jdas doesn't need a listener for das sequence retrieval events

diff --git a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
deleted file mode 100644 (file)
index 0b0a065..0000000
--- a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
+++ /dev/null
@@ -1,165 +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.das;\r
-\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.Sequence;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.ws.dbsources.DasSequenceSource;\r
-\r
-import org.biojava.dasobert.eventmodel.SequenceEvent;\r
-import org.biojava.dasobert.eventmodel.SequenceListener;\r
-\r
-/**\r
- * Listen for sequence fetch events from a dasobert SequenceThread started with\r
- * a query string and collect sequences returned from the DAS sequence source.\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public class DasSequenceSourceListener implements SequenceListener\r
-{\r
-\r
-  String ourAccession = null;\r
-\r
-  DasSequenceSource oursource = null;\r
-\r
-  /**\r
-   * \r
-   * @param source\r
-   *          the DAS Sequence DbProxy object containing database details for\r
-   *          this source\r
-   * @param query\r
-   *          the query string sent to the das source that we should be\r
-   *          listening for.\r
-   */\r
-  public DasSequenceSourceListener(DasSequenceSource source, String query)\r
-  {\r
-    oursource = source;\r
-    ourAccession = query;\r
-  }\r
-\r
-  public void clearSelection()\r
-  {\r
-    // TODO Auto-generated method stub\r
-\r
-  }\r
-\r
-  java.util.Vector seqs = null;\r
-\r
-  public void newSequence(SequenceEvent e)\r
-  {\r
-    if (!e.getAccessionCode().equals(ourAccession))\r
-    {\r
-      System.err\r
-              .println("Warning - received sequence event for strange accession code ("\r
-                      + e.getAccessionCode()\r
-                      + ") - we expected "\r
-                      + ourAccession);\r
-\r
-      return;\r
-    }\r
-    if (seqs == null)\r
-    {\r
-      if (e.getSequence().length() == 0)\r
-      {\r
-        System.err.println("Empty sequence returned for accession code ("\r
-                + e.getAccessionCode() + ") from " + oursource.getDbName());\r
-        called = true;\r
-        noSequences = true;\r
-        return;\r
-      }\r
-      seqs = new java.util.Vector();\r
-    }\r
-    Sequence sq = new Sequence(e.getAccessionCode(), e.getSequence());\r
-    sq.addDBRef(new DBRefEntry(oursource.getDbSource(), oursource\r
-            .getDbVersion() + ":" + e.getVersion(), e.getAccessionCode()));\r
-    seqs.addElement(sq);\r
-    called = true;\r
-  }\r
-\r
-  public void selectedSeqPosition(int position)\r
-  {\r
-    // TODO Auto-generated method stub\r
-\r
-  }\r
-\r
-  public void selectedSeqRange(int start, int end)\r
-  {\r
-    // TODO Auto-generated method stub\r
-\r
-  }\r
-\r
-  public void selectionLocked(boolean flag)\r
-  {\r
-    // TODO Auto-generated method stub\r
-\r
-  }\r
-\r
-  public void newObjectRequested(String accessionCode)\r
-  {\r
-    // TODO Auto-generated method stub\r
-\r
-  }\r
-\r
-  boolean noSequences = false;\r
-\r
-  public void noObjectFound(String accessionCode)\r
-  {\r
-    if (accessionCode.equals(ourAccession))\r
-    {\r
-      noSequences = true;\r
-      called = true;\r
-    }\r
-  }\r
-\r
-  public boolean hasNoSequences()\r
-  {\r
-    return noSequences;\r
-  }\r
-\r
-  boolean called = false;\r
-\r
-  public boolean isNotCalled()\r
-  {\r
-    return !called;\r
-  }\r
-\r
-  public AlignmentI getSequences()\r
-  {\r
-    if (noSequences || 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 (oursource.getSource().hasCapability("features"))\r
-    {\r
-      java.util.Vector src = new java.util.Vector();\r
-      src.addElement(oursource.getSource());\r
-      new jalview.ws.DasSequenceFeatureFetcher(sqs, null, src, false, false);\r
-    }\r
-\r
-    return al;\r
-  }\r
-\r
-}\r