2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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(refseq
72 .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(refseq
89 .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], refseq
98 + start + bounds[0], refseq.getStart() + start
99 + ((bounds[2] == 0) ? -1 : bounds[2]));
100 seq.setDescription(refseq.getDescription());
101 int sstart = seq.getStart(), send = seq.getEnd();
102 // seq.checkValidRange(); probably not needed
103 // recover local properties if present
104 if (seqProps != null)
106 // this recovers dataset sequence reference as well as local features,
107 // names, start/end settings.
108 SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
110 // ensure dataset sequence is up to date from local reference
111 seq.setDatasetSequence(refseq);
112 seq.setStart(sstart);
118 * We don't allow this - refseq is given at construction time only public void
119 * setSeq(SequenceI seq) { this.seq = seq; }
122 * internal constructor - sets seq to a gapless sequence derived from seq and
123 * prepends any 'D' operations needed to get to the first residue of seq.
127 * @param initialDeletion
128 * true to mark initial dataset sequence residues as deleted in
131 * index of first position in seq
133 * index after last position in (possibly gapped) seq
134 * @return true if gaps are present in seq
136 private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
139 boolean hasgaps = false;
142 throw new Error("Implementation Error - _setSeq(null,...)");
146 throw new Error("Implementation Error: _s=" + _s);
148 String seq_string = seq.getSequenceAsString();
149 if (_e == 0 || _e < _s || _e > seq_string.length())
151 _e = seq_string.length();
153 // resolve start and end positions relative to ungapped reference sequence
154 start = seq.findPosition(_s) - seq.getStart();
155 end = seq.findPosition(_e) - seq.getStart();
156 int l_ungapped = end - start;
157 // Find correct sequence to reference and correct start and end - if
159 SequenceI ds = seq.getDatasetSequence();
162 // make a new dataset sequence
163 String ungapped = AlignSeq.extractGaps(
164 jalview.util.Comparison.GapChars, new String(seq_string));
165 l_ungapped = ungapped.length();
166 // check that we haven't just duplicated an ungapped sequence.
167 if (l_ungapped == seq.getLength())
173 ds = new Sequence(seq.getName(), ungapped, seq.getStart(), seq
175 + ungapped.length() - 1);
176 // JBPNote: this would be consistent but may not be useful
177 // seq.setDatasetSequence(ds);
180 // add in offset between seq and the dataset sequence
181 if (ds.getStart() < seq.getStart())
183 int offset = seq.getStart() - ds.getStart();
186 // absolute cigar string
187 addDeleted(_s + offset);
193 // normal behaviour - just mark start and end subsequence
201 // any gaps to process ?
202 if (l_ungapped != (_e - _s))
208 // copy over local properties for the sequence instance of the refseq
209 seqProps = SeqsetUtils.SeqCharacterHash(seq);
211 if (end > ds.getLength())
214 "SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
215 // end = ds.getLength();
222 * directly initialise a cigar object with a sequence of range, operation
223 * pairs and a sequence to apply it to. operation and range should be relative
224 * to the seq.getStart()'th residue of the dataset seq resolved from seq.
233 public SeqCigar(SequenceI seq, char operation[], int range[])
238 throw new Error("Implementation Bug. Null seq !");
240 if (operation.length != range.length)
243 "Implementation Bug. Cigar Operation list!= range list");
246 if (operation != null)
248 this.operation = new char[operation.length + _inc_length];
249 this.range = new int[operation.length + _inc_length];
251 if (_setSeq(seq, false, 0, 0))
254 "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
256 for (int i = this.length, j = 0; j < operation.length; i++, j++)
258 char op = operation[j];
259 if (op != M && op != I && op != D)
261 throw new Error("Implementation Bug. Cigar Operation '" + j
262 + "' '" + op + "' not one of '" + M + "', '" + I
263 + "', or '" + D + "'.");
265 this.operation[i] = op;
266 this.range[i] = range[j];
268 this.length += operation.length;
272 this.operation = null;
275 if (_setSeq(seq, false, 0, 0))
278 "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
284 * add range matched residues to cigar string
289 public void addMatch(int range)
291 this.addOperation(M, range);
295 * Adds insertion and match operations based on seq to the cigar up to the
296 * endpos column of seq.
