applied 2009 GPL license

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

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 86d18ce..8562f37 100644 (file)
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -1,6 +1,6 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  * \r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -29,14 +29,15 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy\r
 {\r
 \r
-  public EmblCdsSouce() {\r
+  public EmblCdsSouce()\r
+  {\r
     super();\r
-    addDbSourceProperty(DBRefSource.CODINGSEQDB); \r
+    addDbSourceProperty(DBRefSource.CODINGSEQDB);\r
   }\r
-  \r
+\r
   public String getAccessionSeparator()\r
   {\r
-   return null;\r
+    return null;\r
   }\r
 \r
   public Regex getAccessionValidator()\r
@@ -52,12 +53,13 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
 \r
   public String getDbVersion()\r
   {\r
-    return "0"; // TODO : this is dynamically set for a returned record - not tied to proxy\r
+    return "0"; // TODO : this is dynamically set for a returned record - not\r
+                // tied to proxy\r
   }\r
 \r
   public AlignmentI getSequenceRecords(String queries) throws Exception\r
-  { \r
-    if (queries.indexOf(".")>-1)\r
+  {\r
+    if (queries.indexOf(".") > -1)\r
     {\r
       queries = queries.substring(0, queries.indexOf("."));\r
     }\r
@@ -66,9 +68,12 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
 \r
   public boolean isValidReference(String accession)\r
   {\r
-    // TODO Auto-generated method stub\r
-    return true;\r
+    // most embl CDS refs look like ..\r
+    // TODO: improve EMBLCDS regex\r
+    return (accession==null || accession.length()<2) ? false : new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+").search(accession);\r
+    \r
   }\r
+\r
   /**\r
    * cDNA for LDHA_CHICK swissprot sequence\r
    */\r
@@ -76,6 +81,7 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
   {\r
     return "CAA37824";\r
   }\r
+\r
   public String getDbName()\r
   {\r
     return "EMBL (CDS)";\r