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
Do a loop for multiple seq matches
[jalview.git]
/
src
/
jalview
/
gui
/
RedundancyPanel.java
diff --git
a/src/jalview/gui/RedundancyPanel.java
b/src/jalview/gui/RedundancyPanel.java
index
b248294
..
5423dc9
100755
(executable)
--- a/
src/jalview/gui/RedundancyPanel.java
+++ b/
src/jalview/gui/RedundancyPanel.java
@@
-44,8
+44,8
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
Stack historyList = new Stack(); // simpler than synching with alignFrame.
\r
float [] redundancy;
\r
SequenceI [] originalSequences;
\r
Stack historyList = new Stack(); // simpler than synching with alignFrame.
\r
float [] redundancy;
\r
SequenceI [] originalSequences;
\r
- Hashtable originalColours;
\r
JInternalFrame frame;
\r
JInternalFrame frame;
\r
+ Vector redundantSeqs;
\r
\r
/**
\r
* Creates a new RedundancyPanel object.
\r
\r
/**
\r
* Creates a new RedundancyPanel object.
\r
@@
-53,10
+53,11
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
* @param ap DOCUMENT ME!
\r
* @param af DOCUMENT ME!
\r
*/
\r
* @param ap DOCUMENT ME!
\r
* @param af DOCUMENT ME!
\r
*/
\r
- public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
\r
+ public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
\r
{
\r
this.ap = ap;
\r
this.af = af;
\r
{
\r
this.ap = ap;
\r
this.af = af;
\r
+ redundantSeqs = new Vector();
\r
\r
slider.addChangeListener(new ChangeListener()
\r
{
\r
\r
slider.addChangeListener(new ChangeListener()
\r
{
\r
@@
-69,7
+70,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
\r
applyButton.setText("Remove");
\r
allGroupsCheck.setVisible(false);
\r
\r
applyButton.setText("Remove");
\r
allGroupsCheck.setVisible(false);
\r
- slider.setMinimum(60);
\r
+ slider.setMinimum(0);
\r
slider.setMaximum(100);
\r
slider.setValue(100);
\r
\r
slider.setMaximum(100);
\r
slider.setValue(100);
\r
\r
@@
-84,7
+85,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
{
\r
public void internalFrameClosing(InternalFrameEvent evt)
\r
{
\r
{
\r
public void internalFrameClosing(InternalFrameEvent evt)
\r
{
\r
- resetColours();
\r
+ ap.idPanel.idCanvas.setHighlighted(null);
\r
}
\r
}
\r
);
\r
}
\r
}
\r
);
\r
@@
-121,7
+122,6
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
SequenceGroup sg = ap.av.getSelectionGroup();
\r
int height;
\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();
\r
int height;
\r
\r
- originalColours = new Hashtable();
\r
int start, end;
\r
\r
if ( (sg != null) && (sg.getSize(false) >= 1))
\r
int start, end;
\r
\r
if ( (sg != null) && (sg.getSize(false) >= 1))
\r
@@
-147,7
+147,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
\r
if (ap.av.hasHiddenColumns)
\r
{
\r
\r
if (ap.av.hasHiddenColumns)
\r
{
\r
- omitHidden = ap.av.getSelectionAsString();
\r
+ omitHidden = ap.av.getViewAsString(sg!=null);
\r
}
\r
\r
\r
}
\r
\r
\r
@@
-157,8
+157,6
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
String seqi, seqj;
\r
for (int i = 0; i < height; i++)
\r
{
\r
String seqi, seqj;
\r
for (int i = 0; i < height; i++)
\r
{
\r
- originalColours.put(originalSequences[i],
\r
- originalSequences[i].getColor());
\r
\r
for (int j = 0; j < i; j++)
\r
{
\r
\r
for (int j = 0; j < i; j++)
\r
{
\r
@@
-209,13
+207,13
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
for(int i=0; i<redundancy.length; i++)
\r
{
\r
if (value > redundancy[i])
\r
for(int i=0; i<redundancy.length; i++)
\r
{
\r
if (value > redundancy[i])
\r
- originalSequences[i].setColor(java.awt.Color.white);
\r
- else
\r
- originalSequences[i].setColor(java.awt.Color.red);
\r
- }
\r
+ redundantSeqs.remove(originalSequences[i]);
\r
+ else if(!redundantSeqs.contains(originalSequences[i]))
\r
+ redundantSeqs.add(originalSequences[i]);
\r
\r
\r
- PaintRefresher.Refresh(null,ap.av.alignment);
\r
+ }
\r
\r
\r
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-272,16
+270,6
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
af.updateEditMenuBar();
\r
}
\r
\r
af.updateEditMenuBar();
\r
}
\r
\r
- void resetColours()
\r
- {
\r
- for(int i=0; i<originalSequences.length; i++)
\r
- {
\r
- SequenceI seq = originalSequences[i];
\r
- seq.setColor( (java.awt.Color)originalColours.get(seq));
\r
- }
\r
-
\r
- PaintRefresher.Refresh(ap.av.alignment);
\r
- }
\r
\r
/**
\r
* DOCUMENT ME!
\r
\r
/**
\r
* DOCUMENT ME!
\r