X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblSource.java;h=6a3b3f79d4707724ec45cd413e0a806a0862d321;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=5ae7a728610023c4ea460e27067293357cc2b68b;hpb=0eda2ac2f334f55f6e5f137789453a9f4dfe4d73;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 5ae7a72..6a3b3f7 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
 
@@ -21,17 +35,20 @@ import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
  * @author JimP
- *
+ * 
  */
 public class EmblSource extends EmblXmlSource implements DbSourceProxy
 {
 
-  public EmblSource() {
+  public EmblSource()
+  {
     addDbSourceProperty(DBRefSource.DNASEQDB);
     addDbSourceProperty(DBRefSource.CODINGSEQDB);
   }
-  
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
   public String getAccessionSeparator()
@@ -40,23 +57,29 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
     return null;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
   public String getDbSource()
   {
     return DBRefSource.EMBL;
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
   public String getDbVersion()
@@ -65,28 +88,40 @@ public class EmblSource 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
   {
     return getEmblSequenceRecords(DBRefSource.EMBL, queries);
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
   public boolean isValidReference(String accession)
   {
-    // TODO Auto-generated method stub
-    return false;
+    // most embl refs look like ..
+
+    return (accession == null || accession.length() < 2) ? false
+            : getAccessionValidator().search(accession);
+
   }
 
   /**
-   * return LHD_CHICK coding gene 
+   * return LHD_CHICK coding gene
    */
   public String getTestQuery()
   {
     return "X53828";
   }
 
+  public String getDbName()
+  {
+    return "EMBL"; // getDbSource();
+  }
 }