From d6ab080a4e9181800bbecb6525e6329c10246aab Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 15 Dec 2008 10:35:09 +0000
Subject: [PATCH] added (and enabled) switch to store gff source string as
 sequencefeature.group rather than add it to description

---
 src/jalview/io/FeaturesFile.java |   28 +++++++++++++++++++++++++---
 1 file changed, 25 insertions(+), 3 deletions(-)

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 5058e5f..17ff88f 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -36,6 +36,11 @@ import jalview.schemes.*;
 public class FeaturesFile extends AlignFile
 {
   /**
+   * work around for GFF interpretation bug where source string becomes description rather than a group
+   */
+  private boolean doGffSource = true;
+
+  /**
    * Creates a new FeaturesFile object.
    */
   public FeaturesFile()
@@ -161,17 +166,34 @@ public class FeaturesFile extends AlignFile
             if (seq != null)
             {
               desc = st.nextToken();
+              String group=null;
+              if (doGffSource && desc.indexOf(' ')==-1) {
+                // could also be a source term rather than description line
+                group = new String(desc);
+              }
               type = st.nextToken();
               try
               {
-                start = Integer.parseInt(st.nextToken());
+                String stt = st.nextToken();
+                if (stt.length()==0 || stt.equals("-"))
+                {
+                  start = 0;
+                } else {
+                start = Integer.parseInt(stt);
+                }
               } catch (NumberFormatException ex)
               {
                 start = 0;
               }
               try
               {
-                end = Integer.parseInt(st.nextToken());
+                String stt = st.nextToken();
+                if (stt.length()==0 || stt.equals("-"))
+                {
+                  end = -1;
+                } else {
+                  end = Integer.parseInt(stt);
+                }
               } catch (NumberFormatException ex)
               {
                 end = -1;
@@ -184,7 +206,7 @@ public class FeaturesFile extends AlignFile
                 score = 0;
               }
 
-              sf = new SequenceFeature(type, desc, start, end, score, null);
+              sf = new SequenceFeature(type, desc, start, end, score, group);
 
               try
               {
-- 
1.7.10.2