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combobox for overlapping features
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
0756e2d
..
7db8f01
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-957,9
+957,12
@@
public class AlignFrame
for (int i = 0; i < alignPanels.size(); i++)
{
AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
for (int i = 0; i < alignPanels.size(); i++)
{
AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager()
+ .removeStructureViewerListener(ap.seqPanel, null);
PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
PaintRefresher.RemoveComponent(ap);
PaintRefresher.RemoveComponent(ap.seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(ap.idPanel.idCanvas);
PaintRefresher.RemoveComponent(ap);
+ ap.av.alignment = null;
}
}
else
}
}
else
@@
-970,6
+973,7
@@
public class AlignFrame
PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
PaintRefresher.RemoveComponent(alignPanel);
PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
PaintRefresher.RemoveComponent(alignPanel);
+ viewport.alignment = null;
alignPanel = null;
viewport = null;
alignPanel = null;
viewport = null;
@@
-1203,14
+1207,6
@@
public class AlignFrame
synchronized void slideSequences(boolean right, int size)
{
synchronized void slideSequences(boolean right, int size)
{
- if(viewport.hasHiddenColumns)
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Slide Sequences not available with hidden columns",
- "Slide Sequence not Available",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
Vector sg = new Vector();
if(viewport.cursorMode)
{
Vector sg = new Vector();
if(viewport.cursorMode)
{
@@
-1297,7
+1293,7
@@
public class AlignFrame
repaint();
}
repaint();
}
-
+
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-1970,6
+1966,8
@@
public class AlignFrame
AlignmentPanel newap =
new Jalview2XML().copyAlignPanel(alignPanel, true);
AlignmentPanel newap =
new Jalview2XML().copyAlignPanel(alignPanel, true);
+ newap.av.gatherViewsHere = false;
+
if (viewport.viewName == null)
{
viewport.viewName = "Original";
if (viewport.viewName == null)
{
viewport.viewName = "Original";
@@
-3309,19
+3307,19
@@
public void showTranslation_actionPerformed(ActionEvent e)
{
///////////////////////////////
// Collect Data to be translated/transferred
{
///////////////////////////////
// Collect Data to be translated/transferred
-
+
SequenceI [] selection = viewport.getSelectionAsNewSequence();
String [] seqstring = viewport.getViewAsString(true);
AlignmentI al = null;
try {
SequenceI [] selection = viewport.getSelectionAsNewSequence();
String [] seqstring = viewport.getViewAsString(true);
AlignmentI al = null;
try {
- al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
- viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
+ al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring, viewport.getViewAsVisibleContigs(true),
+ viewport.getGapCharacter(), viewport.alignment.getAlignmentAnnotation(),
viewport.alignment.getWidth());
} catch (Exception ex) {
al = null;
jalview.bin.Cache.log.debug("Exception during translation.",ex);
}
viewport.alignment.getWidth());
} catch (Exception ex) {
al = null;
jalview.bin.Cache.log.debug("Exception during translation.",ex);
}
- if (al==null)
+ if (al==null)
{
JOptionPane.showMessageDialog(Desktop.desktop,
"Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
{
JOptionPane.showMessageDialog(Desktop.desktop,
"Please select at least three bases in at least one sequence in order to perform a cDNA translation.",