update author list in license for (JAL-826)

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

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 5ae7a72..6a3b3f7 100644 (file)
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.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, J Engelhardt, LM Lui, 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
@@ -21,17 +35,20 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
 \r
 /**\r
  * @author JimP\r
- *\r
+ * \r
  */\r
 public class EmblSource extends EmblXmlSource implements DbSourceProxy\r
 {\r
 \r
-  public EmblSource() {\r
+  public EmblSource()\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
@@ -40,23 +57,29 @@ public class EmblSource 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
   {\r
-    // TODO Auto-generated method stub\r
-    return null;\r
+    return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");\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.EMBL;\r
   }\r
-  /* (non-Javadoc)\r
+\r
+  /*\r
+   * (non-Javadoc)\r
+   * \r
    * @see jalview.ws.DbSourceProxy#getDbVersion()\r
    */\r
   public String getDbVersion()\r
@@ -65,28 +88,40 @@ public class EmblSource 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
     return getEmblSequenceRecords(DBRefSource.EMBL, 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
   {\r
-    // TODO Auto-generated method stub\r
-    return false;\r
+    // most embl refs look like ..\r
+\r
+    return (accession == null || accession.length() < 2) ? false\r
+            : getAccessionValidator().search(accession);\r
+\r
   }\r
 \r
   /**\r
-   * return LHD_CHICK coding gene \r
+   * return LHD_CHICK coding gene\r
    */\r
   public String getTestQuery()\r
   {\r
     return "X53828";\r
   }\r
 \r
+  public String getDbName()\r
+  {\r
+    return "EMBL"; // getDbSource();\r
+  }\r
 }\r