X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=76931429f326be2c619a4492e83df234f090f836;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=76e73e4a827e27d65a797cfaf5098ea47178d7ac;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 76e73e4..7693142 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,490 +1,757 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * 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.
- *
- * 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
- */
-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.datamodel.Mapping;
-import jalview.gui.*;
-import jalview.ws.dbsources.Uniprot;
-import jalview.ws.ebi.EBIFetchClient;
-
-/**
- * Implements a runnable for validating a sequence against external databases
- * and then propagating references and features onto the sequence(s)
- *
- * @author $author$
- * @version $Revision$
- */
-public class DBRefFetcher implements Runnable
-{
- SequenceI[] dataset;
-
- IProgressIndicator af;
-
- CutAndPasteTransfer output = new CutAndPasteTransfer();
-
- StringBuffer sbuffer = new StringBuffer();
-
- boolean running = false;
-
- // /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;
-
- String[] dbSources;
-
- SequenceFetcher sfetcher;
-
- public DBRefFetcher()
- {
- }
-
- /**
- * Creates a new SequenceFeatureFetcher object.
- *
- * @param seqs
- * fetch references for these sequences
- * @param af
- * the parent alignframe for progress bar monitoring.
- */
- public DBRefFetcher(SequenceI[] seqs, AlignFrame af)
- {
- this.af = af;
- SequenceI[] ds = new SequenceI[seqs.length];
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i].getDatasetSequence() != null)
- ds[i] = seqs[i].getDatasetSequence();
- else
- ds[i] = seqs[i];
- }
- 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())
- {
- dbSources = DBRefSource.DNACODINGDBS;
- }
- else
- {
- dbSources = DBRefSource.PROTEINDBS;
- }
- }
-
- /**
- * start the fetcher thread
- *
- * @param waitTillFinished
- * true to block until the fetcher has finished
- */
- public void fetchDBRefs(boolean waitTillFinished)
- {
- Thread thread = new Thread(this);
- thread.start();
- running = true;
-
- if (waitTillFinished)
- {
- while (running)
- {
- try
- {
- Thread.sleep(500);
- } catch (Exception ex)
- {
- }
- }
- }
- }
-
- /**
- * The sequence will be added to a vector of sequences belonging to key which
- * could be either seq name or dbref id
- *
- * @param seq
- * SequenceI
- * @param key
- * String
- */
- void addSeqId(SequenceI seq, String key)
- {
- key = key.toUpperCase();
-
- Vector seqs;
- if (seqRefs.containsKey(key))
- {
- seqs = (Vector) seqRefs.get(key);
-
- if (seqs != null && !seqs.contains(seq))
- {
- seqs.addElement(seq);
- }
- else if (seqs == null)
- {
- seqs = new Vector();
- seqs.addElement(seq);
- }
-
- }
- else
- {
- seqs = new Vector();
- seqs.addElement(seq);
- }
-
- seqRefs.put(key, seqs);
- }
-
- /**
- * DOCUMENT ME!
- */
- public void run()
- {
- if (dbSources == null)
- {
- throw new Error("Implementation error. Must initialise dbSources");
- }
- long startTime = System.currentTimeMillis();
- af.setProgressBar("Fetching db refs", startTime);
- running = true;
- int db = 0;
- Vector sdataset = new Vector();
- for (int s = 0; s < dataset.length; s++)
- {
- sdataset.addElement(dataset[s]);
- }
- while (sdataset.size() > 0 && db < dbSources.length)
- {
- int maxqlen = 1; // default number of queries made to at one time
- System.err.println("Verifying against " + dbSources[db]);
- jalview.ws.seqfetcher.DbSourceProxy dbsource = sfetcher
- .getSourceProxy(dbSources[db]);
- if (dbsource == null)
- {
- System.err.println("No proxy for " + dbSources[db]);
- db++;
- continue;
- }
- if (dbsource.getDbSourceProperties()
- .containsKey(DBRefSource.MULTIACC))
- {
- maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
- DBRefSource.MULTIACC)).intValue();
- }
- else
- {
- maxqlen = 1;
- }
- // iterate through db for each remaining un-verified sequence
- SequenceI[] currSeqs = new SequenceI[sdataset.size()];
- sdataset.copyInto(currSeqs);// seqs that are to be validated against
- // dbSources[db]
