-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.ws;\r
-\r
-import jalview.analysis.AlignSeq;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.Mapping;\r
-import jalview.datamodel.SequenceFeature;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.gui.AlignFrame;\r
-import jalview.gui.CutAndPasteTransfer;\r
-import jalview.gui.Desktop;\r
-import jalview.gui.IProgressIndicator;\r
-import jalview.gui.OOMWarning;\r
-\r
-import java.util.Enumeration;\r
-import java.util.Hashtable;\r
-import java.util.StringTokenizer;\r
-import java.util.Vector;\r
-\r
-import org.biojava.dasobert.dasregistry.DasSource;\r
-\r
-import uk.ac.ebi.picr.model.UPEntry;\r
-\r
-/**\r
- * Implements a runnable for validating a sequence against external databases\r
- * and then propagating references and features onto the sequence(s)\r
- * \r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class DBRefFetcher implements Runnable\r
-{\r
- SequenceI[] dataset;\r
-\r
- IProgressIndicator af;\r
-\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
-\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
- boolean running = false;\r
- /**\r
- * picr client instance\r
- */\r
- uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;\r
-\r
- // /This will be a collection of Vectors of sequenceI refs.\r
- // The key will be the seq name or accession id of the seq\r
- Hashtable seqRefs;\r
-\r
- String[] dbSources;\r
-\r
- SequenceFetcher sfetcher;\r
-\r
- public DBRefFetcher()\r
- {\r
- }\r
-\r
- /**\r
- * Creates a new SequenceFeatureFetcher object and fetches from the\r
- * currently selected set of databases.\r
- * \r
- * @param seqs\r
- * fetch references for these sequences\r
- * @param af\r
- * the parent alignframe for progress bar monitoring.\r
- */\r
- public DBRefFetcher(SequenceI[] seqs, AlignFrame af)\r
- {\r
- this(seqs, af, null);\r
- }\r
- /**\r
- * Creates a new SequenceFeatureFetcher object and fetches from the\r
- * currently selected set of databases.\r
- * \r
- * @param seqs\r
- * fetch references for these sequences\r
- * @param af\r
- * the parent alignframe for progress bar monitoring.\r
- * @param sources array of database source strings to query references from\r
- */\r
- public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)\r
- {\r
- this.af = af;\r
- SequenceI[] ds = new SequenceI[seqs.length];\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- if (seqs[i].getDatasetSequence() != null)\r
- ds[i] = seqs[i].getDatasetSequence();\r
- else\r
- ds[i] = seqs[i];\r
- }\r
- this.dataset = ds;\r
- // TODO Jalview 2.5 lots of this code should be in the gui package!\r
- sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);\r
- if (sources==null)\r
- {\r
- // af.featureSettings_actionPerformed(null);\r
- String[] defdb=null,otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
- Vector selsources = new Vector(), dasselsrc= (af.featureSettings!=null) ? af.featureSettings.getSelectedSources()\r
- : new jalview.gui.DasSourceBrowser().getSelectedSources();\r
- Enumeration en = dasselsrc.elements();\r
- while (en.hasMoreElements())\r
- {\r
- DasSource src = (DasSource) en.nextElement();\r
- selsources.addElement(src.getNickname());\r
- }\r
- int osel = 0;\r
- for (int o=0;otherdb!=null && o<otherdb.length;o++)\r
- {\r
- if (!selsources.contains(otherdb[o]))\r
- {\r
- otherdb[o] = null;\r
- } else {\r
- osel++;\r
- }\r
- }\r
- // select appropriate databases based on alignFrame context.\r
- if (af.getViewport().getAlignment().isNucleotide())\r
- {\r
- defdb = DBRefSource.DNACODINGDBS;\r
- }\r
- else\r
- {\r
- defdb = DBRefSource.PROTEINDBS;\r
- }\r
