2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
\r
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.datamodel;
\r
31 * Copyright: Copyright (c) 2004
\r
35 * Company: Dundee University
\r
38 * @author not attributable
\r
41 public class AlignmentView
\r
44 * Transient object compactly representing a 'view' of an alignment - with
\r
45 * discontinuities marked.
\r
47 private SeqCigar[] sequences = null;
\r
49 private int[] contigs = null;
\r
51 private int width = 0;
\r
53 private int firstCol = 0;
\r
55 public AlignmentView(CigarArray seqcigararray)
\r
57 if (!seqcigararray.isSeqCigarArray())
\r
60 "Implementation Error - can only make an alignment view from a CigarArray of sequences.");
\r
62 // contigs = seqcigararray.applyDeletions();
\r
63 contigs = seqcigararray.getDeletedRegions();
\r
64 sequences = seqcigararray.getSeqCigarArray();
\r
65 width = seqcigararray.getWidth(); // visible width
\r
69 * Create an alignmentView where the first column corresponds with the
\r
70 * 'firstcol' column of some reference alignment
\r
75 public AlignmentView(CigarArray sdata, int firstcol)
\r
78 firstCol = firstcol;
\r
81 public void setSequences(SeqCigar[] sequences)
\r
83 this.sequences = sequences;
\r
86 public void setContigs(int[] contigs)
\r
88 this.contigs = contigs;
\r
91 public SeqCigar[] getSequences()
\r
97 * @see CigarArray.getDeletedRegions
\r
98 * @return int[] { vis_start, sym_start, length }
\r
100 public int[] getContigs()
\r
106 * get the full alignment and a columnselection object marking the hidden
\r
109 * @param gapCharacter
\r
111 * @return Object[] { SequenceI[], ColumnSelection}
\r
113 public Object[] getAlignmentAndColumnSelection(char gapCharacter)
\r
115 ColumnSelection colsel = new ColumnSelection();
\r
117 return new Object[]
\r
119 SeqCigar.createAlignmentSequences(sequences, gapCharacter, colsel,
\r
120 contigs), colsel };
\r
124 * getSequenceStrings
\r
130 public String[] getSequenceStrings(char c)
\r
132 String[] seqs = new String[sequences.length];
\r
133 for (int n = 0; n < sequences.length; n++)
\r
135 String fullseq = sequences[n].getSequenceString(c);
\r
136 if (contigs != null)
\r
140 for (int h = 0; h < contigs.length; h += 3)
\r
142 seqs[n] += fullseq.substring(p, contigs[h + 1]);
\r
143 p = contigs[h + 1] + contigs[h + 2];
\r
145 seqs[n] += fullseq.substring(p);
\r
157 * @return visible number of columns in alignment view
\r
159 public int getWidth()
\r
164 protected void setWidth(int width)
\r
166 this.width = width;
\r
170 * get the contiguous subalignments in an alignment view.
\r
172 * @param gapCharacter
\r
174 * @return SequenceI[][]
\r
176 public SequenceI[][] getVisibleContigs(char gapCharacter)
\r
178 SequenceI[][] smsa;
\r
180 if (sequences == null || width <= 0)
\r
184 if (contigs != null && contigs.length > 0)
\r
188 int fwidth = width;
\r
189 for (int contig = 0; contig < contigs.length; contig += 3)
\r
191 if ((contigs[contig + 1] - start) > 0)
\r
195 fwidth += contigs[contig + 2]; // end up with full region width
\r
196 // (including hidden regions)
\r
197 start = contigs[contig + 1] + contigs[contig + 2];
\r
199 if (start < fwidth)
\r
203 smsa = new SequenceI[njobs][];
\r
206 for (int contig = 0; contig < contigs.length; contig += 3)
\r
208 if (contigs[contig + 1] - start > 0)
\r
210 SequenceI mseq[] = new SequenceI[sequences.length];
\r
211 for (int s = 0; s < mseq.length; s++)
\r
213 mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(
\r
214 start, contigs[contig + 1]);
\r
219 start = contigs[contig + 1] + contigs[contig + 2];
\r
221 if (start < fwidth)
\r
223 SequenceI mseq[] = new SequenceI[sequences.length];
\r
224 for (int s = 0; s < mseq.length; s++)
\r
226 mseq[s] = sequences[s].getSeq(gapCharacter).getSubSequence(start,
\r
235 smsa = new SequenceI[1][];
\r
236 smsa[0] = new SequenceI[sequences.length];
\r
237 for (int s = 0; s < sequences.length; s++)
\r
239 smsa[0][s] = sequences[s].getSeq(gapCharacter);
\r
246 * return full msa and hidden regions with visible blocks replaced with new
\r
252 * AlignmentOrder[] corresponding to each SequenceI[] block.
