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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
8e014fa
..
bd36b0d
100644
(file)
--- a/
src/jalview/appletgui/RedundancyPanel.java
+++ b/
src/jalview/appletgui/RedundancyPanel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-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);
@@
-74,9
+74,10
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
slider.addAdjustmentListener(new AdjustmentListener()
{
slider.addAdjustmentListener(new AdjustmentListener()
{
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- valueField.setText(slider.getValue() + "");
+ valueField.setText(String.valueOf(slider.getValue()));
sliderValueChanged();
}
});
sliderValueChanged();
}
});
@@
-104,6
+105,7
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public void run()
{
label.setText(MessageManager.getString("label.calculating"));
public void run()
{
label.setText(MessageManager.getString("label.calculating"));
@@
-138,8
+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);
@@
-158,7
+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])
@@
-172,6
+174,7
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
}
}
+ @Override
public void applyButton_actionPerformed()
{
Vector del = new Vector();
public void applyButton_actionPerformed()
{
Vector del = new Vector();
@@
-224,12
+227,13
@@
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());
}
}
}
}
+ @Override
public void undoButton_actionPerformed()
{
CommandI command = (CommandI) historyList.pop();
public void undoButton_actionPerformed()
{
CommandI command = (CommandI) historyList.pop();
@@
-239,11
+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)
{
@@
-263,31
+267,38
@@
public class RedundancyPanel extends SliderPanel implements Runnable,
}
}
}
}
+ @Override
public void windowOpened(WindowEvent evt)
{
}
public void windowOpened(WindowEvent evt)
{
}
+ @Override
public void windowClosing(WindowEvent evt)
{
ap.idPanel.idCanvas.setHighlighted(null);
}
public void windowClosing(WindowEvent evt)
{
ap.idPanel.idCanvas.setHighlighted(null);
}
+ @Override
public void windowClosed(WindowEvent evt)
{
}
public void windowClosed(WindowEvent evt)
{
}
+ @Override
public void windowActivated(WindowEvent evt)
{
}
public void windowActivated(WindowEvent evt)
{
}
+ @Override
public void windowDeactivated(WindowEvent evt)
{
}
public void windowDeactivated(WindowEvent evt)
{
}
+ @Override
public void windowIconified(WindowEvent evt)
{
}
public void windowIconified(WindowEvent evt)
{
}
+ @Override
public void windowDeiconified(WindowEvent evt)
{
}
public void windowDeiconified(WindowEvent evt)
{
}