X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=ad8c0f090de983a099e69c82841db784e2a7790a;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=96ac7e8e84c7cc8940bcd901fbe128260986289e;hpb=7d71a7e377e57d614a772ce6a80e8795dd2a3e24;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 96ac7e8..ad8c0f0 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -1,34 +1,45 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.ws; -import java.io.*; -import java.util.*; - -import org.exolab.castor.mapping.*; -import org.exolab.castor.xml.*; -import jalview.analysis.*; -import jalview.datamodel.*; +import jalview.analysis.AlignSeq; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.Mapping; -import jalview.gui.*; -import jalview.ws.dbsources.Uniprot; -import jalview.ws.ebi.EBIFetchClient; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.CutAndPasteTransfer; +import jalview.gui.Desktop; +import jalview.gui.IProgressIndicator; +import jalview.gui.OOMWarning; + +import java.lang.reflect.Array; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; + +import org.biojava.dasobert.dasregistry.DasSource; + +import uk.ac.ebi.picr.model.UPEntry; /** * Implements a runnable for validating a sequence against external databases @@ -49,6 +60,11 @@ public class DBRefFetcher implements Runnable boolean running = false; + /** + * picr client instance + */ + uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null; + // /This will be a collection of Vectors of sequenceI refs. // The key will be the seq name or accession id of the seq Hashtable seqRefs; @@ -57,24 +73,45 @@ public class DBRefFetcher implements Runnable SequenceFetcher sfetcher; + private SequenceI[] alseqs; + public DBRefFetcher() { } /** - * Creates a new SequenceFeatureFetcher object. + * Creates a new SequenceFeatureFetcher object and fetches from the currently + * selected set of databases. * * @param seqs - * fetch references for these sequences + * fetch references for these sequences * @param af - * the parent alignframe for progress bar monitoring. + * the parent alignframe for progress bar monitoring. */ public DBRefFetcher(SequenceI[] seqs, AlignFrame af) { + this(seqs, af, null); + } + + /** + * Creates a new SequenceFeatureFetcher object and fetches from the currently + * selected set of databases. + * + * @param seqs + * fetch references for these sequences + * @param af + * the parent alignframe for progress bar monitoring. + * @param sources + * array of database source strings to query references from + */ + public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources) + { this.af = af; + alseqs = new SequenceI[seqs.length]; SequenceI[] ds = new SequenceI[seqs.length]; for (int i = 0; i < seqs.length; i++) { + alseqs[i] = seqs[i]; if (seqs[i].getDatasetSequence() != null) ds[i] = seqs[i].getDatasetSequence(); else @@ -83,14 +120,83 @@ public class DBRefFetcher implements Runnable this.dataset = ds; // TODO Jalview 2.5 lots of this code should be in the gui package! sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af); - // select appropriate databases based on alignFrame context. - if (af.getViewport().getAlignment().isNucleotide()) + if (sources == null) { - dbSources = DBRefSource.DNACODINGDBS; + // af.featureSettings_actionPerformed(null); + String[] defdb = null, otherdb = sfetcher + .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings + .getSelectedSources() + : new jalview.gui.DasSourceBrowser().getSelectedSources(); + Enumeration en = dasselsrc.elements(); + while (en.hasMoreElements()) + { + DasSource src = (DasSource) en.nextElement(); + selsources.addElement(src.getNickname()); + } + int osel = 0; + for (int o = 0; otherdb != null && o < otherdb.length; o++) + { + if (!selsources.contains(otherdb[o])) + { + otherdb[o] = null; + } + else + { + osel++; + } + } + // select appropriate databases based on alignFrame context. + if (af.getViewport().getAlignment().isNucleotide()) + { + defdb = DBRefSource.DNACODINGDBS; + } + else + { + defdb = DBRefSource.PROTEINDBS; + } + // append the selected sequence sources to the default dbs + dbSources = new String[defdb.length + osel]; + System.arraycopy(defdb, 0, dbSources, 0, defdb.length); + for (int o = 0, op = defdb.length; otherdb != null + && o < otherdb.length; o++) + { + if (otherdb[o] != null) + { + dbSources[op++] = otherdb[o]; + } + } } else { - dbSources = DBRefSource.PROTEINDBS; + // we assume the caller knows what they're doing and ensured that all the + // db source names are valid + dbSources = sources; + } + } + + /** + * retrieve all the das sequence sources and add them to the list of db + * sources to retrieve from + */ + public void appendAllDasSources() + { + if (dbSources == null) + { + dbSources = new String[] + {}; + } + // append additional sources + String[] otherdb = sfetcher + .