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.Comparison;
26 import jalview.util.MessageManager;
27 import jalview.util.ShiftList;
29 import java.util.Enumeration;
30 import java.util.Hashtable;
32 public class SeqCigar extends CigarSimple
35 * start(inclusive) and end(exclusive) of subsequence on refseq
37 private int start, end;
39 private SequenceI refseq = null;
41 private Hashtable seqProps;
44 * Reference dataset sequence for the cigar string
48 public SequenceI getRefSeq()
55 * @return int start index of cigar ops on refSeq
64 * @return int end index (exclusive) of cigar ops on refSeq
72 * Returns sequence as a string with cigar operations applied to it
76 public String getSequenceString(char GapChar)
78 return (length == 0) ? "" : (String) getSequenceAndDeletions(
79 refseq.getSequenceAsString(start, end), GapChar)[0];
83 * recreates a gapped and edited version of RefSeq or null for an empty cigar
88 public SequenceI getSeq(char GapChar)
91 if (refseq == null || length == 0)
95 Object[] edit_result = getSequenceAndDeletions(
96 refseq.getSequenceAsString(start, end), GapChar);
97 if (edit_result == null)
99 throw new Error(MessageManager.getString("error.implementation_error_unexpected_null_from_get_sequence_and_deletions"));
101 int bounds[] = (int[]) edit_result[1];
102 seq = new Sequence(refseq.getName(), (String) edit_result[0],
103 refseq.getStart() + start + bounds[0], refseq.getStart()
104 + start + ((bounds[2] == 0) ? -1 : bounds[2]));
105 seq.setDescription(refseq.getDescription());
106 int sstart = seq.getStart(), send = seq.getEnd();
107 // seq.checkValidRange(); probably not needed
108 // recover local properties if present
109 if (seqProps != null)
111 // this recovers dataset sequence reference as well as local features,
112 // names, start/end settings.
113 SeqsetUtils.SeqCharacterUnhash(seq, seqProps);
115 // ensure dataset sequence is up to date from local reference
116 seq.setDatasetSequence(refseq);
117 seq.setStart(sstart);
123 * We don't allow this - refseq is given at construction time only public void
124 * setSeq(SequenceI seq) { this.seq = seq; }
127 * internal constructor - sets seq to a gapless sequence derived from seq and
128 * prepends any 'D' operations needed to get to the first residue of seq.
132 * @param initialDeletion
133 * true to mark initial dataset sequence residues as deleted in
136 * index of first position in seq
138 * index after last position in (possibly gapped) seq
139 * @return true if gaps are present in seq
141 private boolean _setSeq(SequenceI seq, boolean initialDeletion, int _s,
144 boolean hasgaps = false;
147 throw new Error(MessageManager.getString("error.implementation_error_set_seq_null"));
151 throw new Error(MessageManager.formatMessage("error.implementation_error_s", new String[]{Integer.valueOf(_s).toString()}));
153 String seq_string = seq.getSequenceAsString();
154 if (_e == 0 || _e < _s || _e > seq_string.length())
156 _e = seq_string.length();
158 // resolve start and end positions relative to ungapped reference sequence
159 start = seq.findPosition(_s) - seq.getStart();
160 end = seq.findPosition(_e) - seq.getStart();
161 int l_ungapped = end - start;
162 // Find correct sequence to reference and correct start and end - if
164 SequenceI ds = seq.getDatasetSequence();
167 // make a new dataset sequence
168 String ungapped = AlignSeq.extractGaps(
169 Comparison.GapChars, new String(seq_string));
170 l_ungapped = ungapped.length();
171 // check that we haven't just duplicated an ungapped sequence.
172 if (l_ungapped == seq.getLength())
178 ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
179 seq.getStart() + ungapped.length() - 1);
180 // JBPNote: this would be consistent but may not be useful
181 // seq.setDatasetSequence(ds);
184 // add in offset between seq and the dataset sequence
185 if (ds.getStart() < seq.getStart())
187 int offset = seq.getStart() - ds.getStart();
190 // absolute cigar string
191 addDeleted(_s + offset);
197 // normal behaviour - just mark start and end subsequence
205 // any gaps to process ?
206 if (l_ungapped != (_e - _s))
212 // copy over local properties for the sequence instance of the refseq
213 seqProps = SeqsetUtils.SeqCharacterHash(seq);
215 if (end > ds.getLength())
217 throw new Error(MessageManager.getString("error.implementation_error_seqcigar_possible"));
218 // end = ds.getLength();
225 * directly initialise a cigar object with a sequence of range, operation
226 * pairs and a sequence to apply it to. operation and range should be relative
227 * to the seq.getStart()'th residue of the dataset seq resolved from seq.
