jalviewX
File AlignmentView.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| AlignmentView | 35 | 413 | 172 | 442 | ||
| AlignmentView.ScGroup | 69 | 11 | 6 | 11 |
Contributing tests
This file is covered by 12 tests.
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| 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.datamodel; | |
| 22 | ||
| 23 | import jalview.util.MessageManager; | |
| 24 | import jalview.util.ShiftList; | |
| 25 | ||
| 26 | import java.io.PrintStream; | |
| 27 | import java.util.ArrayList; | |
| 28 | import java.util.List; | |
| 29 | ||
| 30 | /** | |
| 31 | * Transient object compactly representing a 'view' of an alignment - with | |
| 32 | * discontinuities marked. Extended in Jalview 2.7 to optionally record sequence | |
| 33 | * groups and specific selected regions on the alignment. | |
| 34 | */ | |
| 35 | public class AlignmentView | |
| 36 | { | |
| 37 | private SeqCigar[] sequences = null; | |
| 38 | ||
| 39 | private int[] contigs = null; | |
| 40 | ||
| 41 | private int width = 0; | |
| 42 | ||
| 43 | private int firstCol = 0; | |
| 44 | ||
| 45 | /** | |
| 46 | * one or more ScGroup objects, which are referenced by each seqCigar's group | |
| 47 | * membership | |
| 48 | */ | |
| 49 | private List<ScGroup> scGroups = null; | |
| 50 | ||
| 51 | private boolean isNa = false; | |
| 52 | ||
| 53 | /** | |
| 54 | * false if the view concerns peptides | |
| 55 | * | |
| 56 | * @return | |
| 57 | */ | |
| 58 | 0 |  public boolean isNa() |
| 59 | { | |
| 60 | 0 | return isNa; |
| 61 | } | |
| 62 | ||
| 63 | /** | |
| 64 | * Group defined over SeqCigars. Unlike AlignmentI associated groups, each | |
| 65 | * SequenceGroup hold just the essential properties for the group, but no | |
| 66 | * references to the sequences involved. SeqCigars hold references to the | |
| 67 | * seuqenceGroup entities themselves. | |
| 68 | */ | |
| 69 | private class ScGroup | |
| 70 | { | |
| 71 | public List<SeqCigar> seqs; | |
| 72 | ||
| 73 | public SequenceGroup sg; | |
| 74 | ||
| 75 | 11 | ScGroup() |
| 76 | { | |
| 77 | 11 | seqs = new ArrayList<SeqCigar>(); |
| 78 | } | |
| 79 | ||
| 80 | /** | |
| 81 | * @param seq | |
| 82 | * @return true if seq was not a member before and was added to group | |
| 83 | */ | |
| 84 | 33 | public boolean add(SeqCigar seq) |
| 85 | { | |
| 86 | 33 | if (!seq.isMemberOf(this)) |
| 87 | { | |
| 88 | 33 | seqs.add(seq); |
| 89 | 33 | seq.setGroupMembership(this); |
| 90 | 33 | return true; |
| 91 | } | |
| 92 | else | |
| 93 | { | |
| 94 | 0 | return false; |
| 95 | } | |
| 96 | } | |
| 97 | ||
| 98 | /** | |
| 99 | * | |
| 100 | * @param seq | |
| 101 | * @return true if seq was a member and was removed from group | |
| 102 | */ | |
| 103 | 0 | public boolean remove(SeqCigar seq) |
| 104 | { | |
| 105 | 0 | if (seq.removeGroupMembership(this)) |
| 106 | { | |
| 107 | 0 | seqs.remove(seq); |
| 108 | 0 | return true; |
| 109 | } | |
| 110 | 0 | return false; |
| 111 | } | |
| 112 | ||
| 113 | 0 | public int size() |
| 114 | { | |
| 115 | 0 | return seqs.size(); |
| 116 | } | |
| 117 | } | |
| 118 | ||
| 119 | /** | |
| 120 | * vector of selected seqCigars. This vector is also referenced by each | |
| 121 | * seqCigar contained in it. | |
| 122 | */ | |
| 123 | private ScGroup selected; | |
| 124 | ||
| 125 | /** | |
| 126 | * Construct an alignmentView from a live jalview alignment view. Note - | |
| 127 | * hidden rows will be excluded from alignmentView Note: JAL-1179 | |
| 128 | * | |
| 129 | * @param alignment | |
| 130 | * - alignment as referenced by an AlignViewport | |
| 131 | * @param columnSelection | |
| 132 | * - | |
| 133 | * @param selection | |
| 134 | * @param hasHiddenColumns | |
| 135 | * - mark the hidden columns in columnSelection as hidden in the view | |
| 136 | * @param selectedRegionOnly | |
| 137 | * - when set, only include the selected region in the view, | |
| 138 | * otherwise just mark the selected region on the constructed view. | |
| 139 | * @param recordGroups | |
| 140 | * - when set, any groups on the given alignment will be marked on | |
| 141 | * the view | |
| 142 | */ | |
| 143 | 19 | public AlignmentView(AlignmentI alignment, HiddenColumns hidden, |
| 144 | SequenceGroup selection, boolean hasHiddenColumns, | |
| 145 | boolean selectedRegionOnly, boolean recordGroups) | |
| 146 | { | |
| 147 | // refactored from AlignViewport.getAlignmentView(selectedOnly); | |
| 148 | 19 | this(new jalview.datamodel.CigarArray(alignment, |
| 149 | 19 | (hasHiddenColumns ? hidden : null), |
| 150 | 19 | (selectedRegionOnly ? selection : null)), |
| 151 | 19 | (selectedRegionOnly && selection != null) |
| 152 | ? selection.getStartRes() | |
| 153 | : 0); | |
| 154 | 19 | isNa = alignment.isNucleotide(); |
| 155 | // walk down SeqCigar array and Alignment Array - optionally restricted by | |
| 156 | // selected region. | |
| 157 | // test group membership for each sequence in each group, store membership | |
| 158 | // and record non-empty groups in group list. | |
| 159 | // record / sub-select selected region on the alignment view | |
| 160 | 19 | SequenceI[] selseqs; |
| 161 | 19 | if (selection != null && selection.getSize() > 0) |
| 162 | { | |
| 163 | 6 | List<SequenceI> sel = selection.getSequences(null); |