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class); + if (otherdb != null && otherdb.length > 0) + { + String[] newsrc = new String[dbSources.length + otherdb.length]; + System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length); + System + .arraycopy(otherdb, 0, newsrc, dbSources.length, + otherdb.length); + dbSources = newsrc; } } @@ -98,7 +204,7 @@ public class DBRefFetcher implements Runnable * start the fetcher thread * * @param waitTillFinished - * true to block until the fetcher has finished + * true to block until the fetcher has finished */ public void fetchDBRefs(boolean waitTillFinished) { @@ -125,9 +231,9 @@ public class DBRefFetcher implements Runnable * could be either seq name or dbref id * * @param seq - * SequenceI + * SequenceI * @param key - * String + * String */ void addSeqId(SequenceI seq, String key) { @@ -167,9 +273,21 @@ public class DBRefFetcher implements Runnable { throw new Error("Implementation error. Must initialise dbSources"); } + running = true; long startTime = System.currentTimeMillis(); af.setProgressBar("Fetching db refs", startTime); - running = true; + try + { + if (Cache.getDefault("DBREFFETCH_USEPICR", false)) + { + picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator() + .getAccessionMapperPort(); + } + } catch (Exception e) + { + System.err.println("Couldn't locate PICR service instance.\n"); + e.printStackTrace(); + } int db = 0; Vector sdataset = new Vector(); for (int s = 0; s < dataset.length; s++) @@ -213,10 +331,10 @@ public class DBRefFetcher implements Runnable { // Still queries to make for current seqIndex StringBuffer queryString = new StringBuffer(""); - int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size() - : maxqlen; - - while (queries.size()>0 && numq < nqSize) + int numq = 0, nqSize = (maxqlen > queries.size()) ? queries + .size() : maxqlen; + + while (queries.size() > 0 && numq < nqSize) { String query = (String) queries.elementAt(0); if (dbsource.isValidReference(query)) @@ -235,7 +353,9 @@ public class DBRefFetcher implements Runnable { if (jalview.bin.Cache.log.isDebugEnabled()) { - jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'"); + jalview.bin.Cache.log.debug("Querying " + + dbsource.getDbName() + " with : '" + + queryString.toString() + "'"); } retrieved = dbsource.getSequenceRecords(queryString.toString()); } catch (Exception ex) @@ -262,7 +382,7 @@ public class DBRefFetcher implements Runnable { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT // }); // check for existing dbrefs to use - if (uprefs != null && uprefs.length>0) + if (uprefs != null && uprefs.length > 0) { for (int j = 0; j < uprefs.length; j++) { @@ -280,8 +400,43 @@ public class DBRefFetcher implements Runnable while (st.hasMoreTokens()) { String token = st.nextToken(); - addSeqId(sequence, token); - queries.addElement(token.toUpperCase()); + UPEntry[] presp = null; + if (picrClient != null) + { + // resolve the string against PICR to recover valid IDs + try + { + presp = picrClient + .getUPIForAccession(token, null, picrClient + .getMappedDatabaseNames(), null, true); + } catch (Exception e) + { + System.err.println("Exception with Picr for '" + token + + "'\n"); + e.printStackTrace(); + } + } + if (presp != null && presp.length > 0) + { + for (int id = 0; id < presp.length; id++) + { + // construct sequences from response if sequences are + // present, and do a transferReferences + // otherwise transfer non sequence x-references directly. + } + System.out + .println("Validated ID against PICR... (for what its worth):" + + token); + addSeqId(sequence, token); + queries.addElement(token.toUpperCase()); + } + else + { + // if () + // System.out.println("Not querying source with token="+token+"\n"); + addSeqId(sequence, token); + queries.addElement(token.toUpperCase()); + } } } } @@ -319,13 +474,15 @@ public class DBRefFetcher implements Runnable AlignmentI retrievedAl) // File // file) { - if (retrievedAl == null || retrievedAl.getHeight() == 0) { return; } - SequenceI[] retrieved = retrievedAl.getSequencesArray(); + SequenceI[] retrieved = recoverDbSequences(retrievedAl + .getSequencesArray()); SequenceI sequence = null; + boolean transferred = false; + StringBuffer messages = new StringBuffer(); // Vector entries = new