2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.datamodel;
20 import java.util.Hashtable;
22 import jalview.analysis.*;
23 import jalview.util.*;
25 public class SeqCigar extends CigarSimple
28 * start(inclusive) and end(exclusive) of subsequence on refseq
30 private int start, end;
32 private SequenceI refseq = null;
34 private Hashtable seqProps;
37 * Reference dataset sequence for the cigar string
41 public SequenceI getRefSeq()
48 * @return int start index of cigar ops on refSeq
57 * @return int end index (exclusive) of cigar ops on refSeq
65 * Returns sequence as a string with cigar operations applied to it
69 public String getSequenceString(char GapChar)
71 return (length == 0) ? "" : (String) getSequenceAndDeletions(
72 refseq.getSequenceAsString(start, end), GapChar)[0];
76 * recreates a gapped and edited version of RefSeq or null for an empty cigar
81 public SequenceI getSeq(char GapChar)
84 if (refseq == null || length == 0)
88 Object[] edit_result = getSequenceAndDeletions(
89 refseq.getSequenceAsString(start, end), GapChar);
90 if (edit_result == null)
93 "Implementation Error - unexpected null from getSequenceAndDeletions");
95 int bounds[] = (int[]) edit_result[1];
96 seq = new Sequence(refseq.getName(), (String) edit_result[0],
97 refseq.getStart() + start + bounds[0], refseq.getStart()
98 + start + ((bounds[2] == 0) ? -1 : bounds[2]));
99 seq.setDescription(refseq.getDescription());
100 int sstart = seq.getStart(), send = seq.getEnd();
101 // seq.checkValidRange(); probably not needed
102 // recover local properties if present
103 if (seqProps != null)
105 // this recovers dataset sequence reference as well as local features,
106 // names, start/end settings.
107 SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
109 // ensure dataset sequence is up to date from local reference
110 seq.setDatasetSequence(refseq);
111 seq.setStart(sstart);
117 * We don't allow this - refseq is given at construction time only public void
118 * setSeq(SequenceI seq) { this.seq = seq; }
121 * internal constructor - sets seq to a gapless sequence derived from seq and
122 * prepends any 'D' operations needed to get to the first residue of seq.
126 * @param initialDeletion
127 * true to mark initial dataset sequence residues as deleted in
130 * index of first position in seq
132 * index after last position in (possibly gapped) seq
133 * @return true if gaps are present in seq
135 private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
138 boolean hasgaps = false;
141 throw new Error("Implementation Error - _setSeq(null,...)");
145 throw new Error("Implementation Error: _s=" + _s);
147 String seq_string = seq.getSequenceAsString();
148 if (_e == 0 || _e < _s || _e > seq_string.length())
150 _e = seq_string.length();
152 // resolve start and end positions relative to ungapped reference sequence
153 start = seq.findPosition(_s) - seq.getStart();
154 end = seq.findPosition(_e) - seq.getStart();
155 int l_ungapped = end - start;
156 // Find correct sequence to reference and correct start and end - if
158 SequenceI ds = seq.getDatasetSequence();
161 // make a new dataset sequence
162 String ungapped = AlignSeq.extractGaps(
163 jalview.util.Comparison.GapChars, new String(seq_string));
164 l_ungapped = ungapped.length();
165 // check that we haven't just duplicated an ungapped sequence.
166 if (l_ungapped == seq.getLength())
172 ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
173 seq.getStart() + ungapped.length() - 1);
174 // JBPNote: this would be consistent but may not be useful
175 // seq.setDatasetSequence(ds);
178 // add in offset between seq and the dataset sequence
179 if (ds.getStart() < seq.getStart())
181 int offset = seq.getStart() - ds.getStart();
184 // absolute cigar string
185 addDeleted(_s + offset);
191 // normal behaviour - just mark start and end subsequence
199 // any gaps to process ?
200 if (l_ungapped != (_e - _s))
206 // copy over local properties for the sequence instance of the refseq
207 seqProps = SeqsetUtils.SeqCharacterHash(seq);
209 if (end > ds.getLength())
212 "SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
213 // end = ds.getLength();
220 * directly initialise a cigar object with a sequence of range, operation
221 * pairs and a sequence to apply it to. operation and range should be relative
222 * to the seq.getStart()'th residue of the dataset seq resolved from seq.
