From 1470c861a3f837c5206837a89d0b932d2207fcc8 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 30 May 2005 14:58:53 +0000
Subject: [PATCH] more robust parsing for DBset/DBname|id1|id2 type ids

---
 src/jalview/io/FastaFile.java |   22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 4c1ba9e..cd287ff 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -54,13 +54,21 @@ public class FastaFile extends AlignFile {
 
 	    id = str.nextToken();
 	    id = id.substring(1);
-           if(id.indexOf("UniProt/Swiss-Prot")>-1)
-            {
-              id = id.substring(id.indexOf("UniProt/Swiss-Prot|") + 19);
-              if(id.indexOf("|")>-1)
-                id = id.substring(id.indexOf("|") + 1);
-            }
-
+            com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex("[A-Za-z-]+/[A-Za-z-]+\\|(\\w+)\\|(.+)");
+            if (dbId.search(id))
+               {
+                 String dbid = dbId.stringMatched(1);
+                 String idname = dbId.stringMatched(2);
+                 if (idname.length()>0 && idname.indexOf("_") > -1)
+                 {
+                   id = idname; // just use friendly name // JBPNote: we may lose uniprot standardised ID here.
+                 }
+                 else
+                 {
+                   id = dbid; // use dbid to ensure sensible queries
+                 }
+
+               }
 	    if (id.indexOf("/") > 0 ) {
 
 	      StringTokenizer st = new StringTokenizer(id,"/");
-- 
1.7.10.2