X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=132417367797b071225e5d2c02bc9797a2b179d1;hb=8004878db16757b62ee2c35738506bc4509428cf;hp=079f31515fc7c43e013036c8b6e33dca64731f5c;hpb=c4e30ea2141be5b0622cf9cd59eac0366fa47d32;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 079f315..1324173 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -32,7 +32,6 @@ public class AlignFrame extends GAlignFrame
   final AlignViewport viewport;
   public AlignFrame(AlignmentI al)
   {
-    super();
     viewport = new AlignViewport(al,true,true,false);
 
     String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
@@ -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)
@@ -63,22 +70,29 @@ public class AlignFrame extends GAlignFrame
 
   protected void saveAs_actionPerformed(ActionEvent e)
   {
-    String suffix = "";
+    String suffix [] = null;
     if(e.getActionCommand().equals("FASTA"))
-      suffix = "fa";
+      suffix = new String[]{"fa", "fasta"};
     else if(e.getActionCommand().equals("MSF"))
-      suffix = "msf";
+      suffix = new String[]{"msf"};
     else if(e.getActionCommand().equals("CLUSTAL"))
-      suffix = "aln";
+      suffix = new String[]{"aln"};
     else if(e.getActionCommand().equals("BLC"))
-      suffix = "blc";
+      suffix = new String[]{"blc"};
     else if(e.getActionCommand().equals("PIR"))
-      suffix = "pir";
+      suffix = new String[]{"pir"};
     else if(e.getActionCommand().equals("PFAM"))
-      suffix = "pfam";
+      suffix = new String[]{"pfam"};
+
+    if(e.getActionCommand().equals("XML DUMP"))
+    {
+      XMLStore store = new XMLStore();
+      store.store(viewport);
+      return;
+    }
 
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
-        , new String[]{suffix}, e.getActionCommand()+" file");
+        , suffix, e.getActionCommand()+" file");
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file - "+e.getActionCommand() +" format.");
     chooser.setToolTipText("Save");
@@ -116,31 +130,12 @@ public class AlignFrame extends GAlignFrame
 
   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);
+    alignPanel.makePNG();
   }
 
   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())
-    {
-      height = viewport.alignment.getHeight() * viewport.charHeight;
-      width = alignPanel.idPanel.getWidth() + viewport.alignment.getWidth() * viewport.charWidth;
-    }
-
-    alignPanel.makeEPS( width, height);
-
+    alignPanel.makeEPS();
   }
 
 
@@ -185,6 +180,7 @@ public class AlignFrame extends GAlignFrame
 
   Stack historyList = new Stack();
   Stack redoList = new Stack();
+  JMenuBar jMenuBar1 = new JMenuBar();
 
   void updateEditMenuBar()
   {
@@ -246,6 +242,8 @@ public class AlignFrame extends GAlignFrame
       seq = (SequenceI[]) history[1];
       viewport.setAlignment( new Alignment(seq) );
       updateEditMenuBar();
+      viewport.updateConsensus();
+      alignPanel.RefreshPanels();
       alignPanel.RefreshPanels();
   }
 
@@ -358,12 +356,14 @@ 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();
       }
 
@@ -405,6 +405,8 @@ public class AlignFrame extends GAlignFrame
      {
        this.setClosed(true);
      }catch(Exception ex){}
+   viewport.updateConservation();
+   viewport.updateConsensus();
      alignPanel.RefreshPanels();
 
   }
@@ -417,6 +419,8 @@ public class AlignFrame extends GAlignFrame
      SequenceI[] seq = (SequenceI[]) history[1];
      viewport.setAlignment( new Alignment(seq) );
      updateEditMenuBar();
+     viewport.updateConsensus();
+     alignPanel.RefreshPanels();
      alignPanel.RefreshPanels();
   }
 
@@ -481,6 +485,18 @@ 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();
     }
   }
@@ -492,8 +508,19 @@ 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();
     }
@@ -504,6 +531,8 @@ public class AlignFrame extends GAlignFrame
   {
     addHistoryItem("delete gapped columns");
     viewport.getAlignment().removeGaps();
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -524,7 +553,8 @@ public class AlignFrame extends GAlignFrame
           jSize--;
         }
     }
-
+    viewport.updateConservation();
+    viewport.updateConsensus();
     alignPanel.RefreshPanels();
   }
 
@@ -554,7 +584,6 @@ public class AlignFrame extends GAlignFrame
 
   public void font_actionPerformed(ActionEvent e)
   {
-   // JOptionPane op = new JOptionPane();
     JInternalFrame frame = new JInternalFrame();
     FontChooser fc = new FontChooser( alignPanel, frame );
     frame.setContentPane(fc);
@@ -612,9 +641,15 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
-  public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+  public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
+    if(annotationPanelMenuItem.isSelected() && viewport.getWrapAlignment())
+    {
+      annotationPanelMenuItem.setSelected(false);
+      return;
+    }
+    viewport.setShowAnnotation( annotationPanelMenuItem.isSelected() );
+    alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );
   }
 
   public void overviewMenuItem_actionPerformed(ActionEvent e)
@@ -798,6 +833,10 @@ if ( viewport.getConservationSelected() )
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setConservationSelected(conservationMenuItem.isSelected());
+    if(coloursChanging)
+      return;
+
+    coloursChanging = true;
 
     viewport.setAbovePIDThreshold(false);
     abovePIDThreshold.setSelected(false);
@@ -810,11 +849,17 @@ 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);
@@ -831,6 +876,7 @@ if ( viewport.getConservationSelected() )
     else
         changeColour( cs );
 
+    coloursChanging = false;
   }
 
 
@@ -1094,4 +1140,90 @@ if ( viewport.getConservationSelected() )
          g.drawString("Clustal Alignment Web Service running", 30,30);
        }
   }
+  protected void jpred_actionPerformed(ActionEvent e)
+{
+
+    JInternalFrame frame = new JInternalFrame();
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
+    {
+      // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+      SequenceGroup seqs = viewport.getSelectionGroup();
+      if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.getSequenceAt(0));
+      }
+      else
+      {
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+    else
+    {
+      Vector seqs = viewport.getAlignment().getSequences();
+
+      if (seqs.size() == 1 || !viewport.alignment.isAligned())
+      {
+        JPredClient ct = new JPredClient( (SequenceI)
+                                         seqs.elementAt(0));
+      }
+      else
+      {
+        SequenceI[] msa = new SequenceI[seqs.size()];
+        for (int i = 0; i < seqs.size(); i++)
+        {
+          msa[i] = (SequenceI) seqs.elementAt(i);
+        }
+
+        JPredClient ct = new JPredClient(msa);
+      }
+
+    }
+  }
+
+    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();
+      }
+    }
+  }
+
 }