231 public SeqCigar(SequenceI seq, char operation[], int range[])
236 throw new Error("Implementation Bug. Null seq !");
238 if (operation.length != range.length)
241 "Implementation Bug. Cigar Operation list!= range list");
244 if (operation != null)
246 this.operation = new char[operation.length + _inc_length];
247 this.range = new int[operation.length + _inc_length];
249 if (_setSeq(seq, false, 0, 0))
252 "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
254 for (int i = this.length, j = 0; j < operation.length; i++, j++)
256 char op = operation[j];
257 if (op != M && op != I && op != D)
259 throw new Error("Implementation Bug. Cigar Operation '" + j
260 + "' '" + op + "' not one of '" + M + "', '" + I
261 + "', or '" + D + "'.");
263 this.operation[i] = op;
264 this.range[i] = range[j];
266 this.length += operation.length;
270 this.operation = null;
273 if (_setSeq(seq, false, 0, 0))
276 "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
282 * add range matched residues to cigar string
287 public void addMatch(int range)
289 this.addOperation(M, range);
293 * Adds insertion and match operations based on seq to the cigar up to the
294 * endpos column of seq.
304 * @param initialDeletions
305 * if true then initial deletions will be added from start of seq to
308 protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
309 int startpos, int endpos, boolean initialDeletions)
313 int p = 0, res = seq.getLength();
315 if (!initialDeletions)
322 boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
323 .getCharAt(p)) : true;
324 if ((startpos <= p) && (p <= endpos))
328 if (range > 0 && op != I)
330 cigar.addOperation(op, range);
338 if (range > 0 && op != M)
340 cigar.addOperation(op, range);
351 if (range > 0 && op != D)
353 cigar.addOperation(op, range);
361 // do nothing - insertions are not made in flanking regions
368 cigar.addOperation(op, range);
373 * create a cigar string for given sequence
378 public SeqCigar(SequenceI seq)
383 throw new Error("Implementation error for new Cigar(SequenceI)");
385 _setSeq(seq, false, 0, 0);
386 // there is still work to do
387 addSequenceOps(this, seq, 0, seq.getLength() - 1, false);
391 * Create Cigar from a range of gaps and residues on a sequence object
396 * int - first column in range
398 * int - last column in range
400 public SeqCigar(SequenceI seq, int start, int end)
405 throw new Error("Implementation error for new Cigar(SequenceI)");
407 _setSeq(seq, false, start, end + 1);
408 // there is still work to do
409 addSequenceOps(this, seq, start, end, false);
413 * Create a cigar object from a cigar string like '[<I|D|M><range>]+' Will
414 * fail if the given seq already contains gaps (JBPNote: future implementation
418 * SequenceI object resolvable to a dataset sequence
423 public static SeqCigar parseCigar(SequenceI seq, String cigarString)
426 Object[] opsandrange = parseCigarString(cigarString);
427 return new SeqCigar(seq, (char[]) opsandrange[0],
428 (int[]) opsandrange[1]);
436 * @param gapCharacter
438 * @return SequenceI[]
440 public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
441 char gapCharacter, ColumnSelection colsel, int[] segments)
443 SequenceI[] seqs = new SequenceI[alseqs.length];
444 StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
445 String[] alseqs_string = new String[alseqs.length];
446 Object[] gs_regions = new Object[alseqs.length];
447 for (int i = 0; i < alseqs.length; i++)
449 alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
450 alseqs[i].start, alseqs[i].end);
451 gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
452 gapCharacter); // gapped sequence, {start, start col, end.
453 // endcol}, hidden regions {{start, end, col}})
454 if (gs_regions[i] == null)
456 throw new Error("Implementation error: " + i
457 + "'th sequence Cigar has no operations.");
459 g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
464 // Now account for insertions. (well - deletions)
465 // this is complicated because we must keep track of shifted positions in
467 ShiftList shifts = new ShiftList();
468 for (int i = 0; i < alseqs.length; i++)
470 Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]);
471 if (gs_region != null)
474 for (int hr = 0; hr < gs_region.length; hr++)
476 int[] region = (int[]) gs_region[hr];
477 char[] insert = new char[region[1] - region[0] + 1];
478 for (int s = 0; s < insert.length; s++)
480 insert[s] = gapCharacter;
482 int inspos = shifts.shift(region[2]); // resolve insertion position in
483 // current alignment frame of
485 for (int s = 0; s < alseqs.length; s++)
489 if (g_seqs[s].length() <= inspos)
491 // prefix insertion with more gaps.
