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PairwiseAlignPanel | 43 | 126 | 50 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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. | |
11 | * | |
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. | |
16 | * | |
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. | |
20 | */ | |
21 | package jalview.gui; | |
22 | ||
23 | import jalview.analysis.AlignSeq; | |
24 | import jalview.analysis.scoremodels.ScoreMatrix; | |
25 | import jalview.datamodel.Alignment; | |
26 | import jalview.datamodel.AlignmentView; | |
27 | import jalview.datamodel.SequenceGroup; | |
28 | import jalview.datamodel.SequenceI; | |
29 | import jalview.jbgui.GPairwiseAlignPanel; | |
30 | import jalview.util.MessageManager; | |
31 | import jalview.viewmodel.AlignmentViewport; | |
32 | import jalview.math.MiscMath; | |
33 | ||
34 | import java.awt.event.ActionEvent; | |
35 | import java.util.Vector; | |
36 | ||
37 | /** | |
38 | * DOCUMENT ME! | |
39 | * | |
40 | * @author $author$ | |
41 | * @version $Revision$ | |
42 | */ | |
43 | public class PairwiseAlignPanel extends GPairwiseAlignPanel | |
44 | { | |
45 | ||
46 | private static final String DASHES = "---------------------\n"; | |
47 | ||
48 | private float[][] scores; | |
49 | ||
50 | private float[][] alignmentScores; // scores used by PaSiMap | |
51 | ||
52 | private int GAP_OPEN_COST; | |
53 | ||
54 | private int GAP_EXTEND_COST; | |
55 | ||
56 | AlignmentViewport av; | |
57 | ||
58 | Vector<SequenceI> sequences; | |
59 | ||
60 | private String alignmentOutput; | |
61 | ||
62 | private boolean quiet; | |
63 | ||
64 | private boolean discardAlignments; | |
65 | ||
66 | private boolean endGaps; | |
67 | ||
68 | // for listening | |
69 | public static final String TOTAL = "total"; | |
70 | ||
71 | public static final String PROGRESS = "progress"; | |
72 | ||
73 | protected static final String ETA = "eta_in_minutes"; | |
74 | ||
75 | public static final String PROGRESSCOMPLETE = "finished_stop_progress"; | |
76 | public static final String PROGRESSMESSAGE = "message_in_progress"; | |
77 | ||
78 | private volatile boolean cancelled; | |
79 | ||
80 | private long total; | |
81 | ||
82 | private long progress; | |
83 | ||
84 | private SequenceGroup selection; | |
85 | ||
86 | /** | |
87 | * input sequences | |
88 | */ | |
89 | private SequenceI[] seqs = null; | |
90 | ||
91 | private ScoreMatrix scoreMatrix; | |
92 | ||
93 | /** | |
94 | * remaining time | |
95 | */ | |
96 | private double etime=Double.NaN; | |
97 | ||
98 | /** | |
99 | * Creates a new PairwiseAlignPanel object. | |
100 | * | |
101 | * @param viewport | |
102 | * contains selected sequences to align | |
103 | * @param endGaps | |
104 | * ~ toggle gaps and the beginning and end of sequences | |
105 | */ | |
106 | 2 | public PairwiseAlignPanel(AlignmentViewport viewport) |
107 | { | |
108 | 2 | this(viewport, null, false, 120, 20, true, null); // default penalties used |
109 | // in AlignSeq | |
110 | } | |
111 | ||
112 | 0 | public PairwiseAlignPanel(AlignmentViewport viewport, ScoreMatrix params) |
113 | { | |
114 | 0 | this(viewport, null, false, 120, 20, true, params); // default penalties |
115 | // used in AlignSeq | |
116 | } | |
117 | ||
118 | 0 | public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, |
119 | int gapOpenCost, int gapExtendCost) | |
120 | { | |
121 | 0 | this(viewport, null, endGaps, gapOpenCost, gapExtendCost, true, null); |
122 | } | |
123 | ||
124 | /** | |
125 | * Create a new pairwise alignpanel with specified parameters and score model, | |
126 | * and optionally start the calculation | |
