X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FGeneDbSource.java;h=1cbfef891a8b1e0bbeb4fbbc1b2955eb2be5df96;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;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..1cbfef8 100644
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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
+ * 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;
 
@@ -36,18 +35,22 @@ 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()
@@ -56,7 +59,9 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
   public Regex getAccessionValidator()
@@ -65,14 +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()
@@ -81,16 +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)
@@ -100,7 +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()
   {