X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblCdsSouce.java;h=2683ba46480f7d0ea2053536bbf9d0c77eda04b4;hb=a789f790fbb3ab13f1967b42781b837b58bf9bbc;hp=65b4e21b5d0a1a6e1d7d651b7ce6ec291d9aa4e5;hpb=08fbe7c3d40a4077ab519334952a079968c07cd1;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 65b4e21..2683ba4 100644
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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;
 
 import java.util.Hashtable;
@@ -11,20 +28,20 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
 {
 
-  public EmblCdsSouce() {
+  public EmblCdsSouce()
+  {
     super();
-    addDbSourceProperty(DBRefSource.CODINGSEQDB); 
+    addDbSourceProperty(DBRefSource.CODINGSEQDB);
   }
-  
+
   public String getAccessionSeparator()
   {
-   return null;
+    return null;
   }
 
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
   }
 
   public String getDbSource()
@@ -34,12 +51,13 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
 
   public String getDbVersion()
   {
-    return "0"; // TODO : this is dynamically set for a returned record - not tied to proxy
+    return "0"; // TODO : this is dynamically set for a returned record - not
+    // tied to proxy
   }
 
   public AlignmentI getSequenceRecords(String queries) throws Exception
-  { 
-    if (queries.indexOf(".")>-1)
+  {
+    if (queries.indexOf(".") > -1)
     {
       queries = queries.substring(0, queries.indexOf("."));
     }
@@ -48,9 +66,12 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
 
   public boolean isValidReference(String accession)
   {
-    // TODO Auto-generated method stub
-    return true;
+    // most embl CDS refs look like ..
+    // TODO: improve EMBLCDS regex
+    return (accession == null || accession.length() < 2) ? false
+            : getAccessionValidator().search(accession);
   }
+
   /**
    * cDNA for LDHA_CHICK swissprot sequence
    */
@@ -58,6 +79,7 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
   {
     return "CAA37824";
   }
+
   public String getDbName()
   {
     return "EMBL (CDS)";