X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblSource.java;h=08c020e982219696a9ba89e49994323124ae0add;hb=33ddded54e265fccf85851d0ac3ad047ca4a8459;hp=f24579787672b1932e59126a77b1daf228a6e3fd;hpb=08fbe7c3d40a4077ab519334952a079968c07cd1;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index f245797..08c020e 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, 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 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.
  * 
+ * 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
  */
 package jalview.ws.dbsources;
 
@@ -21,17 +36,20 @@ 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 +58,29 @@ 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()
@@ -65,24 +89,31 @@ 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()
   {
@@ -91,6 +122,6 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
 
   public String getDbName()
   {
-    return getDbSource();
+    return "EMBL"; // getDbSource();
   }
 }