2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignSeq;
24 import jalview.datamodel.Alignment;
25 import jalview.datamodel.AlignmentView;
26 import jalview.datamodel.SequenceGroup;
27 import jalview.datamodel.SequenceI;
28 import jalview.jbgui.GPairwiseAlignPanel;
29 import jalview.util.MessageManager;
30 import jalview.viewmodel.AlignmentViewport;
32 import java.awt.event.ActionEvent;
33 import java.util.Vector;
41 public class PairwiseAlignPanel extends GPairwiseAlignPanel
44 private static final String DASHES = "---------------------\n";
46 private float[][] scores;
48 private float[][] alignmentScores; // scores used by PaSiMap
50 private int GAP_OPEN_COST;
52 private int GAP_EXTEND_COST;
56 Vector<SequenceI> sequences;
58 private String alignmentOutput;
60 private boolean suppressTextbox;
62 private boolean discardAlignments;
65 * Creates a new PairwiseAlignPanel object.
69 * @param endGaps ~ toggle gaps and the beginning and end of sequences
71 public PairwiseAlignPanel(AlignmentViewport viewport)
73 this(viewport, false, 120, 20); // default penalties used in AlignSeq
75 public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost)
80 StringBuilder sb = new StringBuilder(1024);
82 sequences = new Vector<SequenceI>();
84 SequenceGroup selectionGroup = viewport.getSelectionGroup();
85 boolean isSelection = selectionGroup != null
86 && selectionGroup.getSize() > 0;
87 AlignmentView view = viewport.getAlignmentView(isSelection);
88 // String[] seqStrings = viewport.getViewAsString(true);
89 String[] seqStrings = view
90 .getSequenceStrings(viewport.getGapCharacter());
95 seqs = (SequenceI[]) view
96 .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
100 seqs = av.getAlignment().getSequencesArray();
103 String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA
106 float[][] scores = new float[seqs.length][seqs.length];
107 float[][] alignmentScores = new float[seqs.length][seqs.length];
108 double totscore = 0D;
109 int count = seqs.length;
110 suppressTextbox = count<10;
111 discardAlignments = count<15;
112 boolean first = true;
114 for (int i = 1; i < count; i++)
116 // fill diagonal alignmentScores with Float.NaN
117 alignmentScores[i - 1][i - 1] = Float.NaN;
118 for (int j = 0; j < i; j++)
120 AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
121 seqStrings[j], type, gapOpenCost, gapExtendCost);
123 if (as.s1str.length() == 0 || as.s2str.length() == 0)
128 as.calcScoreMatrix();
131 as.traceAlignmentWithEndGaps();
141 System.out.println(DASHES);
142 textarea.append(DASHES);
146 if (discardAlignments) {
147 as.printAlignment(System.out);
149 scores[i][j] = as.getMaxScore() / as.getASeq1().length;
150 alignmentScores[i][j] = as.getAlignmentScore();
151 totscore = totscore + scores[i][j];
154 textarea.append(as.getOutput());
155 sb.append(as.getOutput());
157 if (discardAlignments)
159 sequences.add(as.getAlignedSeq1());
160 sequences.add(as.getAlignedSeq2());
164 alignmentScores[count - 1][count - 1] = Float.NaN;
166 this.scores = scores;
167 this.alignmentScores = alignmentScores;
171 printScoreMatrix(seqs, scores, totscore);
174 alignmentOutput = sb.toString();
177 public float[][] getScores()
182 public float[][] getAlignmentScores()
184 return this.alignmentScores;
187 public String getAlignmentOutput()
189 return this.alignmentOutput;
193 * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
199 protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,
203 .println("Pairwise alignment scaled similarity score matrix\n");
205 for (int i = 0; i < seqs.length; i++)
208 String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
212 * table heading columns for sequences 1, 2, 3...
214 System.out.print("\n ");
215 for (int i = 0; i < seqs.length; i++)
217 System.out.print(String.format("%7d", i + 1));
219 System.out.println();
221 for (int i = 0; i < seqs.length; i++)
223 System.out.print(String.format("%3d", i + 1));
224 for (int j = 0; j < i; j++)
227 * as a fraction of tot score, outputs are 0 <= score <= 1
229 System.out.print(String.format("%7.3f", scores[i][j] / totscore));
231 System.out.println();
234 System.out.println("\n");
244 protected void viewInEditorButton_actionPerformed(ActionEvent e)
246 SequenceI[] seq = new SequenceI[sequences.size()];
248 for (int i = 0; i < sequences.size(); i++)
250 seq[i] = sequences.elementAt(i);
253 AlignFrame af = new AlignFrame(new Alignment(seq),
254 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
256 Desktop.addInternalFrame(af,
257 MessageManager.getString("label.pairwise_aligned_sequences"),
258 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);