2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
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
10 * of the License, or (at your option) any later version.
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.
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.
21 package jalview.datamodel;
23 import java.util.Enumeration;
24 import java.util.Hashtable;
26 import jalview.analysis.*;
27 import jalview.util.*;
29 public class SeqCigar extends CigarSimple
32 * start(inclusive) and end(exclusive) of subsequence on refseq
34 private int start, end;
36 private SequenceI refseq = null;
38 private Hashtable seqProps;
41 * Reference dataset sequence for the cigar string
45 public SequenceI getRefSeq()
52 * @return int start index of cigar ops on refSeq
61 * @return int end index (exclusive) of cigar ops on refSeq
69 * Returns sequence as a string with cigar operations applied to it
73 public String getSequenceString(char GapChar)
75 return (length == 0) ? "" : (String) getSequenceAndDeletions(
76 refseq.getSequenceAsString(start, end), GapChar)[0];
80 * recreates a gapped and edited version of RefSeq or null for an empty cigar
85 public SequenceI getSeq(char GapChar)
88 if (refseq == null || length == 0)
92 Object[] edit_result = getSequenceAndDeletions(
93 refseq.getSequenceAsString(start, end), GapChar);
94 if (edit_result == null)
97 "Implementation Error - unexpected null from getSequenceAndDeletions");
99 int bounds[] = (int[]) edit_result[1];
100 seq = new Sequence(refseq.getName(), (String) edit_result[0],
101 refseq.getStart() + start + bounds[0], refseq.getStart()
102 + start + ((bounds[2] == 0) ? -1 : bounds[2]));
103 seq.setDescription(refseq.getDescription());
104 int sstart = seq.getStart(), send = seq.getEnd();
105 // seq.checkValidRange(); probably not needed
106 // recover local properties if present
107 if (seqProps != null)
109 // this recovers dataset sequence reference as well as local features,
110 // names, start/end settings.
111 SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
113 // ensure dataset sequence is up to date from local reference
114 seq.setDatasetSequence(refseq);
115 seq.setStart(sstart);
121 * We don't allow this - refseq is given at construction time only public void
122 * setSeq(SequenceI seq) { this.seq = seq; }
125 * internal constructor - sets seq to a gapless sequence derived from seq and
126 * prepends any 'D' operations needed to get to the first residue of seq.
130 * @param initialDeletion
131 * true to mark initial dataset sequence residues as deleted in
134 * index of first position in seq
136 * index after last position in (possibly gapped) seq
137 * @return true if gaps are present in seq
139 private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
142 boolean hasgaps = false;
145 throw new Error("Implementation Error - _setSeq(null,...)");
149 throw new Error("Implementation Error: _s=" + _s);
151 String seq_string = seq.getSequenceAsString();
152 if (_e == 0 || _e < _s || _e > seq_string.length())
154 _e = seq_string.length();
156 // resolve start and end positions relative to ungapped reference sequence
157 start = seq.findPosition(_s) - seq.getStart();
158 end = seq.findPosition(_e) - seq.getStart();
159 int l_ungapped = end - start;
160 // Find correct sequence to reference and correct start and end - if
162 SequenceI ds = seq.getDatasetSequence();
165 // make a new dataset sequence
166 String ungapped = AlignSeq.extractGaps(
167 jalview.util.Comparison.GapChars, new String(seq_string));
168 l_ungapped = ungapped.length();
169 // check that we haven't just duplicated an ungapped sequence.
170 if (l_ungapped == seq.getLength())
176 ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
177 seq.getStart() + ungapped.length() - 1);
178 // JBPNote: this would be consistent but may not be useful
179 // seq.setDatasetSequence(ds);
182 // add in offset between seq and the dataset sequence
183 if (ds.getStart() < seq.getStart())
185 int offset = seq.getStart() - ds.getStart();
188 // absolute cigar string
189 addDeleted(_s + offset);
195 // normal behaviour - just mark start and end subsequence
203 // any gaps to process ?
204 if (l_ungapped != (_e - _s))
210 // copy over local properties for the sequence instance of the refseq
211 seqProps = SeqsetUtils.SeqCharacterHash(seq);
213 if (end > ds.getLength())
216 "SeqCigar: Possible implementation error: sequence is longer than dataset sequence");
217 // end = ds.getLength();
224 * directly initialise a cigar object with a sequence of range, operation
225 * pairs and a sequence to apply it to. operation and range should be relative
226 * to the seq.getStart()'th residue of the dataset seq resolved from seq.
235 public SeqCigar(SequenceI seq, char operation[], int range[])
240 throw new Error("Implementation Bug. Null seq !");
242 if (operation.length != range.length)
245 "Implementation Bug. Cigar Operation list!= range list");
248 if (operation != null)
250 this.operation = new char[operation.length + _inc_length];
251 this.range = new int[operation.length + _inc_length];
253 if (_setSeq(seq, false, 0, 0))
256 "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
258 for (int i = this.length, j = 0; j < operation.length; i++, j++)
260 char op = operation[j];
261 if (op != M && op != I && op != D)
263 throw new Error("Implementation Bug. Cigar Operation '" + j
264 + "' '" + op + "' not one of '" + M + "', '" + I
265 + "', or '" + D + "'.");
267 this.operation[i] = op;
268 this.range[i] = range[j];
270 this.length += operation.length;
274 this.operation = null;
277 if (_setSeq(seq, false, 0, 0))
280 "NOT YET Implemented: Constructing a Cigar object from a cigar string and a gapped sequence.");
286 * add range matched residues to cigar string
291 public void addMatch(int range)
293 this.addOperation(M, range);
297 * Adds insertion and match operations based on seq to the cigar up to the
298 * endpos column of seq.
