updated jalview version of dasobert 1.53e client and added Das Sequence Source discov...

[jalview.git] / src / jalview / ws / dbsources / DasSequenceSource.java

diff --git a/src/jalview/ws/dbsources/DasSequenceSource.java b/src/jalview/ws/dbsources/DasSequenceSource.java
new file mode 100644 (file)
index 0000000..accb0b9
--- /dev/null
+++ b/src/jalview/ws/dbsources/DasSequenceSource.java
@@ -0,0 +1,125 @@
+package jalview.ws.dbsources;\r
+\r
+import java.util.Hashtable;\r
+\r
+import org.biojava.dasobert.das.SequenceThread;\r
+import org.biojava.dasobert.das2.Das2Source;\r
+import org.biojava.dasobert.dasregistry.Das1Source;\r
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
+import org.biojava.dasobert.dasregistry.DasSource;\r
+import org.biojava.dasobert.eventmodel.SequenceEvent;\r
+import org.biojava.dasobert.eventmodel.SequenceListener;\r
+\r
+import com.stevesoft.pat.Regex;\r
+\r
+import jalview.ws.dbsources.das.DasSequenceSourceListener;\r
+import jalview.ws.seqfetcher.*;\r
+import jalview.datamodel.AlignmentI;\r
+\r
+/**\r
+ * an instance of this class is created for each unique DAS Sequence source (ie 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
+  protected Das1Source source=null;\r
+  protected String dbname="DASCS";\r
+  protected String dbrefname="das:source";\r
+  protected DasCoordinateSystem coordsys = null;\r
+  /**\r
+   * create a new DbSource proxy for a DAS 1 source\r
+   * @param dbnbame Human Readable Name to use when fetching from this source\r
+   * @param dbrefname DbRefName for DbRefs attached to sequences retrieved from this source\r
+   * @param source Das1Source\r
+   * @param coordsys specific coordinate system to use for this source\r
+   * @throws Exception if source is not capable of the 'sequence' command\r
+   */\r
+  public DasSequenceSource(String dbname, String dbrefname, Das1Source source,\r
+            DasCoordinateSystem coordsys) throws Exception\r
+  {\r
+    if (!source.hasCapability("sequence"))\r
+    {\r
+      throw new Exception("Source "+source.getNickname()+" does not support the sequence command.");\r
+    }\r
+    this.source = source;\r
+    this.dbname = dbname;\r
+    this.dbrefname=dbrefname;\r
+    this.coordsys = coordsys;\r
+  }\r
+  public String getAccessionSeparator()\r
+  {\r
+    // cope with single sequences only\r
+    return null;\r
+  }\r
+\r
+  public Regex getAccessionValidator()\r
+  {\r
+    /** ? **/\r
+    return Regex.perlCode("\\S+");\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.getVersion();\r
+  }\r
+\r
+  public AlignmentI getSequenceRecords(String queries) throws Exception\r
+  {\r
+    SequenceThread seqfetcher = new org.biojava.dasobert.das.SequenceThread(queries, source);\r
+    DasSequenceSourceListener ourlistener = new DasSequenceSourceListener(this, queries);\r
+    seqfetcher.addSequenceListener(ourlistener);\r
+    seqfetcher.start();\r
+    try { Thread.sleep(5); } catch (Exception e) {};\r
+    while (ourlistener.isNotCalled() && seqfetcher.isAlive())\r
+    {\r
+      try { Thread.sleep(5); } catch (Exception e) { };\r
+    }\r
+    if (ourlistener.isNotCalled() || ourlistener.hasNoSequences())\r
+    {\r
+      System.err.println("Sequence Query to "+source.getNickname()+" with '"+queries+"' returned no sequences.");\r
+      return null;\r
+    } else {\r
+      return ourlistener.getSequences();\r
+    }\r
+  }\r
+\r
+  public String getTestQuery()\r
+  {\r
+    return coordsys.getTestCode();\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
+   * @return the source\r
+   */\r
+  public Das1Source getSource()\r
+  {\r
+    return source;\r
+  }\r
+  /**\r
+   * @return the coordsys\r
+   */\r
+  public DasCoordinateSystem getCoordsys()\r
+  {\r
+    return coordsys;\r
+  }\r
+}\r