Uniprot().getUniprotEntries(file); @@ -342,6 +499,13 @@ public class DBRefFetcher implements Runnable DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry .getDBRef(), new String[] { dbSource }); + if (entryRefs == null) + { + System.err + .println("Dud dbSource string ? no entryrefs selected for " + + dbSource + " on " + entry.getName()); + continue; + } for (int j = 0; j < entryRefs.length; j++) { String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString(); @@ -418,11 +582,11 @@ public class DBRefFetcher implements Runnable absStart = nonGapped.indexOf(entrySeq); if (absStart == -1) { // verification failed. - sbuffer.append(sequence.getName() + messages.append(sequence.getName() + " SEQUENCE NOT %100 MATCH \n"); continue; } - + transferred = true; sbuffer.append(sequence.getName() + " HAS " + absStart + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n"); // @@ -442,6 +606,7 @@ public class DBRefFetcher implements Runnable } else { + transferred = true; // update start and end of local sequence to place it in entry's // reference frame. // apply identity map map from whole of local sequence to matching @@ -453,20 +618,24 @@ public class DBRefFetcher implements Runnable // absStart+sequence.getStart()+entrySeq.length()-1}, // new int[] { entry.getStart(), entry.getEnd() }, 1, 1); // relocate local features for updated start - if (updateRefFrame && sequence.getSequenceFeatures() != null) + if (updateRefFrame) { - SequenceFeature[] sf = sequence.getSequenceFeatures(); - int start = sequence.getStart(); - int end = sequence.getEnd(); - int startShift = 1 - absStart - start; // how much the features are - // to be shifted by - for (int sfi = 0; sfi < sf.length; sfi++) + if (sequence.getSequenceFeatures() != null) { - if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end) + SequenceFeature[] sf = sequence.getSequenceFeatures(); + int start = sequence.getStart(); + int end = sequence.getEnd(); + int startShift = 1 - absStart - start; // how much the features + // are + // to be shifted by + for (int sfi = 0; sfi < sf.length; sfi++) { - // shift feature along by absstart - sf[sfi].setBegin(sf[sfi].getBegin() + startShift); - sf[sfi].setEnd(sf[sfi].getEnd() + startShift); + if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end) + { + // shift feature along by absstart + sf[sfi].setBegin(sf[sfi].getBegin() + startShift); + sf[sfi].setEnd(sf[sfi].getEnd() + startShift); + } } } } @@ -483,11 +652,74 @@ public class DBRefFetcher implements Runnable // finally, update local sequence reference frame if we're allowed sequence.setStart(absStart); sequence.setEnd(absEnd); + // search for alignment sequences to update coordinate frame for + for (int alsq = 0; alsq < alseqs.length; alsq++) + { + if (alseqs[alsq].getDatasetSequence() == sequence) + { + String ngAlsq = AlignSeq.extractGaps("-. ", + alseqs[alsq].getSequenceAsString()).toUpperCase(); + int oldstrt = alseqs[alsq].getStart(); + alseqs[alsq].setStart(sequence.getSequenceAsString() + .toUpperCase().indexOf(ngAlsq) + + sequence.getStart()); + if (oldstrt != alseqs[alsq].getStart()) + { + alseqs[alsq].setEnd(ngAlsq.length() + + alseqs[alsq].getStart() - 1); + } + } + } + // TODO: search for all other references to this dataset sequence, and + // update start/end + // TODO: update all AlCodonMappings which involve this alignment + // sequence (e.g. Q30167 cdna translation from exon2 product (vamsas + // demo) } // and remove it from the rest // TODO: decide if we should remove annotated sequence from set sdataset.remove(sequence); + // TODO: should we make a note of sequences that have received new DB + // ids, so we can query all enabled DAS servers for them ? + } + } + if (!transferred) + { + // report the ID/sequence mismatches + sbuffer.append(messages); + } + } + + /** + * loop thru and collect additional sequences in Map. + * + * @param sequencesArray + * @return + */ + private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray) + { + Vector nseq = new Vector(); + for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++) + { + nseq.addElement(sequencesArray[i]); + DBRefEntry dbr[] = sequencesArray[i].getDBRef(); + jalview.datamodel.Mapping map = null; + for (int r = 0; (dbr != null) && r < dbr.length; r++) + { + if ((map = dbr[r].getMap()) != null) + { + if (map.getTo() != null && !nseq.contains(map.getTo())) + { + nseq.addElement(map.getTo()); + } + } } } + if (nseq.size() > 0) + { + sequencesArray = new SequenceI[nseq.size()]; + nseq.toArray(sequencesArray); + } + return sequencesArray; } }