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.analysis;
23 import jalview.datamodel.AlignedCodonFrame;
24 import jalview.datamodel.Alignment;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.DBRefEntry;
27 import jalview.datamodel.DBRefSource;
28 import jalview.datamodel.Mapping;
29 import jalview.datamodel.Sequence;
30 import jalview.datamodel.SequenceI;
31 import jalview.util.DBRefUtils;
32 import jalview.ws.SequenceFetcher;
33 import jalview.ws.seqfetcher.ASequenceFetcher;
35 import java.util.ArrayList;
36 import java.util.List;
37 import java.util.Vector;
40 * Functions for cross-referencing sequence databases. user must first specify
41 * if cross-referencing from protein or dna (set dna==true)
49 * Select just the DNA or protein references for a protein or dna sequence
52 * if true, select references from DNA (i.e. Protein databases), else
53 * DNA database references
55 * a set of references to select from
58 public static DBRefEntry[] findXDbRefs(boolean fromDna, DBRefEntry[] refs)
60 return DBRefUtils.selectRefs(refs, fromDna ? DBRefSource.PROTEINDBS
61 : DBRefSource.DNACODINGDBS);
62 // could attempt to find other cross
63 // refs here - ie PDB xrefs
64 // (not dna, not protein seq)
69 * true if seqs are DNA seqs
71 * @return a list of sequence database cross reference source types
73 public static String[] findSequenceXrefTypes(boolean dna, SequenceI[] seqs)
75 return findSequenceXrefTypes(dna, seqs, null);
79 * Indirect references are references from other sequences from the dataset to
80 * any of the direct DBRefEntrys on the given sequences.
83 * true if seqs are DNA seqs
85 * @return a list of sequence database cross reference source types
87 public static String[] findSequenceXrefTypes(boolean dna,
88 SequenceI[] seqs, AlignmentI dataset)
90 String[] dbrefs = null;
91 List<String> refs = new ArrayList<String>();
92 for (SequenceI seq : seqs)
97 while (dss.getDatasetSequence() != null)
99 dss = dss.getDatasetSequence();
101 DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
104 for (DBRefEntry ref : rfs)
106 if (!refs.contains(ref.getSource()))
108 refs.add(ref.getSource());
114 // search for references to this sequence's direct references.
115 DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRef());
116 List<SequenceI> rseqs = new ArrayList<SequenceI>();
117 CrossRef.searchDatasetXrefs(seq, !dna, lrfs, dataset, rseqs,
118 null); // don't need to specify codon frame for mapping here
119 for (SequenceI rs : rseqs)
121 DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
124 for (DBRefEntry ref : xrs)
126 if (!refs.contains(ref.getSource()))
128 refs.add(ref.getSource());
132 // looks like copy and paste - change rfs to xrs?
133 // for (int r = 0; rfs != null && r < rfs.length; r++)
135 // if (!refs.contains(rfs[r].getSource()))
137 // refs.add(rfs[r].getSource());
146 dbrefs = new String[refs.size()];
147 refs.toArray(dbrefs);
152 public static boolean hasCdnaMap(SequenceI[] seqs)
154 // TODO unused - remove?
155 String[] reftypes = findSequenceXrefTypes(false, seqs);
156 for (int s = 0; s < reftypes.length; s++)
158 if (reftypes.equals(DBRefSource.EMBLCDS))
167 public static SequenceI[] getCdnaMap(SequenceI[] seqs)
169 // TODO unused - remove?
170 Vector cseqs = new Vector();
171 for (int s = 0; s < seqs.length; s++)
173 DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRef());
174 for (int c = 0; c < cdna.length; c++)
176 if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
179 .println("TODO: unimplemented sequence retrieval for coding region sequence.");
180 // TODO: retrieve CDS dataset sequences
181 // need global dataset sequence retriever/resolver to reuse refs
182 // and construct Mapping entry.
183 // insert gaps in CDS according to peptide gaps.
184 // add gapped sequence to cseqs
188 if (cseqs.size() > 0)
190 SequenceI[] rsqs = new SequenceI[cseqs.size()];
191 cseqs.copyInto(rsqs);
204 public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
207 return findXrefSequences(seqs, dna, source, null);
213 * sequences whose xrefs are being retrieved
215 * true if sequences are nucleotide
218 * alignment to search for product sequences.
