From: jprocter <Jim Procter>
Date: Thu, 8 Jan 2009 16:01:03 +0000 (+0000)
Subject: fix broken parsing of non-positional features in GFF files
X-Git-Tag: Release_2_5~355
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e5d09d52e9a12fe2c5cd308d50a30e66f00b5b0a;p=jalview.git

fix broken parsing of non-positional features in GFF files
---

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
               {