306 * @param initialDeletions
307 * if true then initial deletions will be added from start of seq to
310 protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
311 int startpos, int endpos, boolean initialDeletions)
315 int p = 0, res = seq.getLength();
317 if (!initialDeletions)
324 boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
325 .getCharAt(p)) : true;
326 if ((startpos <= p) && (p <= endpos))
330 if (range > 0 && op != I)
332 cigar.addOperation(op, range);
340 if (range > 0 && op != M)
342 cigar.addOperation(op, range);
353 if (range > 0 && op != D)
355 cigar.addOperation(op, range);
363 // do nothing - insertions are not made in flanking regions
370 cigar.addOperation(op, range);
375 * create a cigar string for given sequence
380 public SeqCigar(SequenceI seq)
385 throw new Error("Implementation error for new Cigar(SequenceI)");
387 _setSeq(seq, false, 0, 0);
388 // there is still work to do
389 addSequenceOps(this, seq, 0, seq.getLength() - 1, false);
393 * Create Cigar from a range of gaps and residues on a sequence object
398 * int - first column in range
400 * int - last column in range
402 public SeqCigar(SequenceI seq, int start, int end)
407 throw new Error("Implementation error for new Cigar(SequenceI)");
409 _setSeq(seq, false, start, end + 1);
410 // there is still work to do
411 addSequenceOps(this, seq, start, end, false);
415 * Create a cigar object from a cigar string like '[<I|D|M><range>]+' Will
416 * fail if the given seq already contains gaps (JBPNote: future implementation
420 * SequenceI object resolvable to a dataset sequence
425 public static SeqCigar parseCigar(SequenceI seq, String cigarString)
428 Object[] opsandrange = parseCigarString(cigarString);
429 return new SeqCigar(seq, (char[]) opsandrange[0],
430 (int[]) opsandrange[1]);
438 * @param gapCharacter
440 * @return SequenceI[]
442 public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
443 char gapCharacter, ColumnSelection colsel, int[] segments)
445 SequenceI[] seqs = new SequenceI[alseqs.length];
446 StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
447 String[] alseqs_string = new String[alseqs.length];
448 Object[] gs_regions = new Object[alseqs.length];
449 for (int i = 0; i < alseqs.length; i++)
451 alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
452 alseqs[i].start, alseqs[i].end);
453 gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
454 gapCharacter); // gapped sequence, {start, start col, end.
455 // endcol}, hidden regions {{start, end, col}})
456 if (gs_regions[i] == null)
458 throw new Error("Implementation error: " + i
459 + "'th sequence Cigar has no operations.");
461 g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
466 // Now account for insertions. (well - deletions)
467 // this is complicated because we must keep track of shifted positions in
469 ShiftList shifts = new ShiftList();
470 for (int i = 0; i < alseqs.length; i++)
472 Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]);
473 if (gs_region != null)
476 for (int hr = 0; hr < gs_region.length; hr++)
478 int[] region = (int[]) gs_region[hr];
479 char[] insert = new char[region[1] - region[0] + 1];
480 for (int s = 0; s < insert.length; s++)
482 insert[s] = gapCharacter;
484 int inspos = shifts.shift(region[2]); // resolve insertion position in
485 // current alignment frame of
487 for (int s = 0; s < alseqs.length; s++)
491 if (g_seqs[s].length() <= inspos)
493 // prefix insertion with more gaps.