219 * @return products (as dataset sequences)
221 public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
222 String source, AlignmentI dataset)
224 List<SequenceI> rseqs = new ArrayList<SequenceI>();
225 AlignedCodonFrame cf = new AlignedCodonFrame();
226 for (SequenceI seq : seqs)
229 while (dss.getDatasetSequence() != null)
231 dss = dss.getDatasetSequence();
233 boolean found = false;
234 DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRef());
235 if ((xrfs == null || xrfs.length == 0) && dataset != null)
237 System.out.println("Attempting to find ds Xrefs refs.");
238 // FIXME should be dss not seq here?
239 DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRef());
240 // less ambiguous would be a 'find primary dbRefEntry' method.
241 // filter for desired source xref here
242 found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
245 for (int r = 0; xrfs != null && r < xrfs.length; r++)
247 if (source != null && !source.equals(xrfs[r].getSource()))
251 if (xrfs[r].hasMap())
253 if (xrfs[r].getMap().getTo() != null)
255 SequenceI rsq = new Sequence(xrfs[r].getMap().getTo());
257 if (xrfs[r].getMap().getMap().getFromRatio() != xrfs[r]
258 .getMap().getMap().getToRatio())
260 // get sense of map correct for adding to product alignment.
263 // map is from dna seq to a protein product
264 cf.addMap(dss, rsq, xrfs[r].getMap().getMap());
268 // map should be from protein seq to its coding dna
269 cf.addMap(rsq, dss, xrfs[r].getMap().getMap().getInverse());
277 // do a bit more work - search for sequences with references matching
278 // xrefs on this sequence.
281 found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
284 xrfs[r] = null; // we've recovered seqs for this one.
291 if (xrfs != null && xrfs.length > 0)
293 // Try and get the sequence reference...
295 * Ideal world - we ask for a sequence fetcher implementation here if
296 * (jalview.io.RunTimeEnvironment.getSequenceFetcher()) (
298 ASequenceFetcher sftch = new SequenceFetcher();
299 SequenceI[] retrieved = null;
301 for (int r = 0; r < xrfs.length; r++)
303 // filter out any irrelevant or irretrievable references
305 || ((source != null && !source.equals(xrfs[r]
306 .getSource())) || !sftch.isFetchable(xrfs[r]
316 .println("Attempting to retrieve cross referenced sequences.");
317 DBRefEntry[] t = new DBRefEntry[l];
319 for (int r = 0; r < xrfs.length; r++)
329 retrieved = sftch.getSequences(xrfs); // problem here is we don't
330 // know which of xrfs
333 } catch (Exception e)
336 .println("Problem whilst retrieving cross references for Sequence : "
340 if (retrieved != null)
342 for (int rs = 0; rs < retrieved.length; rs++)
344 // TODO: examine each sequence for 'redundancy'
345 DBRefEntry[] dbr = retrieved[rs].getDBRef();
346 if (dbr != null && dbr.length > 0)
348 for (int di = 0; di < dbr.length; di++)
350 // find any entry where we should put in the sequence being
351 // cross-referenced into the map
352 Mapping map = dbr[di].getMap();
355 if (map.getTo() != null && map.getMap() != null)
357 // should search the local dataset to find any existing
358 // candidates for To !
361 // compare ms with dss and replace with dss in mapping
362 // if map is congruent
363 SequenceI ms = map.getTo();
364 int sf = map.getMap().getToLowest();
365 int st = map.getMap().getToHighest();
366 SequenceI mappedrg = ms.getSubSequence(sf, st);
367 SequenceI loc = dss.getSubSequence(sf, st);
368 if (mappedrg.getLength() > 0
369 && mappedrg.getSequenceAsString().equals(
370 loc.getSequenceAsString()))
373 .println("Mapping updated for retrieved crossreference");
374 // method to update all refs of existing To on
375 // retrieved sequence with dss and merge any props
379 } catch (Exception e)
382 .println("Exception when consolidating Mapped sequence set...");
383 e.printStackTrace(System.err);
389 retrieved[rs].updatePDBIds();
390 rseqs.add(retrieved[rs]);
398 Alignment ral = null;
399 if (rseqs.size() > 0)
401 SequenceI[] rsqs = new SequenceI[rseqs.size()];
403 ral = new Alignment(rsqs);
404 if (cf != null && cf.getProtMappings() != null)
406 ral.addCodonFrame(cf);
413 * find references to lrfs in the cross-reference set of each sequence in
414 * dataset (that is not equal to sequenceI) Identifies matching DBRefEntry
415 * based on source and accession string only - Map and Version are nulled.
