-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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 java.io.*;\r
-import java.util.*;\r
-\r
-import org.exolab.castor.mapping.*;\r
-import org.exolab.castor.xml.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class DBRefFetcher\r
- implements Runnable\r
-{\r
- SequenceI [] dataset;\r
- AlignFrame af;\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
- StringBuffer sbuffer = new StringBuffer();\r
- boolean running = false;\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
- public DBRefFetcher()\r
- {}\r
-\r
- public Vector getUniprotEntries(File file)\r
- {\r
- UniprotFile uni = new UniprotFile();\r
- try\r
- {\r
- // 1. Load the mapping information from the file\r
- org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());\r
- java.net.URL url = getClass().getResource("/uniprot_mapping.xml");\r
- map.loadMapping(url);\r
-\r
- // 2. Unmarshal the data\r
- Unmarshaller unmar = new Unmarshaller(uni);\r
- unmar.setIgnoreExtraElements(true);\r
- unmar.setMapping(map);\r
-\r
- uni = (UniprotFile) unmar.unmarshal(new FileReader(file));\r
- }\r
- catch (Exception e)\r
- {\r
- System.out.println("Error getUniprotEntries() " + e);\r
- }\r
-\r
- return uni.getUniprotEntries();\r
- }\r
-\r
- /**\r
- * Creates a new SequenceFeatureFetcher object.\r
- *\r
- * @param align DOCUMENT ME!\r
- * @param ap DOCUMENT ME!\r
- */\r
- public DBRefFetcher(SequenceI [] seqs, AlignFrame af)\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
- }\r
-\r
- public boolean 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
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
- }\r
-\r
- return true;\r
- }\r
-\r
- /**\r
- * The sequence will be added to a vector of sequences\r
- * belonging to key which could be either seq name or dbref id\r
- * @param seq SequenceI\r
- * @param key 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
- long startTime = System.currentTimeMillis();\r
- af.setProgressBar("Fetching db refs", startTime);\r
- running = true;\r
-\r
- seqRefs = new Hashtable();\r
-\r
- try\r
- {\r
- int seqIndex = 0;\r
-\r
- while (seqIndex < dataset.length)\r
- {\r
- StringBuffer queryString = new StringBuffer("uniprot:");\r
-\r
- for (int i = 0; (seqIndex < dataset.length) && (i < 50);\r
- seqIndex++, i++)\r
- {\r
- SequenceI sequence = dataset[seqIndex];\r
- DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.\r
- getDBRef(), new String[]\r
- {\r
- jalview.datamodel.DBRefSource.UNIPROT});\r
- if (uprefs != null)\r
- {\r
- if (uprefs.length + i > 50)\r
- {\r
- break;\r
- }\r
-\r
- for (int j = 0; j < uprefs.length; j++)\r
- {\r
- addSeqId(sequence, uprefs[j].getAccessionId());\r
- queryString.append(uprefs[j].getAccessionId() + ";");\r
- }\r
- }\r
- else\r
- {\r
- StringTokenizer st = new StringTokenizer(sequence.getName(), "|");\r
- if (st.countTokens() + i > 50)\r
- {\r
- //Dont send more than 50 id strings to dbFetch!!\r
- seqIndex--;\r
- }\r
- else\r
- {\r
- while (st.hasMoreTokens())\r
- {\r
- String token = st.nextToken();\r
- addSeqId(sequence, token);\r
- queryString.append(token + ";");\r
- }\r
- }\r
- }\r
- }\r
-\r
- ///////////////////////////////////\r
- ///READ FROM EBI\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile(queryString.toString(), "xml", "raw");\r
- if (file != null)\r
- {\r
- ReadUniprotFile(file);\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- if (sbuffer.length() > 0)\r
- {\r
- output.setText(\r
- "Your sequences have been matched to Uniprot. 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
- * DOCUMENT ME!\r
- *\r
- * @param result DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- * @param align DOCUMENT ME!\r
- */\r
