-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview 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 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.ws.dbsources.das.datamodel;\r
-\r
-import java.util.ArrayList;\r
-import java.util.Arrays;\r
-import java.util.HashMap;\r
-import java.util.List;\r
-import java.util.Map;\r
-import java.util.StringTokenizer;\r
-import java.util.Vector;\r
-\r
-import org.biodas.jdas.client.ConnectionPropertyProviderI;\r
-import org.biodas.jdas.client.SequenceClient;\r
-import org.biodas.jdas.client.adapters.sequence.DasSequenceAdapter;\r
-import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;\r
-import org.biodas.jdas.client.threads.SequenceClientMultipleSources;\r
-import org.biodas.jdas.schema.sequence.SEQUENCE;\r
-import org.biodas.jdas.schema.sources.COORDINATES;\r
-import org.biodas.jdas.schema.sources.SOURCE;\r
-import org.biodas.jdas.schema.sources.VERSION;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.ws.dbsources.das.api.jalviewSourceI;\r
-import jalview.ws.seqfetcher.*;\r
-import jalview.bin.Cache;\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.Sequence;\r
-import jalview.datamodel.SequenceI;\r
-\r
-/**\r
- * an instance of this class is created for each unique DAS Sequence source (ie\r
- * one capable of handling the 'sequence' for a particular MapMaster)\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public class DasSequenceSource extends DbSourceProxyImpl implements\r
- DbSourceProxy\r
-{\r
- private jalviewSourceI jsrc;\r
-\r
- protected SOURCE source = null;\r
-\r
- protected VERSION version = null;\r
-\r
- protected COORDINATES coordsys = null;\r
-\r
- protected String dbname = "DASCS";\r
-\r
- protected String dbrefname = "das:source";\r
-\r
- protected MultipleConnectionPropertyProviderI connprops = null;\r
-\r
- /**\r
- * create a new DbSource proxy for a DAS 1 source\r
- * \r
- * @param dbnbame\r
- * Human Readable Name to use when fetching from this source\r
- * @param dbrefname\r
- * DbRefName for DbRefs attached to sequences retrieved from this\r
- * source\r
- * @param source\r
- * Das1Source\r
- * @param coordsys\r
- * specific coordinate system to use for this source\r
- * @throws Exception\r
- * if source is not capable of the 'sequence' command\r
- */\r
- public DasSequenceSource(String dbname, String dbrefname, SOURCE source,\r
- VERSION version, COORDINATES coordsys,\r
- MultipleConnectionPropertyProviderI connprops) throws Exception\r
- {\r
- if (!(jsrc = new JalviewSource(source, connprops, false))\r
- .isSequenceSource())\r
- {\r
- throw new Exception("Source " + source.getTitle()\r
- + " does not support the sequence command.");\r
- }\r
- this.source = source;\r
- this.dbname = dbname;\r
- this.dbrefname = dbrefname.toUpperCase();\r
- if (coordsys != null)\r
- {\r
- this.coordsys = coordsys;\r
- }\r
- this.connprops = connprops;\r
- }\r
-\r
- public String getAccessionSeparator()\r
- {\r
- return "\t";\r
- }\r
-\r
- public Regex getAccessionValidator()\r
- {\r
- /** ? * */\r
- return Regex.perlCode("m/([^:]+)(:\\d+,\\d+)?/");\r
- }\r
-\r
- public String getDbName()\r
- {\r
- // TODO: map to\r
- return dbname + " (DAS)";\r
- }\r
-\r
- public String getDbSource()\r
- {\r
- return dbrefname;\r
- }\r
-\r
- public String getDbVersion()\r
- {\r
- return coordsys != null ? coordsys.getVersion() : "";\r
- }\r
-\r
- public AlignmentI getSequenceRecords(String queries) throws Exception\r
- {\r
- StringTokenizer st = new StringTokenizer(queries, "\t");\r
- List<String> toks = new ArrayList<String>(), src = new ArrayList<String>(), acIds = new ArrayList<String>();\r
- while (st.hasMoreTokens())\r
- {\r
- String t;\r
- toks.add(t = st.nextToken());\r
- acIds.add(t.replaceAll(":[0-9,]+", ""));\r
- }\r
- src.add(jsrc.getSourceURL());\r
- Map<String, Map<List<String>, DasSequenceAdapter>> resultset = new HashMap<String, Map<List<String>, DasSequenceAdapter>>();\r
- Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();\r
-\r
- // First try multiple sources\r
- boolean multiple = true, retry = false;\r
- do\r
- {\r
- if (!multiple)\r
- {\r
- retry = false;\r
- // slow, fetch one at a time.\r
- for (String sr : src)\r
- {\r
- System.err\r
- .println("Retrieving IDs individually from das source: "\r
- + sr);\r
- org.biodas.jdas.client.SequenceClient sq = new SequenceClient(\r
- connprops.getConnectionPropertyProviderFor(sr));\r
- for (String q : toks)\r
- {\r
- List<String> qset = Arrays.asList(new String[]\r
- { q });\r
- try\r
- {\r
- DasSequenceAdapter s = sq.fetchData(sr, qset);\r
- Map<List<String>, DasSequenceAdapter> dss = resultset.get(sr);\r
- if (dss == null)\r
- {\r
- resultset\r
- .put(sr,\r
- dss = new HashMap<List<String>, DasSequenceAdapter>());\r
- }\r
- dss.put(qset, s);\r
- } catch (Exception x)\r
- {\r
- Map<List<String>, Exception> ers = errors.get(sr);\r
- if (ers == null)\r
- {\r
- errors.put(sr, ers = new HashMap<List<String>, Exception>());\r
- }\r
- ers.put(qset, x);\r
- }\r
- }\r
- }\r
- }\r
- else\r
- {\r
- SequenceClientMultipleSources sclient;\r
- sclient = new SequenceClientMultipleSources();\r
- sclient.fetchData(src, toks, resultset, errors);\r
- sclient.shutDown();\r
- while (!sclient.isTerminated())\r
- {\r
- try\r
- {\r
- Thread.sleep(200);\r
-\r
- } catch (InterruptedException x)\r
- {\r
- }\r
- }\r
- if (resultset.isEmpty() && !errors.isEmpty())\r
- {\r
- retry = true;\r
- multiple = false;\r
- }\r
- }\r
- } while (retry);\r
-\r
- if (resultset.isEmpty())\r
- {\r
- System.err.println("Sequence Query to " + jsrc.getTitle() + " with '"\r
- + queries + "' returned no sequences.");\r
- return null;\r
- }\r
- else\r
- {\r
- Vector<SequenceI> seqs = null;\r
- for (Map.Entry<String, Map<List<String>, DasSequenceAdapter>> resset : resultset\r
- .entrySet())\r
- {\r
- for (Map.Entry<List<String>, DasSequenceAdapter> result : resset\r
- .getValue().entrySet())\r
- {\r
- DasSequenceAdapter dasseqresp = result.getValue();\r
- List<String> accessions = result.getKey();\r
- for (SEQUENCE e : dasseqresp.getSequence())\r
- {\r
- String lbl = e.getId();\r
-\r
- if (acIds.indexOf(lbl) == -1)\r
- {\r
- System.err\r
- .println("Warning - received sequence event for strange accession code ("\r
- + lbl + ")");\r
- }\r
- else\r
- {\r
- if (seqs == null)\r
- {\r
- if (e.getContent().length() == 0)\r
- {\r
- System.err\r
- .println("Empty sequence returned for accession code ("\r
- + lbl\r
- + ") from "\r
- + resset.getKey()\r
- + " (source is " + getDbName());\r
- continue;\r
- }\r
- }\r
- seqs = new java.util.Vector<SequenceI>();\r
- // JDAS returns a sequence complete with any newlines and spaces\r
- // in the XML\r
- Sequence sq = new Sequence(lbl, e.getContent().replaceAll(\r
- "\\s+", ""));\r
- sq.setStart(e.getStart().intValue());\r
- sq.addDBRef(new DBRefEntry(getDbSource(), getDbVersion()\r
- + ":" + e.getVersion(), lbl));\r
- seqs.addElement(sq);\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (seqs == null || seqs.size() == 0)\r
- return null;\r
- SequenceI[] sqs = new SequenceI[seqs.size()];\r
- for (int i = 0, iSize = seqs.size(); i < iSize; i++)\r
- {\r
- sqs[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
- Alignment al = new Alignment(sqs);\r
- if (jsrc.isFeatureSource())\r
- {\r
- java.util.Vector<jalviewSourceI> srcs = new java.util.Vector<jalviewSourceI>();\r
- srcs.addElement(jsrc);\r
- try\r
- {\r
- jalview.ws.DasSequenceFeatureFetcher dssf = new jalview.ws.DasSequenceFeatureFetcher(\r
- sqs, null, srcs, false, false, multiple);\r
- while (dssf.isRunning())\r
- {\r
- try\r
- {\r
- Thread.sleep(200);\r
- } catch (InterruptedException x)\r
- {\r
-\r
- }\r
- }\r
-\r
- } catch (Exception x)\r
- {\r
- Cache.log\r
- .error("Couldn't retrieve features for sequence from its source.",\r
- x);\r
- }\r
- }\r
-\r
- return al;\r
- }\r
- }\r
-\r
- public String getTestQuery()\r
- {\r
- return coordsys == null ? "" : coordsys.getTestRange();\r
- }\r
-\r
- public boolean isValidReference(String accession)\r
- {\r
- // TODO try to validate an accession against source\r
- // We don't really know how to do this without querying source\r
-\r
- return true;\r
- }\r
-\r
- /**\r
- * @return the source\r
- */\r
- public SOURCE getSource()\r
- {\r
- return source;\r
- }\r
-\r
- /**\r
- * @return the coordsys\r
- */\r
- public COORDINATES getCoordsys()\r
- {\r
- return coordsys;\r
- }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ */
+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<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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff