+++ /dev/null
-/*
- * 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.dbsources.das.datamodel;
-
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import org.biodas.jdas.client.SequenceClient;
-import org.biodas.jdas.client.adapters.sequence.DasSequenceAdapter;
-import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
-import org.biodas.jdas.client.threads.SequenceClientMultipleSources;
-import org.biodas.jdas.schema.sequence.SEQUENCE;
-import org.biodas.jdas.schema.sources.COORDINATES;
-import org.biodas.jdas.schema.sources.SOURCE;
-import org.biodas.jdas.schema.sources.VERSION;
-
-import com.stevesoft.pat.Regex;
-
-/**
- * an instance of this class is created for each unique DAS Sequence source (ie
- * one capable of handling the 'sequence' for a particular MapMaster)
- *
- * @author JimP
- *
- */
-public class DasSequenceSource extends DbSourceProxyImpl
- implements DbSourceProxy
-{
- private jalviewSourceI jsrc;
-
- protected SOURCE source = null;
-
- protected VERSION version = null;
-
- protected COORDINATES coordsys = null;
-
- protected String dbname = "DASCS";
-
- protected String dbrefname = "das:source";
-
- protected MultipleConnectionPropertyProviderI connprops = null;
-
- /**
- * DAS sources are tier 1 - if we have a direct DB connection then we should
- * prefer it
- */
- private int tier = 1;
-
- /**
- * create a new DbSource proxy for a DAS 1 source
- *
- * @param dbnbame
- * Human Readable Name to use when fetching from this source
- * @param dbrefname
- * DbRefName for DbRefs attached to sequences retrieved from this
- * source
- * @param source
- * Das1Source
- * @param coordsys
- * specific coordinate system to use for this source
- * @throws Exception
- * if source is not capable of the 'sequence' command
- */
- public DasSequenceSource(String dbname, String dbrefname, SOURCE source,
- VERSION version, COORDINATES coordsys,
- MultipleConnectionPropertyProviderI connprops) throws Exception
- {
- if (!(jsrc = new JalviewSource(source, connprops, false))
- .isSequenceSource())
- {
- throw new Exception(MessageManager.formatMessage(
- "exception.das_source_doesnt_support_sequence_command",
- new String[]
- { source.getTitle() }));
- }
- this.tier = 1 + ((jsrc.isLocal() || jsrc.isReferenceSource()) ? 0 : 1);
- this.source = source;
- this.dbname = dbname;
- this.dbrefname = dbrefname.toUpperCase();
- if (coordsys != null)
- {
- this.coordsys = coordsys;
- }
- this.connprops = connprops;
- }
-
- public String getAccessionSeparator()
- {
- return "\t";
- }
-
- public Regex getAccessionValidator()
- {
- /** ? * */
- return Regex.perlCode("m/([^:]+)(:\\d+,\\d+)?/");
- }
-
- public String getDbName()
- {
- // TODO: map to
- return dbname + " (DAS)";
- }
-
- public String getDbSource()
- {
- return dbrefname;
- }
-
- public String getDbVersion()
- {
- return coordsys != null ? coordsys.getVersion() : "";
- }
-
- public AlignmentI getSequenceRecords(String queries) throws Exception
- {
- StringTokenizer st = new StringTokenizer(queries, "\t");
- List<String> toks = new ArrayList<String>(),
- src = new ArrayList<String>(), acIds = new ArrayList<String>();
- while (st.hasMoreTokens())
- {
- String t;
- toks.add(t = st.nextToken());
- acIds.add(t.replaceAll(":[0-9,]+", ""));
- }
- src.add(jsrc.getSourceURL());
- Map<String, Map<List<String>, DasSequenceAdapter>> resultset = new HashMap<String, Map<List<String>, DasSequenceAdapter>>();
- Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();
-
- // First try multiple sources
- boolean multiple = true, retry = false;
- do
- {
- if (!multiple)
- {
- retry = false;
- // slow, fetch one at a time.
- for (String sr : src)
- {
- System.err.println(
- "Retrieving IDs individually from das source: " + sr);
- org.biodas.jdas.client.SequenceClient sq = new SequenceClient(
- connprops.getConnectionPropertyProviderFor(sr));
- for (String q : toks)
- {
- List<String> qset = Arrays.asList(new String[] { q });
- try
- {
- DasSequenceAdapter s = sq.fetchData(sr, qset);
- Map<List<String>, DasSequenceAdapter> dss = resultset.get(sr);
- if (dss == null)
- {
- resultset.put(sr,
- dss = new HashMap<List<String>, DasSequenceAdapter>());
- }
- dss.put(qset, s);
- } catch (Exception x)
- {
- Map<List<String>, Exception> ers = errors.get(sr);
- if (ers == null)
- {
- errors.put(sr,
- ers = new HashMap<List<String>, Exception>());
- }
- ers.put(qset, x);
- }
- }
- }
- }
- else
- {
- SequenceClientMultipleSources sclient;
- sclient = new SequenceClientMultipleSources();
- sclient.fetchData(src, toks, resultset, errors);
- sclient.shutDown();
- while (!sclient.isTerminated())
- {
- try
- {
- Thread.sleep(200);
-
- } catch (InterruptedException x)
- {
- }
- }
- if (resultset.isEmpty() && !errors.isEmpty())
- {
- retry = true;
- multiple = false;
- }
- }
- } while (retry);
-
- if (resultset.isEmpty())
- {
- System.err.println("Sequence Query to " + jsrc.getTitle() + " with '"
- + queries + "' returned no sequences.");
- return null;
- }
- else
- {
- Vector<SequenceI> seqs = null;
- for (Map.Entry<String, Map<List<String>, DasSequenceAdapter>> resset : resultset
- .entrySet())
- {
- for (Map.Entry<List<String>, DasSequenceAdapter> result : resset
- .getValue().entrySet())
- {
- DasSequenceAdapter dasseqresp = result.getValue();
- List<String> accessions = result.getKey();
- for (SEQUENCE e : dasseqresp.getSequence())
- {
- String lbl = e.getId();
-
- if (acIds.indexOf(lbl) == -1)
- {
- System.err.println(
- "Warning - received sequence event for strange accession code ("
- + lbl + ")");
- }
- else
- {
- if (seqs == null)
- {
- if (e.getContent().length() == 0)
- {
- System.err.println(
- "Empty sequence returned for accession code ("
- + lbl + ") from " + resset.getKey()
- + " (source is " + getDbName());
- continue;
- }
- }
- seqs = new java.util.Vector<SequenceI>();
- // JDAS returns a sequence complete with any newlines and spaces
- // in the XML
- Sequence sq = new Sequence(lbl,
- e.getContent().replaceAll("\\s+", ""));
- sq.setStart(e.getStart().intValue());
- sq.addDBRef(new DBRefEntry(getDbSource(),
- getDbVersion() + ":" + e.getVersion(), lbl));
- seqs.addElement(sq);
- }
- }
- }
- }
-
- if (seqs == null || seqs.size() == 0)
- return null;
- SequenceI[] sqs = new SequenceI[seqs.size()];
- for (int i = 0, iSize = seqs.size(); i < iSize; i++)
- {
- sqs[i] = (SequenceI) seqs.elementAt(i);
- }
- Alignment al = new Alignment(sqs);
- if (jsrc.isFeatureSource())
- {
- java.util.Vector<jalviewSourceI> srcs = new java.util.Vector<jalviewSourceI>();
- srcs.addElement(jsrc);
- try
- {
- jalview.ws.DasSequenceFeatureFetcher dssf = new jalview.ws.DasSequenceFeatureFetcher(
- sqs, null, srcs, false, false, multiple);
- while (dssf.isRunning())
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException x)
- {
-
- }
- }
-
- } catch (Exception x)
- {
- Cache.log.error(
- "Couldn't retrieve features for sequence from its source.",
- x);
- }
- }
-
- return al;
- }
- }
-
- public String getTestQuery()
- {
- return coordsys == null ? "" : coordsys.getTestRange();
- }
-
- public boolean isValidReference(String accession)
- {
- // TODO try to validate an accession against source
- // We don't really know how to do this without querying source
-
- return true;
- }
-
- /**
- * @return the source
- */
- public SOURCE getSource()
- {
- return source;
- }
-
- /**
- * @return the coordsys
- */
- public COORDINATES getCoordsys()
- {
- return coordsys;
- }
-
- @Override
- public int getTier()
- {
- return tier;
- }
-}
git://source.jalview.org / jalview.git / blobdiff