- void ReadUniprotFile(File file)\r
- {\r
- if (!file.exists())\r
- {\r
- return;\r
- }\r
-\r
- SequenceI sequence = null;\r
-\r
- Vector entries = getUniprotEntries(file);\r
-\r
- int i, iSize = entries == null ? 0 : entries.size();\r
- UniprotEntry entry;\r
- for (i = 0; i < iSize; i++)\r
- {\r
- entry = (UniprotEntry) entries.elementAt(i);\r
-\r
- //Work out which sequences this Uniprot file has matches to,\r
- //taking into account all accessionIds and names in the file\r
- Vector sequenceMatches = new Vector();\r
- for (int j = 0; j < entry.getAccession().size(); j++)\r
- {\r
- String accessionId = entry.getAccession().elementAt(j).toString();\r
- if (seqRefs.containsKey(accessionId))\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
- for (int j = 0; j < entry.getName().size(); j++)\r
- {\r
- String name = entry.getName().elementAt(j).toString();\r
- if (seqRefs.containsKey(name))\r
- {\r
- Vector seqs = (Vector) seqRefs.get(name);\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
-\r
- for (int m = 0; m < sequenceMatches.size(); m++)\r
- {\r
- sequence = (SequenceI) sequenceMatches.elementAt(m);\r
- sequence.addDBRef(new DBRefEntry(DBRefSource.UNIPROT,\r
- "0", // TODO: VERSION FROM UNIPROT\r
- entry.getAccession().elementAt(0).\r
- toString()));\r
-\r
- System.out.println("Adding dbref to " + sequence.getName() + " : " +\r
- entry.getAccession().elementAt(0).toString());\r
-\r
- String nonGapped = AlignSeq.extractGaps("-. ",\r
- sequence.getSequenceAsString()).\r
- toUpperCase();\r
-\r
- int absStart = entry.getUniprotSequence().getContent().indexOf(\r
- nonGapped.toString());\r
-\r
- if (absStart == -1)\r
- {\r
- // Is UniprotSequence contained in dataset sequence?\r
- absStart = nonGapped.toString().indexOf(entry.getUniprotSequence().\r
- getContent());\r
- if (absStart == -1)\r
- {\r
- sbuffer.append(sequence.getName() + " SEQUENCE NOT %100 MATCH \n");\r
- continue;\r
- }\r
-\r
- if (entry.getFeature() != null)\r
- {\r
- Enumeration e = entry.getFeature().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- sf.setBegin(sf.getBegin() + absStart + 1);\r
- sf.setEnd(sf.getEnd() + absStart + 1);\r
- }\r
-\r
- sbuffer.append(sequence.getName() +\r
- " HAS " + absStart +\r
- " PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"\r
- + " HAVE BEEN ADJUSTED ACCORDINGLY \n");\r
- absStart = 0;\r
- }\r
-\r
- }\r
-\r
- //unknownSequences.remove(sequence);\r
-\r
- int absEnd = absStart + nonGapped.toString().length();\r
- absStart += 1;\r
-\r
- Enumeration e = entry.getDbReference().elements();\r
- Vector onlyPdbEntries = new Vector();\r
- while (e.hasMoreElements())\r
- {\r
- PDBEntry pdb = (PDBEntry) e.nextElement();\r
- if (!pdb.getType().equals(DBRefSource.PDB))\r
- {\r
- DBRefEntry xref = new DBRefEntry(pdb.getType(), DBRefSource.UNIPROT, pdb.getId());\r
- sequence.addDBRef(xref);\r
- continue;\r
- }\r
- \r
- sequence.addDBRef(new DBRefEntry(DBRefSource.PDB,\r
- "0",\r
- pdb.getId()));\r
-\r
- onlyPdbEntries.addElement(pdb);\r
- }\r
-\r
- sequence.setPDBId(onlyPdbEntries);\r
-\r
- sequence.setStart(absStart);\r
- sequence.setEnd(absEnd);\r
-\r
- }\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 java.util.Locale;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceI;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.gui.FeatureSettings;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import uk.ac.ebi.picr.model.UPEntry;
+import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
+
+/**
+ * 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
+{
+ private static final String NEWLINE = System.lineSeparator();
+
+ public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS";
+
+ public interface FetchFinishedListenerI
