X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b0eca3ebc3952f24a0ff3a67c25a99fbeecd52d5;hb=fe5db5e87fc726b1560d21f97f19b0e04963b72c;hp=63b3787aea773ec8fbabcd5931495287e8e00c42;hpb=4c61bddcb9e367db694e3f2bde9c4d25f114f50b;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 63b3787..b0eca3e 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -11,20 +11,22 @@
 
 package jalview.gui;
 
-import jalview.jbgui.GAlignFrame;
-import jalview.schemes.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.io.*;
-import jalview.ws.*;
+import java.util.*;
+
 import java.awt.*;
+import java.awt.datatransfer.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
 import javax.swing.event.*;
-import java.util.*;
-import java.awt.datatransfer.*;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.ws.*;
+import java.beans.PropertyChangeEvent;
 
 public class AlignFrame extends GAlignFrame
 {
@@ -76,14 +78,14 @@ public class AlignFrame extends GAlignFrame
     if(value == JalviewFileChooser.APPROVE_OPTION)
     {
       currentFileFormat  = chooser.getSelectedFormat();
+      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat);
 
       if (currentFileFormat.equals("Jalview"))
       {
         String shortName = title.replace('/', '_');
         title = title.replace('\\', '_');
         String choice = chooser.getSelectedFile().getPath();
-        Jalview2XML.SaveState(this, System.currentTimeMillis(), shortName,
-                              choice);
+        Jalview2XML.SaveState(this, choice, shortName);
         // USE Jalview2XML to save this file
         return;
       }
@@ -103,18 +105,14 @@ public class AlignFrame extends GAlignFrame
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     JInternalFrame frame = new JInternalFrame();
-     cap.formatForOutput();
-     frame.setContentPane(cap);
-     Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
+     CutAndPasteTransfer cap = new CutAndPasteTransfer();
+     Desktop.addInternalFrame(cap, "Alignment output - "+e.getActionCommand(), 600, 500);
      cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
   }
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport);
-    htmlOutput = null;
+    new HTMLOutput(viewport);
   }
 
   protected void createPNG_actionPerformed(ActionEvent e)
@@ -169,6 +167,7 @@ public class AlignFrame extends GAlignFrame
 
   Stack historyList = new Stack();
   Stack redoList = new Stack();
+  private int treeCount = 0;
 
   void updateEditMenuBar()
    {
@@ -237,7 +236,6 @@ public class AlignFrame extends GAlignFrame
           SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
           if(restore.getLength()==0)
           {
-            System.out.println(hi.getHidden().elementAt(i));
             restore.setSequence(hi.getHidden().elementAt(i).toString());
             viewport.alignment.getSequences().insertElementAt(
                restore,
@@ -252,13 +250,13 @@ public class AlignFrame extends GAlignFrame
             viewport.alignment.deleteSequence(i);
         }
       }
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+      updateEditMenuBar();
 
-       updateEditMenuBar();
-
-       viewport.updateConsensus();
-       viewport.updateConservation();
-       alignPanel.repaint();
-   }
+      viewport.updateConsensus();
+      viewport.updateConservation();
+      alignPanel.repaint();
+  }
 
   public void moveSelectedSequences(boolean up)
   {
@@ -397,6 +395,7 @@ public class AlignFrame extends GAlignFrame
       }
       else
       {
+        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
         viewport.updateConservation();
@@ -417,26 +416,32 @@ public class AlignFrame extends GAlignFrame
 
   protected void delete_actionPerformed(ActionEvent e)
   {
-    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
+    boolean seqsdeleted=false;
 
     if (viewport.getSelectionGroup() == null)
       return;
 
+    addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE));
+
      SequenceGroup sg = viewport.getSelectionGroup();
      for (int i=0;i < sg.sequences.size(); i++)
      {
        SequenceI seq = sg.getSequenceAt(i);
        int index = viewport.getAlignment().findIndex(seq);
-       seq.deleteChars(sg.getStartRes(), sg.getEndRes()+1);
+       seq.deleteChars(sg.getStartRes(),sg.getEndRes()+1);
 