| 164 | 6 | this.selected = new ScGroup(); |
| 165 | 6 | selseqs = selection.getSequencesInOrder(alignment, |
| 166 | selectedRegionOnly); | |
| 167 | } | |
| 168 | else | |
| 169 | { | |
| 170 | 13 | selseqs = alignment.getSequencesArray(); |
| 171 | } | |
| 172 | ||
| 173 | 19 | List<List<SequenceI>> seqsets = new ArrayList<List<SequenceI>>(); |
| 174 | // get the alignment's group list and make a copy | |
| 175 | 19 | List<SequenceGroup> grps = new ArrayList<SequenceGroup>(); |
| 176 | 19 | List<SequenceGroup> gg = alignment.getGroups(); |
| 177 | 19 | grps.addAll(gg); |
| 178 | 19 | ScGroup[] sgrps = null; |
| 179 | 19 | boolean addedgps[] = null; |
| 180 | 19 | if (grps != null) |
| 181 | { | |
| 182 | 19 | if (selection != null && selectedRegionOnly) |
| 183 | { | |
| 184 | // trim annotation to the region being stored. | |
| 185 | // strip out any groups that do not actually intersect with the | |
| 186 | // visible and selected region | |
| 187 | 6 | int ssel = selection.getStartRes(), esel = selection.getEndRes(); |
| 188 | 6 | List<SequenceGroup> isg = new ArrayList<SequenceGroup>(); |
| 189 | 6 | for (SequenceGroup sg : grps) |
| 190 | { | |
| 191 | 0 | if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel)) |
| 192 | { | |
| 193 | // adjust bounds of new group, if necessary. | |
| 194 | 0 | if (sg.getStartRes() < ssel) |
| 195 | { | |
| 196 | 0 | sg.setStartRes(ssel); |
| 197 | } | |
| 198 | 0 | if (sg.getEndRes() > esel) |
| 199 | { | |
| 200 | 0 | sg.setEndRes(esel); |
| 201 | } | |
| 202 | 0 | sg.setStartRes(sg.getStartRes() - ssel + 1); |
| 203 | 0 | sg.setEndRes(sg.getEndRes() - ssel + 1); |
| 204 | ||
| 205 | 0 | isg.add(sg); |
| 206 | } | |
| 207 | } | |
| 208 | 6 | grps = isg; |
| 209 | } | |
| 210 | ||
| 211 | 19 | sgrps = new ScGroup[grps.size()]; |
| 212 | 19 | addedgps = new boolean[grps.size()]; |
| 213 | 24 | for (int g = 0; g < sgrps.length; g++) |
| 214 | { | |
| 215 | 5 | SequenceGroup sg = grps.get(g); |
| 216 | 5 | sgrps[g] = new ScGroup(); |
| 217 | 5 | sgrps[g].sg = new SequenceGroup(sg); |
| 218 | 5 | addedgps[g] = false; |
| 219 | // can't set entry 0 in an empty list | |
| 220 | // seqsets.set(g, sg.getSequences(null)); | |
| 221 | 5 | seqsets.add(sg.getSequences()); |
| 222 | } | |
| 223 | // seqsets now contains vectors (should be sets) for each group, so we can | |
| 224 | // track when we've done with the group | |
| 225 | } | |
| 226 | 19 | int csi = 0; |
| 227 | 84 | for (int i = 0; i < selseqs.length; i++) |
| 228 | { | |
| 229 | 65 | if (selseqs[i] != null) |
| 230 | { | |
| 231 | 65 | if (selection != null && selection.getSize() > 0 |
| 232 | && !selectedRegionOnly) | |
| 233 | { | |
| 234 | 0 | selected.add(sequences[csi]); |
| 235 | } | |
| 236 | 65 | if (seqsets != null) |
| 237 | { | |
| 238 | 230 | for (int sg = 0; sg < sgrps.length; sg++) |
| 239 | { | |
| 240 | 165 | if ((seqsets.get(sg)).contains(selseqs[i])) |
| 241 | { | |
| 242 | 33 | sgrps[sg].sg.deleteSequence(selseqs[i], false); |
| 243 | 33 | sgrps[sg].add(sequences[csi]); |
| 244 | 33 | if (!addedgps[sg]) |
| 245 | { | |
| 246 | 5 | if (scGroups == null) |
| 247 | { | |
| 248 | 1 | scGroups = new ArrayList<ScGroup>(); |
| 249 | } | |
| 250 | 5 | addedgps[sg] = true; |
| 251 | 5 | scGroups.add(sgrps[sg]); |
| 252 | } | |
| 253 | } | |
| 254 | } | |
| 255 | } | |
| 256 | 65 | csi++; |
| 257 | } | |
| 258 | } | |
| 259 | // finally, delete the remaining sequences (if any) not selected | |
| 260 | 24 | for (int sg = 0; sg < sgrps.length; sg++) |
| 261 | { | |
| 262 | 5 | SequenceI[] sqs = sgrps[sg].sg.getSequencesAsArray(null); |
| 263 | 5 | for (int si = 0; si < sqs.length; si++) |
| 264 | { | |
| 265 | 0 | sgrps[sg].sg.deleteSequence(sqs[si], false); |
| 266 | } | |
| 267 | 5 | sgrps[sg] = null; |
| 268 | } | |
| 269 | } | |
| 270 | ||
| 271 | /** | |
| 272 | * construct an alignmentView from a SeqCigarArray. Errors are thrown if the | |
| 273 | * seqcigararray.isSeqCigarArray() flag is not set. | |
| 274 | */ | |
| 275 | 20 | public AlignmentView(CigarArray seqcigararray) |
| 276 | { | |
| 277 | 20 | if (!seqcigararray.isSeqCigarArray()) |
| 278 | { | |
| 279 | 0 | throw new Error( |
| 280 | "Implementation Error - can only make an alignment view from a CigarArray of sequences."); | |
| 281 | } | |
| 282 | // contigs = seqcigararray.applyDeletions(); | |
| 283 | 20 | contigs = seqcigararray.getDeletedRegions(); |
| 284 | 20 | sequences = seqcigararray.getSeqCigarArray(); |
| 285 | 20 | width = seqcigararray.getWidth(); // visible width |
| 286 | } | |
| 287 | ||
| 288 | /** | |
| 289 | * Create an alignmentView where the first column corresponds with the | |
| 290 | * 'firstcol' column of some reference alignment | |
| 291 | * | |
| 292 | * @param sdata | |
| 293 | * @param firstcol | |
| 294 | */ | |
| 295 | 19 | public AlignmentView(CigarArray sdata, int firstcol) |
| 296 | { | |
| 297 | 19 | this(sdata); |
| 298 | 19 | firstCol = firstcol; |
| 299 | } | |
| 300 | ||
| 301 | 0 | public void setSequences(SeqCigar[] sequences) |
| 302 | { | |
| 303 | 0 | this.sequences = sequences; |
| 304 | } | |
| 305 | ||
| 306 | 0 | public void setContigs(int[] contigs) |
| 307 | { | |
| 308 | 0 | this.contigs = contigs; |
| 309 | } | |
| 310 | ||
| 311 | 6 | public SeqCigar[] getSequences() |
| 312 | { | |
