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
JAL-629 example files from nf-core
[jalview.git]
/
src
/
jalview
/
appletgui
/
RedundancyPanel.java
diff --git
a/src/jalview/appletgui/RedundancyPanel.java
b/src/jalview/appletgui/RedundancyPanel.java
index
6be416c
..
bd36b0d
100644
(file)
--- a/
src/jalview/appletgui/RedundancyPanel.java
+++ b/
src/jalview/appletgui/RedundancyPanel.java
@@
-40,8
+40,8
@@
import java.util.List;
import java.util.Stack;
import java.util.Vector;
import java.util.Stack;
import java.util.Vector;
-public class RedundancyPanel extends SliderPanel implements Runnable,
- WindowListener
+public class RedundancyPanel extends SliderPanel
+ implements Runnable, WindowListener
{
Stack historyList = new Stack(); // simpler than synching with alignFrame.
{
Stack historyList = new Stack(); // simpler than synching with alignFrame.
@@
-63,8
+63,8
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
applyButton.setVisible(true);
allGroupsCheck.setVisible(false);
applyButton.setVisible(true);
allGroupsCheck.setVisible(false);
- label.setText(MessageManager
- .getString("label.enter_redundancy_threshold"));
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
valueField.setText("100");
slider.setVisibleAmount(1);
valueField.setText("100");
slider.setVisibleAmount(1);
@@
-140,8
+140,8
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
omitHidden, start, end, false);
redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
omitHidden, start, end, false);
- label.setText(MessageManager
- .getString("label.enter_redundancy_threshold"));
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
@@
-160,7
+160,7
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
float value = slider.getValue();
float value = slider.getValue();
- List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
+ List<SequenceI> redundantSequences = new ArrayList<>();
for (int i = 0; i < redundancy.length; i++)
{
if (value <= redundancy[i])
for (int i = 0; i < redundancy.length; i++)
{
if (value <= redundancy[i])
@@
-227,8
+227,8
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
ap.alignFrame.addHistoryItem(cut);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
}
}
@@
-243,11
+243,11
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
{
ap.av.getHistoryList().remove(command);
ap.alignFrame.updateEditMenuBar();
{
ap.av.getHistoryList().remove(command);
ap.alignFrame.updateEditMenuBar();
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
if (historyList.size() == 0)
{
if (historyList.size() == 0)
{