/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
+import jalview.analysis.AlignSeq;
+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
{
- AlignmentPanel ap;
-
Stack historyList = new Stack(); // simpler than synching with alignFrame.
float[] redundancy;
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);
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);
*/
public void run()
{
- label.setText("Calculating....");
+ label.setText(MessageManager.getString("label.calculating"));
slider.setVisible(false);
applyButton.setEnabled(false);
if ((sg != null) && (sg.getSize() >= 1))
{
- originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+ originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
start = sg.getStartRes();
end = sg.getEndRes();
}
else
{
- originalSequences = ap.av.alignment.getSequencesArray();
+ originalSequences = ap.av.getAlignment().getSequencesArray();
start = 0;
- end = ap.av.alignment.getWidth();
+ end = ap.av.getAlignment().getWidth();
}
height = originalSequences.length;
- redundancy = new float[height];
- for (int i = 0; i < height; i++)
- {
- redundancy[i] = 0f;
- }
-
- // if (ap.av.hasHiddenColumns)
- {
- // omitHidden = ap.av.getSelectionAsString();
- }
-
- // long start = System.currentTimeMillis();
-
- float pid;
- String seqi, seqj;
- for (int i = 0; i < height; i++)
- {
- for (int j = 0; j < i; j++)
- {
- if (i == j)
- {
- continue;
- }
-
- if (omitHidden == null)
- {
- seqi = originalSequences[i].getSequenceAsString(start, end);
- seqj = originalSequences[j].getSequenceAsString(start, end);
- }
- else
- {
- seqi = omitHidden[i];
- seqj = omitHidden[j];
- }
-
- pid = jalview.util.Comparison.PID(seqi, seqj);
-
- if (seqj.length() < seqi.length())
- {
- redundancy[j] = Math.max(pid, redundancy[j]);
- }
- else
- {
- redundancy[i] = Math.max(pid, redundancy[i]);
- }
-
- }
- }
-
- 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));
}
float value = slider.getValue();
+ List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
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);
}
}
}
- EditCommand cut = new EditCommand("Remove Redundancy",
- EditCommand.CUT, deleted, 0, width, ap.av.alignment);
-
+ 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++)
{
- ap.av.alignment.deleteSequence(deleted[i]);
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+ alignment.deleteSequence(deleted[i]);
if (sg != null)
{
sg.deleteSequence(deleted[i], false);
ap.alignFrame.addHistoryItem(cut);
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
.getSequences());
}
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);
git://source.jalview.org / jalview.git / blobdiff