| 313 | 6 | return sequences; |
| 314 | } | |
| 315 | ||
| 316 | /** | |
| 317 | * @see CigarArray.getDeletedRegions | |
| 318 | * @return int[] { vis_start, sym_start, length } | |
| 319 | */ | |
| 320 | 0 | public int[] getContigs() |
| 321 | { | |
| 322 | 0 | return contigs; |
| 323 | } | |
| 324 | ||
| 325 | /** | |
| 326 | * get the full alignment and a columnselection object marking the hidden | |
| 327 | * regions | |
| 328 | * | |
| 329 | * @param gapCharacter | |
| 330 | * char | |
| 331 | * @return Object[] { SequenceI[], ColumnSelection} | |
| 332 | */ | |
| 333 | 3 | public Object[] getAlignmentAndHiddenColumns(char gapCharacter) |
| 334 | { | |
| 335 | 3 | HiddenColumns hidden = new HiddenColumns(); |
| 336 | ||
| 337 | 3 | return new Object[] { SeqCigar.createAlignmentSequences(sequences, |
| 338 | gapCharacter, hidden, contigs), | |
| 339 | hidden }; | |
| 340 | } | |
| 341 | ||
| 342 | /** | |
| 343 | * return the visible alignment corresponding to this view. Sequences in this | |
| 344 | * alignment are edited versions of the parent sequences - where hidden | |
| 345 | * regions have been removed. NOTE: the sequence data in this alignment is not | |
| 346 | * complete! | |
| 347 | * | |
| 348 | * @param c | |
| 349 | * @return | |
| 350 | */ | |
| 351 | 2 | public AlignmentI getVisibleAlignment(char c) |
| 352 | { | |
| 353 | 2 | SequenceI[] aln = getVisibleSeqs(c); |
| 354 | ||
| 355 | 2 | AlignmentI vcal = new Alignment(aln); |
| 356 | 2 | addPrunedGroupsInOrder(vcal, -1, -1, true); |
| 357 | 2 | return vcal; |
| 358 | } | |
| 359 | ||
| 360 | /** | |
| 361 | * add groups from view to the given alignment | |
| 362 | * | |
| 363 | * @param vcal | |
| 364 | * @param gstart | |
| 365 | * -1 or 0 to width-1 | |
| 366 | * @param gend | |
| 367 | * -1 or gstart to width-1 | |
| 368 | * @param viscontigs | |
| 369 | * - true if vcal is alignment of the visible regions of the view | |
| 370 | * (e.g. as returned from getVisibleAlignment) | |
| 371 | */ | |
| 372 | 4 | private void addPrunedGroupsInOrder(AlignmentI vcal, int gstart, int gend, |
| 373 | boolean viscontigs) | |
| 374 | { | |
| 375 | 4 | boolean r = false; |
| 376 | 4 | if (gstart > -1 && gstart <= gend) |
| 377 | { | |
| 378 | 2 | r = true; |
| 379 | } | |
| 380 | ||
| 381 | 4 | SequenceI[] aln = vcal.getSequencesArray(); |
| 382 | { | |
| 383 | /** | |
| 384 | * prune any groups to the visible coordinates of the alignment. | |
| 385 | */ | |
| 386 | { | |
| 387 | 4 | int nvg = (scGroups != null) ? scGroups.size() : 0; |
| 388 | 4 | if (nvg > 0) |
| 389 | { | |
| 390 | 2 | SequenceGroup[] nsg = new SequenceGroup[nvg]; |
| 391 | 12 | for (int g = 0; g < nvg; g++) |
| 392 | { | |
| 393 | 10 | SequenceGroup sg = scGroups.get(g).sg; |
| 394 | 10 | if (r) |
| 395 | { | |
| 396 | 10 | if (sg.getStartRes() > gend || sg.getEndRes() < gstart) |
| 397 | { | |
| 398 | // Skip this group | |
| 399 | 0 | nsg[g] = null; |
| 400 | 0 | continue; |
| 401 | } | |
| 402 | } | |
| 403 | ||
| 404 | // clone group properties | |
| 405 | 10 | nsg[g] = new SequenceGroup(sg); |
| 406 | ||
| 407 | // may need to shift/trim start and end ? | |
| 408 | 10 | if (r && !viscontigs) |
| 409 | { | |
| 410 | // Not fully tested code - routine not yet called with | |
| 411 | // viscontigs==false | |
| 412 | 0 | if (nsg[g].getStartRes() < gstart) |
| 413 | { | |
| 414 | 0 | nsg[g].setStartRes(0); |
| 415 | } | |
| 416 | else | |
| 417 | { | |
| 418 | 0 | nsg[g].setStartRes(nsg[g].getStartRes() - gstart); |
| 419 | 0 | nsg[g].setEndRes(nsg[g].getEndRes() - gstart); |
| 420 | } | |
| 421 | 0 | if (nsg[g].getEndRes() > (gend - gstart)) |
| 422 | { | |
| 423 | 0 | nsg[g].setEndRes(gend - gstart); |
| 424 | } | |
| 425 | } | |
| 426 | } | |
| 427 | 2 | if (viscontigs) |
| 428 | { | |
| 429 | // prune groups to cover just the visible positions between | |
| 430 | // gstart/gend. | |
| 431 | 2 | if (contigs != null) |
| 432 | { | |
| 433 | 0 | int p = 0; |
| 434 | 0 | ShiftList prune = new ShiftList(); |
| 435 | 0 | if (r) |
| 436 | { | |
| 437 | // adjust for start of alignment within visible window. | |
| 438 | 0 | prune.addShift(gstart, -gstart); // |
| 439 | } | |
| 440 | 0 | for (int h = 0; h < contigs.length; h += 3) |
| 441 | { | |
| 442 | { | |
| 443 | 0 | prune.addShift(p + contigs[h + 1], |
| 444 | contigs[h + 2] - contigs[h + 1]); | |
| 445 | } | |
| 446 | 0 | p = contigs[h + 1] + contigs[h + 2]; |
| 447 | } | |
| 448 | 0 | for (int g = 0; g < nsg.length; g++) |
| 449 | { | |
| 450 | 0 | if (nsg[g] != null) |
| 451 | { | |
| 452 | 0 | int s = nsg[g].getStartRes(), t = nsg[g].getEndRes(); |
| 453 | 0 | int w = 1 + t - s; |
| 454 | 0 | if (r) |
| 455 | { | |
| 456 | 0 | if (s < gstart) |
| 457 | { | |
| 458 | 0 | s = gstart; |
| 459 | } | |
| 460 | 0 | if (t > gend) |
| 461 | { | |
| 462 | 0 | t = gend; |
| 463 | } | |
| 464 | } | |
| 465 | 0 | s = prune.shift(s); |
| 466 | 0 | t = prune.shift(t); |
| 467 | 0 | nsg[g].setStartRes(s); |
| 468 | 0 | nsg[g].setEndRes(t); |
| 469 | } | |
| 470 | } | |
| 471 | } | |
| 472 | } | |
| 473 | ||
| 474 | 68 | for (int nsq = 0; nsq < aln.length; nsq++) |
| 475 | { | |
| 476 | 396 | for (int g = 0; g < nvg; g++) |
| 477 | { | |
| 478 | 330 | if (nsg[g] != null |
| 479 | && sequences[nsq].isMemberOf(scGroups.get(g))) | |