- Vector queries = new Vector(); // generated queries curSeq
- seqRefs = new Hashtable();
-
- int seqIndex = 0;
-
- while (queries.size() > 0 || seqIndex < currSeqs.length)
- {
- if (queries.size() > 0)
- {
- // Still queries to make for current seqIndex
- StringBuffer queryString = new StringBuffer("");
- int nqSize = (maxqlen > queries.size()) ? queries.size()
- : maxqlen;
- for (int nq = 0, numq = 0; nq < nqSize; nq++)
- {
- String query = (String) queries.elementAt(nq);
- if (dbsource.isValidReference(query))
- {
- queryString.append((nq == 0) ? "" : dbsource
- .getAccessionSeparator());
- queryString.append(query);
- numq++;
- }
- }
- for (int nq = 0; nq < nqSize; nq++)
- {
- queries.removeElementAt(0);
- }
- // make the queries and process the response
- AlignmentI retrieved = null;
- try
- {
- retrieved = dbsource.getSequenceRecords(queryString.toString());
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } catch (OutOfMemoryError err)
- {
- new OOMWarning("retrieving database references ("
- + queryString.toString() + ")", err);
- }
- if (retrieved != null)
- {
- transferReferences(sdataset, dbSources[db], retrieved);
- }
- }
- else
- {
- // make some more strings for use as queries
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
- {
- SequenceI sequence = dataset[seqIndex];
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- sequence.getDBRef(), new String[]
- { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT
- // });
- // check for existing dbrefs to use
- if (uprefs != null)
- {
- for (int j = 0; j < uprefs.length; j++)
- {
- addSeqId(sequence, uprefs[j].getAccessionId());
- queries
- .addElement(uprefs[j].getAccessionId()
- .toUpperCase());
- }
- }
- else
- {
- // generate queries from sequence ID string
- StringTokenizer st = new StringTokenizer(sequence.getName(),
- "|");
- while (st.hasMoreTokens())
- {
- String token = st.nextToken();
- addSeqId(sequence, token);
- queries.addElement(token.toUpperCase());
- }
- }
- }
- }
- }
- // advance to next database
- db++;
- } // all databases have been queries.
- if (sbuffer.length() > 0)
- {
- output
- .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
- + "altered, most likely the start/end residue will have been updated.\n"
- + "Save your alignment to maintain the updated id.\n\n"
- + sbuffer.toString());
- Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
- // The above is the dataset, we must now find out the index
- // of the viewed sequence
-
- }
-
- af.setProgressBar("DBRef search completed", startTime);
- // promptBeforeBlast();
-
- running = false;
-
- }
-
- /**
- * Verify local sequences in seqRefs against the retrieved sequence database
- * records.
- *
- */
- void transferReferences(Vector sdataset, String dbSource,
- AlignmentI retrievedAl) // File
- // file)
- {
-
- if (retrievedAl == null || retrievedAl.getHeight() == 0)
- {
- return;
- }
- SequenceI[] retrieved = retrievedAl.getSequencesArray();
- SequenceI sequence = null;
-
- // Vector entries = new Uniprot().getUniprotEntries(file);
-
- int i, iSize = retrieved.length; // entries == null ? 0 : entries.size();
- // UniprotEntry entry;
- for (i = 0; i < iSize; i++)
- {
- SequenceI entry = retrieved[i]; // (UniprotEntry) entries.elementAt(i);
-
- // Work out which sequences this sequence matches,
- // taking into account all accessionIds and names in the file
- Vector sequenceMatches = new Vector();
- // look for corresponding accession ids
- DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry
- .getDBRef(), new String[]
- { dbSource });
- 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++)
- {
- 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
- Enumeration e = seqRefs.keys();
- while (e.hasMoreElements())
- {
- Vector sqs = (Vector) seqRefs.get(e.nextElement());
- if (sqs != null && sqs.size() > 0)
- {
- Enumeration sqe = sqs.elements();
- while (sqe.hasMoreElements())
- {
- sequenceMatches.addElement(sqe.nextElement());
- }
- }
- }
- }
- // look for corresponding names
- // this is uniprot specific ?
- // could be useful to extend this so we try to find any 'significant'
- // information in common between two sequence objects.
