From 167476e350f385aa0fcb334b79722ddaa1b3a368 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 18 Jul 2008 15:05:30 +0000
Subject: [PATCH] resolve 1:many mappings from feature sequence ID to
 alignment sequence(s) with same ID

---
 src/jalview/io/FeaturesFile.java |   22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 03a7a83..3e0314a 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -148,7 +148,7 @@ public class FeaturesFile extends AlignFile
           }
           continue;
         }
-
+        String seqId="";
         while (st.hasMoreElements())
         {
 
@@ -156,8 +156,8 @@ public class FeaturesFile extends AlignFile
           {
             // Still possible this is an old Jalview file,
             // which does not have type colours at the beginning
-            token = st.nextToken();
-            seq = align.findName(token, true);
+            seqId = token = st.nextToken();
+            seq = align.findName(seqId, true);
             if (seq != null)
             {
               desc = st.nextToken();
@@ -205,7 +205,10 @@ public class FeaturesFile extends AlignFile
               }
 
               seq.addSequenceFeature(sf);
-
+              while ((seq=align.findName(seq, seqId, true))!=null)
+              {
+                seq.addSequenceFeature(new SequenceFeature(sf));
+              }
               break;
             }
           }
@@ -231,11 +234,12 @@ public class FeaturesFile extends AlignFile
 
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
-            seq = align.findName(token, true);
+            seq = align.findName(seqId=token, true);
             st.nextToken();
           }
           else
           {
+            seqId=null;
             try
             {
               index = Integer.parseInt(st.nextToken());
@@ -266,8 +270,6 @@ public class FeaturesFile extends AlignFile
 
           sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
-          seq.addSequenceFeature(sf);
-
           if (groupLink != null && removeHTML)
           {
             sf.addLink(groupLink);
@@ -281,6 +283,12 @@ public class FeaturesFile extends AlignFile
 
           parseDescriptionHTML(sf, removeHTML);
 
+          seq.addSequenceFeature(sf);
+
+          while (seqId!=null && (seq=align.findName(seq, seqId, false))!=null)
+          {
+            seq.addSequenceFeature(new SequenceFeature(sf));
+          }
           // If we got here, its not a GFFFile
           GFFFile = false;
         }
-- 
1.7.10.2