X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=bd36b0d4b6dfb5b76c107ad228f8fa6cdfa20354;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=b42075881b3acfcfc4e244a82e72de580f7e328d;hpb=e851b6e27ddf19394510347c1af298f1c377f101;p=jalview.git
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
old mode 100755
new mode 100644
index b420758..bd36b0d
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -1,33 +1,47 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
-
-public class RedundancyPanel extends SliderPanel implements Runnable,
- WindowListener
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+public class RedundancyPanel extends SliderPanel
+ implements Runnable, WindowListener
{
Stack historyList = new Stack(); // simpler than synching with alignFrame.
@@ -49,7 +63,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
applyButton.setVisible(true);
allGroupsCheck.setVisible(false);
- label.setText("Enter the redundancy threshold");
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
valueField.setText("100");
slider.setVisibleAmount(1);
@@ -59,17 +74,18 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
slider.addAdjustmentListener(new AdjustmentListener()
{
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- valueField.setText(slider.getValue() + "");
+ valueField.setText(String.valueOf(slider.getValue()));
sliderValueChanged();
}
});
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame,
- "Redundancy threshold selection", 400, 100);
+ jalview.bin.JalviewLite.addFrame(frame, MessageManager
+ .getString("label.redundancy_threshold_selection"), 400, 100);
frame.addWindowListener(this);
@@ -89,9 +105,10 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
*
* @return DOCUMENT ME!
*/
+ @Override
public void run()
{
- label.setText("Calculating....");
+ label.setText(MessageManager.getString("label.calculating"));
slider.setVisible(false);
applyButton.setEnabled(false);
@@ -121,13 +138,16 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
height = originalSequences.length;
- redundancy = AlignSeq.computeRedundancyMatrix(originalSequences, omitHidden, start, end, false);
- label.setText("Enter the redundancy threshold");
+ redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+ omitHidden, start, end, false);
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println("blob done "+ (System.currentTimeMillis()-start));
}
@@ -140,23 +160,21 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
float value = slider.getValue();
+ List redundantSequences = new ArrayList<>();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.removeElement(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.addElement(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
}
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
}
+ @Override
public void applyButton_actionPerformed()
{
Vector del = new Vector();
@@ -191,13 +209,13 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
}
}
- EditCommand cut = new EditCommand("Remove Redundancy",
- EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
- AlignmentI alignment=ap.av.getAlignment();
+ EditCommand cut = new EditCommand(
+ MessageManager.getString("action.remove_redundancy"),
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());
+ AlignmentI alignment = ap.av.getAlignment();
for (int i = 0; i < del.size(); i++)
{
alignment.deleteSequence(deleted[i]);
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
if (sg != null)
{
sg.deleteSequence(deleted[i], false);
@@ -208,24 +226,28 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
ap.alignFrame.addHistoryItem(cut);
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
- .getSequences());
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
}
+ @Override
public void undoButton_actionPerformed()
{
CommandI command = (CommandI) historyList.pop();
command.undoCommand(null);
- if (ap.av.historyList.contains(command))
+ if (ap.av.getHistoryList().contains(command))
{
- ap.av.historyList.removeElement(command);
+ ap.av.getHistoryList().remove(command);
ap.alignFrame.updateEditMenuBar();
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
if (historyList.size() == 0)
{
@@ -245,31 +267,38 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
}
}
+ @Override
public void windowOpened(WindowEvent evt)
{
}
+ @Override
public void windowClosing(WindowEvent evt)
{
ap.idPanel.idCanvas.setHighlighted(null);
}
+ @Override
public void windowClosed(WindowEvent evt)
{
}
+ @Override
public void windowActivated(WindowEvent evt)
{
}
+ @Override
public void windowDeactivated(WindowEvent evt)
{
}
+ @Override
public void windowIconified(WindowEvent evt)
{
}
+ @Override
public void windowDeiconified(WindowEvent evt)
{
}