- // append the selected sequence sources to the default dbs \r
- dbSources = new String[defdb.length+osel];\r
- System.arraycopy(defdb, 0, dbSources, 0, defdb.length);\r
- for (int o=0,op=defdb.length; otherdb!=null && o<otherdb.length; o++)\r
- {\r
- if (otherdb[o]!=null)\r
- {\r
- dbSources[op++] = otherdb[o];\r
- }\r
- }\r
- } else {\r
- // we assume the caller knows what they're doing and ensured that all the db source names are valid\r
- dbSources = sources;\r
- }\r
- }\r
- /**\r
- * retrieve all the das sequence sources and add them to the list of db sources to retrieve from \r
- */\r
- public void appendAllDasSources()\r
- {\r
- if (dbSources == null)\r
- {\r
- dbSources = new String[] {};\r
- }\r
- // append additional sources\r
- String[] otherdb = sfetcher.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
- if (otherdb!=null && otherdb.length>0)\r
- {\r
- String[] newsrc = new String[dbSources.length+otherdb.length];\r
- System.arraycopy(dbSources, 0, newsrc,0,dbSources.length);\r
- System.arraycopy(otherdb, 0, newsrc,dbSources.length, otherdb.length);\r
- dbSources = newsrc;\r
- }\r
- }\r
- /**\r
- * start the fetcher thread\r
- * \r
- * @param waitTillFinished\r
- * true to block until the fetcher has finished\r
- */\r
- public void fetchDBRefs(boolean waitTillFinished)\r
- {\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- running = true;\r
-\r
- if (waitTillFinished)\r
- {\r
- while (running)\r
- {\r
- try\r
- {\r
- Thread.sleep(500);\r
- } catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * The sequence will be added to a vector of sequences belonging to key which\r
- * could be either seq name or dbref id\r
- * \r
- * @param seq\r
- * SequenceI\r
- * @param key\r
- * String\r
- */\r
- void addSeqId(SequenceI seq, String key)\r
- {\r
- key = key.toUpperCase();\r
-\r
- Vector seqs;\r
- if (seqRefs.containsKey(key))\r
- {\r
- seqs = (Vector) seqRefs.get(key);\r
-\r
- if (seqs != null && !seqs.contains(seq))\r
- {\r
- seqs.addElement(seq);\r
- }\r
- else if (seqs == null)\r
- {\r
- seqs = new Vector();\r
- seqs.addElement(seq);\r
- }\r
-\r
- }\r
- else\r
- {\r
- seqs = new Vector();\r
- seqs.addElement(seq);\r
- }\r
-\r
- seqRefs.put(key, seqs);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- if (dbSources == null)\r
- {\r
- throw new Error("Implementation error. Must initialise dbSources");\r
- }\r
- running = true;\r
- long startTime = System.currentTimeMillis();\r
- af.setProgressBar("Fetching db refs", startTime);\r
- try {\r
- picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator().getAccessionMapperPort(); \r
- } catch (Exception e)\r
- {\r
- System.err.println("Couldn't locate PICR service instance.\n");\r
- e.printStackTrace();\r
- }\r
- int db = 0;\r
- Vector sdataset = new Vector();\r
- for (int s = 0; s < dataset.length; s++)\r
- {\r
- sdataset.addElement(dataset[s]);\r
- }\r
- while (sdataset.size() > 0 && db < dbSources.length)\r
- {\r
- int maxqlen = 1; // default number of queries made to at one time\r
- System.err.println("Verifying against " + dbSources[db]);\r
- jalview.ws.seqfetcher.DbSourceProxy dbsource = sfetcher\r
- .getSourceProxy(dbSources[db]);\r
- if (dbsource == null)\r
- {\r
- System.err.println("No proxy for " + dbSources[db]);\r
- db++;\r
- continue;\r
- }\r
- if (dbsource.getDbSourceProperties()\r
- .containsKey(DBRefSource.MULTIACC))\r
- {\r
- maxqlen = ((Integer) dbsource.getDbSourceProperties().get(\r
- DBRefSource.MULTIACC)).intValue();\r
- }\r
- else\r
- {\r
- maxqlen = 1;\r
- }\r
- // iterate through db for each remaining un-verified sequence\r
- SequenceI[] currSeqs = new SequenceI[sdataset.size()];\r