\r
255 public Object[] getUpdatedView(SequenceI[][] nvismsa,
\r
256 AlignmentOrder[] orders, char gapCharacter)
\r
258 if (sequences == null || width <= 0)
\r
260 throw new Error("empty view cannot be updated.");
\r
262 if (nvismsa == null)
\r
265 "nvismsa==null. use getAlignmentAndColumnSelection() instead.");
\r
267 if (contigs != null && contigs.length > 0)
\r
269 SequenceI[] alignment = new SequenceI[sequences.length];
\r
270 ColumnSelection columnselection = new ColumnSelection();
\r
271 if (contigs != null && contigs.length > 0)
\r
275 int owidth = width;
\r
277 for (int contig = 0; contig < contigs.length; contig += 3)
\r
279 owidth += contigs[contig + 2]; // recover final column width
\r
280 if (contigs[contig + 1] - start > 0)
\r
282 int swidth = 0; // subalignment width
\r
283 if (nvismsa[j] != null)
\r
285 SequenceI mseq[] = nvismsa[j];
\r
286 AlignmentOrder order = (orders == null) ? null : orders[j];
\r
288 if (mseq.length != sequences.length)
\r
291 "Mismatch between number of sequences in block "
\r
292 + j + " (" + mseq.length
\r
293 + ") and the original view ("
\r
294 + sequences.length + ")");
\r
296 swidth = mseq[0].getLength(); // JBPNote: could ensure padded
\r
298 for (int s = 0; s < mseq.length; s++)
\r
300 if (alignment[s] == null)
\r
302 alignment[s] = mseq[s];
\r
306 alignment[s].setSequence(alignment[s]
\r
307 .getSequenceAsString()
\r
308 + mseq[s].getSequenceAsString());
\r
309 if (mseq[s].getStart() <= mseq[s].getEnd())
\r
311 alignment[s].setEnd(mseq[s].getEnd());
\r
315 order.updateSequence(mseq[s], alignment[s]);
\r
322 // recover original alignment block or place gaps
\r
325 // recover input data
\r
326 for (int s = 0; s < sequences.length; s++)
\r
328 SequenceI oseq = sequences[s].getSeq(gapCharacter)
\r
329 .getSubSequence(start, contigs[contig + 1]);
\r
330 if (swidth < oseq.getLength())
\r
332 swidth = oseq.getLength();
\r
334 if (alignment[s] == null)
\r
336 alignment[s] = oseq;
\r
340 alignment[s].setSequence(alignment[s]
\r
341 .getSequenceAsString()
\r
342 + oseq.getSequenceAsString());
\r
343 if (oseq.getEnd() >= oseq.getStart())
\r
345 alignment[s].setEnd(oseq.getEnd());
\r
355 // advance to begining of visible region
\r
356 start = contigs[contig + 1] + contigs[contig + 2];
\r
357 // add hidden segment to right of next region
\r
358 for (int s = 0; s < sequences.length; s++)
\r
360 SequenceI hseq = sequences[s].getSeq(gapCharacter)
\r
361 .getSubSequence(contigs[contig + 1], start);
\r
362 if (alignment[s] == null)
\r
364 alignment[s] = hseq;
\r
368 alignment[s].setSequence(alignment[s].getSequenceAsString()
\r
369 + hseq.getSequenceAsString());
\r
370 if (hseq.getEnd() >= hseq.getStart())
\r
372 alignment[s].setEnd(hseq.getEnd());
\r
376 // mark hidden segment as hidden in the new alignment
\r
377 columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2]
\r
379 nwidth += contigs[contig + 2];
\r
381 // Do final segment - if it exists
\r