+ {
+ void finished();
+ }
+
+ SequenceI[] dataset;
+
+ IProgressIndicator progressWindow;
+
+ CutAndPasteTransfer output = new CutAndPasteTransfer();
+
+ /**
+ * 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<String, Vector<SequenceI>> seqRefs;
+
+ DbSourceProxy[] dbSources;
+
+ SequenceFetcher sfetcher;
+
+ private List<FetchFinishedListenerI> listeners;
+
+ private SequenceI[] alseqs;
+
+ /*
+ * when true - retrieved sequences will be trimmed to cover longest derived
+ * alignment sequence
+ */
+ private boolean trimDsSeqs = true;
+
+ /**
+ * Creates a new DBRefFetcher object and fetches from the currently selected
+ * set of databases, if this is null then it fetches based on feature settings
+ *
+ * @param seqs
+ * fetch references for these SequenceI array
+ * @param progressIndicatorFrame
+ * the frame for progress bar monitoring
+ * @param sources
+ * array of DbSourceProxy to query references form
+ * @param featureSettings
+ * FeatureSettings to get alternative DbSourceProxy from
+ * @param isNucleotide
+ * indicates if the array of SequenceI are Nucleotides or not
+ */
+ public DBRefFetcher(SequenceI[] seqs,
+ IProgressIndicator progressIndicatorFrame,
+ DbSourceProxy[] sources, FeatureSettings featureSettings,
+ boolean isNucleotide)
+ {
+ listeners = new ArrayList<>();
+ this.progressWindow = progressIndicatorFrame;
+ 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();
+ // set default behaviour for transferring excess sequence data to the
+ // dataset
+ trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
+ if (sources == null)
+ {
+ setDatabaseSources(featureSettings, isNucleotide);
+ }
+ else
+ {
+ // we assume the caller knows what they're doing and ensured that all the
+ // db source names are valid
+ dbSources = sources;
+ }
+ }
+
+ /**
+ * Helper method to configure the list of database sources to query
+ *
+ * @param featureSettings
+ * @param forNucleotide
+ */
+ void setDatabaseSources(FeatureSettings featureSettings,
+ boolean forNucleotide)
+ {
+ // af.featureSettings_actionPerformed(null);
+ String[] defdb = null;
+ List<DbSourceProxy> selsources = new ArrayList<>();
+ // select appropriate databases based on alignFrame context.
+ if (forNucleotide)
+ {
+ defdb = DBRefSource.DNACODINGDBS;
+ }
+ else
+ {
+ defdb = DBRefSource.PROTEINDBS;
+ }
+ List<DbSourceProxy> srces = new ArrayList<>();
+ for (String ddb : defdb)
+ {
+ List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+ if (srcesfordb != null)
+ {
+ for (DbSourceProxy src : srcesfordb)
+ {
+ if (!srces.contains(src))
+ {
+ srces.addAll(srcesfordb);
+ }
+ }
+ }
+ }
+ // append the PDB data source, since it is 'special', catering for both
+ // nucleotide and protein
+ // srces.addAll(sfetcher.getSourceProxy(DBRefSource.PDB));
+
+ srces.addAll(selsources);
+ dbSources = srces.toArray(new DbSourceProxy[srces.size()]);
+ }
+
+ /**
+ * Constructor with only sequences provided
+ *
+ * @param sequences
+ */
+ public DBRefFetcher(SequenceI[] sequences)
+ {
+ this(sequences, null, null, null, false);
+ }
+
+ /**
+ * Add a listener to be notified when sequence fetching is complete
+ *
+ * @param l
+ */
+ public void addListener(FetchFinishedListenerI l)
+ {
+ listeners.add(l);
+ }
+
+ /**
+ * start the fetcher thread
+ *
+ * @param waitTillFinished
+ * true to block until the fetcher has finished
+ */
+ public void fetchDBRefs(boolean waitTillFinished)
+ {
+ if (waitTillFinished)
+ {
+ run();
+ }
+ else
+ {
+ new Thread(this).start();
+ }
+ }
+
+ /**
+ * 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(Locale.ROOT);
+
+ Vector<SequenceI> seqs;
+ if (seqRefs.containsKey(key))
+ {
+ seqs = 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!
