From a497d3031bbc2ae601295bdd03e240c38261e15c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 5 Dec 2005 13:38:26 +0000
Subject: [PATCH] Use regex on seq names

---
 src/jalview/datamodel/Sequence.java |   26 +++++++++++---------------
 1 file changed, 11 insertions(+), 15 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 05a2b73..80dfda5 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -66,24 +66,20 @@ public class Sequence implements SequenceI
       checkValidRange();
     }
 
+    static com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+                        "[/][0-9]{1,}[-][0-9]{1,}$");
+    static com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
+                        "[0-9]{1,}$");
+
     void parseId()
     {
-         // Remove /start-end from sequence
-         if (name.indexOf("/") > 0)
+        // Does sequence have the /start-end signiature?
+         if(limitrx.search(name))
          {
-           String limits = name.substring(name.lastIndexOf("/")+1);
-           try
-           {
-             StringTokenizer st = new StringTokenizer(limits, "-");
-             setStart(Integer.valueOf(st.nextToken()).intValue());
-             setEnd(Integer.valueOf(st.nextToken()).intValue());
-
-             // If we're still in this loop, parsing of start and end was ok
-             // Therefore remove it from the sequence name
-             name = name.substring(0, name.lastIndexOf("/"));
-           }
-           catch (NumberFormatException ex)
-           {      }
+            name = limitrx.left();
+            endrx.search(limitrx.stringMatched());
+            setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));
+            setEnd(   Integer.parseInt( endrx.stringMatched() ));
          }
     }
 
-- 
1.7.10.2