updated das sequence source for jdas client and refactored to implementation package

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

diff --git a/src/jalview/ws/dbsources/DasSequenceSource.java b/src/jalview/ws/dbsources/DasSequenceSource.java
deleted file mode 100644 (file)
index dc0f0a5..0000000
--- a/src/jalview/ws/dbsources/DasSequenceSource.java
+++ /dev/null
@@ -1,168 +0,0 @@
-/*\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;\r
-\r
-import java.util.Hashtable;\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\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
-  protected Das1Source source = null;\r
-\r
-  protected String dbname = "DASCS";\r
-\r
-  protected String dbrefname = "das:source";\r
-\r
-  protected DasCoordinateSystem coordsys = 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,\r
-          Das1Source source, DasCoordinateSystem coordsys) throws Exception\r
-  {\r
-    if (!source.hasCapability("sequence"))\r
-    {\r
-      throw new Exception("Source " + source.getNickname()\r
-              + " 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
-\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(\r
-            queries, source);\r
-    DasSequenceSourceListener ourlistener = new DasSequenceSourceListener(\r
-            this, queries);\r
-    seqfetcher.addSequenceListener(ourlistener);\r
-    seqfetcher.start();\r
-    try\r
-    {\r
-      Thread.sleep(5);\r
-    } catch (Exception e)\r
-    {\r
-    }\r
-    ;\r
-    while (ourlistener.isNotCalled() && seqfetcher.isAlive())\r
-    {\r
-      try\r
-      {\r
-        Thread.sleep(5);\r
-      } catch (Exception e)\r
-      {\r
-      }\r
-      ;\r
-    }\r
-    if (ourlistener.isNotCalled() || ourlistener.hasNoSequences())\r
-    {\r
-      System.err.println("Sequence Query to " + source.getNickname()\r
-              + " with '" + queries + "' returned no sequences.");\r
-      return null;\r
-    }\r
-    else\r
-    {\r
-      return ourlistener.getSequences();\r
-    }\r
-  }\r
-\r
-  public String getTestQuery()\r
-  {\r
-    return coordsys.getTestCode();\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 Das1Source getSource()\r
-  {\r
-    return source;\r
-  }\r
-\r
-  /**\r
-   * @return the coordsys\r
-   */\r
-  public DasCoordinateSystem getCoordsys()\r
-  {\r
-    return coordsys;\r
-  }\r
-}\r