From 6f1b2c4f5a6ec44e7b1840c93cee4696426f9674 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 4 Sep 2007 13:34:05 +0000
Subject: [PATCH] gff parsing when no start or end position is defined.

---
 src/jalview/io/FeaturesFile.java |   22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 6b9ee67..78e796e 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -25,9 +25,11 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 
 /**
- * DOCUMENT ME!
- *
- * @author $author$
+ * Parse and create Jalview Features files
+ * Detects GFF format features files and parses.
+ * Does not implement standard print() - call specific printFeatures or printGFF.
+ * Uses AlignmentI.findSequence(String id) to find the sequence object for the features annotation - this normally works on an exact match.
+ * @author AMW
  * @version $Revision$
  */
 public class FeaturesFile
@@ -156,8 +158,19 @@ public class FeaturesFile
             {
               desc = st.nextToken();
               type = st.nextToken();
+              try {
               start = Integer.parseInt(st.nextToken());
-              end = Integer.parseInt(st.nextToken());
+              } catch (NumberFormatException ex)
+              {
+                start=0;
+              }
+              try {
+                end = Integer.parseInt(st.nextToken());
+              }
+              catch (NumberFormatException ex)
+              {
+                end=-1;
+              } 
               try
               {
                 score = new Float(st.nextToken()).floatValue();
@@ -265,6 +278,7 @@ public class FeaturesFile
     {
       System.out.println(line);
       System.out.println("Error parsing feature file: " + ex + "\n" + line);
+      ex.printStackTrace(System.err);
       return false;
     }
 
-- 
1.7.10.2