X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=581901a5450a2f9655ea2bf278ab694c988f27db;hb=dc734ef1e078af1a0329000fb6839e2e08b7e16b;hp=96ac7e8e84c7cc8940bcd901fbe128260986289e;hpb=7d71a7e377e57d614a772ce6a80e8795dd2a3e24;p=jalview.git diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java index 96ac7e8..581901a 100644 --- a/src/jalview/ws/DBRefFetcher.java +++ b/src/jalview/ws/DBRefFetcher.java @@ -1,6 +1,6 @@ /* - * 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 (Development Version 2.4.1) + * Copyright (C) 2009 AM Waterhouse, J Procter, 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 @@ -18,17 +18,29 @@ */ 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 +61,11 @@ 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 +74,45 @@ 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 +121,83 @@ 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 +205,7 @@ 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 +232,9 @@ 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 +274,21 @@ 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 +332,10 @@ 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 +354,9 @@ 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 +383,7 @@ 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 +401,43 @@ 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 +475,15 @@ 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); @@ -342,27 +500,31 @@ 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(); - // match up on accessionId - if (seqRefs.containsKey(accessionId.toUpperCase())) { - Vector seqs = (Vector) seqRefs.get(accessionId); - for (int jj = 0; jj < seqs.size(); jj++) + String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString(); + // match up on accessionId + if (seqRefs.containsKey(accessionId.toUpperCase())) { - sequence = (SequenceI) seqs.elementAt(jj); - if (!sequenceMatches.contains(sequence)) + Vector seqs = (Vector) seqRefs.get(accessionId); + for (int jj = 0; jj < seqs.size(); jj++) { - sequenceMatches.addElement(sequence); + sequence = (SequenceI) seqs.elementAt(jj); + if (!sequenceMatches.contains(sequence)) + { + sequenceMatches.addElement(sequence); + } } } } - } - if (sequenceMatches.size() == 0) - { - // failed to match directly on accessionId==query so just compare all - // sequences to entry + if (sequenceMatches.size() == 0) + { + // failed to match directly on accessionId==query so just compare all + // sequences to entry Enumeration e = seqRefs.keys(); while (e.hasMoreElements()) { @@ -418,11 +580,11 @@ 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 +604,7 @@ 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 @@ -453,8 +616,9 @@ 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) { + if (sequence.getSequenceFeatures() != null) + { SequenceFeature[] sf = sequence.getSequenceFeatures(); int start = sequence.getStart(); int end = sequence.getEnd(); @@ -469,6 +633,7 @@ public class DBRefFetcher implements Runnable sf[sfi].setEnd(sf[sfi].getEnd() + startShift); } } + } } } @@ -483,11 +648,67 @@ 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 0) + { + sequencesArray = new SequenceI[nseq.size()]; + nseq.toArray(sequencesArray); + } + return sequencesArray; } }