127 | * | |
128 | * @param viewport | |
129 | * @param selection | |
130 | * @param endGaps | |
131 | * @param gapOpenCost | |
132 | * @param gapExtendCost | |
133 | * @param run | |
134 | * @param scoreMatrix | |
135 | */ | |
136 | 2 | public PairwiseAlignPanel(AlignmentViewport viewport, |
137 | SequenceGroup selection, boolean endGaps, int gapOpenCost, | |
138 | int gapExtendCost, boolean run, ScoreMatrix scoreMatrix) | |
139 | { | |
140 | 2 | super(); |
141 | 2 | this.av = viewport; |
142 | 2 | this.GAP_OPEN_COST = gapOpenCost; |
143 | 2 | this.GAP_EXTEND_COST = gapExtendCost; |
144 | 2 | this.endGaps = endGaps; |
145 | 2 | this.selection = selection; |
146 | 2 | this.total = av.getAlignment().getHeight(); |
147 | 2 | total = (total*total-total)/2; |
148 | 2 | this.scoreMatrix = scoreMatrix; |
149 | 2 | if (run) |
150 | { | |
151 | 2 | calculate(); |
152 | } | |
153 | } | |
154 | ||
155 | 2 | public void calculate() |
156 | { | |
157 | 2 | calculate(scoreMatrix); |
158 | } | |
159 | ||
160 | 2 | public void calculate(ScoreMatrix sm) |
161 | { | |
162 | 2 | cancelled=false; |
163 | 2 | StringBuilder sb = new StringBuilder(1024); |
164 | ||
165 | 2 | sequences = new Vector<SequenceI>(); |
166 | 2 | String[] seqStrings; |
167 | 2 | seqs = null; |
168 | ||
169 | 2 | if (selection != null) |
170 | { | |
171 | // given a set of sequences to compare | |
172 | 0 | seqs = selection.getSelectionAsNewSequences(av.getAlignment()); |
173 | 0 | seqStrings = new String[seqs.length]; |
174 | 0 | int s = 0; |
175 | 0 | for (SequenceI seq : seqs) |
176 | { | |
177 | 0 | seqStrings[s++] = seq.getSequenceAsString(); |
178 | } | |
179 | } | |
180 | else | |
181 | { | |
182 | 2 | SequenceGroup selectionGroup = av.getSelectionGroup(); |
183 | 2 | boolean isSelection = selectionGroup != null |
184 | && selectionGroup.getSize() > 0; | |
185 | 2 | AlignmentView view = av.getAlignmentView(isSelection); |
186 | 2 | seqStrings = view.getSequenceStrings(av.getGapCharacter()); |
187 | 2 | if (isSelection) |
188 | { | |
189 | 1 | seqs = (SequenceI[]) view |
190 | .getAlignmentAndHiddenColumns(av.getGapCharacter())[0]; | |
191 | } | |
192 | else | |
193 | { | |
194 | 1 | seqs = av.getAlignment().getSequencesArray(); |
195 | } | |
196 | } | |
197 | ||
198 | 2 | String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA |
199 | : AlignSeq.PEP; | |
200 | ||
201 | 2 | float[][] scores = new float[seqs.length][seqs.length]; |
202 | 2 | float[][] alignmentScores = new float[seqs.length][seqs.length]; |
203 | 2 | double totscore = 0D; |
204 | 2 | int count = seqs.length; |
205 | 2 | int fracprogress=0; |
206 | 2 | boolean first = true; |
207 | 2 | long time=System.currentTimeMillis(); |
208 | 2 | long fprogress = 0; |
209 | 2 | firePropertyChange(TOTAL, 0, 500); |
210 | ||
211 | 4 | for (int i = 1; i < count; i++) |
212 | { | |
213 | // fill diagonal alignmentScores with Float.NaN | |
214 | 2 | alignmentScores[i - 1][i - 1] = Float.NaN; |
215 | 4 | for (int j = 0; j < i; j++) |
216 | { | |
217 | 2 | if (cancelled) |
218 | { | |
219 | 0 | alignmentOutput = "Alignment was cancelled."; |
220 | 0 | return; |
221 | } | |
222 | 2 | AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j], |
223 | seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST); | |
224 | ||
225 | 2 | if (sm != null) |
226 | { | |
227 | 0 | as.setScoreMatrix(sm); |
228 | } | |
229 | ||
230 | 2 | if (as.s1str.length() == 0 || as.s2str.length() == 0) |
231 | { | |
232 | 0 | continue; |
233 | } | |
234 | ||
235 | 2 | as.calcScoreMatrix(); |
236 | 2 | if (endGaps) |
237 | { | |
238 | 0 | as.traceAlignmentWithEndGaps(); |