- sdataset.copyInto(currSeqs);// seqs that are to be validated against\r
- // dbSources[db]\r
- Vector queries = new Vector(); // generated queries curSeq\r
- seqRefs = new Hashtable();\r
-\r
- int seqIndex = 0;\r
-\r
- while (queries.size() > 0 || seqIndex < currSeqs.length)\r
- {\r
- if (queries.size() > 0)\r
- {\r
- // Still queries to make for current seqIndex\r
- StringBuffer queryString = new StringBuffer("");\r
- int numq=0,nqSize = (maxqlen > queries.size()) ? queries.size()\r
- : maxqlen;\r
- \r
- while (queries.size()>0 && numq < nqSize)\r
- {\r
- String query = (String) queries.elementAt(0);\r
- if (dbsource.isValidReference(query))\r
- {\r
- queryString.append((numq == 0) ? "" : dbsource\r
- .getAccessionSeparator());\r
- queryString.append(query);\r
- numq++;\r
- }\r
- // remove the extracted query string\r
- queries.removeElementAt(0);\r
- }\r
- // make the queries and process the response\r
- AlignmentI retrieved = null;\r
- try\r
- {\r
- if (jalview.bin.Cache.log.isDebugEnabled())\r
- {\r
- jalview.bin.Cache.log.debug("Querying "+dbsource.getDbName()+" with : '"+queryString.toString()+"'");\r
- }\r
- retrieved = dbsource.getSequenceRecords(queryString.toString());\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- } catch (OutOfMemoryError err)\r
- {\r
- new OOMWarning("retrieving database references ("\r
- + queryString.toString() + ")", err);\r
- }\r
- if (retrieved != null)\r
- {\r
- transferReferences(sdataset, dbSources[db], retrieved);\r
- }\r
- }\r
- else\r
- {\r
- // make some more strings for use as queries\r
- for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)\r
- {\r
- SequenceI sequence = dataset[seqIndex];\r
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(\r
- sequence.getDBRef(), new String[]\r
- { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT\r
- // });\r
- // check for existing dbrefs to use\r
- if (uprefs != null && uprefs.length>0)\r
- {\r
- for (int j = 0; j < uprefs.length; j++)\r
- {\r
- addSeqId(sequence, uprefs[j].getAccessionId());\r
- queries\r
- .addElement(uprefs[j].getAccessionId()\r
- .toUpperCase());\r
- }\r
- }\r
- else\r
- {\r
- // generate queries from sequence ID string\r
- StringTokenizer st = new StringTokenizer(sequence.getName(),\r
- "|");\r
- while (st.hasMoreTokens())\r
- {\r
- String token = st.nextToken();\r
- UPEntry[] presp = null;\r
- try {\r
- presp=picrClient.getUPIForAccession(token, null, picrClient.getMappedDatabaseNames(), null, true);\r
- } catch (Exception e) {\r
- System.err.println("Exception with Picr for '"+token+"'\n");\r
- e.printStackTrace();\r
- }\r
- if (presp!=null && presp.length>0)\r
- {\r
- for (int id=0;id<presp.length; id++)\r
- {\r
- // construct sequences from response if sequences are present, and do a transferReferences\r
- // otherwise transfer non sequence x-references directly.\r
- }\r
- addSeqId(sequence, token);\r
- queries.addElement(token.toUpperCase());\r
- } else {\r
- System.out.println("Not querying source with token="+token+"\n");\r
- //addSeqId(sequence, token);\r
- //queries.addElement(token.toUpperCase());\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
- // advance to next database\r
- db++;\r
- } // all databases have been queries.\r
- if (sbuffer.length() > 0)\r
- {\r
- output\r
- .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"\r
- + "altered, most likely the start/end residue will have been updated.\n"\r
- + "Save your alignment to maintain the updated id.\n\n"\r
- + sbuffer.toString());\r
- Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
- // The above is the dataset, we must now find out the index\r