-       if(seq.getSequence().length()<1)
-          viewport.getAlignment().deleteSequence(seq);
-      else
-          viewport.getAlignment().getSequences().setElementAt(seq, index);
+       if(seq.getSequence().length()<1) {
+         seqsdeleted=true;
+         viewport.getAlignment().deleteSequence(seq);
+        } else {
+         viewport.getAlignment().getSequences().setElementAt(seq, index);
+       }
      }
 
      viewport.setSelectionGroup(null);
      viewport.alignment.deleteGroup(sg);
+     if (seqsdeleted)
+       viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
      viewport.resetSeqLimits( alignPanel.seqPanel.seqCanvas.getHeight());
      if(viewport.getAlignment().getHeight()<1)
      try
@@ -445,9 +450,8 @@ public class AlignFrame extends GAlignFrame
      }catch(Exception ex){}
    viewport.updateConservation();
    viewport.updateConsensus();
-     alignPanel.repaint();
-
-  }
+   alignPanel.repaint();
+ }
 
 
   protected void deleteGroups_actionPerformed(ActionEvent e)
@@ -545,6 +549,7 @@ public class AlignFrame extends GAlignFrame
     addHistoryItem(new HistoryItem("Remove Gapped Columns",
                                    viewport.alignment,
                                    HistoryItem.HIDE));
+
     viewport.getAlignment().removeGaps();
     viewport.updateConservation();
     viewport.updateConsensus();
@@ -576,6 +581,26 @@ public class AlignFrame extends GAlignFrame
   }
 
 
+  public void padGapsMenuitem_actionPerformed(ActionEvent e)
+    {
+      addHistoryItem(new HistoryItem("Pad Gaps",
+                                     viewport.alignment,
+                                     HistoryItem.HIDE));
+      SequenceI current;
+      int Width = viewport.getAlignment().getWidth()-1;
+      for (int i=0; i < viewport.getAlignment().getSequences().size();i++)
+      {
+        current = viewport.getAlignment().getSequenceAt(i);
+
+        if (current.getLength()<Width)
+          current.insertCharAt(Width, viewport.getGapCharacter());
+      }
+      viewport.updateConservation();
+      viewport.updateConsensus();
+      alignPanel.repaint();
+  }
+
+
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
     JInternalFrame frame = new JInternalFrame();
@@ -709,7 +734,6 @@ public class AlignFrame extends GAlignFrame
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-    abovePIDThreshold.setSelected(false);
     changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
   }
 
@@ -806,7 +830,7 @@ public class AlignFrame extends GAlignFrame
       ccs.setConsensus( viewport.vconsensus );
       viewport.setGlobalColourScheme(ccs);
 
-      SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+      ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
 
     }
     else
@@ -825,16 +849,16 @@ public class AlignFrame extends GAlignFrame
       {
         SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
 
-        if (cs instanceof ClustalxColourScheme)
-        {
+        if(cs==null)
+          sg.cs = null;
+        else if (cs instanceof ClustalxColourScheme)
           sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
-        }
-        else if(cs!=null)
-        {
+        else if (cs instanceof UserColourScheme)
+          sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
+        else
           try{
             sg.cs = (ColourSchemeI) cs.getClass().newInstance();
-          }catch(Exception ex){ex.printStackTrace();}
-        }
+          }catch(Exception ex){}
 
         if(viewport.getAbovePIDThreshold())
         {
@@ -931,7 +955,7 @@ public class AlignFrame extends GAlignFrame
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
-    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
+    new UserDefinedColours( alignPanel, null);
   }
 
   public void PIDColour_actionPerformed(ActionEvent e)
@@ -971,7 +995,7 @@ public class AlignFrame extends GAlignFrame
 
