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formatAdapter.formatSequences and maintain annotation after undo
author
amwaterhouse
<Andrew Waterhouse>
Tue, 3 May 2005 12:49:40 +0000
(12:49 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 3 May 2005 12:49:40 +0000
(12:49 +0000)
src/jalview/gui/AlignFrame.java
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diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
cabb24f
..
4fbdb72
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-94,7
+94,7
@@
public class AlignFrame extends GAlignFrame
{
\r
String choice = chooser.getSelectedFile().getPath();
\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
{
\r
String choice = chooser.getSelectedFile().getPath();
\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
- String output = FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences());
\r
+ String output = FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences());
\r
try{
\r
java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
\r
out.println(output);
\r
try{
\r
java.io.PrintWriter out = new java.io.PrintWriter( new java.io.FileWriter( choice ) );
\r
out.println(output);
\r
@@
-112,7
+112,7
@@
public class AlignFrame extends GAlignFrame
cap.formatForOutput();
\r
frame.setContentPane(cap);
\r
Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
\r
cap.formatForOutput();
\r
frame.setContentPane(cap);
\r
Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
\r
- cap.setText( FormatAdapter.get(e.getActionCommand(), viewport.getAlignment().getSequences()));
\r
+ cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
\r
}
\r
\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
}
\r
\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)
\r
@@
-232,9
+232,13
@@
public class AlignFrame extends GAlignFrame
redoList.add(0, new Object[] {history[0], seq});
\r
\r
seq = (SequenceI[]) history[1];
\r
redoList.add(0, new Object[] {history[0], seq});
\r
\r
seq = (SequenceI[]) history[1];
\r
+ AlignmentAnnotation [] old = viewport.alignment.getAlignmentAnnotation();
\r
viewport.setAlignment( new Alignment(seq) );
\r
updateEditMenuBar();
\r
viewport.setAlignment( new Alignment(seq) );
\r
updateEditMenuBar();
\r
+ for(int i=0; i<old.length; i++)
\r
+ viewport.alignment.addAnnotation(old[i]);
\r
viewport.updateConsensus();
\r
viewport.updateConsensus();
\r
+ viewport.updateConservation();
\r
alignPanel.repaint();
\r
}
\r
\r
alignPanel.repaint();
\r
}
\r
\r
@@
-617,7
+621,7
@@
public class AlignFrame extends GAlignFrame
viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
\r
{
\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());
\r
if(viewport.showSequenceFeatures && !((Alignment)viewport.alignment).featuresAdded)
\r
{
\r
- AlignmentUtil.fetchSequenceFeatures( viewport.alignment , alignPanel);
\r
+ SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.alignment, alignPanel);
\r
((Alignment)viewport.alignment).featuresAdded = true;
\r
}
\r
alignPanel.repaint();
\r
((Alignment)viewport.alignment).featuresAdded = true;
\r
}
\r
alignPanel.repaint();
\r