X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FGeneDbSource.java;h=ae11a6892e498105e6bf875bb26618195967d064;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=7cea53208f787f2e9feeb668db70265cea1c023e;hpb=08fbe7c3d40a4077ab519334952a079968c07cd1;p=jalview.git

diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index 7cea532..ae11a68 100644
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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;
 
@@ -20,18 +34,23 @@ 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() {
+  public GeneDbSource()
+  {
     addDbSourceProperty(DBRefSource.DNASEQDB);
     addDbSourceProperty(DBRefSource.CODINGSEQDB);
   }
-  
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
   public String getAccessionSeparator()
@@ -40,7 +59,9 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
   public Regex getAccessionValidator()
@@ -49,14 +70,19 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
   public String getDbSource()
   {
     return DBRefSource.GENEDB;
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
   public String getDbVersion()
@@ -65,16 +91,22 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
     return "0";
   }
 
-  /* (non-Javadoc)
+  /*
+   * (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
+    // query of form
+    // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
     // 
     return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
   public boolean isValidReference(String accession)
@@ -84,7 +116,7 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
   }
 
   /**
-   * return T.Brucei Mannosyl-Transferase TbPIG-M 
+   * return T.Brucei Mannosyl-Transferase TbPIG-M
    */
   public String getTestQuery()
   {
@@ -93,6 +125,6 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
 
   public String getDbName()
   {
-    return getDbSource();
+    return "GeneDB"; // getDbSource();
   }
 }