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.Enumeration;
21 import java.util.Hashtable;
22 import java.util.Vector;
24 import jalview.analysis.*;
25 import jalview.util.*;
27 public class SeqCigar extends CigarSimple
30 * start(inclusive) and end(exclusive) of subsequence on refseq
32 private int start, end;
34 private SequenceI refseq = null;
36 private Hashtable seqProps;
39 * Reference dataset sequence for the cigar string
43 public SequenceI getRefSeq()
50 * @return int start index of cigar ops on refSeq
59 * @return int end index (exclusive) of cigar ops on refSeq
67 * Returns sequence as a string with cigar operations applied to it
71 public String getSequenceString(char GapChar)
73 return (length == 0) ? "" : (String) getSequenceAndDeletions(
74 refseq.getSequenceAsString(start, end), GapChar)[0];
78 * recreates a gapped and edited version of RefSeq or null for an empty cigar
83 public SequenceI getSeq(char GapChar)
86 if (refseq == null || length == 0)
90 Object[] edit_result = getSequenceAndDeletions(
91 refseq.getSequenceAsString(start, end), GapChar);
92 if (edit_result == null)
95 "Implementation Error - unexpected null from getSequenceAndDeletions");
97 int bounds[] = (int[]) edit_result[1];
98 seq = new Sequence(refseq.getName(), (String) edit_result[0],
99 refseq.getStart() + start + bounds[0], refseq.getStart()
100 + start + ((bounds[2] == 0) ? -1 : bounds[2]));
101 seq.setDescription(refseq.getDescription());
102 int sstart = seq.getStart(), send = seq.getEnd();
103 // seq.checkValidRange(); probably not needed
104 // recover local properties if present
105 if (seqProps != null)
107 // this recovers dataset sequence reference as well as local features,
108 // names, start/end settings.
109 SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
111 // ensure dataset sequence is up to date from local reference
112 seq.setDatasetSequence(refseq);
113 seq.setStart(sstart);
119 * We don't allow this - refseq is given at construction time only public void
120 * setSeq(SequenceI seq) { this.seq = seq; }
123 * internal constructor - sets seq to a gapless sequence derived from seq and
124 * prepends any 'D' operations needed to get to the first residue of seq.
128 * @param initialDeletion
129 * true to mark initial dataset sequence residues as deleted in
132 * index of first position in seq
134 * index after last position in (possibly gapped) seq
135 * @return true if gaps are present in seq
137 private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
140 boolean hasgaps = false;
143 throw new Error("Implementation Error - _setSeq(null,...)");
147 throw new Error("Implementation Error: _s=" + _s);
149 String seq_string = seq.getSequenceAsString();
150 if (_e == 0 || _e < _s || _e > seq_string.length())
152 _e = seq_string.length();
154 // resolve start and end positions relative to ungapped reference sequence
155 start = seq.findPosition(_s) - seq.getStart();
156 end = seq.findPosition(_e) - seq.getStart();
157 int l_ungapped = end - start;
158 // Find correct sequence to reference and correct start and end - if
160 SequenceI ds = seq.getDatasetSequence();
163 // make a new dataset sequence
164 String ungapped = AlignSeq.extractGaps(
165 jalview.util.Comparison.GapChars, new String(seq_string));
166 l_ungapped = ungapped.length();
167 // check that we haven't just duplicated an ungapped sequence.
168 if (l_ungapped == seq.getLength())
174 ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
175 seq.getStart() + 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]);
434 * create an alignment from the given array of cigar sequences and gap
435 * character, and marking the given segments as visible in the given
439 * @param gapCharacter
441 * - columnSelection where hidden regions are marked
443 * - visible regions of alignment
444 * @return SequenceI[]
446 public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
447 char gapCharacter, ColumnSelection colsel, int[] segments)
449 SequenceI[] seqs = new SequenceI[alseqs.length];
450 StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
451 String[] alseqs_string = new String[alseqs.length];
452 Object[] gs_regions = new Object[alseqs.length];
453 for (int i = 0; i < alseqs.length; i++)
455 alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
456 alseqs[i].start, alseqs[i].end);
457 gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
458 gapCharacter); // gapped sequence, {start, start col, end.