| 480 | { | |
| 481 | 66 | nsg[g].addSequence(aln[nsq], false); |
| 482 | } | |
| 483 | } | |
| 484 | } | |
| 485 | 12 | for (int g = 0; g < nvg; g++) |
| 486 | { | |
| 487 | 10 | if (nsg[g] != null && nsg[g].getSize() > 0) |
| 488 | { | |
| 489 | 10 | vcal.addGroup(nsg[g]); |
| 490 | } | |
| 491 | 10 | nsg[g] = null; |
| 492 | } | |
| 493 | } | |
| 494 | } | |
| 495 | } | |
| 496 | } | |
| 497 | ||
| 498 | /** | |
| 499 | * generate sequence array corresponding to the visible parts of the | |
| 500 | * alignment. | |
| 501 | * | |
| 502 | * @param c | |
| 503 | * gap character to use to recreate the alignment | |
| 504 | * @return | |
| 505 | */ | |
| 506 | 2 | private SequenceI[] getVisibleSeqs(char c) |
| 507 | { | |
| 508 | 2 | SequenceI[] aln = new SequenceI[sequences.length]; |
| 509 | 5 | for (int i = 0, j = sequences.length; i < j; i++) |
| 510 | { | |
| 511 | 3 | aln[i] = sequences[i].getSeq(c); |
| 512 | // Remove hidden regions from sequence | |
| 513 | 3 | aln[i].setSequence(getASequenceString(c, i)); |
| 514 | } | |
| 515 | 2 | return aln; |
| 516 | } | |
| 517 | ||
| 518 | /** | |
| 519 | * creates new alignment objects for all contiguous visible segments | |
| 520 | * | |
| 521 | * @param c | |
| 522 | * @param start | |
| 523 | * @param end | |
| 524 | * @param regionOfInterest | |
| 525 | * specify which sequences to include (or null to include all | |
| 526 | * sequences) | |
| 527 | * @return AlignmentI[] - all alignments where each sequence is a subsequence | |
| 528 | * constructed from visible contig regions of view | |
| 529 | */ | |
| 530 | 2 | public AlignmentI[] getVisibleContigAlignments(char c) |
| 531 | { | |
| 532 | 2 | int nvc = 0; |
| 533 | 2 | int[] vcontigs = getVisibleContigs(); |
| 534 | 2 | SequenceI[][] contigviews = getVisibleContigs(c); |
| 535 | 2 | AlignmentI[] vcals = new AlignmentI[contigviews.length]; |
| 536 | 4 | for (nvc = 0; nvc < contigviews.length; nvc++) |
| 537 | { | |
| 538 | 2 | vcals[nvc] = new Alignment(contigviews[nvc]); |
| 539 | 2 | if (scGroups != null && scGroups.size() > 0) |
| 540 | { | |
| 541 | 2 | addPrunedGroupsInOrder(vcals[nvc], vcontigs[nvc * 2], |
| 542 | vcontigs[nvc * 2 + 1], true); | |
| 543 | } | |
| 544 | } | |
| 545 | 2 | return vcals; |
| 546 | } | |
| 547 | ||
| 548 | /** | |
| 549 | * build a string excluding hidden regions from a particular sequence in the | |
| 550 | * view | |
| 551 | * | |
| 552 | * @param c | |
| 553 | * @param n | |
| 554 | * @return | |
| 555 | */ | |
| 556 | 9 | private String getASequenceString(char c, int n) |
| 557 | { | |
| 558 | 9 | String sqn; |
| 559 | 9 | String fullseq = sequences[n].getSequenceString(c); |
| 560 | 9 | if (contigs != null) |
| 561 | { | |
| 562 | 0 | sqn = ""; |
| 563 | 0 | int p = 0; |
| 564 | 0 | for (int h = 0; h < contigs.length; h += 3) |
| 565 | { | |
| 566 | 0 | sqn += fullseq.substring(p, contigs[h + 1]); |
| 567 | 0 | p = contigs[h + 1] + contigs[h + 2]; |
| 568 | } | |
| 569 | 0 | sqn += fullseq.substring(p); |
| 570 | } | |
| 571 | else | |
| 572 | { | |
| 573 | 9 | sqn = fullseq; |
| 574 | } | |
| 575 | 9 | return sqn; |
| 576 | } | |
| 577 | ||
| 578 | /** | |
| 579 | * get an array of visible sequence strings for a view on an alignment using | |
| 580 | * the given gap character uses getASequenceString | |
| 581 | * | |
| 582 | * @param c | |
| 583 | * char | |
| 584 | * @return String[] | |
| 585 | */ | |
| 586 | 4 | public String[] getSequenceStrings(char c) |
| 587 | { | |
| 588 | 4 | String[] seqs = new String[sequences.length]; |
| 589 | 10 | for (int n = 0; n < sequences.length; n++) |
| 590 | { | |
| 591 | 6 | seqs[n] = getASequenceString(c, n); |
| 592 | } | |
| 593 | 4 | return seqs; |
| 594 | } | |
| 595 | ||
| 596 | /** | |
| 597 | * | |
| 598 | * @return visible number of columns in alignment view | |
| 599 | */ | |
| 600 | 0 | public int getWidth() |
| 601 | { | |
| 602 | 0 | return width; |
| 603 | } | |
| 604 | ||
| 605 | 0 | protected void setWidth(int width) |
| 606 | { | |
| 607 | 0 | this.width = width; |
| 608 | } | |
| 609 | ||
| 610 | /** | |
| 611 | * get the contiguous subalignments in an alignment view. | |
| 612 | * | |
| 613 | * @param gapCharacter | |
| 614 | * char | |
| 615 | * @return SequenceI[][] | |
| 616 | */ | |
| 617 | 2 | public SequenceI[][] getVisibleContigs(char gapCharacter) |
| 618 | { | |
| 619 | 2 | SequenceI[][] smsa; |
| 620 | 2 | int njobs = 1; |
| 621 | 2 | if (sequences == null || width <= 0) |
| 622 | { | |
| 623 | 0 | return null; |
| 624 | } | |
| 625 | 2 | if (contigs != null && contigs.length > 0) |
| 626 | { | |
| 627 | 0 | int start = 0; |
| 628 | 0 | njobs = 0; |
| 629 | 0 | int fwidth = width; |
| 630 | 0 | for (int contig = 0; contig < contigs.length; contig += 3) |
| 631 | { | |
| 632 | 0 | if ((contigs[contig + 1] - start) > 0) |
| 633 | { | |
| 634 | 0 | njobs++; |
| 635 | } | |
| 636 | 0 | fwidth += contigs[contig + 2]; // end up with full region width |
| 637 | // (including hidden regions) | |
| 638 | 0 | start = contigs[contig + 1] + contigs[contig + 2]; |
| 639 | } | |
| 640 | 0 | if (start < fwidth) |
| 641 | { | |
| 642 | 0 | njobs++; |
| 643 | } | |
| 644 | 0 | smsa = new SequenceI[njobs][]; |
| 645 | 0 | start = 0; |
| 646 | 0 | int j = 0; |
| 647 | 0 | for (int contig = 0; contig < contigs.length; contig += 3) |