236 public SeqCigar(SequenceI seq, char operation[], int range[])
241 throw new Error(MessageManager.getString("error.implmentation_bug_seq_null"));
243 if (operation.length != range.length)
245 throw new Error(MessageManager.getString("error.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))
255 throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
257 for (int i = this.length, j = 0; j < operation.length; i++, j++)
259 char op = operation[j];
260 if (op != M && op != I && op != D)
262 throw new Error(MessageManager.formatMessage("error.implementation_bug_cigar_operation", new String[]{Integer.valueOf(j).toString(),Integer.valueOf(op).toString(),Integer.valueOf(M).toString(),Integer.valueOf(I).toString(),Integer.valueOf(D).toString()}));
264 this.operation[i] = op;
265 this.range[i] = range[j];
267 this.length += operation.length;
271 this.operation = null;
274 if (_setSeq(seq, false, 0, 0))
276 throw new Error(MessageManager.getString("error.not_yet_implemented_cigar_object_from_cigar_string"));
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) ? 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(MessageManager.getString("error.implementation_error_for_new_cigar"));
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(MessageManager.getString("error.implementation_error_for_new_cigar"));
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]);
432 * create an alignment from the given array of cigar sequences and gap
433 * character, and marking the given segments as visible in the given
437 * @param gapCharacter
439 * - columnSelection where hidden regions are marked
441 * - visible regions of alignment
442 * @return SequenceI[]
444 public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
445 char gapCharacter, ColumnSelection colsel, int[] segments)
447 SequenceI[] seqs = new SequenceI[alseqs.length];
448 StringBuffer[] g_seqs = new StringBuffer[alseqs.length];
449 String[] alseqs_string = new String[alseqs.length];
450 Object[] gs_regions = new Object[alseqs.length];
451 for (int i = 0; i < alseqs.length; i++)
453 alseqs_string[i] = alseqs[i].getRefSeq().getSequenceAsString(
454 alseqs[i].start, alseqs[i].end);
455 gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
456 gapCharacter); // gapped sequence, {start, start col, end.
457 // endcol}, hidden regions {{start, end, col}})
458 if (gs_regions[i] == null)
460 throw new Error(MessageManager.formatMessage("error.implementation_error_cigar_seq_no_operations", new String[]{Integer.valueOf(i).toString()}));
462 g_seqs[i] = new StringBuffer((String) ((Object[]) gs_regions[i])[0]); // the
467 // Now account for insertions. (well - deletions)
468 // this is complicated because we must keep track of shifted positions in
470 ShiftList shifts = new ShiftList();
471 for (int i = 0; i < alseqs.length; i++)
473 Object[] gs_region = ((Object[]) ((Object[]) gs_regions[i])[2]);
474 if (gs_region != null)
477 for (int hr = 0; hr < gs_region.length; hr++)
479 int[] region = (int[]) gs_region[hr];
480 char[] insert = new char[region[1] - region[0] + 1];
481 for (int s = 0; s < insert.length; s++)
483 insert[s] = gapCharacter;
485 int inspos = shifts.shift(region[2]); // resolve insertion position in
486 // current alignment frame of
488 for (int s = 0; s < alseqs.length; s++)
492 if (g_seqs[s].length() <= inspos)
494 // prefix insertion with more gaps.
495 for (int l = inspos - g_seqs[s].length(); l > 0; l--)
497 g_seqs[s].append(gapCharacter); // to debug - use a diffferent
498 // gap character here
501 g_seqs[s].insert(inspos, insert);
505 g_seqs[s].insert(inspos,
506 alseqs_string[i].substring(region[0], region[1] + 1));
509 shifts.addShift(region[2], insert.length); // update shift in
510 // alignment frame of
512 if (segments == null)
514 // add a hidden column for this deletion
515 colsel.hideColumns(inspos, inspos + insert.length - 1);
520 for (int i = 0; i < alseqs.length; i++)
522 int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
523 SequenceI ref = alseqs[i].getRefSeq();
524 seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
525 ref.getStart() + 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 * references to entities that this sequence cigar is associated with.
546 private Hashtable selGroups = null;
548 public void setGroupMembership(Object group)
550 if (selGroups == null)
552 selGroups = new Hashtable();
554 selGroups.put(group, new int[0]);
558 * Test for and if present remove association to group.
561 * @return true if group was associated and it was removed
563 public boolean removeGroupMembership(Object group)
565 if (selGroups != null && selGroups.containsKey(group))
567 selGroups.remove(group);
574 * forget all associations for this sequence.
576 public void clearMemberships()
578 if (selGroups != null)
587 * @return null or array of all associated entities
589 public Object[] getAllMemberships()
591 if (selGroups == null)
595 Object[] mmbs = new Object[selGroups.size()];
596 Enumeration en = selGroups.keys();
597 for (int i = 0; en.hasMoreElements(); i++)
599 mmbs[i] = en.nextElement();
605 * Test for group membership
608 * - a selection group or some other object that may be associated
610 * @return true if sgr is associated with this seqCigar
612 public boolean isMemberOf(Object sgr)
614 return (selGroups != null) && selGroups.get(sgr) != null;