492 for (int l = inspos - g_seqs[s].length(); l > 0; l--)
494 g_seqs[s].append(gapCharacter); // to debug - use a diffferent
495 // gap character here
498 g_seqs[s].insert(inspos, insert);
502 g_seqs[s].insert(inspos,
503 alseqs_string[i].substring(region[0], region[1] + 1));
506 shifts.addShift(region[2], insert.length); // update shift in
507 // alignment frame of
509 if (segments == null)
511 // add a hidden column for this deletion
512 colsel.hideColumns(inspos, inspos + insert.length - 1);
517 for (int i = 0; i < alseqs.length; i++)
519 int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
520 SequenceI ref = alseqs[i].getRefSeq();
521 seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
522 ref.getStart() + alseqs[i].start + bounds[0], ref.getStart()
523 + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
524 seqs[i].setDatasetSequence(ref);
525 seqs[i].setDescription(ref.getDescription());
527 if (segments != null)
529 for (int i = 0; i < segments.length; i += 3)
531 // int start=shifts.shift(segments[i]-1)+1;
532 // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
533 colsel.hideColumns(segments[i + 1], segments[i + 1]
534 + segments[i + 2] - 1);
541 * non rigorous testing
547 * @param ex_cs_gapped
551 public static String testCigar_string(Sequence seq, String ex_cs_gapped)
553 SeqCigar c_sgapped = new SeqCigar(seq);
554 String cs_gapped = c_sgapped.getCigarstring();
555 if (!cs_gapped.equals(ex_cs_gapped))
557 System.err.println("Failed getCigarstring: incorect string '"
558 + cs_gapped + "' != " + ex_cs_gapped);
563 public static boolean testSeqRecovery(SeqCigar gen_sgapped,
566 // this is non-rigorous - start and end recovery is not tested.
567 SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
568 if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
570 System.err.println("Couldn't reconstruct sequence.\n"
571 + gen_sgapped_s.getSequenceAsString() + "\n"
572 + s_gapped.getSequenceAsString());
578 public static void main(String argv[]) throws Exception
581 Sequence s = new Sequence("MySeq",
582 o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
584 Sequence s_gapped = new Sequence(
586 orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
588 String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
589 s_gapped.setDatasetSequence(s);
591 Sequence s_subsequence_gapped = new Sequence(
593 sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
596 s_subsequence_gapped.setDatasetSequence(s);
597 SeqCigar c_null = new SeqCigar(s);
598 String cs_null = c_null.getCigarstring();
599 if (!cs_null.equals("42M"))
602 .println("Failed to recover ungapped sequence cigar operations:"
603 + ((cs_null == "") ? "empty string" : cs_null));
605 testCigar_string(s_gapped, ex_cs_gapped);
606 SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
607 if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
609 System.err.println("Failed parseCigar(" + ex_cs_gapped
610 + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
613 testSeqRecovery(gen_sgapped, s_gapped);
614 // Test dataset resolution
615 SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
616 if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
619 .println("Failed recovery for subsequence of dataset sequence");
622 if (sub_gapped.getWidth() != sub_gapped_s.length())
624 System.err.println("Failed getWidth()");
627 sub_gapped.getFullWidth();
628 if (sub_gapped.hasDeletedRegions())
630 System.err.println("hasDeletedRegions is incorrect.");
632 // Test start-end region SeqCigar
633 SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
634 if (sub_se_gp.getWidth() != 41)
637 .println("SeqCigar(seq, start, end) not properly clipped alignsequence.");
639 System.out.println("Original sequence align:\n" + sub_gapped_s
640 + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
641 + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
642 + sub_se_gp.getCigarstring() + "\n");
643 SequenceI ssgp = sub_se_gp.getSeq('-');
644 System.out.println("\t " + ssgp.getSequenceAsString());
645 for (int r = 0; r < 10; r++)
647 sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
648 int sl = sub_se_gp.getWidth();
650 for (int rs = 0; rs < 10; rs++)
653 sub_se_gp.deleteRange(st, e);
654 String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
655 System.out.println(st + "," + e + "\t:" + ssgapedseq);
660 SeqCigar[] set = new SeqCigar[]
661 { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
662 new SeqCigar(s_gapped) };
663 Alignment al = new Alignment(set);
664 for (int i = 0; i < al.getHeight(); i++)
666 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
667 + al.getSequenceAt(i).getStart() + "\t"
668 + al.getSequenceAt(i).getEnd() + "\t"
669 + al.getSequenceAt(i).getSequenceAsString());
673 System.out.println("Gapped.");
674 SeqCigar[] set = new SeqCigar[]
675 { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
676 new SeqCigar(s_gapped) };
677 set[0].deleteRange(20, 25);
678 Alignment al = new Alignment(set);
679 for (int i = 0; i < al.getHeight(); i++)
681 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
682 + al.getSequenceAt(i).getStart() + "\t"
683 + al.getSequenceAt(i).getEnd() + "\t"
684 + al.getSequenceAt(i).getSequenceAsString());
687 // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
688 // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());