X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=4fbdb7224e15b862d04942d42b1d28e3b61492ba;hb=24ad8bbb87343e317452c0dcb22efd800e7986d6;hp=b217e9c99a1c198f45cb181b023bc49a60c9d294;hpb=fdaf66178c7596335c3675ec3db0da8503dc61b2;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b217e9c..4fbdb72 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -38,31 +38,20 @@ public class AlignFrame extends GAlignFrame
     try{
       String ip = java.net.InetAddress.getLocalHost().getHostAddress();
       if( !ip.startsWith("10."))
-        alignMenu.setVisible(false);
+        webService.setVisible(false);
     }
     catch(java.net.UnknownHostException e){}
-    viewport = new AlignViewport(al,true,true,false);
-
-    String fontName = jalview.bin.Cache.getProperty("FONT_NAME");
-    String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");
-    String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");
-    if(fontName!=null && fontStyle!=null && fontSize!=null)
-      viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
-
-    // add conservation graph to alignment
-    viewport.updateConservation();
-    viewport.updateConsensus();
+    viewport = new AlignViewport(al);
 
 
     alignPanel = new AlignmentPanel(this, viewport);
-
     alignPanel.annotationPanel.adjustPanelHeight();
     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());
+    alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );
 
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
 
-
     addInternalFrameListener(new InternalFrameAdapter()
    {
      public void internalFrameActivated(InternalFrameEvent evt)
@@ -105,7 +94,7 @@ public class AlignFrame extends GAlignFrame
     {
       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(e.getActionCommand(), viewport.getAlignment().getSequences());
       try{
         java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice )  );
         out.println(output);
@@ -123,7 +112,7 @@ 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)
@@ -184,7 +173,6 @@ public class AlignFrame extends GAlignFrame
 
   Stack historyList = new Stack();
   Stack redoList = new Stack();
-  JMenuBar jMenuBar1 = new JMenuBar();
 
   void updateEditMenuBar()
   {
@@ -244,9 +232,13 @@ 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) );
       updateEditMenuBar();
+      for(int i=0; i<old.length; i++)
+        viewport.alignment.addAnnotation(old[i]);
       viewport.updateConsensus();
+      viewport.updateConservation();
       alignPanel.repaint();
   }
 
@@ -448,6 +440,8 @@ public class AlignFrame extends GAlignFrame
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
     viewport.setSelectionGroup(null);
+    viewport.getColumnSelection().clear();
+    viewport.setSelectionGroup(null);
     PaintRefresher.Refresh(null);
   }
 
@@ -460,13 +454,6 @@ public class AlignFrame extends GAlignFrame
     PaintRefresher.Refresh(null);
   }
 
-
-  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
-  {
-    viewport.getColumnSelection().clear();
-    repaint();
-  }
-
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
     addHistoryItem("delete columns");
@@ -549,19 +536,6 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();
   }
 
-  public void setGapCharMenuItem_actionPerformed(ActionEvent e)
-  {
-    char thisChar = '-';
-    char nextChar = '.';
-    if(viewport.getGapCharacter()=='-')
-    {
-      thisChar = '.';
-      nextChar = '-';
-    }
-    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");
-    viewport.setGapCharacter(thisChar);
-    alignPanel.repaint();
-  }
 
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
@@ -576,13 +550,7 @@ public class AlignFrame extends GAlignFrame
 
   public void font_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    FontChooser fc = new FontChooser( alignPanel, frame );
-    frame.setContentPane(fc);
-    Desktop.addInternalFrame(frame, "Change Font", 480,100, false);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    if(alignPanel.getOverviewPanel()!=null)
-      alignPanel.getOverviewPanel().updateOverviewImage();
+    FontChooser fc = new FontChooser( alignPanel );
   }
 
   protected void fullSeqId_actionPerformed(ActionEvent e)
@@ -653,7 +621,7 @@ 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();
@@ -928,10 +896,7 @@ public class AlignFrame extends GAlignFrame
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);
-    frame.setContentPane(chooser);
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );
+    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
@@ -1188,6 +1153,39 @@ public class AlignFrame extends GAlignFrame
 
     }
   }
+  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
+  {
+    // TODO:resolve which menu item was actually selected
+    // Now, check we have enough sequences
+      if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+      {
+        // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+        SequenceGroup seqs = viewport.getSelectionGroup();
+        int sz;
+        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        for (int i = 0; i < sz; i++)
+        {
+          msa[i] = (SequenceI) seqs.getSequenceAt(i);
+        }
+
+        MsaWSClient ct = new jalview.ws.MsaWSClient(msa);
+      }
+      else
+      {
+        Vector seqs = viewport.getAlignment().getSequences();
+
+        if (seqs.size() > 1) {
+          SequenceI[] msa = new SequenceI[seqs.size()];
+          for (int i = 0; i < seqs.size(); i++)
+          {
+            msa[i] = (SequenceI) seqs.elementAt(i);
+          }
+
+          MsaWSClient ct = new MsaWSClient(msa);
+        }
+
+      }
+    }
 
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
     // Pick the tree file