From 450598e6efcebb8a81ba774762a237e1ccea802f Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 18 Apr 2013 10:48:40 +0100
Subject: [PATCH] fix for cases with semi-colon characters in reference name
---
uk/ac/sanger/artemis/io/IndexFastaStream.java | 15 ++++++++++++---
1 file changed, 12 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/IndexFastaStream.java b/uk/ac/sanger/artemis/io/IndexFastaStream.java
index bd9cf0fe9..6197339ea 100644
--- a/uk/ac/sanger/artemis/io/IndexFastaStream.java
+++ b/uk/ac/sanger/artemis/io/IndexFastaStream.java
@@ -193,8 +193,12 @@ public class IndexFastaStream extends StreamSequence
Object obj = it.next();
if(i == seqIndex)
{
- String size = obj.toString().split(";")[2].substring(5).trim();
- return Integer.parseInt(size);
+ String parts[] = obj.toString().split(";");
+ for(String part: parts)
+ {
+ if(part.trim().startsWith("size"))
+ return Integer.parseInt(part.substring(5).trim());
+ }
}
i++;
}
@@ -209,7 +213,12 @@ public class IndexFastaStream extends StreamSequence
{
Object obj = it.next();
if(i == seqIndex)
- return obj.toString().split(";")[0].substring(6).trim();
+ {
+ String c = obj.toString().split(" ")[1];
+ if(c.endsWith(";"))
+ c = c.substring(0, c.length()-1);
+ return c;
+ }
i++;
}
return null;
--
GitLab