308 * @param initialDeletions
309 * if true then initial deletions will be added from start of seq to
312 protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
313 int startpos, int endpos, boolean initialDeletions)
317 int p = 0, res = seq.getLength();
319 if (!initialDeletions)
326 boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
327 .getCharAt(p)) : true;
328 if ((startpos <= p) && (p <= endpos))
332 if (range > 0 && op != I)
334 cigar.addOperation(op, range);
342 if (range > 0 && op != M)
344 cigar.addOperation(op, range);
355 if (range > 0 && op != D)
357 cigar.addOperation(op, range);
365 // do nothing - insertions are not made in flanking regions
372 cigar.addOperation(op, range);
377 * create a cigar string for given sequence
382 public SeqCigar(SequenceI seq)
387 throw new Error("Implementation error for new Cigar(SequenceI)");
389 _setSeq(seq, false, 0, 0);
390 // there is still work to do
391 addSequenceOps(this, seq, 0, seq.getLength() - 1, false);
395 * Create Cigar from a range of gaps and residues on a sequence object
400 * int - first column in range
402 * int - last column in range
404 public SeqCigar(SequenceI seq, int start, int end)
409 throw new Error("Implementation error for new Cigar(SequenceI)");
411 _setSeq(seq, false, start, end + 1);
412 // there is still work to do
413 addSequenceOps(this, seq, start, end, false);
417 * Create a cigar object from a cigar string like '[<I|D|M><range>]+' Will
418 * fail if the given seq already contains gaps (JBPNote: future implementation
422 * SequenceI object resolvable to a dataset sequence
427 public static SeqCigar parseCigar(SequenceI seq, String cigarString)
430 Object[] opsandrange = parseCigarString(cigarString);
431 return new SeqCigar(seq, (char[]) opsandrange[0],
432 (int[]) opsandrange[1]);
436 * create an alignment from the given array of cigar sequences and gap
437 * character, and marking the given segments as visible in the given
441 * @param gapCharacter
443 * - columnSelection where hidden regions are marked
445 * - visible regions of alignment
446 * @return SequenceI[]
448 public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
449 char gapCharacter, ColumnSelection colsel, int[] segments)
451 SequenceI[] seqs = new SequenceI[alseqs.length];
452 StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
453 String[] alseqs_string = new String[alseqs.length];
454 Object[] gs_regions = new Object[alseqs.length];
455 for (int i = 0; i < alseqs.length; i++)
457 alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
458 alseqs[i].start, alseqs[i].end);
459 gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
460 gapCharacter); // gapped sequence, {start, start col, end.
461 // endcol}, hidden regions {{start, end, col}})
462 if (gs_regions[i] == null)
464 throw new Error("Implementation error: " + i
465 + "'th sequence Cigar has no operations.");
467 g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
472 // Now account for insertions. (well - deletions)
473 // this is complicated because we must keep track of shifted positions in
475 ShiftList shifts = new ShiftList();
476 for (int i = 0; i < alseqs.length; i++)
478 Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]);
479 if (gs_region != null)
482 for (int hr = 0; hr < gs_region.length; hr++)
484 int[] region = (int[]) gs_region[hr];
485 char[] insert = new char[region[1] - region[0] + 1];
486 for (int s = 0; s < insert.length; s++)
488 insert[s] = gapCharacter;
490 int inspos = shifts.shift(region[2]); // resolve insertion position in
491 // current alignment frame of
493 for (int s = 0; s < alseqs.length; s++)
497 if (g_seqs[s].length() <= inspos)
499 // prefix insertion with more gaps.
500 for (int l = inspos - g_seqs[s].length(); l > 0; l--)
502 g_seqs[s].append(gapCharacter); // to debug - use a diffferent
503 // gap character here
506 g_seqs[s].insert(inspos, insert);
510 g_seqs[s].insert(inspos,
511 alseqs_string[i].substring(region[0], region[1] + 1));
514 shifts.addShift(region[2], insert.length); // update shift in
515 // alignment frame of
517 if (segments == null)
519 // add a hidden column for this deletion
520 colsel.hideColumns(inspos, inspos + insert.length - 1);
525 for (int i = 0; i < alseqs.length; i++)
527 int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
528 SequenceI ref = alseqs[i].getRefSeq();
529 seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
530 ref.getStart() + alseqs[i].start + bounds[0], ref.getStart()
531 + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
532 seqs[i].setDatasetSequence(ref);
533 seqs[i].setDescription(ref.getDescription());
535 if (segments != null)
537 for (int i = 0; i < segments.length; i += 3)
539 // int start=shifts.shift(segments[i]-1)+1;
540 // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
541 colsel.hideColumns(segments[i + 1], segments[i + 1]
542 + segments[i + 2] - 1);
549 * non rigorous testing
555 * @param ex_cs_gapped
559 public static String testCigar_string(Sequence seq, String ex_cs_gapped)
561 SeqCigar c_sgapped = new SeqCigar(seq);
562 String cs_gapped = c_sgapped.getCigarstring();
563 if (!cs_gapped.equals(ex_cs_gapped))
565 System.err.println("Failed getCigarstring: incorect string '"
566 + cs_gapped + "' != " + ex_cs_gapped);
571 public static boolean testSeqRecovery(SeqCigar gen_sgapped,
574 // this is non-rigorous - start and end recovery is not tested.
