2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.gui;
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22 import jalview.datamodel.*;
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23 import jalview.jbgui.GPairwiseAlignPanel;
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24 import jalview.analysis.*;
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25 import java.awt.event.*;
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26 import javax.swing.*;
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30 public class PairwiseAlignPanel extends GPairwiseAlignPanel
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32 Vector sequences = new Vector();
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35 public PairwiseAlignPanel(AlignViewport av)
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39 Vector selsubset = new Vector();
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40 for (int i=0, j=av.getSelectionGroup().getSize(); i<j; i++)
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41 if (av.getAlignment().getSequences().contains(av.getSelectionGroup().getSequenceAt(i)))
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42 selsubset.add(av.getSelectionGroup().getSequenceAt(i));
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43 float scores[][] = new float[selsubset.size()][selsubset.size()];
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44 double totscore = 0;
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45 int count = selsubset.size();
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48 for (int i = 1; i < count; i++)
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50 for (int j = 0; j < i; j++)
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53 AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),
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54 (SequenceI) selsubset.elementAt(j), "pep");
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55 as.calcScoreMatrix();
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56 as.traceAlignment();
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57 as.printAlignment();
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58 scores[i][j] = (float) as.getMaxScore() /
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59 (float) as.getASeq1().length;
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60 totscore = totscore + scores[i][j];
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62 textarea.append(as.getOutput());
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63 sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
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64 sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
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69 System.out.println("Pairwise alignment scaled similarity score matrix\n");
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70 for (int i = 0; i < count;i++)
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71 jalview.util.Format.print(System.out, "%s \n", (""+i)+" "+((SequenceI) selsubset.elementAt(i)).getName());
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72 System.out.println("\n");
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73 for (int i = 0; i < count;i++)
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74 for (int j = 0; j < i; j++)
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75 jalview.util.Format.print(System.out,"%7.3f",scores[i][j]/totscore);
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76 System.out.println("\n");
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82 protected void viewInEditorButton_actionPerformed(ActionEvent e)
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85 Sequence [] seq = new Sequence[sequences.size()];
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87 for (int i=0;i<sequences.size();i++)
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88 seq[i] = (Sequence) sequences.elementAt(i);
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91 AlignFrame af = new AlignFrame(new Alignment(seq));
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92 Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
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93 AlignFrame.NEW_WINDOW_WIDTH,
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94 AlignFrame.NEW_WINDOW_HEIGHT);
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