apply version 2.7 copyright

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

diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index 7cea532..1cbfef8 100644 (file)
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -1,5 +1,19 @@
-/**\r
+/*\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
@@ -20,18 +34,23 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 \r
 /**\r
+ * Test class for accessing GeneDB - not yet finished.\r
+ * \r
  * @author JimP\r
- *\r
+ * \r
  */\r
 public class GeneDbSource extends EmblXmlSource implements DbSourceProxy\r
 {\r
 \r
-  public GeneDbSource() {\r
+  public GeneDbSource()\r
+  {\r
     addDbSourceProperty(DBRefSource.DNASEQDB);\r
     addDbSourceProperty(DBRefSource.CODINGSEQDB);\r
   }\r
-  \r
-  /* (non-Javadoc)\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
    */\r
   public String getAccessionSeparator()\r
@@ -40,7 +59,9 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
     return null;\r
   }\r
 \r
-  /* (non-Javadoc)\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
    */\r
   public Regex getAccessionValidator()\r
@@ -49,14 +70,19 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
     return null;\r
   }\r
 \r
-  /* (non-Javadoc)\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getDbSource()\r
    */\r
   public String getDbSource()\r
   {\r
     return DBRefSource.GENEDB;\r
   }\r
-  /* (non-Javadoc)\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getDbVersion()\r
    */\r
   public String getDbVersion()\r
@@ -65,16 +91,22 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
     return "0";\r
   }\r
 \r
-  /* (non-Javadoc)\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
    */\r
   public AlignmentI getSequenceRecords(String queries) throws Exception\r
   {\r
-    // query of form http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL\r
-    // \r
+    // query of form\r
+    // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL\r
+    //\r
     return getEmblSequenceRecords(DBRefSource.GENEDB, queries);\r
   }\r
-  /* (non-Javadoc)\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
    */\r
   public boolean isValidReference(String accession)\r
@@ -84,7 +116,7 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
   }\r
 \r
   /**\r
-   * return T.Brucei Mannosyl-Transferase TbPIG-M \r
+   * return T.Brucei Mannosyl-Transferase TbPIG-M\r
    */\r
   public String getTestQuery()\r
   {\r
@@ -93,6 +125,6 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
 \r
   public String getDbName()\r
   {\r
-    return getDbSource();\r
+    return "GeneDB"; // getDbSource();\r
   }\r
 }\r