- /*
- * DBRefEntry[] entryRefs =
- * jalview.util.DBRefUtils.selectRefs(entry.getDBRef(), new String[] {
- * dbSource }); for (int j = 0; j < entry.getName().size(); j++) { String
- * name = entry.getName().elementAt(j).toString(); if
- * (seqRefs.containsKey(name)) { Vector seqs = (Vector) seqRefs.get(name);
- * for (int jj = 0; jj < seqs.size(); jj++) { sequence = (SequenceI)
- * seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) {
- * sequenceMatches.addElement(sequence); } } } }
- */
- // sequenceMatches now contains the set of all sequences associated with
- // the returned db record
- String entrySeq = entry.getSequenceAsString().toUpperCase();
- for (int m = 0; m < sequenceMatches.size(); m++)
- {
- sequence = (SequenceI) sequenceMatches.elementAt(m);
- // only update start and end positions and shift features if there are
- // no existing references
- // TODO: test for legacy where uniprot or EMBL refs exist but no
- // mappings are made (but content matches retrieved set)
- boolean updateRefFrame = sequence.getDBRef() == null
- || sequence.getDBRef().length == 0;
- // verify sequence against the entry sequence
-
- String nonGapped = AlignSeq.extractGaps("-. ",
- sequence.getSequenceAsString()).toUpperCase();
-
- int absStart = entrySeq.indexOf(nonGapped);
- int mapStart = entry.getStart();
- jalview.datamodel.Mapping mp;
-
- if (absStart == -1)
- {
- // Is local sequence contained in dataset sequence?
- absStart = nonGapped.indexOf(entrySeq);
- if (absStart == -1)
- { // verification failed.
- sbuffer.append(sequence.getName()
- + " SEQUENCE NOT %100 MATCH \n");
- continue;
- }
-
- sbuffer.append(sequence.getName() + " HAS " + absStart
- + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
- //
- // + " - ANY SEQUENCE FEATURES"
- // + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
- // absStart = 0;
- // create valid mapping between matching region of local sequence and
- // the mapped sequence
- mp = new Mapping(null, new int[]
- { sequence.getStart() + absStart,
- sequence.getStart() + absStart + entrySeq.length() - 1 },
- new int[]
- { entry.getStart(),
- entry.getStart() + entrySeq.length() - 1 }, 1, 1);
- updateRefFrame = false; // mapping is based on current start/end so
- // don't modify start and end
- }
- else
- {
- // 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
- // region of database
- // sequence
- mp = null; // Mapping.getIdentityMap();
- // new Mapping(null,
- // new int[] { absStart+sequence.getStart(),
- // 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)
- {
- 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 (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);
- }
- }
- }
- }
-
- System.out.println("Adding dbrefs to " + sequence.getName()
- + " from " + dbSource + " sequence : " + entry.getName());
- sequence.transferAnnotation(entry, mp);
- // unknownSequences.remove(sequence);
- int absEnd = absStart + nonGapped.length();
- absStart += 1;
- if (updateRefFrame)
- {
- // finally, update local sequence reference frame if we're allowed
- sequence.setStart(absStart);
- sequence.setEnd(absEnd);
- }
- // and remove it from the rest
- // TODO: decide if we should remove annotated sequence from set
- sdataset.remove(sequence);
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws;
+
+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.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 jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import uk.ac.ebi.picr.model.UPEntry;
+
+/**
+ * Implements a runnable for validating a sequence against external databases
+ * and then propagating references and features onto the sequence(s)
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class DBRefFetcher implements Runnable
+{
+ SequenceI[] dataset;
+
+ IProgressIndicator af;
+
+ CutAndPasteTransfer output = new CutAndPasteTransfer();
+
+ StringBuffer sbuffer = new StringBuffer();
+
+ 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;
+
+ DbSourceProxy[] dbSources;
+
+ SequenceFetcher sfetcher;
+
+ private SequenceI[] alseqs;
+
+ /**
+ * when true - retrieved sequences will be trimmed to cover longest derived
+ * alignment sequence
+ */
+ private boolean trimDsSeqs = true;
+
+ public DBRefFetcher()
+ {
+ }
+
+ /**
+ * 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.
+ */
+ 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,
+ DbSourceProxy[] 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
+ ds[i] = seqs[i];
+ }
+ this.dataset = ds;
+ // TODO Jalview 2.5 lots of this code should be in the gui package!
+ sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
+ // set default behaviour for transferring excess sequence data to the
+ // dataset
+ trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
+ if (sources == null)
+ {
+ // af.featureSettings_actionPerformed(null);
+ String[] defdb = null, otherdb = sfetcher
+ .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+ List selsources = new ArrayList();
+ Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings
+ .getSelectedSources() : new jalview.gui.DasSourceBrowser()
+ .getSelectedSources();
+ Enumeration en = dasselsrc.elements();
+ while (en.hasMoreElements())
+ {
+ jalviewSourceI src = en.nextElement();
+ List sp = src.getSequenceSourceProxies();
+ if (sp != null)
+ {
+ selsources.addAll(sp);
+ if (sp.size() > 1)
+ {
+ Cache.log.debug("Added many Db Sources for :" + src.getTitle());
+ }
+ }
+ }
+ // select appropriate databases based on alignFrame context.
+ if (af.getViewport().getAlignment().isNucleotide())
+ {
+ defdb = DBRefSource.DNACODINGDBS;
+ }
+ else
+ {
+ defdb = DBRefSource.PROTEINDBS;
+ }
+ List srces = new ArrayList();
+ for (String ddb : defdb)
+ {
+ List srcesfordb = sfetcher.getSourceProxy(ddb);
+ if (srcesfordb != null)
+ {
+ srces.addAll(srcesfordb);
+ }
+ }
+
+ // append the selected sequence sources to the default dbs
+ srces.addAll(selsources);
+ dbSources = srces.toArray(new DbSourceProxy[0]);
+ }
+ else
+ {
+ // 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 DbSourceProxy[0];
+ }
+ // append additional sources
+ DbSourceProxy[] otherdb = sfetcher
+ .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+ if (otherdb != null && otherdb.length > 0)
+ {
+ DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
+ + otherdb.length];
+ System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
+ System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);
+ dbSources = newsrc;
+ }
+ }
+
+ /**
+ * start the fetcher thread
+ *
+ * @param waitTillFinished
+ * true to block until the fetcher has finished
+ */
+ public void fetchDBRefs(boolean waitTillFinished)
+ {
+ Thread thread = new Thread(this);
+ thread.start();
+ running = true;
+
+ if (waitTillFinished)
+ {
+ while (running)
+ {
+ try
+ {
+ Thread.sleep(500);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+
+ /**
+ * The sequence will be added to a vector of sequences belonging to key which
+ * could be either seq name or dbref id
+ *
+ * @param seq
+ * SequenceI
+ * @param key
+ * String
+ */
+ void addSeqId(SequenceI seq, String key)
+ {
+ key = key.toUpperCase();
+
+ Vector seqs;
+ if (seqRefs.containsKey(key))
+ {
+ seqs = (Vector) seqRefs.get(key);
+
+ if (seqs != null && !seqs.contains(seq))
+ {
+ seqs.addElement(seq);
+ }
+ else if (seqs == null)
+ {
+ seqs = new Vector();
+ seqs.addElement(seq);
+ }
+
+ }
+ else
+ {
+ seqs = new Vector();
+ seqs.addElement(seq);
+ }
+
+ seqRefs.put(key, seqs);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run()
+ {
+ if (dbSources == null)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_must_init_dbsources"));
+ }
+ running = true;
+ long startTime = System.currentTimeMillis();
+ af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+ startTime);
+ 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++)
+ {
+ sdataset.addElement(dataset[s]);
+ }
+ while (sdataset.size() > 0 && db < dbSources.length)
+ {
+ int maxqlen = 1; // default number of queries made to at one time
+ System.err.println("Verifying against " + dbSources[db].getDbName());
+ boolean dn = false;
+
+ // iterate through db for each remaining un-verified sequence
+ SequenceI[] currSeqs = new SequenceI[sdataset.size()];
+ sdataset.copyInto(currSeqs);// seqs that are to be validated against
+ // dbSources[db]
+ Vector queries = new Vector(); // generated queries curSeq
+ seqRefs = new Hashtable();
+
+ int seqIndex = 0;
+
+ jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];
+ {
+ // for moment, we dumbly iterate over all retrieval sources for a
+ // particular database
+ // TODO: introduce multithread multisource queries and logic to remove a
+ // query from other sources if any source for a database returns a
+ // record
+ if (dbsource.getDbSourceProperties().containsKey(