239 | } | |
240 | else | |
241 | { | |
242 | 2 | as.traceAlignment(); |
243 | } | |
244 | 2 | as.scoreAlignment(); |
245 | ||
246 | 2 | if (!first && !quiet) |
247 | { | |
248 | 0 | jalview.bin.Console.outPrintln(DASHES); |
249 | 0 | textarea.append(DASHES); |
250 | 0 | sb.append(DASHES); |
251 | } | |
252 | 2 | first = false; |
253 | 2 | if (!discardAlignments) |
254 | { | |
255 | 2 | as.printAlignment(System.out); |
256 | } | |
257 | 2 | scores[i][j] = as.getMaxScore() / as.getASeq1().length; |
258 | 2 | alignmentScores[i][j] = as.getAlignmentScore(); |
259 | 2 | totscore = totscore + scores[i][j]; |
260 | 2 | if (!quiet) |
261 | { | |
262 | 2 | textarea.append(as.getOutput()); |
263 | 2 | sb.append(as.getOutput()); |
264 | } | |
265 | 2 | if (!discardAlignments) |
266 | { | |
267 | 2 | sequences.add(as.getAlignedSeq1()); |
268 | 2 | sequences.add(as.getAlignedSeq2()); |
269 | } | |
270 | 2 | ++fprogress; |
271 | } | |
272 | 2 | if (i<count) |
273 | { | |
274 | 2 | int newfracprogress=(int) Math.floor((500.0*(double)fprogress)/((double)total)); |
275 | // need to fake a different starting value until we have an ETA calculated | |
276 | 2 | firePropertyChange(PROGRESS, fracprogress, newfracprogress); |
277 | 2 | fracprogress = newfracprogress; |
278 | 2 | progress=fprogress; |
279 | // remaining time in minutes ~ is remaining*(elapsed time)/progress; | |
280 | 2 | double lasteta=etime; |
281 | 2 | double rate = ((double)(System.currentTimeMillis()-time))/(double)progress; |
282 | 2 | etime = rate*(total-progress)/60000; |
283 | 2 | firePropertyChange(ETA, lasteta,etime); |
284 | } | |
285 | } | |
286 | 2 | alignmentScores[count - 1][count - 1] = Float.NaN; |
287 | // done - mark progress as indeterminate again | |
288 | 2 | firePropertyChange(TOTAL, -1, -2); |
289 | ||
290 | ||
291 | 2 | this.scores = scores; |
292 | 2 | this.alignmentScores = alignmentScores; |
293 | ||
294 | 2 | if (count > 2 && !quiet) |
295 | { | |
296 | 0 | printScoreMatrix(seqs, scores, totscore); |
297 | } | |
298 | ||
299 | 2 | alignmentOutput = sb.toString(); |
300 | } | |
301 | ||
302 | 0 | public boolean hasEta() |
303 | { | |
304 | 0 | return etime>0; |
305 | } | |
306 | 0 | public double getEta() |
307 | { | |
308 | 0 | return etime; |
309 | } | |
310 | /** | |
311 | * stops the run() loop ASAP | |
312 | */ | |
313 | 0 | public void cancel() |
314 | { | |
315 | 0 | cancelled=true; |
316 | } | |
317 | ||
318 | 0 | public float[][] getScores() |
319 | { | |
320 | 0 | return this.scores; |
321 | } | |
322 | ||
323 | 0 | public float[][] getAlignmentScores() |
324 | { | |
325 | 0 | return this.alignmentScores; |
326 | } | |
327 | ||
328 | 0 | public String getAlignmentOutput() |
329 | { | |
330 | 0 | return this.alignmentOutput; |
331 | } | |
332 | ||
333 | /** | |
334 | * Prints a matrix of seqi-seqj pairwise alignment scores to sysout | |
335 | * | |
336 | * @param seqs | |
337 | * @param scores | |
338 | * @param totscore | |
339 | */ | |
340 | 0 | protected void printScoreMatrix(SequenceI[] seqs, float[][] scores, |
341 | double totscore) | |
342 | { | |
343 | 0 | System.out |
344 | .println("Pairwise alignment scaled similarity score matrix "+getPairwiseSimscoresAsString()+"\n"); | |
345 | ||
346 | 0 | for (int i = 0; i < seqs.length; i++) |
347 | { | |
348 | 0 | jalview.bin.Console.outPrintln( |
349 | String.format("%3d %s", i + 1, seqs[i].getDisplayId(true))); | |
350 | } | |
351 | ||
352 | /* | |
353 | * table heading columns for sequences 1, 2, 3... | |
354 | */ | |
355 | 0 | System.out.print("\n "); |
356 | 0 | for (int i = 0; i < seqs.length; i++) |
357 | { | |