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel);
+    RedundancyPanel sp = new RedundancyPanel(alignPanel,this);
     JInternalFrame frame = new JInternalFrame();
     frame.setContentPane(sp);
     Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, 100, false);
@@ -1035,7 +1059,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
   {
-    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+    NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
   }
 
   void NewTreePanel(String type, String pwType, String title)
@@ -1043,7 +1067,9 @@ public class AlignFrame extends GAlignFrame
     //are the sequences aligned?
     if(!viewport.alignment.isAligned())
     {
-      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.",
+      JOptionPane.showMessageDialog(Desktop.desktop, "The sequences must be aligned before creating a tree.\n"
+                                   +"Try using the Pad function in the edit menu,\n"
+                                  +"or one of the multiple sequence alignment web services.",
                                     "Sequences not aligned", JOptionPane.WARNING_MESSAGE);
       return;
     }
@@ -1068,8 +1094,8 @@ public class AlignFrame extends GAlignFrame
   }
 
   public void addSortByOrderMenuItem(String title, final AlignmentOrder order) {
-    final JMenuItem item = new JMenuItem(title);
-    sortByTreeMenu.add(item);
+    final JMenuItem item = new JMenuItem("by "+title);
+    sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1086,6 +1112,12 @@ public class AlignFrame extends GAlignFrame
   void addTreeMenuItem(final TreePanel treePanel, String title)
   {
     final JMenuItem item = new JMenuItem(title);
+
+    treeCount++;
+
+    if (treeCount==1)
+      sort.add(sortByTreeMenu);
+
     sortByTreeMenu.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
@@ -1102,10 +1134,23 @@ public class AlignFrame extends GAlignFrame
     {
       public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
       {
+        treeCount--;
         sortByTreeMenu.remove(item);
+        if (treeCount==0)
+          sort.remove(sortByTreeMenu);
       };
     });
+    viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() {
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        if (evt.getPropertyName().equals("alignment")) {
+          treePanel.getTree().UpdatePlaceHolders( (Vector) evt.getNewValue());
+          treePanel.repaint();
+        }
+      }
 
+    }
+    );
   }
 
 
@@ -1147,6 +1192,8 @@ public class AlignFrame extends GAlignFrame
 
   protected void jpred_actionPerformed(ActionEvent e)
 {
+    SequenceI seq=null;
+    SequenceI[] msa=null;
 
     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
     {
@@ -1154,20 +1201,17 @@ public class AlignFrame extends GAlignFrame
       SequenceGroup seqs = viewport.getSelectionGroup();
       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
       {
-        JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
+        seq = (SequenceI)seqs.getSequenceAt(0);
       }
       else
       {
         int sz;
-        SequenceI[] msa = new SequenceI[sz=seqs.getSize()];
+        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
     {
@@ -1175,20 +1219,24 @@ public class AlignFrame extends GAlignFrame
 
       if (seqs.size() == 1 || !viewport.alignment.isAligned())
       {
-        JPredClient ct = new JPredClient( (SequenceI)
-                                         seqs.elementAt(0));
+        seq = (SequenceI) seqs.elementAt(0);
       }
       else
       {
-        SequenceI[] msa = new SequenceI[seqs.size()];
+        msa = new SequenceI[seqs.size()];
         for (int i = 0; i < seqs.size(); i++)
         {
           msa[i] = (SequenceI) seqs.elementAt(i);
         }
-
-        JPredClient ct = new JPredClient(msa);
       }
-
+    }
+    if (msa!=null) {
+      JPredClient ct = new JPredClient(title, msa);
+    } else
+    if (seq!=null) {
+      JPredClient ct = new JPredClient(title, seq);
+    } else {
+      System.err.print("JALVIEW ERROR! - Unexpected JPred selection state!\n");
     }
   }
   protected void msaAlignMenuItem_actionPerformed(ActionEvent e)
@@ -1271,5 +1319,4 @@ public class AlignFrame extends GAlignFrame
      }catch(Exception ex){ex.printStackTrace();}
   }
 
-
 }