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;
31 import jalview.math.MiscMath;
33 import java.beans.PropertyChangeListener;
34 import java.awt.event.ActionEvent;
35 import java.util.Vector;
36 import javax.swing.event.SwingPropertyChangeSupport;
44 public class PairwiseAlignPanel extends GPairwiseAlignPanel
47 private static final String DASHES = "---------------------\n";
49 private float[][] scores;
51 private float[][] alignmentScores; // scores used by PaSiMap
53 private int GAP_OPEN_COST;
55 private int GAP_EXTEND_COST;
59 Vector<SequenceI> sequences;
61 private String alignmentOutput;
63 private boolean suppressTextbox;
65 private boolean discardAlignments;
67 private boolean endGaps;
70 public static final String TOTAL = "total";
72 public static final String PROGRESS = "progress";
79 * Creates a new PairwiseAlignPanel object.
83 * @param endGaps ~ toggle gaps and the beginning and end of sequences
85 public PairwiseAlignPanel(AlignmentViewport viewport)
87 this(viewport, false, 120, 20, true); // default penalties used in AlignSeq
89 public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost)
91 this(viewport, endGaps, gapOpenCost, gapExtendCost, true);
93 public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost, boolean run)
97 this.GAP_OPEN_COST = gapOpenCost;
98 this.GAP_EXTEND_COST = gapExtendCost;
99 this.endGaps = endGaps;
100 this.total = MiscMath.combinations(av.getAlignment().getHeight(), 2);
104 System.out.println("Creating pap");
107 public void calculate()
110 SequenceGroup selectionGroup = av.getSelectionGroup();
111 StringBuilder sb = new StringBuilder(1024);
113 sequences = new Vector<SequenceI>();
115 boolean isSelection = selectionGroup != null
116 && selectionGroup.getSize() > 0;
117 AlignmentView view = av.getAlignmentView(isSelection);
118 // String[] seqStrings = av.getViewAsString(true);
119 String[] seqStrings = view
120 .getSequenceStrings(av.getGapCharacter());
125 seqs = (SequenceI[]) view
126 .getAlignmentAndHiddenColumns(av.getGapCharacter())[0];
130 seqs = av.getAlignment().getSequencesArray();
133 String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
136 float[][] scores = new float[seqs.length][seqs.length];
137 float[][] alignmentScores = new float[seqs.length][seqs.length];
138 double totscore = 0D;
139 int count = seqs.length;
140 boolean first = true;
143 firePropertyChange(TOTAL, 0, total);
145 suppressTextbox = count<10;
146 discardAlignments = count<15;
148 for (int i = 1; i < count; i++)
150 // fill diagonal alignmentScores with Float.NaN
151 alignmentScores[i - 1][i - 1] = Float.NaN;
152 for (int j = 0; j < i; j++)
154 AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
155 seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST);
157 if (as.s1str.length() == 0 || as.s2str.length() == 0)
162 as.calcScoreMatrix();
165 as.traceAlignmentWithEndGaps();
173 System.out.println(DASHES);
174 textarea.append(DASHES);
178 if (discardAlignments) {
179 as.printAlignment(System.out);
181 scores[i][j] = as.getMaxScore() / as.getASeq1().length;
182 alignmentScores[i][j] = as.getAlignmentScore();
183 totscore = totscore + scores[i][j];
187 textarea.append(as.getOutput());
188 sb.append(as.getOutput());
190 if (discardAlignments)
192 sequences.add(as.getAlignedSeq1());
193 sequences.add(as.getAlignedSeq2());
196 firePropertyChange(PROGRESS, progress, ++progress);
199 alignmentScores[count - 1][count - 1] = Float.NaN;
201 this.scores = scores;
202 this.alignmentScores = alignmentScores;
206 printScoreMatrix(seqs, scores, totscore);
209 alignmentOutput = sb.toString();
212 public float[][] getScores()
217 public float[][] getAlignmentScores()
219 return this.alignmentScores;
222 public String getAlignmentOutput()
224 return this.alignmentOutput;
228 * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
234 protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,
238 .println("Pairwise alignment scaled similarity score matrix\n");
240 for (int i = 0; i < seqs.length; i++)
243 String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
247 * table heading columns for sequences 1, 2, 3...
249 System.out.print("\n ");
250 for (int i = 0; i < seqs.length; i++)
252 System.out.print(String.format("%7d", i + 1));
254 System.out.println();
256 for (int i = 0; i < seqs.length; i++)
258 System.out.print(String.format("%3d", i + 1));
259 for (int j = 0; j < i; j++)
262 * as a fraction of tot score, outputs are 0 <= score <= 1
264 System.out.print(String.format("%7.3f", scores[i][j] / totscore));
266 System.out.println();
269 System.out.println("\n");
279 protected void viewInEditorButton_actionPerformed(ActionEvent e)
281 SequenceI[] seq = new SequenceI[sequences.size()];
283 for (int i = 0; i < sequences.size(); i++)
285 seq[i] = sequences.elementAt(i);
288 AlignFrame af = new AlignFrame(new Alignment(seq),
289 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
291 Desktop.addInternalFrame(af,
292 MessageManager.getString("label.pairwise_aligned_sequences"),
293 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
296 public long getTotal()
301 public long getProgress()