421 * @return true if matches were found.
423 private static boolean searchDatasetXrefs(SequenceI sequenceI,
424 boolean dna, DBRefEntry[] lrfs, AlignmentI dataset,
425 List<SequenceI> rseqs, AlignedCodonFrame cf)
427 boolean found = false;
432 for (int i = 0; i < lrfs.length; i++)
434 DBRefEntry xref = new DBRefEntry(lrfs[i]);
436 xref.setVersion(null);
438 found = searchDataset(sequenceI, xref, dataset, rseqs, cf, false, dna);
444 * search a given sequence dataset for references matching cross-references to
451 * set of unique sequences
453 * @return true if one or more unique sequences were found and added
455 public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
456 AlignmentI dataset, List<SequenceI> rseqs, AlignedCodonFrame cf)
458 return searchDataset(sequenceI, xrf, dataset, rseqs, cf, true, false);
462 * TODO: generalise to different protein classifications Search dataset for
463 * DBRefEntrys matching the given one (xrf) and add the associated sequence to
471 * - search all references or only subset
473 * search dna or protein xrefs (if direct=false)
474 * @return true if relationship found and sequence added.
476 public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
477 AlignmentI dataset, List<SequenceI> rseqs, AlignedCodonFrame cf,
478 boolean direct, boolean dna)
480 boolean found = false;
481 SequenceI[] typer = new SequenceI[1];
486 if (dataset.getSequences() == null)
488 System.err.println("Empty dataset sequence set - NO VECTOR");
492 synchronized (ds = dataset.getSequences())
494 for (SequenceI nxt : ds)
498 if (nxt.getDatasetSequence() != null)
501 .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
503 if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
505 // check if this is the correct sequence type
508 boolean isDna = jalview.util.Comparison.isNucleotide(typer);
509 if ((direct && isDna == dna) || (!direct && isDna != dna))
511 // skip this sequence because it is same molecule type
516 // look for direct or indirect references in common
517 DBRefEntry[] poss = nxt.getDBRef(), cands = null;
520 cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
524 poss = CrossRef.findXDbRefs(dna, poss); //
525 cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
529 if (!rseqs.contains(nxt))
532 boolean foundmap = cf != null;
533 // don't search if we aren't given a codon map object
534 for (int r = 0; foundmap && r < cands.length; r++)
536 if (cands[r].hasMap())
538 if (cands[r].getMap().getTo() != null
539 && cands[r].getMap().getMap().getFromRatio() != cands[r]
540 .getMap().getMap().getToRatio())
543 // get sense of map correct for adding to product
547 // map is from dna seq to a protein product
548 cf.addMap(sequenceI, nxt, cands[r].getMap()
553 // map should be from protein seq to its coding dna
554 cf.addMap(nxt, sequenceI, cands[r].getMap()
555 .getMap().getInverse());
560 // TODO: add mapping between sequences if necessary
573 * precalculate different products that can be found for seqs in dataset and
580 * - don't actually build lists - just get types
581 * @return public static Object[] buildXProductsList(boolean dna, SequenceI[]
582 * seqs, AlignmentI dataset, boolean fake) { String types[] =
583 * jalview.analysis.CrossRef.findSequenceXrefTypes( dna, seqs,
584 * dataset); if (types != null) { System.out.println("Xref Types for:
585 * "+(dna ? "dna" : "prot")); for (int t = 0; t < types.length; t++) {
586 * System.out.println("Type: " + types[t]); SequenceI[] prod =
587 * jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);
588 * System.out.println("Found " + ((prod == null) ? "no" : "" +
589 * prod.length) + " products"); if (prod!=null) { for (int p=0;
590 * p<prod.length; p++) { System.out.println("Prod "+p+":
591 * "+prod[p].getDisplayId(true)); } } } } else {
592 * System.out.println("Trying getProducts for
593 * "+al.getSequenceAt(0).getDisplayId(true));
594 * System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));
595 * // have a bash at finding the products amongst all the retrieved
596 * sequences. SequenceI[] prod =
597 * jalview.analysis.CrossRef.findXrefSequences(al
598 * .getSequencesArray(), dna, null, ds); System.out.println("Found " +
599 * ((prod == null) ? "no" : "" + prod.length) + " products"); if
600 * (prod!=null) { // select non-equivalent sequences from dataset list
601 * for (int p=0; p<prod.length; p++) { System.out.println("Prod "+p+":
602 * "+prod[p].getDisplayId(true)); } } } }