From 664a775152a1ed48b706038423627e79fd14e572 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 19 Oct 2017 15:01:56 +0100
Subject: [PATCH] JAL-2755 put chromosomal dbref first in report

---
 src/jalview/io/SequenceAnnotationReport.java |   10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index f1ebcac..13f41d4 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -58,7 +58,7 @@ public class SequenceAnnotationReport
 
   /*
    * Comparator to order DBRefEntry by Source + accession id (case-insensitive),
-   * with 'Primary' sources placed before others
+   * with 'Primary' sources placed before others, and 'chromosome' first of all
    */
   private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
   {
@@ -66,6 +66,14 @@ public class SequenceAnnotationReport
     @Override
     public int compare(DBRefEntry ref1, DBRefEntry ref2)
     {
+      if (ref1.isChromosome())
+      {
+        return -1;
+      }
+      if (ref2.isChromosome())
+      {
+        return 1;
+      }
       String s1 = ref1.getSource();
       String s2 = ref2.getSource();
       boolean s1Primary = isPrimarySource(s1);
-- 
1.7.10.2