X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblSource.java;h=ec75b04b4d70c1b2c556b369cb090bb20bad3175;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=e5f0c6282b230f9878ab11e64c15d423824e20c3;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index e5f0c62..ec75b04 100644
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,23 +20,24 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.util.Platform;
+
+import com.stevesoft.pat.Regex;
 
 /**
  * @author JimP
  * 
  */
-public class EmblSource extends EmblXmlSource implements DbSourceProxy
+public class EmblSource extends EmblXmlSource
 {
 
+  private static Regex ACCESSION_REGEX;
+
   public EmblSource()
   {
-    addDbSourceProperty(DBRefSource.DNASEQDB);
-    addDbSourceProperty(DBRefSource.CODINGSEQDB);
+    super();
   }
 
   /*
@@ -44,6 +45,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
+  @Override
   public String getAccessionSeparator()
   {
     // TODO Auto-generated method stub
@@ -55,9 +57,14 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
+  @Override
   public Regex getAccessionValidator()
   {
-    return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
+    if (ACCESSION_REGEX == null)
+    {
+      ACCESSION_REGEX = Platform.newRegex("^[A-Z]+[0-9]+", null);
+    }
+    return ACCESSION_REGEX;
   }
 
   /*
@@ -65,6 +72,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
+  @Override
   public String getDbSource()
   {
     return DBRefSource.EMBL;
@@ -75,6 +83,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
+  @Override
   public String getDbVersion()
   {
     // TODO Auto-generated method stub
@@ -86,6 +95,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     return getEmblSequenceRecords(DBRefSource.EMBL, queries);
@@ -96,6 +106,7 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     // most embl refs look like ..
@@ -108,11 +119,13 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
   /**
    * return LHD_CHICK coding gene
    */
+  @Override
   public String getTestQuery()
   {
     return "X53828";
   }
 
+  @Override
   public String getDbName()
   {
     return "EMBL"; // getDbSource();