+ DBRefSource.MULTIACC))
+ {
+ maxqlen = ((Integer) dbsource.getDbSourceProperties().get(
+ DBRefSource.MULTIACC)).intValue();
+ }
+ else
+ {
+ maxqlen = 1;
+ }
+ while (queries.size() > 0 || seqIndex < currSeqs.length)
+ {
+ if (queries.size() > 0)
+ {
+ // 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)
+ {
+ String query = (String) queries.elementAt(0);
+ if (dbsource.isValidReference(query))
+ {
+ queryString.append((numq == 0) ? "" : dbsource
+ .getAccessionSeparator());
+ queryString.append(query);
+ numq++;
+ }
+ // remove the extracted query string
+ queries.removeElementAt(0);
+ }
+ // make the queries and process the response
+ AlignmentI retrieved = null;
+ try
+ {
+ if (jalview.bin.Cache.log.isDebugEnabled())
+ {
+ jalview.bin.Cache.log.debug("Querying "
+ + dbsource.getDbName() + " with : '"
+ + queryString.toString() + "'");
+ }
+ retrieved = dbsource.getSequenceRecords(queryString
+ .toString());
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ } catch (OutOfMemoryError err)
+ {
+ new OOMWarning("retrieving database references ("
+ + queryString.toString() + ")", err);
+ }
+ if (retrieved != null)
+ {
+ transferReferences(sdataset, dbsource.getDbSource(),
+ retrieved, trimDsSeqs);
+ }
+ }
+ else
+ {
+ // make some more strings for use as queries
+ for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
+ {
+ SequenceI sequence = dataset[seqIndex];
+ DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
+ sequence.getDBRef(),
+ new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ // });
+ // check for existing dbrefs to use
+ if (uprefs != null && uprefs.length > 0)
+ {
+ for (int j = 0; j < uprefs.length; j++)
+ {
+ addSeqId(sequence, uprefs[j].getAccessionId());
+ queries.addElement(uprefs[j].getAccessionId()
+ .toUpperCase());
+ }
+ }
+ else
+ {
+ // generate queries from sequence ID string
+ StringTokenizer st = new StringTokenizer(
+ sequence.getName(), "|");
+ while (st.hasMoreTokens())
+ {
+ String token = st.nextToken();
+ 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());
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ // advance to next database
+ db++;
+ } // all databases have been queries.
+ if (sbuffer.length() > 0)
+ {
+ output.setText(MessageManager
+ .getString("label.your_sequences_have_been_verified")
+ + sbuffer.toString());
+ Desktop.addInternalFrame(output,
+ MessageManager.getString("label.sequence_names_updated"),
+ 600, 300);
+ // The above is the dataset, we must now find out the index
+ // of the viewed sequence
+
+ }
+
+ af.setProgressBar(
+ MessageManager.getString("label.dbref_search_completed"),
+ startTime);
+ // promptBeforeBlast();
+
+ running = false;
+
+ }
+
+ /**
+ * Verify local sequences in seqRefs against the retrieved sequence database
+ * records.
+ *
+ * @param trimDatasetSeqs
+ *
+ */
+ void transferReferences(Vector sdataset, String dbSource,
+ AlignmentI retrievedAl, boolean trimDatasetSeqs) // File
+ // file)
+ {
+ System.out.println("trimming ? " + trimDatasetSeqs);
+ if (retrievedAl == null || retrievedAl.getHeight() == 0)
+ {
+ return;
+ }
+ SequenceI[] retrieved = recoverDbSequences(retrievedAl
+ .getSequencesArray());
+ SequenceI sequence = null;
+ boolean transferred = false;
+ StringBuffer messages = new StringBuffer();
+
+ // Vector entries = new Uniprot().getUniprotEntries(file);
+
+ int i, iSize = retrieved.length; // entries == null ? 0 : entries.size();
+ // UniprotEntry entry;
+ for (i = 0; i < iSize; i++)
+ {
+ SequenceI entry = retrieved[i]; // (UniprotEntry) entries.elementAt(i);
+
+ // Work out which sequences this sequence matches,
+ // taking into account all accessionIds and names in the file
+ Vector sequenceMatches = new Vector();
+ // look for corresponding accession ids
+ 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++)
+ {
+ 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
+ Enumeration e = seqRefs.keys();
+ while (e.hasMoreElements())
+ {
+ Vector sqs = (Vector) seqRefs.get(e.nextElement());
+ if (sqs != null && sqs.size() > 0)
+ {
+ Enumeration sqe = sqs.elements();
+ while (sqe.hasMoreElements())
+ {
+ sequenceMatches.addElement(sqe.nextElement());
+ }
+ }
+ }
+ }
+ // look for corresponding names
+ // this is uniprot specific ?
+ // could be useful to extend this so we try to find any 'significant'
+ // information in common between two sequence objects.
+ /*
+ * DBRefEntry[] entryRefs =
+ * jalview.util.DBRefUtils.selectRefs(entry.getDBRef(), new String[] {
+ * dbSource }); for (int j = 0; j < entry.getName().size(); j++) { String
+ * name = entry.getName().elementAt(j).toString(); if
+ * (seqRefs.containsKey(name)) { Vector seqs = (Vector) seqRefs.get(name);
+ * for (int jj = 0; jj < seqs.size(); jj++) { sequence = (SequenceI)
+ * seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) {
+ * sequenceMatches.addElement(sequence); } } } }
+ */
+ // sequenceMatches now contains the set of all sequences associated with
+ // the returned db record
+ String entrySeq = entry.getSequenceAsString().toUpperCase();
+ for (int m = 0; m < sequenceMatches.size(); m++)
+ {
+ sequence = (SequenceI) sequenceMatches.elementAt(m);
+ // only update start and end positions and shift features if there are
+ // no existing references
+ // TODO: test for legacy where uniprot or EMBL refs exist but no
+ // mappings are made (but content matches retrieved set)
+ boolean updateRefFrame = sequence.getDBRef() == null
+ || sequence.getDBRef().length == 0;
+ // TODO:
+ // verify sequence against the entry sequence
+
+ String nonGapped = AlignSeq.extractGaps("-. ",
+ sequence.getSequenceAsString()).toUpperCase();
+
+ int absStart = entrySeq.indexOf(nonGapped);
+ int mapStart = entry.getStart();
+ jalview.datamodel.Mapping mp;
+
+ if (absStart == -1)
+ {
+ // Is local sequence contained in dataset sequence?
+ absStart = nonGapped.indexOf(entrySeq);
+ if (absStart == -1)
+ { // verification failed.
+ messages.append(sequence.getName()
+ + " SEQUENCE NOT %100 MATCH \n");
+ continue;
+ }
+ transferred = true;
+ sbuffer.append(sequence.getName() + " HAS " + absStart
+ + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");
+ //
+ // + " - ANY SEQUENCE FEATURES"
+ // + " HAVE BEEN ADJUSTED ACCORDINGLY \n");
+ // absStart = 0;
+ // create valid mapping between matching region of local sequence and
+ // the mapped sequence
+ mp = new Mapping(null, new int[] {
+ sequence.getStart() + absStart,
+ sequence.getStart() + absStart + entrySeq.length() - 1 },
+ new int[] { entry.getStart(),
+ entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+ updateRefFrame = false; // mapping is based on current start/end so
+ // don't modify start and end
+ }
+ 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
+ // region of database
+ // sequence
+ mp = null; // Mapping.getIdentityMap();
+ // new Mapping(null,
+ // new int[] { absStart+sequence.getStart(),
+ // absStart+sequence.getStart()+entrySeq.length()-1},
+ // new int[] { entry.getStart(), entry.getEnd() }, 1, 1);
+ // relocate local features for updated start
+ if (updateRefFrame)
+ {
+ if (sequence.getSequenceFeatures() != null)
+ {
+ 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 (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);
+ }
+ }
+ }
+ }
+ }
+
+ System.out.println("Adding dbrefs to " + sequence.getName()
+ + " from " + dbSource + " sequence : " + entry.getName());
+ sequence.transferAnnotation(entry, mp);
+ // unknownSequences.remove(sequence);
+ int absEnd = absStart + nonGapped.length();
+ absStart += 1;
+ if (!trimDatasetSeqs)
+ {
+ // insert full length sequence from record
+ sequence.setSequence(entry.getSequenceAsString());
+ sequence.setStart(entry.getStart());
+ }
+ if (updateRefFrame)
+ {
+ // finally, update local sequence reference frame if we're allowed
+ if (trimDatasetSeqs)
+ {
+ // just fix start/end
+ 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;
+ }
+}