494 for (int l = inspos - g_seqs[s].length(); l > 0; l--)
496 g_seqs[s].append(gapCharacter); // to debug - use a diffferent
497 // gap character here
500 g_seqs[s].insert(inspos, insert);
504 g_seqs[s].insert(inspos, alseqs_string[i].substring(
505 region[0], region[1] + 1));
508 shifts.addShift(region[2], insert.length); // update shift in
509 // alignment frame of
511 if (segments == null)
513 // add a hidden column for this deletion
514 colsel.hideColumns(inspos, inspos + insert.length - 1);
519 for (int i = 0; i < alseqs.length; i++)
521 int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
522 SequenceI ref = alseqs[i].getRefSeq();
523 seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(), ref
525 + alseqs[i].start + bounds[0], ref.getStart()
526 + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
527 seqs[i].setDatasetSequence(ref);
528 seqs[i].setDescription(ref.getDescription());
530 if (segments != null)
532 for (int i = 0; i < segments.length; i += 3)
534 // int start=shifts.shift(segments[i]-1)+1;
535 // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
536 colsel.hideColumns(segments[i + 1], segments[i + 1]
537 + segments[i + 2] - 1);
544 * non rigorous testing
550 * @param ex_cs_gapped
554 public static String testCigar_string(Sequence seq, String ex_cs_gapped)
556 SeqCigar c_sgapped = new SeqCigar(seq);
557 String cs_gapped = c_sgapped.getCigarstring();
558 if (!cs_gapped.equals(ex_cs_gapped))
560 System.err.println("Failed getCigarstring: incorect string '"
561 + cs_gapped + "' != " + ex_cs_gapped);
566 public static boolean testSeqRecovery(SeqCigar gen_sgapped,
569 // this is non-rigorous - start and end recovery is not tested.
570 SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
571 if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
573 System.err.println("Couldn't reconstruct sequence.\n"
574 + gen_sgapped_s.getSequenceAsString() + "\n"
575 + s_gapped.getSequenceAsString());
581 public static void main(String argv[]) throws Exception
584 Sequence s = new Sequence("MySeq",
585 o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
587 Sequence s_gapped = new Sequence(
589 orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
591 String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
592 s_gapped.setDatasetSequence(s);
594 Sequence s_subsequence_gapped = new Sequence(
596 sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
599 s_subsequence_gapped.setDatasetSequence(s);
600 SeqCigar c_null = new SeqCigar(s);
601 String cs_null = c_null.getCigarstring();
602 if (!cs_null.equals("42M"))
605 .println("Failed to recover ungapped sequence cigar operations:"
606 + ((cs_null == "") ? "empty string" : cs_null));
608 testCigar_string(s_gapped, ex_cs_gapped);
609 SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
610 if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
612 System.err.println("Failed parseCigar(" + ex_cs_gapped
613 + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
616 testSeqRecovery(gen_sgapped, s_gapped);
617 // Test dataset resolution
618 SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
619 if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
622 .println("Failed recovery for subsequence of dataset sequence");
625 if (sub_gapped.getWidth() != sub_gapped_s.length())
627 System.err.println("Failed getWidth()");
630 sub_gapped.getFullWidth();
631 if (sub_gapped.hasDeletedRegions())
633 System.err.println("hasDeletedRegions is incorrect.");
635 // Test start-end region SeqCigar
636 SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
637 if (sub_se_gp.getWidth() != 41)
640 .println("SeqCigar(seq, start, end) not properly clipped alignsequence.");
642 System.out.println("Original sequence align:\n" + sub_gapped_s
643 + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
644 + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
645 + sub_se_gp.getCigarstring() + "\n");
646 SequenceI ssgp = sub_se_gp.getSeq('-');
647 System.out.println("\t " + ssgp.getSequenceAsString());
648 for (int r = 0; r < 10; r++)
650 sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
651 int sl = sub_se_gp.getWidth();
653 for (int rs = 0; rs < 10; rs++)
656 sub_se_gp.deleteRange(st, e);
657 String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
658 System.out.println(st + "," + e + "\t:" + ssgapedseq);
663 SeqCigar[] set = new SeqCigar[]
664 { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
665 new SeqCigar(s_gapped) };
666 Alignment al = new Alignment(set);
667 for (int i = 0; i < al.getHeight(); i++)
669 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
670 + al.getSequenceAt(i).getStart() + "\t"
671 + al.getSequenceAt(i).getEnd() + "\t"
672 + al.getSequenceAt(i).getSequenceAsString());
676 System.out.println("Gapped.");
677 SeqCigar[] set = new SeqCigar[]
678 { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
679 new SeqCigar(s_gapped) };
680 set[0].deleteRange(20, 25);
681 Alignment al = new Alignment(set);
682 for (int i = 0; i < al.getHeight(); i++)
684 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
685 + al.getSequenceAt(i).getStart() + "\t"
686 + al.getSequenceAt(i).getEnd() + "\t"
687 + al.getSequenceAt(i).getSequenceAsString());
690 // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
691 // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());