git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
When saving, use print instead of println
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
fc59062
..
bdcea36
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-97,11
+97,9
@@
public class AlignFrame
/* Set up intrinsic listeners for dynamically generated GUI bits. */
\r
private void addServiceListeners()
\r
{
\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */
\r
private void addServiceListeners()
\r
{
\r
-
\r
- final AlignFrame thisFrame = this;
\r
final java.beans.PropertyChangeListener thisListener;
\r
// Do this once to get current state
\r
final java.beans.PropertyChangeListener thisListener;
\r
// Do this once to get current state
\r
- thisFrame.BuildWebServiceMenu();
\r
+ BuildWebServiceMenu();
\r
Desktop.discoverer.addPropertyChangeListener(
\r
thisListener = new java.beans.PropertyChangeListener()
\r
{
\r
Desktop.discoverer.addPropertyChangeListener(
\r
thisListener = new java.beans.PropertyChangeListener()
\r
{
\r
@@
-111,7
+109,7
@@
public class AlignFrame
if (evt.getPropertyName().equals("services"))
\r
{
\r
// System.out.println("Rebuilding web service menu");
\r
if (evt.getPropertyName().equals("services"))
\r
{
\r
// System.out.println("Rebuilding web service menu");
\r
- thisFrame.BuildWebServiceMenu();
\r
+ BuildWebServiceMenu();
\r
}
\r
}
\r
});
\r
}
\r
}
\r
});
\r
@@
-123,6
+121,7
@@
public class AlignFrame
{
\r
// System.out.println("deregistering discoverer listener");
\r
Desktop.discoverer.removePropertyChangeListener(thisListener);
\r
{
\r
// System.out.println("deregistering discoverer listener");
\r
Desktop.discoverer.removePropertyChangeListener(thisListener);
\r
+ closeMenuItem_actionPerformed(null);
\r
}
\r
;
\r
});
\r
}
\r
;
\r
});
\r
@@
-264,7
+263,8
@@
public class AlignFrame
{
\r
java.io.PrintWriter out = new java.io.PrintWriter(
\r
new java.io.FileWriter(file));
\r
{
\r
java.io.PrintWriter out = new java.io.PrintWriter(
\r
new java.io.FileWriter(file));
\r
- out.println(output);
\r
+
\r
+ out.print(output);
\r
out.close();
\r
return true;
\r
}
\r
out.close();
\r
return true;
\r
}
\r
@@
-348,6
+348,7
@@
public class AlignFrame
{
\r
try
\r
{
\r
{
\r
try
\r
{
\r
+ PaintRefresher.components.remove(viewport.alignment);
\r
this.setClosed(true);
\r
}
\r
catch (Exception ex)
\r
this.setClosed(true);
\r
}
\r
catch (Exception ex)
\r
@@
-1448,7
+1449,9
@@
public class AlignFrame
}
\r
}
\r
\r
}
\r
}
\r
\r
- if (viewport.getAbovePIDThreshold())
\r
+ if (viewport.getAbovePIDThreshold()
\r
+ || cs instanceof PIDColourScheme
\r
+ || cs instanceof Blosum62ColourScheme)
\r
{
\r
sg.cs.setThreshold(threshold,
\r
viewport.getIgnoreGapsConsensus());
\r
{
\r
sg.cs.setThreshold(threshold,
\r
viewport.getIgnoreGapsConsensus());
\r
@@
-2109,6
+2112,11
@@
public class AlignFrame
}
\r
}
\r
\r
}
\r
}
\r
\r
+
\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
+ {
\r
+ return ShowNewickTree(nf,title,600,500,4,5);
\r
+ }
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
@@
-2117,7
+2125,7
@@
public class AlignFrame
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public TreePanel ShowNewickTree(NewickFile nf, String title)
\r
+ public TreePanel ShowNewickTree(NewickFile nf, String title, int w,int h,int x, int y)
\r
{
\r
TreePanel tp = null;
\r
\r
{
\r
TreePanel tp = null;
\r
\r
@@
-2131,7
+2139,14
@@
public class AlignFrame
viewport.getAlignment().getSequences(), nf,
\r
"FromFile",
\r
title);
\r
viewport.getAlignment().getSequences(), nf,
\r
"FromFile",
\r
title);
\r
- Desktop.addInternalFrame(tp, title, 600, 500);
\r
+
\r
+ tp.setSize(w,h);
\r
+
\r
+ if(x>0 && y>0)
\r
+ tp.setLocation(x,y);
\r
+
\r
+
\r
+ Desktop.addInternalFrame(tp, title, w, h);
\r
addTreeMenuItem(tp, title);
\r
}
\r
}
\r
addTreeMenuItem(tp, title);
\r
}
\r
}
\r