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;
61 * Creates a new PairwiseAlignPanel object.
65 * @param endGaps ~ toggle gaps and the beginning and end of sequences
67 public PairwiseAlignPanel(AlignmentViewport viewport)
69 this(viewport, false, 120, 20); // default penalties used in AlignSeq
71 public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost)
76 StringBuilder sb = new StringBuilder(1024);
78 sequences = new Vector<SequenceI>();
80 SequenceGroup selectionGroup = viewport.getSelectionGroup();
81 boolean isSelection = selectionGroup != null
82 && selectionGroup.getSize() > 0;
83 AlignmentView view = viewport.getAlignmentView(isSelection);
84 // String[] seqStrings = viewport.getViewAsString(true);
85 String[] seqStrings = view
86 .getSequenceStrings(viewport.getGapCharacter());
91 seqs = (SequenceI[]) view
92 .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
96 seqs = av.getAlignment().getSequencesArray();
99 String type = (viewport.getAlignment().isNucleotide()) ? AlignSeq.DNA
102 float[][] scores = new float[seqs.length][seqs.length];
103 float[][] alignmentScores = new float[seqs.length][seqs.length];
104 double totscore = 0D;
105 int count = seqs.length;
106 boolean first = true;
108 for (int i = 1; i < count; i++)
110 // fill diagonal alignmentScores with Float.NaN
111 alignmentScores[i-1][i-1] = Float.NaN;
112 for (int j = 0; j < i; j++)
114 AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
115 seqStrings[j], type, gapOpenCost, gapExtendCost);
117 if (as.s1str.length() == 0 || as.s2str.length() == 0)
122 as.calcScoreMatrix();
125 as.traceAlignmentWithEndGaps();
133 System.out.println(DASHES);
134 textarea.append(DASHES);
138 as.printAlignment(System.out);
139 scores[i][j] = as.getMaxScore() / as.getASeq1().length;
140 alignmentScores[i][j] = as.getAlignmentScore();
141 totscore = totscore + scores[i][j];
143 textarea.append(as.getOutput());
144 sb.append(as.getOutput());
145 sequences.add(as.getAlignedSeq1());
146 sequences.add(as.getAlignedSeq2());
149 alignmentScores[count-1][count-1] = Float.NaN;
151 this.scores = scores;
152 this.alignmentScores = alignmentScores;
156 printScoreMatrix(seqs, scores, totscore);
159 alignmentOutput = sb.toString();
162 public float[][] getScores()
167 public float[][] getAlignmentScores()
169 return this.alignmentScores;
172 public String getAlignmentOutput()
174 return this.alignmentOutput;
178 * Prints a matrix of seqi-seqj pairwise alignment scores to sysout
184 protected void printScoreMatrix(SequenceI[] seqs, float[][] scores,
188 .println("Pairwise alignment scaled similarity score matrix\n");
190 for (int i = 0; i < seqs.length; i++)
193 String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
197 * table heading columns for sequences 1, 2, 3...
199 System.out.print("\n ");
200 for (int i = 0; i < seqs.length; i++)
202 System.out.print(String.format("%7d", i + 1));
204 System.out.println();
206 for (int i = 0; i < seqs.length; i++)
208 System.out.print(String.format("%3d", i + 1));
209 for (int j = 0; j < i; j++)
212 * as a fraction of tot score, outputs are 0 <= score <= 1
214 System.out.print(String.format("%7.3f", scores[i][j] / totscore));
216 System.out.println();
219 System.out.println("\n");
229 protected void viewInEditorButton_actionPerformed(ActionEvent e)
231 SequenceI[] seq = new SequenceI[sequences.size()];
233 for (int i = 0; i < sequences.size(); i++)
235 seq[i] = sequences.elementAt(i);
238 AlignFrame af = new AlignFrame(new Alignment(seq),
239 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
241 Desktop.addInternalFrame(af,
242 MessageManager.getString("label.pairwise_aligned_sequences"),
243 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);