2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.AlignSeq;
24 import jalview.analysis.SeqsetUtils;
25 import jalview.util.MessageManager;
26 import jalview.util.ShiftList;
28 import java.util.Enumeration;
29 import java.util.Hashtable;
31 public class SeqCigar extends CigarSimple
34 * start(inclusive) and end(exclusive) of subsequence on refseq
36 private int start, end;
38 private SequenceI refseq = null;
40 private Hashtable seqProps;
43 * Reference dataset sequence for the cigar string
47 public SequenceI getRefSeq()
54 * @return int start index of cigar ops on refSeq
63 * @return int end index (exclusive) of cigar ops on refSeq
71 * Returns sequence as a string with cigar operations applied to it
75 public String getSequenceString(char GapChar)
77 return (length == 0) ? "" : (String) getSequenceAndDeletions(
78 refseq.getSequenceAsString(start, end), GapChar)[0];
82 * recreates a gapped and edited version of RefSeq or null for an empty cigar
87 public SequenceI getSeq(char GapChar)
90 if (refseq == null || length == 0)
94 Object[] edit_result = getSequenceAndDeletions(
95 refseq.getSequenceAsString(start, end), GapChar);
96 if (edit_result == null)
100 .getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
102 int bounds[] = (int[]) edit_result[1];
103 seq = new Sequence(refseq.getName(), (String) edit_result[0],
104 refseq.getStart() + start + bounds[0], refseq.getStart()
105 + start + ((bounds[2] == 0) ? -1 : bounds[2]));
106 seq.setDescription(refseq.getDescription());
107 int sstart = seq.getStart(), send = seq.getEnd();
108 // seq.checkValidRange(); probably not needed
109 // recover local properties if present
110 if (seqProps != null)
112 // this recovers dataset sequence reference as well as local features,
113 // names, start/end settings.
114 SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
116 // ensure dataset sequence is up to date from local reference
117 seq.setDatasetSequence(refseq);
118 seq.setStart(sstart);
124 * We don't allow this - refseq is given at construction time only public void
125 * setSeq(SequenceI seq) { this.seq = seq; }
128 * internal constructor - sets seq to a gapless sequence derived from seq and
129 * prepends any 'D' operations needed to get to the first residue of seq.
133 * @param initialDeletion
134 * true to mark initial dataset sequence residues as deleted in
137 * index of first position in seq
139 * index after last position in (possibly gapped) seq
140 * @return true if gaps are present in seq
142 private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
145 boolean hasgaps = false;
150 .getString("error.implementation_error_set_seq_null"));
154 throw new Error(MessageManager.formatMessage(
155 "error.implementation_error_s", new String[] { Integer
156 .valueOf(_s).toString() }));
158 String seq_string = seq.getSequenceAsString();
159 if (_e == 0 || _e < _s || _e > seq_string.length())
161 _e = seq_string.length();
163 // resolve start and end positions relative to ungapped reference sequence
164 start = seq.findPosition(_s) - seq.getStart();
165 end = seq.findPosition(_e) - seq.getStart();
166 int l_ungapped = end - start;
167 // Find correct sequence to reference and correct start and end - if
169 SequenceI ds = seq.getDatasetSequence();
172 // make a new dataset sequence
173 String ungapped = AlignSeq.extractGaps(
174 jalview.util.Comparison.GapChars, new String(seq_string));
175 l_ungapped = ungapped.length();
176 // check that we haven't just duplicated an ungapped sequence.
177 if (l_ungapped == seq.getLength())
183 ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
184 seq.getStart() + ungapped.length() - 1);
185 // JBPNote: this would be consistent but may not be useful
186 // seq.setDatasetSequence(ds);
189 // add in offset between seq and the dataset sequence
190 if (ds.getStart() < seq.getStart())
192 int offset = seq.getStart() - ds.getStart();
195 // absolute cigar string
196 addDeleted(_s + offset);
202 // normal behaviour - just mark start and end subsequence
210 // any gaps to process ?
