From b1314f2aa829a8ccbb1816c6254c28f988967154 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 28 Jul 2006 11:08:11 +0000
Subject: [PATCH] output source in gff file

---
 src/jalview/io/FeaturesFile.java |   29 +++++++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d7c3775..7299628 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -173,7 +173,17 @@ public class FeaturesFile extends AlignFile
                 catch (Exception ex)
                 {}
 
-                seq.getDatasetSequence().addSequenceFeature(sf);
+                if(st.hasMoreTokens())
+                {
+                  StringBuffer attributes = new StringBuffer();
+                  while (st.hasMoreTokens())
+                  {
+                    attributes.append("\t"+st.nextElement());
+                  }
+                  sf.setValue("ATTRIBUTES", attributes.toString());
+                }
+
+                seq.addSequenceFeature(sf);
 
                 break;
               }
@@ -403,6 +413,7 @@ public class FeaturesFile extends AlignFile
     {
       StringBuffer out = new StringBuffer();
       SequenceFeature [] next;
+      String source;
 
       for(int i=0; i<seqs.length; i++)
       {
@@ -414,8 +425,12 @@ public class FeaturesFile extends AlignFile
             if(!visible.containsKey(next[j].type))
               continue;
 
+            source = next[j].featureGroup;
+            if(source==null)
+              source = next[j].getDescription();
+
             out.append(seqs[i].getName() + "\t"
-                       + next[j].description + "\t"
+                       + source + "\t"
                        + next[j].type  + "\t"
                        + next[j].begin + "\t"
                        + next[j].end   + "\t"
@@ -426,10 +441,16 @@ public class FeaturesFile extends AlignFile
               out.append(next[j].getValue("STRAND")+"\t");
             else
               out.append(".\t");
+
             if(next[j].getValue("FRAME")!=null)
-              out.append(next[j].getValue("FRAME")+"\n");
+              out.append(next[j].getValue("FRAME"));
             else
-              out.append(".\n");
+              out.append(".");
+
+            if(next[j].getValue("ATTRIBUTES")!=null)
+              out.append(next[j].getValue("ATTRIBUTES"));
+
+            out.append("\n");
 
           }
         }
-- 
1.7.10.2