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.*;
public class AlignFrame extends GAlignFrame
Stack historyList = new Stack();
Stack redoList = new Stack();
+ private int treeCount = 0;
void updateEditMenuBar()
{
{
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);
}
+ 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();
}
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)
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()
{
{
public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
{
+ treeCount--;
sortByTreeMenu.remove(item);
+ if (treeCount==0)
+ sort.remove(sortByTreeMenu);
};
});
msa[i] = (SequenceI) seqs.getSequenceAt(i);
}
- JPredClient ct = new JPredClient(msa);
+ JPredClient ct = new JPredClient(title, msa);
}
}
msa[i] = (SequenceI) seqs.elementAt(i);
}
- JPredClient ct = new JPredClient(msa);
+ JPredClient ct = new JPredClient(title, msa);
}
}
}catch(Exception ex){ex.printStackTrace();}
}
-
}