575 SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
576 if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
578 System.err.println("Couldn't reconstruct sequence.\n"
579 + gen_sgapped_s.getSequenceAsString() + "\n"
580 + s_gapped.getSequenceAsString());
586 public static void main(String argv[]) throws Exception
589 Sequence s = new Sequence("MySeq",
590 o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
592 Sequence s_gapped = new Sequence(
594 orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
596 String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
597 s_gapped.setDatasetSequence(s);
599 Sequence s_subsequence_gapped = new Sequence(
601 sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
604 s_subsequence_gapped.setDatasetSequence(s);
605 SeqCigar c_null = new SeqCigar(s);
606 String cs_null = c_null.getCigarstring();
607 if (!cs_null.equals("42M"))
610 .println("Failed to recover ungapped sequence cigar operations:"
611 + ((cs_null == "") ? "empty string" : cs_null));
613 testCigar_string(s_gapped, ex_cs_gapped);
614 SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
615 if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
617 System.err.println("Failed parseCigar(" + ex_cs_gapped
618 + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
621 testSeqRecovery(gen_sgapped, s_gapped);
622 // Test dataset resolution
623 SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
624 if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
627 .println("Failed recovery for subsequence of dataset sequence");
630 if (sub_gapped.getWidth() != sub_gapped_s.length())
632 System.err.println("Failed getWidth()");
635 sub_gapped.getFullWidth();
636 if (sub_gapped.hasDeletedRegions())
638 System.err.println("hasDeletedRegions is incorrect.");
640 // Test start-end region SeqCigar
641 SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
642 if (sub_se_gp.getWidth() != 41)
645 .println("SeqCigar(seq, start, end) not properly clipped alignsequence.");
647 System.out.println("Original sequence align:\n" + sub_gapped_s
648 + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
649 + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
650 + sub_se_gp.getCigarstring() + "\n");
651 SequenceI ssgp = sub_se_gp.getSeq('-');
652 System.out.println("\t " + ssgp.getSequenceAsString());
653 for (int r = 0; r < 10; r++)
655 sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
656 int sl = sub_se_gp.getWidth();
658 for (int rs = 0; rs < 10; rs++)
661 sub_se_gp.deleteRange(st, e);
662 String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
663 System.out.println(st + "," + e + "\t:" + ssgapedseq);
668 SeqCigar[] set = new SeqCigar[]
669 { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
670 new SeqCigar(s_gapped) };
671 Alignment al = new Alignment(set);
672 for (int i = 0; i < al.getHeight(); i++)
674 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
675 + al.getSequenceAt(i).getStart() + "\t"
676 + al.getSequenceAt(i).getEnd() + "\t"
677 + al.getSequenceAt(i).getSequenceAsString());
681 System.out.println("Gapped.");
682 SeqCigar[] set = new SeqCigar[]
683 { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
684 new SeqCigar(s_gapped) };
685 set[0].deleteRange(20, 25);
686 Alignment al = new Alignment(set);
687 for (int i = 0; i < al.getHeight(); i++)
689 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
690 + al.getSequenceAt(i).getStart() + "\t"
691 + al.getSequenceAt(i).getEnd() + "\t"
692 + al.getSequenceAt(i).getSequenceAsString());
695 // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
696 // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
700 * references to entities that this sequence cigar is associated with.
702 private Hashtable selGroups = null;
704 public void setGroupMembership(Object group)
706 if (selGroups == null)
708 selGroups = new Hashtable();
710 selGroups.put(group, new int[0]);
714 * Test for and if present remove association to group.
717 * @return true if group was associated and it was removed
719 public boolean removeGroupMembership(Object group)
721 if (selGroups != null && selGroups.containsKey(group))
723 selGroups.remove(group);
730 * forget all associations for this sequence.
732 public void clearMemberships()
734 if (selGroups != null)
743 * @return null or array of all associated entities
745 public Object[] getAllMemberships()
747 if (selGroups == null)
751 Object[] mmbs = new Object[selGroups.size()];
752 Enumeration en = selGroups.keys();
753 for (int i = 0; en.hasMoreElements(); i++)
755 mmbs[i] = en.nextElement();
761 * Test for group membership
764 * - a selection group or some other object that may be associated
766 * @return true if sgr is associated with this seqCigar
768 public boolean isMemberOf(Object sgr)
770 return (selGroups != null) && selGroups.get(sgr) != null;