382 if (j < nvismsa.length)
\r
385 if (nvismsa[j] != null)
\r
387 SequenceI mseq[] = nvismsa[j];
\r
388 AlignmentOrder order = (orders != null) ? orders[j] : null;
\r
389 swidth = mseq[0].getLength();
\r
390 for (int s = 0; s < mseq.length; s++)
\r
392 if (alignment[s] == null)
\r
394 alignment[s] = mseq[s];
\r
398 alignment[s].setSequence(alignment[s].getSequenceAsString()
\r
399 + mseq[s].getSequenceAsString());
\r
400 if (mseq[s].getEnd() >= mseq[s].getStart())
\r
402 alignment[s].setEnd(mseq[s].getEnd());
\r
406 order.updateSequence(mseq[s], alignment[s]);
\r
413 if (start < owidth)
\r
415 // recover input data or place gaps
\r
418 // recover input data
\r
419 for (int s = 0; s < sequences.length; s++)
\r
421 SequenceI oseq = sequences[s].getSeq(gapCharacter)
\r
422 .getSubSequence(start, owidth + 1);
\r
423 if (swidth < oseq.getLength())
\r
425 swidth = oseq.getLength();
\r
427 if (alignment[s] == null)
\r
429 alignment[s] = oseq;
\r
433 alignment[s].setSequence(alignment[s]
\r
434 .getSequenceAsString()
\r
435 + oseq.getSequenceAsString());
\r
436 if (oseq.getEnd() >= oseq.getStart())
\r
438 alignment[s].setEnd(oseq.getEnd());
\r
447 throw new Error("Padding not yet implemented.");
\r
453 return new Object[]
\r
454 { alignment, columnselection };
\r
458 if (nvismsa.length != 1)
\r
461 "Mismatch between visible blocks to update and number of contigs in view (contigs=0,blocks="
\r
464 if (nvismsa[0] != null)
\r
466 return new Object[]
\r
467 { nvismsa[0], new ColumnSelection() };
\r
471 return getAlignmentAndColumnSelection(gapCharacter);
\r
477 * returns simple array of start end positions of visible range on alignment.
\r
478 * vis_start and vis_end are inclusive - use
\r
479 * SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence
\r
480 * from underlying alignment.
\r
482 * @return int[] { start_i, end_i } for 1<i<n visible regions.
\r
484 public int[] getVisibleContigs()
\r
486 if (contigs != null && contigs.length > 0)
\r
490 int fwidth = width;
\r
491 for (int contig = 0; contig < contigs.length; contig += 3)
\r
493 if ((contigs[contig + 1] - start) > 0)
\r
497 fwidth += contigs[contig + 2]; // end up with full region width
\r
498 // (including hidden regions)
\r
499 start = contigs[contig + 1] + contigs[contig + 2];
\r
501 if (start < fwidth)
\r
505 int viscontigs[] = new int[nvis * 2];
\r
508 for (int contig = 0; contig < contigs.length; contig += 3)
\r
510 if ((contigs[contig + 1] - start) > 0)
\r
512 viscontigs[nvis] = start;
\r
513 viscontigs[nvis + 1] = contigs[contig + 1] - 1; // end is inclusive
\r
516 start = contigs[contig + 1] + contigs[contig + 2];
\r
518 if (start < fwidth)
\r
520 viscontigs[nvis] = start;
\r
521 viscontigs[nvis + 1] = fwidth; // end is inclusive
\r
535 * @return position of first visible column of AlignmentView within its
\r
536 * parent's alignment reference frame
\r
538 public int getAlignmentOrigin()
\r
540 // TODO Auto-generated method stub
\r