/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
import java.util.*;
-
+import java.util.List;
import java.awt.*;
import java.awt.event.*;
+import jalview.analysis.AlignSeq;
import jalview.commands.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
-public class RedundancyPanel
- extends SliderPanel implements Runnable, WindowListener
+public class RedundancyPanel extends SliderPanel implements Runnable,
+ WindowListener
{
- AlignmentPanel ap;
-
Stack historyList = new Stack(); // simpler than synching with alignFrame.
+
float[] redundancy;
+
SequenceI[] originalSequences;
+
Frame frame;
+
Vector redundantSeqs;
public RedundancyPanel(AlignmentPanel ap)
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);
}
/**
- * This is a copy of remove redundancy in jalivew.datamodel.Alignment
- * except we dont want to remove redundancy, just calculate once
- * so we can use the slider to dynamically hide redundant sequences
- *
- * @param threshold DOCUMENT ME!
- * @param sel DOCUMENT ME!
- *
+ * This is a copy of remove redundancy in jalivew.datamodel.Alignment except
+ * we dont want to remove redundancy, just calculate once so we can use the
+ * slider to dynamically hide redundant sequences
+ *
+ * @param threshold
+ * DOCUMENT ME!
+ * @param sel
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public void run()
{
- label.setText("Calculating....");
+ label.setText(MessageManager.getString("label.calculating"));
slider.setVisible(false);
applyButton.setEnabled(false);
int start, end;
- if ( (sg != null) && (sg.getSize() >= 1))
+ 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);
- PaintRefresher.Refresh(this,
- ap.av.getSequenceSetId(),
- true,
- true);
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
}
}
}
- // This has to be done before the restoreHistoryItem method of alignFrame will
+ // This has to be done before the restoreHistoryItem method of alignFrame
+ // will
// actually restore these sequences.
if (del.size() > 0)
{
}
EditCommand cut = new EditCommand("Remove Redundancy",
- EditCommand.CUT, deleted, 0, width,
- ap.av.alignment);
-
+ EditCommand.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);
- 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());
}
}
{
int i = Integer.parseInt(valueField.getText());
slider.setValue(i);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
valueField.setText(slider.getValue() + "");
}
}
public void windowOpened(WindowEvent evt)
- {}
+ {
+ }
public void windowClosing(WindowEvent evt)
{
}
public void windowClosed(WindowEvent evt)
- {}
+ {
+ }
public void windowActivated(WindowEvent evt)
- {}
+ {
+ }
public void windowDeactivated(WindowEvent evt)
- {}
+ {
+ }
public void windowIconified(WindowEvent evt)
- {}
+ {
+ }
public void windowDeiconified(WindowEvent evt)
- {}
+ {
+ }
}
git://source.jalview.org / jalview.git / blobdiff