X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=8bf2fba4e6b267de7b5c54de7d57855ba3f7451b;hb=bd894ca9f2aae448653d7431ab8a170e1105e85c;hp=f0a4f91a503e3b1a3082f94e6ca2f7714b49ae9d;hpb=e851b6e27ddf19394510347c1af298f1c377f101;p=jalview.git
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index f0a4f91..8bf2fba 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -1,33 +1,46 @@
/*
- * 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.gui;
-import java.util.*;
-
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
import jalview.analysis.AlignSeq;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.util.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GSliderPanel;
+import jalview.util.MessageManager;
+
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JProgressBar;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
/**
* DOCUMENT ME!
@@ -41,7 +54,9 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
AlignmentPanel ap;
- Stack historyList = new Stack(); // simpler than synching with alignFrame.
+ Stack historyList = new Stack();
+
+ // simpler than synching with alignFrame.
float[] redundancy;
@@ -67,6 +82,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
valueField.setText(slider.getValue() + "");
@@ -74,7 +90,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
}
});
- applyButton.setText("Remove");
+ applyButton.setText(MessageManager.getString("action.remove"));
allGroupsCheck.setVisible(false);
slider.setMinimum(0);
slider.setMaximum(100);
@@ -85,13 +101,16 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
- 100, false);
+ Desktop.addInternalFrame(frame,
+ MessageManager
+ .getString("label.redundancy_threshold_selection"),
+ 400, 100, false);
frame.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent evt)
{
- ap.idPanel.idCanvas.setHighlighted(null);
+ ap.getIdPanel().getIdCanvas().setHighlighted(null);
}
});
@@ -109,13 +128,14 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
*
* @return DOCUMENT ME!
*/
+ @Override
public void run()
{
JProgressBar progress = new JProgressBar();
progress.setIndeterminate(true);
southPanel.add(progress, java.awt.BorderLayout.SOUTH);
- label.setText("Calculating....");
+ label.setText(MessageManager.getString("label.calculating"));
slider.setVisible(false);
applyButton.setEnabled(false);
@@ -148,18 +168,21 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
{
omitHidden = ap.av.getViewAsString(sg != null);
}
- redundancy = AlignSeq.computeRedundancyMatrix(originalSequences, omitHidden, start, end, false);
+ redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+ omitHidden, start, end, false);
progress.setIndeterminate(false);
progress.setVisible(false);
progress = null;
- label.setText("Enter the redundancy threshold");
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
slider.setVisible(true);
applyButton.setEnabled(true);
valueField.setVisible(true);
validate();
+ sliderValueChanged();
// System.out.println((System.currentTimeMillis()-start));
}
@@ -171,21 +194,15 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
}
float value = slider.getValue();
-
+ List redundantSequences = new ArrayList();
for (int i = 0; i < redundancy.length; i++)
{
- if (value > redundancy[i])
- {
- redundantSeqs.remove(originalSequences[i]);
- }
- else if (!redundantSeqs.contains(originalSequences[i]))
+ if (value <= redundancy[i])
{
- redundantSeqs.add(originalSequences[i]);
+ redundantSequences.add(originalSequences[i]);
}
-
}
-
- ap.idPanel.idCanvas.setHighlighted(redundantSeqs);
+ ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
}
/**
@@ -194,6 +211,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
* @param e
* DOCUMENT ME!
*/
+ @Override
public void applyButton_actionPerformed(ActionEvent e)
{
Vector del = new Vector();
@@ -228,13 +246,13 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
}
}
- EditCommand cut = new EditCommand("Remove Redundancy",
- EditCommand.CUT, deleted, 0, width, ap.av.getAlignment());
+ EditCommand cut = new EditCommand(
+ MessageManager.getString("action.remove_redundancy"),
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());
for (int i = 0; i < del.size(); i++)
{
ap.av.getAlignment().deleteSequence(deleted[i]);
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
if (sg != null)
{
sg.deleteSequence(deleted[i], false);
@@ -245,8 +263,9 @@ public class RedundancyPanel extends GSliderPanel 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());
}
}
@@ -257,14 +276,22 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
* @param e
* DOCUMENT ME!
*/
+ @Override
public void undoButton_actionPerformed(ActionEvent e)
{
- CommandI command = (CommandI) historyList.pop();
- command.undoCommand(af.getViewAlignments());
+ if (historyList == null || historyList.isEmpty())
+ {
+ undoButton.setEnabled(false);
+ return;
+ }
- if (ap.av.historyList.contains(command))
+ CommandI command = historyList.pop();
+ if (ap.av.getHistoryList().contains(command))
{
- ap.av.historyList.remove(command);
+ command.undoCommand(af.getViewAlignments());
+ ap.av.getHistoryList().remove(command);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
af.updateEditMenuBar();
}
@@ -276,22 +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() + "");
- }
- }
-
}