211 if (l_ungapped != (_e - _s))
217 // copy over local properties for the sequence instance of the refseq
218 seqProps = SeqsetUtils.SeqCharacterHash(seq);
220 if (end > ds.getLength())
224 .getString("error.implementation_error_seqcigar_possible"));
225 // end = ds.getLength();
232 * directly initialise a cigar object with a sequence of range, operation
233 * pairs and a sequence to apply it to. operation and range should be relative
234 * to the seq.getStart()'th residue of the dataset seq resolved from seq.
243 public SeqCigar(SequenceI seq, char operation[], int range[])
249 MessageManager.getString("error.implmentation_bug_seq_null"));
251 if (operation.length != range.length)
255 .getString("error.implementation_bug_cigar_operation_list_range_list"));
258 if (operation != null)
260 this.operation = new char[operation.length + _inc_length];
261 this.range = new int[operation.length + _inc_length];
263 if (_setSeq(seq, false, 0, 0))
267 .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
269 for (int i = this.length, j = 0; j < operation.length; i++, j++)
271 char op = operation[j];
272 if (op != M && op != I && op != D)
274 throw new Error(MessageManager.formatMessage(
275 "error.implementation_bug_cigar_operation", new String[] {
276 Integer.valueOf(j).toString(),
277 Integer.valueOf(op).toString(),
278 Integer.valueOf(M).toString(),
279 Integer.valueOf(I).toString(),
280 Integer.valueOf(D).toString() }));
282 this.operation[i] = op;
283 this.range[i] = range[j];
285 this.length += operation.length;
289 this.operation = null;
292 if (_setSeq(seq, false, 0, 0))
296 .getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
302 * add range matched residues to cigar string
307 public void addMatch(int range)
309 this.addOperation(M, range);
313 * Adds insertion and match operations based on seq to the cigar up to the
314 * endpos column of seq.
324 * @param initialDeletions
325 * if true then initial deletions will be added from start of seq to
328 protected static void addSequenceOps(CigarBase cigar, SequenceI seq,
329 int startpos, int endpos, boolean initialDeletions)
333 int p = 0, res = seq.getLength();
335 if (!initialDeletions)
342 boolean isGap = (p < res) ? jalview.util.Comparison.isGap(seq
343 .getCharAt(p)) : true;
344 if ((startpos <= p) && (p <= endpos))
348 if (range > 0 && op != I)
350 cigar.addOperation(op, range);
358 if (range > 0 && op != M)
360 cigar.addOperation(op, range);
371 if (range > 0 && op != D)
373 cigar.addOperation(op, range);
381 // do nothing - insertions are not made in flanking regions
388 cigar.addOperation(op, range);
393 * create a cigar string for given sequence
398 public SeqCigar(SequenceI seq)
405 .getString("error.implementation_error_for_new_cigar"));
407 _setSeq(seq, false, 0, 0);
408 // there is still work to do
409 addSequenceOps(this, seq, 0, seq.getLength() - 1, false);
413 * Create Cigar from a range of gaps and residues on a sequence object
418 * int - first column in range
420 * int - last column in range
422 public SeqCigar(SequenceI seq, int start, int end)
429 .getString("error.implementation_error_for_new_cigar"));
431 _setSeq(seq, false, start, end + 1);
432 // there is still work to do
433 addSequenceOps(this, seq, start, end, false);
437 * Create a cigar object from a cigar string like '[<I|D|M><range>]+' Will
438 * fail if the given seq already contains gaps (JBPNote: future implementation
442 * SequenceI object resolvable to a dataset sequence
447 public static SeqCigar parseCigar(SequenceI seq, String cigarString)
450 Object[] opsandrange = parseCigarString(cigarString);
451 return new SeqCigar(seq, (char[]) opsandrange[0],
452 (int[]) opsandrange[1]);
456 * create an alignment from the given array of cigar sequences and gap
457 * character, and marking the given segments as visible in the given
461 * @param gapCharacter
463 * - columnSelection where hidden regions are marked
465 * - visible regions of alignment
466 * @return SequenceI[]
468 public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
469 char gapCharacter, ColumnSelection colsel, int[] segments)
471 SequenceI[] seqs = new SequenceI[alseqs.length];
472 StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
473 String[] alseqs_string = new String[alseqs.length];
474 Object[] gs_regions = new Object[alseqs.length];
475 for (int i = 0; i < alseqs.length; i++)
477 alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
478 alseqs[i].start, alseqs[i].end);
479 gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
480 gapCharacter); // gapped sequence, {start, start col, end.
