From: jprocter <Jim Procter>
Date: Tue, 4 Nov 2008 13:29:50 +0000 (+0000)
Subject: implemented embl validation properly
X-Git-Tag: Jalview_2_4_0b2~45
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=18099e521fde283ebe0f03491876c686333adf81;p=jalview.git

implemented embl validation properly
---

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 1ac5c76..0dfc924 100644
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -68,8 +68,10 @@ 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 : new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+").search(accession);
+    
   }
 
   /**
diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 5eac1c0..344182f 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -99,7 +99,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
   {
     return getEmblSequenceRecords(DBRefSource.EMBL, queries);
   }
-
+  
   /*
    * (non-Javadoc)
    * 
@@ -107,8 +107,10 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
    */
   public boolean isValidReference(String accession)
   {
-    // TODO Auto-generated method stub
-    return false;
+    // most embl refs look like ..
+    
+    return (accession==null || accession.length()<2) ? false : new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+$").search(accession);
+    
   }
 
   /**