+ */
+ @Override
+ public void run()
+ {
+ if (dbSources == null)
+ {
+ throw new Error(MessageManager
+ .getString("error.implementation_error_must_init_dbsources"));
+ }
+ long startTime = System.currentTimeMillis();
+ if (progressWindow != null)
+ {
+ progressWindow.setProgressBar(
+ MessageManager.getString("status.fetching_db_refs"),
+ startTime);
+ }
+ try
+ {
+ if (Cache.getDefault("DBREFFETCH_USEPICR", false))
+ {
+ picrClient = new AccessionMapperServiceLocator()
+ .getAccessionMapperPort();
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Couldn't locate PICR service instance.\n");
+ e.printStackTrace();
+ }
+
+ Vector<SequenceI> sdataset = new Vector<>(
+ Arrays.asList(dataset));
+ List<String> warningMessages = new ArrayList<>();
+
+ // clear any old feature display settings recorded from past sessions
+ featureDisplaySettings = null;
+
+ int db = 0;
+ while (sdataset.size() > 0 && db < dbSources.length)
+ {
+ int maxqlen = 1; // default number of queries made at one time
+ System.out.println("Verifying against " + dbSources[db].getDbName());
+
+ // 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<String> queries = new Vector<>(); // generated queries curSeq
+ seqRefs = new Hashtable<>();
+
+ int seqIndex = 0;
+
+ 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
+ maxqlen = dbsource.getMaximumQueryCount();
+
+ 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;
+ int nqSize = (maxqlen > queries.size()) ? queries.size()
+ : maxqlen;
+
+ while (queries.size() > 0 && numq < nqSize)
+ {
+ String query = 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 (Console.isDebugEnabled())
+ {
+ Console.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, retrieved,
+ trimDsSeqs, warningMessages);
+ }
+ }
+ else
+ {
+ // make some more strings for use as queries
+ for (int i = 0; (seqIndex < dataset.length)
+ && (i < 50); seqIndex++, i++)
+ {
+ SequenceI sequence = dataset[seqIndex];
+ List<DBRefEntry> uprefs = DBRefUtils
+ .selectRefs(sequence.getDBRefs(), new String[]
+ { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
+ // });
+ // check for existing dbrefs to use
+ if (uprefs != null && uprefs.size() > 0)
+ {
+ for (int j = 0, n = uprefs.size(); j < n; j++)
+ {
+ DBRefEntry upref = uprefs.get(j);
+ addSeqId(sequence, upref.getAccessionId());
+ queries.addElement(
+ upref.getAccessionId().toUpperCase(Locale.ROOT));
+ }
+ }
+ else
+ {
+ Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
+ // generate queries from sequence ID string
+ Matcher tokens = possibleIds.matcher(sequence.getName());
+ int p=0;
+ while (tokens.find(p))
+ {
+ String token = tokens.group();
+ p = tokens.end();
+ 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(Locale.ROOT));
+ }
+ else
+ {
+ // if ()
+ // System.out.println("Not querying source with
+ // token="+token+"\n");
+ addSeqId(sequence, token);
+ queries.addElement(token.toUpperCase(Locale.ROOT));
+ }
+ }
+ }
+ }
+ }
+ }
+ // advance to next database
+ db++;
+ } // all databases have been queried
+ if (!warningMessages.isEmpty())
+ {
+ StringBuilder sb = new StringBuilder(warningMessages.size() * 30);
+ sb.append(MessageManager
+ .getString("label.your_sequences_have_been_verified"));
+ for (String msg : warningMessages)
+ {
+ sb.append(msg).append(NEWLINE);
+ }
+ output.setText(sb.toString());
+
+ Desktop.addInternalFrame(output,
+ MessageManager.getString("label.sequences_updated"), 600,
+ 300);
+ // The above is the dataset, we must now find out the index
+ // of the viewed sequence
+
+ }
+ if (progressWindow != null)
+ {
+ progressWindow.setProgressBar(
+ MessageManager.getString("label.dbref_search_completed"),
+ startTime);
+ }
+
+ for (FetchFinishedListenerI listener : listeners)
+ {
+ listener.finished();
+ }
+ }
+
+ /**
+ * Verify local sequences in seqRefs against the retrieved sequence database
+ * records. Returns true if any sequence was modified as a result (start/end
+ * changed and/or sequence enlarged), else false.
