent e)
   {
+    if(coloursChanging)
+      return;
+
+    coloursChanging = true;
     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
 
     conservationMenuItem.setSelected(false);
@@ -797,6 +864,7 @@ if ( viewport.getConservationSelected() )
     else
         changeColour( cs );
 
+    coloursChanging = false;
   }
 
 
@@ -870,7 +938,7 @@ 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 +950,8 @@ 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 +1007,9 @@ 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
@@ -1059,4 +1128,50 @@ if ( viewport.getConservationSelected() )
          g.drawString("Clustal Alignment Web Service running", 30,30);
        }
   }
+  protected void jpred_actionPerformed(ActionEvent e)
+{
+
+
+      JInternalFrame frame = new JInternalFrame();
+      JPredClient ct = new JPredClient((SequenceI)
+                                       viewport.getAlignment().getSequences().elementAt(0));
+    }
+
+    protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Select a newick-like tree file");
+    chooser.setToolTipText("Load a tree file");
+    int value = chooser.showOpenDialog(null);
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      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);
+        }
+      }
+      catch (Exception ex)
+      {
+        JOptionPane.showMessageDialog(Desktop.desktop,
+                                      "Problem reading tree file",
+                                      ex.getMessage(),
+                                      JOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
+      }
+    }
+  }
+
 }