481 // endcol}, hidden regions {{start, end, col}})
482 if (gs_regions[i] == null)
484 throw new Error(MessageManager.formatMessage(
485 "error.implementation_error_cigar_seq_no_operations",
486 new String[] { Integer.valueOf(i).toString() }));
488 g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
493 // Now account for insertions. (well - deletions)
494 // this is complicated because we must keep track of shifted positions in
496 ShiftList shifts = new ShiftList();
497 for (int i = 0; i < alseqs.length; i++)
499 Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]);
500 if (gs_region != null)
503 for (int hr = 0; hr < gs_region.length; hr++)
505 int[] region = (int[]) gs_region[hr];
506 char[] insert = new char[region[1] - region[0] + 1];
507 for (int s = 0; s < insert.length; s++)
509 insert[s] = gapCharacter;
511 int inspos = shifts.shift(region[2]); // resolve insertion position in
512 // current alignment frame of
514 for (int s = 0; s < alseqs.length; s++)
518 if (g_seqs[s].length() <= inspos)
520 // prefix insertion with more gaps.
521 for (int l = inspos - g_seqs[s].length(); l > 0; l--)
523 g_seqs[s].append(gapCharacter); // to debug - use a diffferent
524 // gap character here
527 g_seqs[s].insert(inspos, insert);
531 g_seqs[s].insert(inspos,
532 alseqs_string[i].substring(region[0], region[1] + 1));
535 shifts.addShift(region[2], insert.length); // update shift in
536 // alignment frame of
538 if (segments == null)
540 // add a hidden column for this deletion
541 colsel.hideColumns(inspos, inspos + insert.length - 1);
546 for (int i = 0; i < alseqs.length; i++)
548 int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
549 SequenceI ref = alseqs[i].getRefSeq();
550 seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
551 ref.getStart() + alseqs[i].start + bounds[0], ref.getStart()
552 + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
553 seqs[i].setDatasetSequence(ref);
554 seqs[i].setDescription(ref.getDescription());
556 if (segments != null)
558 for (int i = 0; i < segments.length; i += 3)
560 // int start=shifts.shift(segments[i]-1)+1;
561 // int end=shifts.shift(segments[i]+segments[i+1]-1)-1;
562 colsel.hideColumns(segments[i + 1], segments[i + 1]
563 + segments[i + 2] - 1);
570 * references to entities that this sequence cigar is associated with.
572 private Hashtable selGroups = null;
574 public void setGroupMembership(Object group)
576 if (selGroups == null)
578 selGroups = new Hashtable();
580 selGroups.put(group, new int[0]);
584 * Test for and if present remove association to group.
587 * @return true if group was associated and it was removed
589 public boolean removeGroupMembership(Object group)
591 if (selGroups != null && selGroups.containsKey(group))
593 selGroups.remove(group);
600 * forget all associations for this sequence.
602 public void clearMemberships()
604 if (selGroups != null)
613 * @return null or array of all associated entities
615 public Object[] getAllMemberships()
617 if (selGroups == null)
621 Object[] mmbs = new Object[selGroups.size()];
622 Enumeration en = selGroups.keys();
623 for (int i = 0; en.hasMoreElements(); i++)
625 mmbs[i] = en.nextElement();
631 * Test for group membership
634 * - a selection group or some other object that may be associated
636 * @return true if sgr is associated with this seqCigar
638 public boolean isMemberOf(Object sgr)
640 return (selGroups != null) && selGroups.get(sgr) != null;