From e5d09d52e9a12fe2c5cd308d50a30e66f00b5b0a Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 8 Jan 2009 16:01:03 +0000
Subject: [PATCH] fix broken parsing of non-positional features in GFF files

---
 src/jalview/io/FeaturesFile.java |   10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 2bc3b4b..ef70efa 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -190,13 +190,19 @@ public class FeaturesFile extends AlignFile
                 String stt = st.nextToken();
                 if (stt.length()==0 || stt.equals("-"))
                 {
-                  end = -1;
+                  end = 0;
                 } else {
                   end = Integer.parseInt(stt);
                 }
               } catch (NumberFormatException ex)
               {
-                end = -1;
+                end = 0;
+              }
+              // TODO: decide if non positional feature assertion for input data where end==0 is generally valid
+              if (end==0)
+              {
+                // treat as non-positional feature, regardless.
+	        start=0;
               }
               try
               {
-- 
1.7.10.2