- // of the viewed sequence\r
-\r
- }\r
-\r
- af.setProgressBar("DBRef search completed", startTime);\r
- // promptBeforeBlast();\r
-\r
- running = false;\r
-\r
- }\r
-\r
- /**\r
- * Verify local sequences in seqRefs against the retrieved sequence database\r
- * records.\r
- * \r
- */\r
- void transferReferences(Vector sdataset, String dbSource,\r
- AlignmentI retrievedAl) // File\r
- // file)\r
- {\r
-\r
- if (retrievedAl == null || retrievedAl.getHeight() == 0)\r
- {\r
- return;\r
- }\r
- SequenceI[] retrieved = retrievedAl.getSequencesArray();\r
- SequenceI sequence = null;\r
-\r
- // Vector entries = new Uniprot().getUniprotEntries(file);\r
-\r
- int i, iSize = retrieved.length; // entries == null ? 0 : entries.size();\r
- // UniprotEntry entry;\r
- for (i = 0; i < iSize; i++)\r
- {\r
- SequenceI entry = retrieved[i]; // (UniprotEntry) entries.elementAt(i);\r
-\r
- // Work out which sequences this sequence matches,\r
- // taking into account all accessionIds and names in the file\r
- Vector sequenceMatches = new Vector();\r
- // look for corresponding accession ids\r
- DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry\r
- .getDBRef(), new String[]\r
- { dbSource });\r
- for (int j = 0; j < entryRefs.length; j++)\r
- {\r
- String accessionId = entryRefs[j].getAccessionId(); // .getAccession().elementAt(j).toString();\r
- // match up on accessionId\r
- if (seqRefs.containsKey(accessionId.toUpperCase()))\r
- {\r
- Vector seqs = (Vector) seqRefs.get(accessionId);\r
- for (int jj = 0; jj < seqs.size(); jj++)\r
- {\r
- sequence = (SequenceI) seqs.elementAt(jj);\r
- if (!sequenceMatches.contains(sequence))\r
- {\r
- sequenceMatches.addElement(sequence);\r
- }\r
- }\r
- }\r
- }\r
- if (sequenceMatches.size() == 0)\r
- {\r
- // failed to match directly on accessionId==query so just compare all\r
- // sequences to entry\r
- Enumeration e = seqRefs.keys();\r
- while (e.hasMoreElements())\r
- {\r
- Vector sqs = (Vector) seqRefs.get(e.nextElement());\r
- if (sqs != null && sqs.size() > 0)\r
- {\r
- Enumeration sqe = sqs.elements();\r
- while (sqe.hasMoreElements())\r
- {\r
- sequenceMatches.addElement(sqe.nextElement());\r
- }\r
- }\r
- }\r
- }\r
- // look for corresponding names\r
- // this is uniprot specific ?\r
- // could be useful to extend this so we try to find any 'significant'\r
- // information in common between two sequence objects.\r
- /*\r
- * DBRefEntry[] entryRefs =\r
- * jalview.util.DBRefUtils.selectRefs(entry.getDBRef(), new String[] {\r
- * dbSource }); for (int j = 0; j < entry.getName().size(); j++) { String\r
- * name = entry.getName().elementAt(j).toString(); if\r
- * (seqRefs.containsKey(name)) { Vector seqs = (Vector) seqRefs.get(name);\r
- * for (int jj = 0; jj < seqs.size(); jj++) { sequence = (SequenceI)\r
- * seqs.elementAt(jj); if (!sequenceMatches.contains(sequence)) {\r
- * sequenceMatches.addElement(sequence); } } } }\r
- */\r
- // sequenceMatches now contains the set of all sequences associated with\r
- // the returned db record\r
- String entrySeq = entry.getSequenceAsString().toUpperCase();\r
- for (int m = 0; m < sequenceMatches.size(); m++)\r
- {\r
- sequence = (SequenceI) sequenceMatches.elementAt(m);\r
- // only update start and end positions and shift features if there are\r
- // no existing references\r
- // TODO: test for legacy where uniprot or EMBL refs exist but no\r
- // mappings are made (but content matches retrieved set)\r
- boolean updateRefFrame = sequence.getDBRef() == null\r
- || sequence.getDBRef().length == 0;\r
- // verify sequence against the entry sequence\r
-\r