358 | 0 | System.out.print(String.format("%7d", i + 1)); |
359 | } | |
360 | 0 | jalview.bin.Console.outPrintln(); |
361 | ||
362 | 0 | for (int i = 0; i < seqs.length; i++) |
363 | { | |
364 | 0 | System.out.print(String.format("%3d", i + 1)); |
365 | 0 | for (int j = 0; j < i; j++) |
366 | { | |
367 | /* | |
368 | * as a fraction of tot score, outputs are 0 <= score <= 1 | |
369 | */ | |
370 | 0 | System.out.print(String.format("%7.3f", scores[i][j] / totscore)); |
371 | } | |
372 | 0 | jalview.bin.Console.outPrintln(); |
373 | } | |
374 | ||
375 | 0 | jalview.bin.Console.outPrintln("\n"); |
376 | } | |
377 | ||
378 | 0 | public String getPairwiseSimscoresAsString() |
379 | { | |
380 | 0 | return (scoreMatrix != null |
381 | ? " (" + scoreMatrix.getName() + ", open=" + GAP_OPEN_COST | |
382 | + ", extend=" + GAP_EXTEND_COST | |
383 | 0 | + (endGaps ? ", with endGaps" : ", no endGaps") + ")" |
384 | : ""); | |
385 | } | |
386 | ||
387 | /** | |
388 | * DOCUMENT ME! | |
389 | * | |
390 | * @param e | |
391 | * DOCUMENT ME! | |
392 | */ | |
393 | 0 | @Override |
394 | protected void viewInEditorButton_actionPerformed(ActionEvent e) | |
395 | { | |
396 | 0 | SequenceI[] seq = new SequenceI[sequences.size()]; |
397 | ||
398 | 0 | for (int i = 0; i < sequences.size(); i++) |
399 | { | |
400 | 0 | seq[i] = sequences.elementAt(i); |
401 | } | |
402 | ||
403 | 0 | AlignFrame af = new AlignFrame(new Alignment(seq), |
404 | AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); | |
405 | ||
406 | 0 | Desktop.addInternalFrame(af, |
407 | MessageManager.getString("label.pairwise_aligned_sequences")+" "+getPairwiseSimscoresAsString(), | |
408 | AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); | |
409 | } | |
410 | ||
411 | 0 | public long getTotal() |
412 | { | |
413 | 0 | return total; |
414 | } | |
415 | ||
416 | 0 | public long getProgress() |
417 | { | |
418 | 0 | return progress; |
419 | } | |
420 | ||
421 | 0 | public SequenceI[] getInputSequences() |
422 | { | |
423 | 0 | return seqs; |
424 | } | |
425 | ||
426 | /** | |
427 | * Set to true to suppress output of progress to Console.stdout or GUI | |
428 | * | |
429 | * @param quiet | |
430 | */ | |
431 | 0 | public void setQuiet(boolean quiet) |
432 | { | |
433 | 0 | this.quiet = quiet; |
434 | } | |
435 | ||
436 | /** | |
437 | * @return true if no textual alignment report was generated | |
438 | */ | |
439 | 0 | public boolean isQuiet() |
440 | { | |
441 | 0 | return quiet; |
442 | } | |
443 | ||
444 | /** | |
445 | * set this if you are only interested in final alignment scores | |
446 | * | |
447 | * @param discard | |
448 | */ | |
449 | 0 | public void setDiscardAlignments(boolean discard) |
450 | { | |
451 | 0 | discardAlignments = discard; |
452 | } | |
453 | ||
454 | /** | |
455 | * @return true if no alignments were saved | |
456 | * @return | |
457 | */ | |
458 | 0 | public boolean isDiscardAlignments() |
459 | { | |
460 | 0 | return discardAlignments; |
461 | } | |
462 | ||
463 | /** | |
464 | * | |
465 | * @return true if the calculation was cancelled before completion | |
466 | */ | |
467 | 0 | public boolean isCancelled() |
468 | { | |
469 | 0 | return cancelled; |
470 | } | |
471 | ||
472 | /** | |
473 | * sends status updates to the progress bar for this panel | |
474 | * @param type - PROGRESSMESSAGE or PROGRESSCOMPLETE | |
475 | * @param message - the message (may be internationalised key) | |
476 | */ | |
477 | 0 | public void updateProgress(String type, String message) |
478 | { | |
479 | 0 | firePropertyChange(type, "", MessageManager.getStringOrReturn("progress", message)); |
480 | } | |
481 | } |