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Padgap history
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
b2c8901
..
ccf7303
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-263,7
+263,7
@@
public class AlignFrame
java.io.File.separatorChar) + 1);
\r
}
\r
\r
java.io.File.separatorChar) + 1);
\r
}
\r
\r
- Jalview2XML.SaveAlignment(this, file, shortName);
\r
+ new Jalview2XML().SaveAlignment(this, file, shortName);
\r
\r
// USE Jalview2XML to save this file
\r
return true;
\r
\r
// USE Jalview2XML to save this file
\r
return true;
\r
@@
-912,6
+912,11
@@
public class AlignFrame
*/
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
{
\r
*/
\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
\r
{
\r
+ if(viewport.cursorMode)
\r
+ {
\r
+ alignPanel.seqPanel.keyboardNo1 = null;
\r
+ alignPanel.seqPanel.keyboardNo2 = null;
\r
+ }
\r
viewport.setSelectionGroup(null);
\r
viewport.getColumnSelection().clear();
\r
viewport.setSelectionGroup(null);
\r
viewport.setSelectionGroup(null);
\r
viewport.getColumnSelection().clear();
\r
viewport.setSelectionGroup(null);
\r
@@
-1134,7
+1139,10
@@
public class AlignFrame
\r
public void alignmentChanged()
\r
{
\r
\r
public void alignmentChanged()
\r
{
\r
- if(viewport.vconsensus!=null)
\r
+ if(viewport.padGaps)
\r
+ viewport.getAlignment().padGaps();
\r
+
\r
+ if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
\r
{
\r
viewport.updateConsensus();
\r
viewport.updateConservation();
\r
{
\r
viewport.updateConsensus();
\r
viewport.updateConservation();
\r
@@
-1196,8
+1204,11
@@
public class AlignFrame
{
\r
addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
HistoryItem.HIDE));
\r
{
\r
addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
\r
HistoryItem.HIDE));
\r
- if (viewport.getAlignment().padGaps())
\r
- alignmentChanged();
\r
+
\r
+ viewport.padGaps = padGapsMenuitem.isSelected();
\r
+
\r
+ // if (viewport.padGaps)
\r
+ alignmentChanged();
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-1928,6
+1939,13
@@
public class AlignFrame
new PCAPanel(viewport);
\r
}
\r
\r
new PCAPanel(viewport);
\r
}
\r
\r
+
\r
+ public void autoCalculate_actionPerformed(ActionEvent e)
\r
+ {
\r
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();
\r
+ }
\r
+
\r
+
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
@@
-1977,7
+1995,7
@@
public class AlignFrame
*/
\r
void NewTreePanel(String type, String pwType, String title)
\r
{
\r
*/
\r
void NewTreePanel(String type, String pwType, String title)
\r
{
\r
- final TreePanel tp;
\r
+ TreePanel tp;
\r
\r
if ( (viewport.getSelectionGroup() != null) &&
\r
(viewport.getSelectionGroup().getSize() > 3))
\r
\r
if ( (viewport.getSelectionGroup() != null) &&
\r
(viewport.getSelectionGroup().getSize() > 3))
\r
@@
-2029,7
+2047,6
@@
public class AlignFrame
}
\r
\r
addTreeMenuItem(tp, title);
\r
}
\r
\r
addTreeMenuItem(tp, title);
\r
- viewport.setCurrentTree(tp.getTree());
\r
\r
Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
}
\r
\r
Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
\r
}
\r
@@
-2725,10
+2742,10
@@
public void drop(DropTargetDropEvent evt)
}
\r
\r
// This method will attempt to load a "dropped" file first by testing
\r
}
\r
\r
// This method will attempt to load a "dropped" file first by testing
\r
- // whether its and Annotation file, then group file. If both are
\r
+ // whether its and Annotation file, then features file. If both are
\r
// false then the user may have dropped an alignment file onto this
\r
// AlignFrame
\r
// false then the user may have dropped an alignment file onto this
\r
// AlignFrame
\r
- void loadJalviewDataFile(String file)
\r
+ public void loadJalviewDataFile(String file)
\r
{
\r
try{
\r
boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.
\r
{
\r
try{
\r
boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.
\r