459 // endcol}, hidden regions {{start, end, col}})
460 if (gs_regions[i] == null)
462 throw new Error("Implementation error: " + i
463 + "'th sequence Cigar has no operations.");
465 g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
470 // Now account for insertions. (well - deletions)
471 // this is complicated because we must keep track of shifted positions in
473 ShiftList shifts = new ShiftList();
474 for (int i = 0; i < alseqs.length; i++)
476 Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]);
477 if (gs_region != null)
480 for (int hr = 0; hr < gs_region.length; hr++)
482 int[] region = (int[]) gs_region[hr];
483 char[] insert = new char[region[1] - region[0] + 1];
484 for (int s = 0; s < insert.length; s++)
486 insert[s] = gapCharacter;
488 int inspos = shifts.shift(region[2]); // resolve insertion position in
489 // current alignment frame of
491 for (int s = 0; s < alseqs.length; s++)
495 if (g_seqs[s].length() <= inspos)
497 // prefix insertion with more gaps.
498 for (int l = inspos - g_seqs[s].length(); l > 0; l--)
500 g_seqs[s].append(gapCharacter); // to debug - use a diffferent
501 // gap character here
504 g_seqs[s].insert(inspos, insert);
508 g_seqs[s].insert(inspos,
509 alseqs_string[i].substring(region[0], region[1] + 1));
512 shifts.addShift(region[2], insert.length); // update shift in
513 // alignment frame of
515 if (segments == null)
517 // add a hidden column for this deletion
518 colsel.hideColumns(inspos, inspos + insert.length - 1);
523 for (int i = 0; i < alseqs.length; i++)
525 int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
526 SequenceI ref = alseqs[i].getRefSeq();
527 seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
528 ref.getStart() + alseqs[i].start + bounds[0], ref.getStart()
529 + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
530 seqs[i].setDatasetSequence(ref);
531 seqs[i].setDescription(ref.getDescription());
533 if (segments != null)
535 for (int i = 0; i < segments.length; i += 3)
537 // int start=shifts.shift(segments[i]-1)+1;
538 // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
539 colsel.hideColumns(segments[i + 1], segments[i + 1]
540 + segments[i + 2] - 1);
547 * non rigorous testing
553 * @param ex_cs_gapped
557 public static String testCigar_string(Sequence seq, String ex_cs_gapped)
559 SeqCigar c_sgapped = new SeqCigar(seq);
560 String cs_gapped = c_sgapped.getCigarstring();
561 if (!cs_gapped.equals(ex_cs_gapped))
563 System.err.println("Failed getCigarstring: incorect string '"
564 + cs_gapped + "' != " + ex_cs_gapped);
569 public static boolean testSeqRecovery(SeqCigar gen_sgapped,
572 // this is non-rigorous - start and end recovery is not tested.
