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JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...
[jalview.git]
/
src
/
jalview
/
gui
/
RedundancyPanel.java
diff --git
a/src/jalview/gui/RedundancyPanel.java
b/src/jalview/gui/RedundancyPanel.java
index
69a7ec1
..
c4390c0
100755
(executable)
--- a/
src/jalview/gui/RedundancyPanel.java
+++ b/
src/jalview/gui/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.
*
@@
-54,7
+54,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
AlignmentPanel ap;
AlignmentPanel ap;
- Stack<CommandI> historyList = new Stack<CommandI>();
+ Stack<CommandI> historyList = new Stack<>();
// simpler than synching with alignFrame.
// simpler than synching with alignFrame.
@@
-82,6
+82,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
slider.addChangeListener(new ChangeListener()
{
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
valueField.setText(slider.getValue() + "");
public void stateChanged(ChangeEvent evt)
{
valueField.setText(slider.getValue() + "");
@@
-100,11
+101,13
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
frame = new JInternalFrame();
frame.setContentPane(this);
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, MessageManager
- .getString("label.redundancy_threshold_selection"), 400, 100,
- false);
+ Desktop.addInternalFrame(frame,
+ MessageManager
+ .getString("label.redundancy_threshold_selection"),
+ 400, 100, false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
frame.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent evt)
{
ap.getIdPanel().getIdCanvas().setHighlighted(null);
public void internalFrameClosing(InternalFrameEvent evt)
{
ap.getIdPanel().getIdCanvas().setHighlighted(null);
@@
-125,6
+128,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
+ @Override
public void run()
{
JProgressBar progress = new JProgressBar();
public void run()
{
JProgressBar progress = new JProgressBar();
@@
-171,8
+175,8
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
progress.setVisible(false);
progress = null;
progress.setVisible(false);
progress = null;
- label.setText(MessageManager
- .getString("label.enter_redundancy_thereshold"));
+ 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);
@@
-190,7
+194,7
@@
public class RedundancyPanel extends GSliderPanel 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])
@@
-207,6
+211,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
* @param e
* DOCUMENT ME!
*/
* @param e
* DOCUMENT ME!
*/
+ @Override
public void applyButton_actionPerformed(ActionEvent e)
{
Vector del = new Vector();
public void applyButton_actionPerformed(ActionEvent e)
{
Vector del = new Vector();
@@
-259,8
+264,8
@@
public class RedundancyPanel extends GSliderPanel 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());
}
}
}
}
@@
-271,6
+276,7
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
* @param e
* DOCUMENT ME!
*/
* @param e
* DOCUMENT ME!
*/
+ @Override
public void undoButton_actionPerformed(ActionEvent e)
{
if (historyList == null || historyList.isEmpty())
public void undoButton_actionPerformed(ActionEvent e)
{
if (historyList == null || historyList.isEmpty())
@@
-284,12
+290,12
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
{
command.undoCommand(af.getViewAlignments());
ap.av.getHistoryList().remove(command);
{
command.undoCommand(af.getViewAlignments());
ap.av.getHistoryList().remove(command);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
af.updateEditMenuBar();
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
if (historyList.size() == 0)
{
if (historyList.size() == 0)
{
@@
-297,22
+303,4
@@
public class RedundancyPanel extends GSliderPanel implements Runnable
}
}
}
}
- /**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
- */
- public void valueField_actionPerformed(ActionEvent e)
- {
- try
- {
- int i = Integer.parseInt(valueField.getText());
- slider.setValue(i);
- } catch (Exception ex)
- {
- valueField.setText(slider.getValue() + "");
- }
- }
-
}
}