/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* This file is part of Jalview.
*
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
{
- AlignmentPanel ap;
-
Stack historyList = new Stack(); // simpler than synching with alignFrame.
float[] redundancy;
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]);
- }
-
- }
- }
-
+ redundancy = AlignSeq.computeRedundancyMatrix(originalSequences, omitHidden, start, end, false);
label.setText("Enter the redundancy threshold");
slider.setVisible(true);
applyButton.setEnabled(true);
}
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]);
+ alignment.deleteSequence(deleted[i]);
PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
if (sg != null)
{