+ *
+ * @param sdataset
+ * dataset sequences we are retrieving for
+ * @param dbSource
+ * database source we are retrieving from
+ * @param retrievedAl
+ * retrieved sequences as alignment
+ * @param trimDatasetSeqs
+ * if true, sequences will not be enlarged to match longer retrieved
+ * sequences, only their start/end adjusted
+ * @param warningMessages
+ * a list of messages to add to
+ */
+ boolean transferReferences(Vector<SequenceI> sdataset,
+ DbSourceProxy dbSourceProxy,
+ AlignmentI retrievedAl, boolean trimDatasetSeqs,
+ List<String> warningMessages)
+ {
+ // System.out.println("trimming ? " + trimDatasetSeqs);
+ if (retrievedAl == null || retrievedAl.getHeight() == 0)
+ {
+ return false;
+ }
+
+ String dbSource = dbSourceProxy.getDbName();
+ boolean modified = false;
+ SequenceI[] retrieved = recoverDbSequences(
+ retrievedAl.getSequencesArray());
+ SequenceI sequence = null;
+
+ for (SequenceI retrievedSeq : retrieved)
+ {
+ // Work out which sequences this sequence matches,
+ // taking into account all accessionIds and names in the file
+ Vector<SequenceI> sequenceMatches = new Vector<>();
+ // look for corresponding accession ids
+ List<DBRefEntry> entryRefs = DBRefUtils
+ .selectRefs(retrievedSeq.getDBRefs(), new String[]
+ { dbSource });
+ if (entryRefs == null)
+ {
+ System.err
+ .println("Dud dbSource string ? no entryrefs selected for "
+ + dbSource + " on " + retrievedSeq.getName());
+ continue;
+ }
+ for (int j = 0, n = entryRefs.size(); j < n; j++)
+ {
+ DBRefEntry ref = entryRefs.get(j);
+ String accessionId = ref.getAccessionId();
+ // match up on accessionId
+ if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
+ {
+ Vector<SequenceI> seqs = seqRefs.get(accessionId);
+ for (int jj = 0; jj < seqs.size(); jj++)
+ {
+ sequence = seqs.elementAt(jj);
+ if (!sequenceMatches.contains(sequence))
+ {
+ sequenceMatches.addElement(sequence);
+ }
+ }
+ }
+ }
+ if (sequenceMatches.isEmpty())
+ {
+ // failed to match directly on accessionId==query so just compare all
+ // sequences to entry
+ Enumeration<String> e = seqRefs.keys();
+ while (e.hasMoreElements())
+ {
+ Vector<SequenceI> sqs = seqRefs.get(e.nextElement());
+ if (sqs != null && sqs.size() > 0)
+ {
+ Enumeration<SequenceI> 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.
+ /*
+ * List<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); } } } }
+ */
+ if (sequenceMatches.size() > 0)
+ {
+ addFeatureSettings(dbSourceProxy);
+ }
+ // sequenceMatches now contains the set of all sequences associated with
+ // the returned db record
+ final String retrievedSeqString = retrievedSeq.getSequenceAsString();
+ String entrySeq = retrievedSeqString.toUpperCase(Locale.ROOT);
+ for (int m = 0; m < sequenceMatches.size(); m++)
+ {
+ sequence = 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.getDBRefs() == null
+ || sequence.getDBRefs().size() == 0;
+ // TODO:
+ // verify sequence against the entry sequence
+
+ Mapping mp;
+ final int sequenceStart = sequence.getStart();
+
+ boolean remoteEnclosesLocal = false;
+ String nonGapped = AlignSeq
+ .extractGaps("-. ", sequence.getSequenceAsString())
+ .toUpperCase(Locale.ROOT);
+ int absStart = entrySeq.indexOf(nonGapped);
+ if (absStart == -1)
+ {
+ // couldn't find local sequence in sequence from database, so check if
+ // the database sequence is a subsequence of local sequence
+ absStart = nonGapped.indexOf(entrySeq);
+ if (absStart == -1)
+ {
+ // verification failed. couldn't find any relationship between
+ // entrySeq and local sequence
+ // messages suppressed as many-to-many matches are confusing
+ // String msg = sequence.getName()
+ // + " Sequence not 100% match with "
+ // + retrievedSeq.getName();
+ // addWarningMessage(warningMessages, msg);
+ continue;
+ }
+ /*
+ * retrieved sequence is a proper subsequence of local sequence
+ */
+ String msg = sequence.getName() + " has " + absStart
+ + " prefixed residues compared to "
+ + retrievedSeq.getName();
+ addWarningMessage(warningMessages, msg);
+
+ /*
+ * So create a mapping to the external entry from the matching region of
+ * the local sequence, and leave local start/end untouched.
+ */
+ mp = new Mapping(null,
+ new int[]
+ { sequenceStart + absStart,
+ sequenceStart + absStart + entrySeq.length() - 1 },
+ new int[]
+ { retrievedSeq.getStart(),
+ retrievedSeq.getStart() + entrySeq.length() - 1 },
+ 1, 1);
+ updateRefFrame = false;
+ }
+ else
+ {
+ /*
+ * local sequence is a subsequence of (or matches) retrieved sequence
+ */
+ remoteEnclosesLocal = true;
+ mp = null;
+
+ if (updateRefFrame)
+ {
+ /*
+ * relocate existing sequence features by offset
+ */
+ int startShift = absStart - sequenceStart + 1;
+ if (startShift != 0)
+ {
+ modified |= sequence.getFeatures().shiftFeatures(1,
+ startShift);
+ }
+ }
+ }
+
+ System.out.println("Adding dbrefs to " + sequence.getName()
+ + " from " + dbSource + " sequence : "
+ + retrievedSeq.getName());
+ sequence.transferAnnotation(retrievedSeq, mp);
+
+ absStart += retrievedSeq.getStart();
+ int absEnd = absStart + nonGapped.length() - 1;
+ if (!trimDatasetSeqs)
+ {
+ /*
+ * update start position and/or expand to longer retrieved sequence
+ */
+ if (!retrievedSeqString.equals(sequence.getSequenceAsString())
+ && remoteEnclosesLocal)
+ {
+ sequence.setSequence(retrievedSeqString);
+ modified = true;
+ addWarningMessage(warningMessages,
+ "Sequence for " + sequence.getName() + " expanded from "
+ + retrievedSeq.getName());
+ }
+ if (sequence.getStart() != retrievedSeq.getStart())
+ {
+ sequence.setStart(retrievedSeq.getStart());
+ modified = true;
+ if (absStart != sequenceStart)
+ {
+ addWarningMessage(warningMessages,
+ "Start/end position for " + sequence.getName()
+ + " updated from " + retrievedSeq.getName());
+ }
+ }
+ }
+ if (updateRefFrame)
+ {
+ // finally, update local sequence reference frame if we're allowed
+ if (trimDatasetSeqs)
+ {
+ // just fix start/end
+ if (sequence.getStart() != absStart
+ || sequence.getEnd() != absEnd)
+ {
+ sequence.setStart(absStart);
+ sequence.setEnd(absEnd);
+ modified = true;
+ addWarningMessage(warningMessages,
+ "Start/end for " + sequence.getName()
+ + " updated from " + retrievedSeq.getName());
+ }
+ }
+ // 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(Locale.ROOT);
+ int oldstrt = alseqs[alsq].getStart();
+ alseqs[alsq].setStart(sequence.getSequenceAsString()
+ .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
+ if (oldstrt != alseqs[alsq].getStart())
+ {
+ alseqs[alsq].setEnd(
+ ngAlsq.length() + alseqs[alsq].getStart() - 1);
+ modified = true;
+ }
+ }
+ }
+ // 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);
+ }
+ }
+ return modified;
+ }
+
+ Map<String, FeatureSettingsModelI> featureDisplaySettings = null;
+
+ private void addFeatureSettings(DbSourceProxy dbSourceProxy)
+ {
+ FeatureSettingsModelI fsettings = dbSourceProxy
+ .getFeatureColourScheme();
+ if (fsettings != null)
+ {
+ if (featureDisplaySettings == null)
+ {
+ featureDisplaySettings = new HashMap<>();
+ }
+ featureDisplaySettings.put(dbSourceProxy.getDbName(), fsettings);
+ }
+ }
+
+ /**
+ *
+ * @return any feature settings associated with sources that have provided sequences
+ */
+ public List<FeatureSettingsModelI>getFeatureSettingsModels()
+ {
+ return featureDisplaySettings == null
+ ? Arrays.asList(new FeatureSettingsModelI[0])
+ : Arrays.asList(featureDisplaySettings.values()
+ .toArray(new FeatureSettingsModelI[1]));
+ }
+ /**
+ * Adds the message to the list unless it already contains it
+ *
+ * @param messageList
+ * @param msg
+ */
+ void addWarningMessage(List<String> messageList, String msg)
+ {
+ if (!messageList.contains(msg))
+ {
+ messageList.add(msg);
+ }
+ }
+
+ /**
+ * loop thru and collect additional sequences in Map.
+ *
+ * @param sequencesArray
+ * @return
+ */
+ private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
+ {
+ int n;
+ if (sequencesArray == null || (n = sequencesArray.length) == 0)
+ return sequencesArray;
+ ArrayList<SequenceI> nseq = new ArrayList<>();
+ for (int i = 0;i < n; i++)
+ {
+ nseq.add(sequencesArray[i]);
+ List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
+ Mapping map = null;
+ if (dbr != null)
+ {
+ for (int r = 0, rn = dbr.size(); r < rn; r++)
+ {
+ if ((map = dbr.get(r).getMap()) != null)
+ {
+ if (map.getTo() != null && !nseq.contains(map.getTo()))
+ {
+ nseq.add(map.getTo());
+ }
+ }
+ }
+ }
+ }
+ // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found?
+ if (nseq.size() > 0)
+ {
+ return nseq.toArray(new SequenceI[nseq.size()]);
+ }
+ return sequencesArray;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff