X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FGeneDbSource.java;h=ce21ad029b9ae6f81cc9eee4c66f725abe787ca3;hb=d943fcd0dc04fd4974344eddd13902c89fb595b2;hp=ab779f6fb00293895ef488802357ec4e8e3f6921;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index ab779f6..ce21ad0 100644
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -1,114 +1,135 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- * 
- * This program 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 2
- * of the License, or (at your option) any later version.
- * 
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.ws.dbsources;
-
-import java.io.File;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.StringTokenizer;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.embl.EmblEntry;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
-
-/**
- * Test class for accessing GeneDB - not yet finished.
- * @author JimP
- *
- */
-public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
-{
-
-  public GeneDbSource() {
-    addDbSourceProperty(DBRefSource.DNASEQDB);
-    addDbSourceProperty(DBRefSource.CODINGSEQDB);
-  }
-  
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
-   */
-  public String getAccessionSeparator()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
-   */
-  public Regex getAccessionValidator()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbSource()
-   */
-  public String getDbSource()
-  {
-    return DBRefSource.GENEDB;
-  }
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getDbVersion()
-   */
-  public String getDbVersion()
-  {
-    // TODO Auto-generated method stub
-    return "0";
-  }
-
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
-   */
-  public AlignmentI getSequenceRecords(String queries) throws Exception
-  {
-    // query of form http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
-    // 
-    return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
-  }
-  /* (non-Javadoc)
-   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
-   */
-  public boolean isValidReference(String accession)
-  {
-    // TODO Auto-generated method stub
-    return false;
-  }
-
-  /**
-   * return T.Brucei Mannosyl-Transferase TbPIG-M 
-   */
-  public String getTestQuery()
-  {
-    return "Tb927.6.3300";
-  }
-
-  public String getDbName()
-  {
-    return "GeneDB"; // getDbSource();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * Test class for accessing GeneDB - not yet finished.
+ * 
+ * @author JimP
+ * 
+ */
+public class GeneDbSource extends EmblXmlSource
+{
+
+  public GeneDbSource()
+  {
+    super();
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+   */
+  @Override
+  public String getAccessionSeparator()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+   */
+  @Override
+  public Regex getAccessionValidator()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbSource()
+   */
+  @Override
+  public String getDbSource()
+  {
+    return DBRefSource.GENEDB;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getDbVersion()
+   */
+  @Override
+  public String getDbVersion()
+  {
+    // TODO Auto-generated method stub
+    return "0";
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+   */
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    // query of form
+    // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
+    //
+    return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+   */
+  @Override
+  public boolean isValidReference(String accession)
+  {
+    // TODO Auto-generated method stub
+    return false;
+  }
+
+  /**
+   * return T.Brucei Mannosyl-Transferase TbPIG-M
+   */
+  @Override
+  public String getTestQuery()
+  {
+    return "Tb927.6.3300";
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "GeneDB"; // getDbSource();
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+}