- String nonGapped = AlignSeq.extractGaps("-. ",\r
- sequence.getSequenceAsString()).toUpperCase();\r
-\r
- int absStart = entrySeq.indexOf(nonGapped);\r
- int mapStart = entry.getStart();\r
- jalview.datamodel.Mapping mp;\r
-\r
- if (absStart == -1)\r
- {\r
- // Is local sequence contained in dataset sequence?\r
- absStart = nonGapped.indexOf(entrySeq);\r
- if (absStart == -1)\r
- { // verification failed.\r
- sbuffer.append(sequence.getName()\r
- + " SEQUENCE NOT %100 MATCH \n");\r
- continue;\r
- }\r
-\r
- sbuffer.append(sequence.getName() + " HAS " + absStart\r
- + " PREFIXED RESIDUES COMPARED TO " + dbSource + "\n");\r
- //\r
- // + " - ANY SEQUENCE FEATURES"\r
- // + " HAVE BEEN ADJUSTED ACCORDINGLY \n");\r
- // absStart = 0;\r
- // create valid mapping between matching region of local sequence and\r
- // the mapped sequence\r
- mp = new Mapping(null, new int[]\r
- { sequence.getStart() + absStart,\r
- sequence.getStart() + absStart + entrySeq.length() - 1 },\r
- new int[]\r
- { entry.getStart(),\r
- entry.getStart() + entrySeq.length() - 1 }, 1, 1);\r
- updateRefFrame = false; // mapping is based on current start/end so\r
- // don't modify start and end\r
- }\r
- else\r
- {\r
- // update start and end of local sequence to place it in entry's\r
- // reference frame.\r
- // apply identity map map from whole of local sequence to matching\r
- // region of database\r
- // sequence\r
- mp = null; // Mapping.getIdentityMap();\r
- // new Mapping(null,\r
- // new int[] { absStart+sequence.getStart(),\r
- // absStart+sequence.getStart()+entrySeq.length()-1},\r
- // new int[] { entry.getStart(), entry.getEnd() }, 1, 1);\r
- // relocate local features for updated start\r
- if (updateRefFrame && sequence.getSequenceFeatures() != null)\r
- {\r
- SequenceFeature[] sf = sequence.getSequenceFeatures();\r
- int start = sequence.getStart();\r
- int end = sequence.getEnd();\r
- int startShift = 1 - absStart - start; // how much the features are\r
- // to be shifted by\r
- for (int sfi = 0; sfi < sf.length; sfi++)\r
- {\r
- if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)\r
- {\r
- // shift feature along by absstart\r
- sf[sfi].setBegin(sf[sfi].getBegin() + startShift);\r
- sf[sfi].setEnd(sf[sfi].getEnd() + startShift);\r
- }\r
- }\r
- }\r
- }\r
-\r
- System.out.println("Adding dbrefs to " + sequence.getName()\r
- + " from " + dbSource + " sequence : " + entry.getName());\r
- sequence.transferAnnotation(entry, mp);\r
- // unknownSequences.remove(sequence);\r
- int absEnd = absStart + nonGapped.length();\r
- absStart += 1;\r
- if (updateRefFrame)\r
- {\r
- // finally, update local sequence reference frame if we're allowed\r
- sequence.setStart(absStart);\r
- sequence.setEnd(absEnd);\r
- }\r
- // and remove it from the rest\r
- // TODO: decide if we should remove annotated sequence from set\r
- sdataset.remove(sequence);\r
- // TODO: should we make a note of sequences that have received new DB ids, so we can query all enabled DAS servers for them ?\r
- }\r
- }\r
- }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
+ Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings
+ .getSelectedSources() : new jalview.gui.DasSourceBrowser()
+ .getSelectedSources();
+ Enumeration<jalviewSourceI> en = dasselsrc.elements();
+ while (en.hasMoreElements())
+ {
+ jalviewSourceI src = en.nextElement();
+ List<DbSourceProxy> 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<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+ for (String ddb : defdb)
+ {
+ List<DbSourceProxy> 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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff