X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FDasSequenceSource.java;h=f9b4c480226c6537d94a542d070825070503025a;hb=59d682209891099d46b960509907c79e3fb276fe;hp=eeaccf4cd2befe6376f49f13b56cbb2d7ebf534f;hpb=d1b697c33b69a6dfe55df789eec5ac9881013681;p=jalview.git
diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index eeaccf4..f9b4c48 100644
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -1,338 +1,338 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-package jalview.ws.dbsources.das.datamodel;
-
-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.ConnectionPropertyProviderI;
-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;
-
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.*;
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-
-/**
- * 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;
-
- /**
- * 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("Source " + source.getTitle()
- + " does not support the sequence command.");
- }
- 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 toks = new ArrayList(), src = new ArrayList(), acIds = new ArrayList();
- while (st.hasMoreTokens())
- {
- String t;
- toks.add(t = st.nextToken());
- acIds.add(t.replaceAll(":[0-9,]+", ""));
- }
- src.add(jsrc.getSourceURL());
- Map, DasSequenceAdapter>> resultset = new HashMap, DasSequenceAdapter>>();
- Map, Exception>> errors = new HashMap, 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 qset = Arrays.asList(new String[]
- { q });
- try
- {
- DasSequenceAdapter s = sq.fetchData(sr, qset);
- Map, DasSequenceAdapter> dss = resultset.get(sr);
- if (dss == null)
- {
- resultset
- .put(sr,
- dss = new HashMap, DasSequenceAdapter>());
- }
- dss.put(qset, s);
- } catch (Exception x)
- {
- Map, Exception> ers = errors.get(sr);
- if (ers == null)
- {
- errors.put(sr, ers = new HashMap, 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 seqs = null;
- for (Map.Entry, DasSequenceAdapter>> resset : resultset
- .entrySet())
- {
- for (Map.Entry, DasSequenceAdapter> result : resset
- .getValue().entrySet())
- {
- DasSequenceAdapter dasseqresp = result.getValue();
- List 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();
- // 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 srcs = new java.util.Vector();
- 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;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+package jalview.ws.dbsources.das.datamodel;
+
+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.ConnectionPropertyProviderI;
+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;
+
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.*;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+/**
+ * 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;
+
+ /**
+ * 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("Source " + source.getTitle()
+ + " does not support the sequence command.");
+ }
+ 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 toks = new ArrayList(), src = new ArrayList(), acIds = new ArrayList();
+ while (st.hasMoreTokens())
+ {
+ String t;
+ toks.add(t = st.nextToken());
+ acIds.add(t.replaceAll(":[0-9,]+", ""));
+ }
+ src.add(jsrc.getSourceURL());
+ Map, DasSequenceAdapter>> resultset = new HashMap, DasSequenceAdapter>>();
+ Map, Exception>> errors = new HashMap, 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 qset = Arrays.asList(new String[]
+ { q });
+ try
+ {
+ DasSequenceAdapter s = sq.fetchData(sr, qset);
+ Map, DasSequenceAdapter> dss = resultset.get(sr);
+ if (dss == null)
+ {
+ resultset
+ .put(sr,
+ dss = new HashMap, DasSequenceAdapter>());
+ }
+ dss.put(qset, s);
+ } catch (Exception x)
+ {
+ Map, Exception> ers = errors.get(sr);
+ if (ers == null)
+ {
+ errors.put(sr, ers = new HashMap, 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 seqs = null;
+ for (Map.Entry, DasSequenceAdapter>> resset : resultset
+ .entrySet())
+ {
+ for (Map.Entry, DasSequenceAdapter> result : resset
+ .getValue().entrySet())
+ {
+ DasSequenceAdapter dasseqresp = result.getValue();
+ List 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();
+ // 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 srcs = new java.util.Vector();
+ 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;
+ }
+}