| 648 | { | |
| 649 | 0 | if (contigs[contig + 1] - start > 0) |
| 650 | { | |
| 651 | 0 | SequenceI mseq[] = new SequenceI[sequences.length]; |
| 652 | 0 | for (int s = 0; s < mseq.length; s++) |
| 653 | { | |
| 654 | 0 | mseq[s] = sequences[s].getSeq(gapCharacter) |
| 655 | .getSubSequence(start, contigs[contig + 1]); | |
| 656 | } | |
| 657 | 0 | smsa[j] = mseq; |
| 658 | 0 | j++; |
| 659 | } | |
| 660 | 0 | start = contigs[contig + 1] + contigs[contig + 2]; |
| 661 | } | |
| 662 | 0 | if (start < fwidth) |
| 663 | { | |
| 664 | 0 | SequenceI mseq[] = new SequenceI[sequences.length]; |
| 665 | 0 | for (int s = 0; s < mseq.length; s++) |
| 666 | { | |
| 667 | 0 | mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start, |
| 668 | fwidth + 1); | |
| 669 | } | |
| 670 | 0 | smsa[j] = mseq; |
| 671 | 0 | j++; |
| 672 | } | |
| 673 | } | |
| 674 | else | |
| 675 | { | |
| 676 | 2 | smsa = new SequenceI[1][]; |
| 677 | 2 | smsa[0] = new SequenceI[sequences.length]; |
| 678 | 68 | for (int s = 0; s < sequences.length; s++) |
| 679 | { | |
| 680 | 66 | smsa[0][s] = sequences[s].getSeq(gapCharacter); |
| 681 | } | |
| 682 | } | |
| 683 | 2 | return smsa; |
| 684 | } | |
| 685 | ||
| 686 | /** | |
| 687 | * return full msa and hidden regions with visible blocks replaced with new | |
| 688 | * sub alignments | |
| 689 | * | |
| 690 | * @param nvismsa | |
| 691 | * SequenceI[][] | |
| 692 | * @param orders | |
| 693 | * AlignmentOrder[] corresponding to each SequenceI[] block. | |
| 694 | * @return Object[] | |
| 695 | */ | |
| 696 | 0 | public Object[] getUpdatedView(SequenceI[][] nvismsa, |
| 697 | AlignmentOrder[] orders, char gapCharacter) | |
| 698 | { | |
| 699 | 0 | if (sequences == null || width <= 0) |
| 700 | { | |
| 701 | 0 | throw new Error(MessageManager |
| 702 | .getString("error.empty_view_cannot_be_updated")); | |
| 703 | } | |
| 704 | 0 | if (nvismsa == null) |
| 705 | { | |
| 706 | 0 | throw new Error( |
| 707 | "nvismsa==null. use getAlignmentAndColumnSelection() instead."); | |
| 708 | } | |
| 709 | 0 | if (contigs != null && contigs.length > 0) |
| 710 | { | |
| 711 | 0 | SequenceI[] alignment = new SequenceI[sequences.length]; |
| 712 | // ColumnSelection columnselection = new ColumnSelection(); | |
| 713 | 0 | HiddenColumns hidden = new HiddenColumns(); |
| 714 | 0 | if (contigs != null && contigs.length > 0) |
| 715 | { | |
| 716 | 0 | int start = 0; |
| 717 | 0 | int nwidth = 0; |
| 718 | 0 | int owidth = width; |
| 719 | 0 | int j = 0; |
| 720 | 0 | for (int contig = 0; contig < contigs.length; contig += 3) |
| 721 | { | |
| 722 | 0 | owidth += contigs[contig + 2]; // recover final column width |
| 723 | 0 | if (contigs[contig + 1] - start > 0) |
| 724 | { | |
| 725 | 0 | int swidth = 0; // subalignment width |
| 726 | 0 | if (nvismsa[j] != null) |
| 727 | { | |
| 728 | 0 | SequenceI mseq[] = nvismsa[j]; |
| 729 | 0 | AlignmentOrder order = (orders == null) ? null : orders[j]; |
| 730 | 0 | j++; |
| 731 | 0 | if (mseq.length != sequences.length) |
| 732 | { | |
| 733 | 0 | throw new Error(MessageManager.formatMessage( |
| 734 | "error.mismatch_between_number_of_sequences_in_block", | |
| 735 | new String[] | |
| 736 | { Integer.valueOf(j).toString(), | |
| 737 | Integer.valueOf(mseq.length).toString(), | |
| 738 | Integer.valueOf(sequences.length) | |
| 739 | .toString() })); | |
| 740 | } | |
| 741 | 0 | swidth = mseq[0].getLength(); // JBPNote: could ensure padded |
| 742 | // here. | |
| 743 | 0 | for (int s = 0; s < mseq.length; s++) |
| 744 | { | |
| 745 | 0 | if (alignment[s] == null) |
| 746 | { | |
| 747 | 0 | alignment[s] = mseq[s]; |
| 748 | } | |
| 749 | else | |
| 750 | { | |
| 751 | 0 | alignment[s] |
| 752 | .setSequence(alignment[s].getSequenceAsString() | |
| 753 | + mseq[s].getSequenceAsString()); | |
| 754 | 0 | if (mseq[s].getStart() <= mseq[s].getEnd()) |
| 755 | { | |
| 756 | 0 | alignment[s].setEnd(mseq[s].getEnd()); |
| 757 | } | |
| 758 | 0 | if (order != null) |
| 759 | { | |
| 760 | 0 | order.updateSequence(mseq[s], alignment[s]); |
| 761 | } | |
| 762 | } | |
| 763 | } | |
| 764 | } | |
| 765 | else | |
| 766 | { | |
| 767 | // recover original alignment block or place gaps | |
| 768 | 0 | if (true) |
| 769 | { | |
| 770 | // recover input data | |
| 771 | 0 | for (int s = 0; s < sequences.length; s++) |
| 772 | { | |
| 773 | 0 | SequenceI oseq = sequences[s].getSeq(gapCharacter) |
| 774 | .getSubSequence(start, contigs[contig + 1]); | |
| 775 | 0 | if (swidth < oseq.getLength()) |
| 776 | { | |
| 777 | 0 | swidth = oseq.getLength(); |
| 778 | } | |
| 779 | 0 | if (alignment[s] == null) |
| 780 | { | |
| 781 | 0 | alignment[s] = oseq; |
| 782 | } | |
| 783 | else | |
| 784 | { | |
| 785 | 0 | alignment[s] |
| 786 | .setSequence(alignment[s].getSequenceAsString() | |
| 787 | + oseq.getSequenceAsString()); | |
| 788 | 0 | if (oseq.getEnd() >= oseq.getStart()) |
| 789 | { | |
| 790 | 0 | alignment[s].setEnd(oseq.getEnd()); |
| 791 | } | |
| 792 | } | |
| 793 | } | |
| 794 | ||
| 795 | } | |
| 796 | 0 | j++; |
| 797 | } | |
| 798 | 0 | nwidth += swidth; |
| 799 | } | |
| 800 | // advance to begining of visible region | |
| 801 | 0 | start = contigs[contig + 1] + contigs[contig + 2]; |
| 802 | // add hidden segment to right of next region | |
| 803 | 0 | for (int s = 0; s < sequences.length; s++) |
| 804 | { | |
| 805 | 0 | SequenceI hseq = sequences[s].getSeq(gapCharacter) |
| 806 | .getSubSequence(contigs[contig + 1], start); | |
| 807 | 0 | if (alignment[s] == null) |
| 808 | { | |
| 809 | 0 | alignment[s] = hseq; |
| 810 | } | |
| 811 | else | |
| 812 | { | |
| 813 | 0 | alignment[s].setSequence(alignment[s].getSequenceAsString() |
| 814 | + hseq.getSequenceAsString()); | |
| 815 | 0 | if (hseq.getEnd() >= hseq.getStart()) |
| 816 | { | |
| 817 | 0 | alignment[s].setEnd(hseq.getEnd()); |
| 818 | } | |
| 819 | } | |
| 820 | } | |
| 821 | // mark hidden segment as hidden in the new alignment | |
| 822 | 0 | hidden.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1); |
| 823 | 0 | nwidth += contigs[contig + 2]; |
| 824 | } | |
| 825 | // Do final segment - if it exists | |
| 826 | 0 | if (j < nvismsa.length) |
| 827 | { | |
| 828 | 0 | int swidth = 0; |
| 829 | 0 | if (nvismsa[j] != null) |
| 830 | { | |
| 831 | 0 | SequenceI mseq[] = nvismsa[j]; |
| 832 | 0 | AlignmentOrder order = (orders != null) ? orders[j] : null; |
| 833 | 0 | swidth = mseq[0].getLength(); |
| 834 | 0 | for (int s = 0; s < mseq.length; s++) |
| 835 | { | |
| 836 | 0 | if (alignment[s] == null) |
| 837 | { | |
| 838 | 0 | alignment[s] = mseq[s]; |
| 839 | } | |
| 840 | else | |
| 841 | { | |
| 842 | 0 | alignment[s].setSequence(alignment[s].getSequenceAsString() |
| 843 | + mseq[s].getSequenceAsString()); | |
| 844 | 0 | if (mseq[s].getEnd() >= mseq[s].getStart()) |
| 845 | { | |
| 846 | 0 | alignment[s].setEnd(mseq[s].getEnd()); |
| 847 | } | |
| 848 | 0 | if (order != null) |
| 849 | { | |
| 850 | 0 | order.updateSequence(mseq[s], alignment[s]); |
| 851 | } | |
| 852 | } | |
| 853 | } | |
| 854 | } | |
| 855 | else | |
| 856 | { | |
| 857 | 0 | if (start < owidth) |
| 858 | { | |
| 859 | // recover input data or place gaps | |
| 860 | 0 | if (true) |
| 861 | { | |
| 862 | // recover input data | |
| 863 | 0 | for (int s = 0; s < sequences.length; s++) |
| 864 | { | |
| 865 | 0 | SequenceI oseq = sequences[s].getSeq(gapCharacter) |
| 866 | .getSubSequence(start, owidth + 1); | |
| 867 | 0 | if (swidth < oseq.getLength()) |
| 868 | { | |
| 869 | 0 | swidth = oseq.getLength(); |
| 870 | } | |
| 871 | 0 | if (alignment[s] == null) |
| 872 | { | |
| 873 | 0 | alignment[s] = oseq; |
| 874 | } | |
| 875 | else | |
| 876 | { | |
| 877 | 0 | alignment[s] |
| 878 | .setSequence(alignment[s].getSequenceAsString() | |
| 879 | + oseq.getSequenceAsString()); | |
| 880 | 0 | if (oseq.getEnd() >= oseq.getStart()) |
| 881 | { | |
| 882 | 0 | alignment[s].setEnd(oseq.getEnd()); |
| 883 | } | |
| 884 | } | |
| 885 | } | |
| 886 | 0 | nwidth += swidth; |
| 887 | } | |
| 888 | else | |
| 889 | { | |
| 890 | // place gaps. | |
| 891 | 0 | throw new Error(MessageManager |
| 892 | .getString("error.padding_not_yet_implemented")); | |
| 893 | } | |
| 894 | } | |
| 895 | } | |
| 896 | } | |
| 897 | } | |
| 898 | 0 | return new Object[] { alignment, hidden }; |
| 899 | } | |
| 900 | else | |
| 901 | { | |
| 902 | 0 | if (nvismsa.length != 1) |
| 903 | { | |
| 904 | 0 | throw new Error(MessageManager.formatMessage( |
| 905 | "error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view", | |
| 906 | new String[] | |
| 907 | { Integer.valueOf(nvismsa.length).toString() })); | |
| 908 | } | |
| 909 | 0 | if (nvismsa[0] != null) |
| 910 | { | |
| 911 | 0 | return new Object[] { nvismsa[0], new HiddenColumns() }; |
| 912 | } | |
| 913 | else | |
| 914 | { | |
| 915 | 0 | return getAlignmentAndHiddenColumns(gapCharacter); |
| 916 | } | |
| 917 | } | |
| 918 | } | |
| 919 | ||
| 920 | /** | |
| 921 | * returns simple array of start end positions of visible range on alignment. | |
| 922 | * vis_start and vis_end are inclusive - use | |
| 923 | * SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence | |
| 924 | * from underlying alignment. | |
| 925 | * | |
| 926 | * @return int[] { start_i, end_i } for 1<i<n visible regions. | |
| 927 | */ | |
| 928 | 19 | public int[] getVisibleContigs() |
| 929 | { | |
| 930 | 19 | if (contigs != null && contigs.length > 0) |
| 931 | { | |
| 932 | 8 | int start = 0; |
| 933 | 8 | int nvis = 0; |
| 934 | 8 | int fwidth = width; |
| 935 | 22 | for (int contig = 0; contig < contigs.length; contig += 3) |
| 936 | { | |
| 937 | 14 | if ((contigs[contig + 1] - start) > 0) |
| 938 | { | |
| 939 | 7 | nvis++; |
| 940 | } | |
| 941 | 14 | fwidth += contigs[contig + 2]; // end up with full region width |
| 942 | // (including hidden regions) | |
| 943 | 14 | start = contigs[contig + 1] + contigs[contig + 2]; |
| 944 | } | |
| 945 | 8 | if (start < fwidth) |
| 946 | { | |
| 947 | 3 | nvis++; |
| 948 | } | |
| 949 | 8 | int viscontigs[] = new int[nvis * 2]; |
| 950 | 8 | nvis = 0; |
| 951 | 8 | start = 0; |
| 952 | 22 | for (int contig = 0; contig < contigs.length; contig += 3) |
| 953 | { | |
| 954 | 14 | if ((contigs[contig + 1] - start) > 0) |
| 955 | { | |
| 956 | 7 | viscontigs[nvis] = start; |
| 957 | 7 | viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive |
| 958 | 7 | nvis += 2; |
| 959 | } | |
| 960 | 14 | start = contigs[contig + 1] + contigs[contig + 2]; |
| 961 | } | |
| 962 | 8 | if (start < fwidth) |
| 963 | { | |
| 964 | 3 | viscontigs[nvis] = start; |
| 965 | 3 | viscontigs[nvis + 1] = fwidth - 1; // end is inclusive |
| 966 | 3 | nvis += 2; |
| 967 | } | |
| 968 | 8 | return viscontigs; |
| 969 | } | |
| 970 | else | |
| 971 | { | |
| 972 | 11 | return new int[] { 0, width - 1 }; |
| 973 | } | |
| 974 | } | |
| 975 | ||
| 976 | /** | |
| 977 | * | |
| 978 | * @return position of first visible column of AlignmentView within its | |
| 979 | * parent's alignment reference frame | |
| 980 | */ | |
| 981 | 0 | public int getAlignmentOrigin() |
| 982 | { | |
| 983 | 0 | return firstCol; |
| 984 | } | |
| 985 | ||
| 986 | /** | |
| 987 | * compute a deletion map for the current view according to the given | |
| 988 | * gap/match map | |
| 989 | * | |
| 990 | * @param gapMap | |
| 991 | * (as returned from SequenceI.gapMap()) | |
| 992 | * @return int[] {intersection of visible regions with gapMap) | |
| 993 | */ | |
| 994 | 0 | public int[] getVisibleContigMapFor(int[] gapMap) |
| 995 | { | |
| 996 | 0 | int[] delMap = null; |
| 997 | 0 | int[] viscontigs = getVisibleContigs(); |
| 998 | 0 | int spos = 0; |
| 999 | 0 | int i = 0; |
| 1000 | 0 | if (viscontigs != null) |
| 1001 | { | |
| 1002 | // viscontigs maps from a subset of the gapMap to the gapMap, so it will | |
| 1003 | // always be equal to or shorter than gapMap | |
| 1004 | 0 | delMap = new int[gapMap.length]; |
| 1005 | 0 | for (int contig = 0; contig < viscontigs.length; contig += 2) |
| 1006 | { | |
| 1007 | ||
| 1008 | 0 | while (spos < gapMap.length && gapMap[spos] < viscontigs[contig]) |
| 1009 | { | |
| 1010 | 0 | spos++; |
| 1011 | } | |
| 1012 | 0 | while (spos < gapMap.length |
| 1013 | && gapMap[spos] <= viscontigs[contig + 1]) | |
| 1014 | { | |
| 1015 | 0 | delMap[i++] = spos++; |
| 1016 | } | |
| 1017 | } | |
| 1018 | 0 | int tmap[] = new int[i]; |
| 1019 | 0 | System.arraycopy(delMap, 0, tmap, 0, i); |
| 1020 | 0 | delMap = tmap; |
| 1021 | } | |
| 1022 | 0 | return delMap; |
| 1023 | } | |
| 1024 | ||
| 1025 | /** | |
| 1026 | * apply the getSeq(gc) method to each sequence cigar, and return the array of | |
| 1027 | * edited sequences, optionally with hidden regions removed. | |
| 1028 | * | |
| 1029 | * @param gc | |
| 1030 | * gap character to use for insertions | |
| 1031 | * @param delete | |
| 1032 | * remove hidden regions from sequences. Note: currently implemented | |
| 1033 | * in a memory inefficient way - space needed is 2*result set for | |
| 1034 | * deletion | |
| 1035 | * | |
| 1036 | * @return SequenceI[] | |
| 1037 | */ | |
| 1038 | 0 | public SequenceI[] getEditedSequences(char gc, boolean delete) |
| 1039 | { | |
| 1040 | 0 | SeqCigar[] msf = getSequences(); |
| 1041 | 0 | SequenceI[] aln = new SequenceI[msf.length]; |
| 1042 | 0 | for (int i = 0, j = msf.length; i < j; i++) |
| 1043 | { | |
| 1044 | 0 | aln[i] = msf[i].getSeq(gc); |
| 1045 | } | |
| 1046 | 0 | if (delete) |
| 1047 | { | |
| 1048 | 0 | String[] sqs = getSequenceStrings(gc); |
| 1049 | 0 | for (int i = 0; i < sqs.length; i++) |
| 1050 | { | |
| 1051 | 0 | aln[i].setSequence(sqs[i]); |
| 1052 | 0 | sqs[i] = null; |
| 1053 | } | |
| 1054 | } | |
| 1055 | 0 | return aln; |
| 1056 | } | |
| 1057 | ||
| 1058 | 0 | public static void summariseAlignmentView(AlignmentView view, |
| 1059 | PrintStream os) | |
| 1060 | { | |
| 1061 | 0 | os.print("View has " + view.sequences.length + " of which "); |
| 1062 | 0 | if (view.selected == null) |
| 1063 | { | |
| 1064 | 0 | os.print("None"); |
| 1065 | } | |
| 1066 | else | |
| 1067 | { | |
| 1068 | 0 | os.print(" " + view.selected.size()); |
| 1069 | } | |
| 1070 | 0 | os.println(" are selected."); |
| 1071 | 0 | os.print("View is " + view.getWidth() + " columns wide"); |
| 1072 | 0 | int viswid = 0; |
| 1073 | 0 | int[] contigs = view.getContigs(); |
| 1074 | 0 | if (contigs != null) |
| 1075 | { | |
| 1076 | 0 | viswid = view.width; |
| 1077 | 0 | for (int i = 0; i < contigs.length; i += 3) |
| 1078 | { | |
| 1079 | 0 | viswid += contigs[i + 2]; |
| 1080 | } | |
| 1081 | 0 | os.println("with " + viswid + " visible columns spread over " |
| 1082 | + contigs.length / 3 + " regions."); | |
| 1083 | } | |
| 1084 | else | |
| 1085 | { | |
| 1086 | 0 | viswid = view.width; |
| 1087 | 0 | os.println("."); |
| 1088 | } | |
| 1089 | 0 | if (view.scGroups != null) |
| 1090 | { | |
| 1091 | 0 | os.println("There are " + view.scGroups.size() |
| 1092 | + " groups defined on the view."); | |
| 1093 | 0 | for (int g = 0; g < view.scGroups.size(); g++) |
| 1094 | { | |
| 1095 | 0 | ScGroup sgr = view.scGroups.get(g); |
| 1096 | 0 | os.println("Group " + g + ": Name = " + sgr.sg.getName() |
| 1097 | + " Contains " + sgr.seqs.size() + " Seqs."); | |
| 1098 | 0 | os.println("This group runs from " + sgr.sg.getStartRes() + " to " |
| 1099 | + sgr.sg.getEndRes()); | |
| 1100 | 0 | for (int s = 0; s < sgr.seqs.size(); s++) |
| 1101 | { | |
| 1102 | // JBPnote this should be a unit test for ScGroup | |
| 1103 | 0 | if (!sgr.seqs.get(s).isMemberOf(sgr)) |
| 1104 | { | |
| 1105 | 0 | os.println("** WARNING: sequence " + sgr.seqs.get(s).toString() |
| 1106 | + " is not marked as member of group."); | |
| 1107 | } | |
| 1108 | } | |
| 1109 | } | |
| 1110 | 0 | AlignmentI visal = view.getVisibleAlignment('-'); |
| 1111 | 0 | if (visal != null) |
| 1112 | { | |
| 1113 | 0 | os.println("Vis. alignment is " + visal.getWidth() |
| 1114 | + " wide and has " + visal.getHeight() + " seqs."); | |
| 1115 | 0 | if (visal.getGroups() != null && visal.getGroups().size() > 0) |
| 1116 | { | |
| 1117 | ||
| 1118 | 0 | int i = 1; |
| 1119 | 0 | for (SequenceGroup sg : visal.getGroups()) |
| 1120 | { | |
| 1121 | 0 | os.println("Group " + (i++) + " begins at column " |
| 1122 | + sg.getStartRes() + " and ends at " + sg.getEndRes()); | |
| 1123 | } | |
| 1124 | } | |
| 1125 | } | |
| 1126 | } | |
| 1127 | } | |
| 1128 | ||
| 1129 | 0 | public static void testSelectionViews(AlignmentI alignment, |
| 1130 | HiddenColumns hidden, SequenceGroup selection) | |
| 1131 | { | |
| 1132 | 0 | System.out.println("Testing standard view creation:\n"); |
| 1133 | 0 | AlignmentView view = null; |
| 1134 | 0 | try |
| 1135 | { | |
| 1136 | 0 | System.out.println( |
| 1137 | "View with no hidden columns, no limit to selection, no groups to be collected:"); | |
| 1138 | 0 | view = new AlignmentView(alignment, hidden, selection, false, false, |
| 1139 | false); | |
| 1140 | 0 | summariseAlignmentView(view, System.out); |
| 1141 | ||
| 1142 | } catch (Exception e) | |
| 1143 | { | |
| 1144 | 0 | e.printStackTrace(); |
| 1145 | 0 | System.err.println( |
| 1146 | "Failed to generate alignment with selection but no groups marked."); | |
| 1147 | } | |
| 1148 | 0 | try |
| 1149 | { | |
| 1150 | 0 | System.out.println( |
| 1151 | "View with no hidden columns, no limit to selection, and all groups to be collected:"); | |
| 1152 | 0 | view = new AlignmentView(alignment, hidden, selection, false, false, |
| 1153 | true); | |
| 1154 | 0 | summariseAlignmentView(view, System.out); |
| 1155 | } catch (Exception e) | |
| 1156 | { | |
| 1157 | 0 | e.printStackTrace(); |
| 1158 | 0 | System.err.println( |
| 1159 | "Failed to generate alignment with selection marked but no groups marked."); | |
| 1160 | } | |
| 1161 | 0 | try |
| 1162 | { | |
| 1163 | 0 | System.out.println( |
| 1164 | "View with no hidden columns, limited to selection and no groups to be collected:"); | |
| 1165 | 0 | view = new AlignmentView(alignment, hidden, selection, false, true, |
| 1166 | false); | |
| 1167 | 0 | summariseAlignmentView(view, System.out); |
| 1168 | } catch (Exception e) | |
| 1169 | { | |
| 1170 | 0 | e.printStackTrace(); |
| 1171 | 0 | System.err.println( |
| 1172 | "Failed to generate alignment with selection restricted but no groups marked."); | |
| 1173 | } | |
| 1174 | 0 | try |
| 1175 | { | |
| 1176 | 0 | System.out.println( |
| 1177 | "View with no hidden columns, limited to selection, and all groups to be collected:"); | |
| 1178 | 0 | view = new AlignmentView(alignment, hidden, selection, false, true, |
| 1179 | true); | |
| 1180 | 0 | summariseAlignmentView(view, System.out); |
| 1181 | } catch (Exception e) | |
| 1182 | { | |
| 1183 | 0 | e.printStackTrace(); |
| 1184 | 0 | System.err.println( |
| 1185 | "Failed to generate alignment with selection restricted and groups marked."); | |
| 1186 | } | |
| 1187 | 0 | try |
| 1188 | { | |
| 1189 | 0 | System.out.println( |
| 1190 | "View *with* hidden columns, no limit to selection, no groups to be collected:"); | |
| 1191 | 0 | view = new AlignmentView(alignment, hidden, selection, true, false, |
| 1192 | false); | |
| 1193 | 0 | summariseAlignmentView(view, System.out); |
| 1194 | } catch (Exception e) | |
| 1195 | { | |
| 1196 | 0 | e.printStackTrace(); |
| 1197 | 0 | System.err.println( |
| 1198 | "Failed to generate alignment with selection but no groups marked."); | |
| 1199 | } | |
| 1200 | 0 | try |
| 1201 | { | |
| 1202 | 0 | System.out.println( |
| 1203 | "View *with* hidden columns, no limit to selection, and all groups to be collected:"); | |
| 1204 | 0 | view = new AlignmentView(alignment, hidden, selection, true, false, |
| 1205 | true); | |
| 1206 | 0 | summariseAlignmentView(view, System.out); |
| 1207 | } catch (Exception e) | |
| 1208 | { | |
| 1209 | 0 | e.printStackTrace(); |
| 1210 | 0 | System.err.println( |
| 1211 | "Failed to generate alignment with selection marked but no groups marked."); | |
| 1212 | } | |
| 1213 | 0 | try |
| 1214 | { | |
| 1215 | 0 | System.out.println( |
| 1216 | "View *with* hidden columns, limited to selection and no groups to be collected:"); | |
| 1217 | 0 | view = new AlignmentView(alignment, hidden, selection, true, true, |
| 1218 | false); | |
| 1219 | 0 | summariseAlignmentView(view, System.out); |
| 1220 | } catch (Exception e) | |
| 1221 | { | |
| 1222 | 0 | e.printStackTrace(); |
| 1223 | 0 | System.err.println( |
| 1224 | "Failed to generate alignment with selection restricted but no groups marked."); | |
| 1225 | } | |
| 1226 | 0 | try |
| 1227 | { | |
| 1228 | 0 | System.out.println( |
| 1229 | "View *with* hidden columns, limited to selection, and all groups to be collected:"); | |
| 1230 | 0 | view = new AlignmentView(alignment, hidden, selection, true, true, |
| 1231 | true); | |
| 1232 | 0 | summariseAlignmentView(view, System.out); |
| 1233 | } catch (Exception e) | |
| 1234 | { | |
| 1235 | 0 | e.printStackTrace(); |
| 1236 | 0 | System.err.println( |
| 1237 | "Failed to generate alignment with selection restricted and groups marked."); | |
| 1238 | } | |
| 1239 | ||
| 1240 | } | |
| 1241 | } |