573 SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
574 if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
576 System.err.println("Couldn't reconstruct sequence.\n"
577 + gen_sgapped_s.getSequenceAsString() + "\n"
578 + s_gapped.getSequenceAsString());
584 public static void main(String argv[]) throws Exception
587 Sequence s = new Sequence("MySeq",
588 o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt", 39, 80);
590 Sequence s_gapped = new Sequence(
592 orig_gapped = "----asdf------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhttt",
594 String ex_cs_gapped = "4I4M6I6M3I11M4I12M4I9M";
595 s_gapped.setDatasetSequence(s);
597 Sequence s_subsequence_gapped = new Sequence(
599 sub_gapped_s = "------ktryas---dtqwrtsasll----dddptyipqqwa----slchvh",
602 s_subsequence_gapped.setDatasetSequence(s);
603 SeqCigar c_null = new SeqCigar(s);
604 String cs_null = c_null.getCigarstring();
605 if (!cs_null.equals("42M"))
608 .println("Failed to recover ungapped sequence cigar operations:"
609 + ((cs_null == "") ? "empty string" : cs_null));
611 testCigar_string(s_gapped, ex_cs_gapped);
612 SeqCigar gen_sgapped = SeqCigar.parseCigar(s, ex_cs_gapped);
613 if (!gen_sgapped.getCigarstring().equals(ex_cs_gapped))
615 System.err.println("Failed parseCigar(" + ex_cs_gapped
616 + ")->getCigarString()->'" + gen_sgapped.getCigarstring()
619 testSeqRecovery(gen_sgapped, s_gapped);
620 // Test dataset resolution
621 SeqCigar sub_gapped = new SeqCigar(s_subsequence_gapped);
622 if (!testSeqRecovery(sub_gapped, s_subsequence_gapped))
625 .println("Failed recovery for subsequence of dataset sequence");
628 if (sub_gapped.getWidth() != sub_gapped_s.length())
630 System.err.println("Failed getWidth()");
633 sub_gapped.getFullWidth();
634 if (sub_gapped.hasDeletedRegions())
636 System.err.println("hasDeletedRegions is incorrect.");
638 // Test start-end region SeqCigar
639 SeqCigar sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
640 if (sub_se_gp.getWidth() != 41)
643 .println("SeqCigar(seq, start, end) not properly clipped alignsequence.");
645 System.out.println("Original sequence align:\n" + sub_gapped_s
646 + "\nReconstructed window from 8 to 48\n" + "XXXXXXXX"
647 + sub_se_gp.getSequenceString('-') + "..." + "\nCigar String:"
648 + sub_se_gp.getCigarstring() + "\n");
649 SequenceI ssgp = sub_se_gp.getSeq('-');
650 System.out.println("\t " + ssgp.getSequenceAsString());
651 for (int r = 0; r < 10; r++)
653 sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
654 int sl = sub_se_gp.getWidth();
656 for (int rs = 0; rs < 10; rs++)
659 sub_se_gp.deleteRange(st, e);
660 String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
661 System.out.println(st + "," + e + "\t:" + ssgapedseq);
666 SeqCigar[] set = new SeqCigar[]
667 { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
668 new SeqCigar(s_gapped) };
669 Alignment al = new Alignment(set);
670 for (int i = 0; i < al.getHeight(); i++)
672 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
673 + al.getSequenceAt(i).getStart() + "\t"
674 + al.getSequenceAt(i).getEnd() + "\t"
675 + al.getSequenceAt(i).getSequenceAsString());
679 System.out.println("Gapped.");
680 SeqCigar[] set = new SeqCigar[]
681 { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
682 new SeqCigar(s_gapped) };
683 set[0].deleteRange(20, 25);
684 Alignment al = new Alignment(set);
685 for (int i = 0; i < al.getHeight(); i++)
687 System.out.println("" + al.getSequenceAt(i).getName() + "\t"
688 + al.getSequenceAt(i).getStart() + "\t"
689 + al.getSequenceAt(i).getEnd() + "\t"
690 + al.getSequenceAt(i).getSequenceAsString());
693 // if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))
694 // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
698 * references to entities that this sequence cigar is associated with.
700 private Hashtable selGroups = null;
702 public void setGroupMembership(Object group)
704 if (selGroups == null)
706 selGroups = new Hashtable();
708 selGroups.put(group, new int[0]);
712 * Test for and if present remove association to group.
715 * @return true if group was associated and it was removed
717 public boolean removeGroupMembership(Object group)
719 if (selGroups != null && selGroups.containsKey(group))
721 selGroups.remove(group);
728 * forget all associations for this sequence.
730 public void clearMemberships()
732 if (selGroups != null)
741 * @return null or array of all associated entities
743 public Object[] getAllMemberships()
745 if (selGroups == null)
749 Object[] mmbs = new Object[selGroups.size()];
750 Enumeration en = selGroups.keys();
751 for (int i = 0; en.hasMoreElements(); i++)
753 mmbs[i] = en.nextElement();
759 * Test for group membership
762 * - a selection group or some other object that may be associated
764 * @return true if sgr is associated with this seqCigar
766 public boolean isMemberOf(Object sgr)
768 return (selGroups != null) && selGroups.get(sgr) != null;