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group.getSize should be ab.alignment.getGroups
[jalview.git]
/
src
/
jalview
/
appletgui
/
RedundancyPanel.java
diff --git
a/src/jalview/appletgui/RedundancyPanel.java
b/src/jalview/appletgui/RedundancyPanel.java
index
7608cb9
..
efabb9b
100755
(executable)
--- a/
src/jalview/appletgui/RedundancyPanel.java
+++ b/
src/jalview/appletgui/RedundancyPanel.java
@@
-35,13
+35,14
@@
public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
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
Frame frame;
\r
Frame frame;
\r
+ Vector redundantSeqs;
\r
\r
public RedundancyPanel(AlignmentPanel ap)
\r
{
\r
super(ap, 0, false, null);
\r
\r
\r
public RedundancyPanel(AlignmentPanel ap)
\r
{
\r
super(ap, 0, false, null);
\r
\r
+ redundantSeqs = new Vector();
\r
this.ap = ap;
\r
undoButton.setVisible(true);
\r
applyButton.setVisible(true);
\r
this.ap = ap;
\r
undoButton.setVisible(true);
\r
applyButton.setVisible(true);
\r
@@
-51,7
+52,7
@@
public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
valueField.setText("100");
\r
\r
slider.setVisibleAmount(1);
\r
valueField.setText("100");
\r
\r
slider.setVisibleAmount(1);
\r
- slider.setMinimum(40);
\r
+ slider.setMinimum(0);
\r
slider.setMaximum(100+slider.getVisibleAmount());
\r
slider.setValue(100);
\r
\r
slider.setMaximum(100+slider.getVisibleAmount());
\r
slider.setValue(100);
\r
\r
@@
-99,7
+100,6
@@
public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
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
@@
-135,9
+135,6
@@
public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
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
if(i==j)
\r
for (int j = 0; j < i; j++)
\r
{
\r
if(i==j)
\r
@@
-184,11
+181,13
@@
public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
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
+ redundantSeqs.removeElement(originalSequences[i]);
\r
+ else if(!redundantSeqs.contains(originalSequences[i]))
\r
+ redundantSeqs.addElement(originalSequences[i]);
\r
}
\r
\r
}
\r
\r
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
\r
+
\r
PaintRefresher.Refresh(null,ap.av.alignment);
\r
\r
}
\r
PaintRefresher.Refresh(null,ap.av.alignment);
\r
\r
}
\r
@@
-273,13
+272,7
@@
public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
\r
public void windowClosing(WindowEvent evt)
\r
{
\r
\r
public void windowClosing(WindowEvent evt)
\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
+ ap.idPanel.idCanvas.setHighlighted(null);
\r
}
\r
\r
public void windowClosed(WindowEvent evt)
\r
}
\r
\r
public void windowClosed(WindowEvent evt)
\r