From e6ee9bdb5c3a632b0b9de544f64380b0714e5169 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 7 Oct 2015 11:03:47 +0100
Subject: [PATCH] JAL-1499 corrected domainend parsing, add gene name to
 domain desc

---
 src/jalview/io/MegaFile.java      |   24 ++++++++++++++----------
 test/jalview/io/MegaFileTest.java |   18 +++++++++---------
 2 files changed, 23 insertions(+), 19 deletions(-)

diff --git a/src/jalview/io/MegaFile.java b/src/jalview/io/MegaFile.java
index 58961f8..c7caa3b 100644
--- a/src/jalview/io/MegaFile.java
+++ b/src/jalview/io/MegaFile.java
@@ -362,22 +362,26 @@ public class MegaFile extends AlignFile
   protected void processGeneOrDomain(String gene, String domain,
           String property, String codonStart)
   {
+    boolean domainEnd = "domainend".equalsIgnoreCase(property);
+
     /*
-     * If we have been processing a Gene or Domain, and this does not continue
-     * it, then close it off (generate sequence features for it)
+     * If we have been processing a Domain or Gene, and this does not continue
+     * it, then close it off (generate sequence features for it). Do Domain
+     * first as it is in the context of the enclosing gene if any.
      */
-    if (this.currentGene != null && !this.currentGene.equals(gene))
-    {
-      createFeature(GENE, currentGene, geneStart);
-    }
     if (this.currentDomain != null)
     {
-      if (!this.currentDomain.equals(domain)
-              || "domainend".equalsIgnoreCase(property))
+      if (!this.currentDomain.equals(domain) || domainEnd)
       {
-        createFeature(DOMAIN, currentDomain, domainStart);
+        String description = currentDomain
+                + (currentGene == null ? "" : " (" + currentGene + ")");
+        createFeature(DOMAIN, description, domainStart);
       }
     }
+    if (this.currentGene != null && !this.currentGene.equals(gene))
+    {
+      createFeature(GENE, currentGene, geneStart);
+    }
 
     /*
      * and if we have declared a Gene or Domain which does not continue the
@@ -393,7 +397,7 @@ public class MegaFile extends AlignFile
     }
 
     currentGene = gene;
-    currentDomain = domain;
+    currentDomain = domainEnd ? null : domain;
   }
 
   /**
diff --git a/test/jalview/io/MegaFileTest.java b/test/jalview/io/MegaFileTest.java
index 14cb27e..2766610 100644
--- a/test/jalview/io/MegaFileTest.java
+++ b/test/jalview/io/MegaFileTest.java
@@ -655,24 +655,24 @@ public class MegaFileTest
     for (SequenceI seq : seqs) {
       SequenceFeature[] sfs = seq.getSequenceFeatures();
       // features are added in the order in which their end is found
-      // (Gene before Domain when they end together)
+      // (Domain before Gene when they end together)
       assertEquals(5, sfs.length);
       // TODO settle which way round type/description go!
-      assertEquals("Exon1", sfs[0].type);
+      assertEquals("Exon1 (Adh)", sfs[0].type);
       assertEquals("Domain", sfs[0].description);
       assertEquals(7, sfs[0].begin);
       assertEquals(12, sfs[0].end);
-      assertEquals("Intron1", sfs[1].type);
+      assertEquals("Intron1 (Adh)", sfs[1].type);
       assertEquals("Domain", sfs[1].description);
       assertEquals(13, sfs[1].begin);
       assertEquals(18, sfs[1].end);
-      assertEquals("Adh", sfs[2].type);
-      assertEquals("Gene", sfs[2].description);
-      assertEquals(7, sfs[2].begin);
+      assertEquals("Exon2 (Adh)", sfs[2].type);
+      assertEquals("Domain", sfs[2].description);
+      assertEquals(19, sfs[2].begin);
       assertEquals(24, sfs[2].end);
-      assertEquals("Exon2", sfs[3].type);
-      assertEquals("Domain", sfs[3].description);
-      assertEquals(19, sfs[3].begin);
+      assertEquals("Adh", sfs[3].type);
+      assertEquals("Gene", sfs[3].description);
+      assertEquals(7, sfs[3].begin);
       assertEquals(24, sfs[3].end);
       assertEquals("BindingSite", sfs[4].type);
       assertEquals("Domain", sfs[4].description);
-- 
1.7.10.2