From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 15 Mar 2016 14:27:12 +0000 (+0000)
Subject: JAL-1705 code tidy/comment only
X-Git-Tag: Release_2_10_0~296^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6fb341da6a316869ba5fc87c146c30d1279f06fa;p=jalview.git

JAL-1705 code tidy/comment only
---

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 3b32797..0cecc59 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -328,19 +328,19 @@ public class EnsemblGene extends EnsemblSeqProxy
     List<int[]> mapTo = new ArrayList<int[]>();
     mapTo.add(new int[] { 1, transcriptLength });
     MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
-    new EnsemblCdna(getDomain()).transferFeatures(
-            gene.getSequenceFeatures(), transcript.getDatasetSequence(),
-            mapping, parentId);
+    EnsemblCdna cdna = new EnsemblCdna(getDomain());
+    cdna.transferFeatures(gene.getSequenceFeatures(),
+            transcript.getDatasetSequence(), mapping, parentId);
 
     /*
      * fetch and save cross-references
      */
-    new EnsemblCdna(getDomain()).getCrossReferences(transcript);
+    cdna.getCrossReferences(transcript);
 
     /*
      * and finally fetch the protein product and save as a cross-reference
      */
-    new EnsemblCdna(getDomain()).addProteinProduct(transcript);
+    cdna.addProteinProduct(transcript);
 
     return transcript;
   }
diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index c442b6f..e9bcf24 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -655,14 +655,17 @@ public class MapListTest
   @Test(groups = { "Functional" })
   public void testIsFromForwardStrand()
   {
+    // [3-9] declares forward strand
     MapList ml = new MapList(new int[] { 2, 2, 3, 9, 12, 11 },
             new int[] { 20, 11 }, 1, 1);
     assertTrue(ml.isFromForwardStrand());
 
+    // [11-5] declares reverse strand ([13-14] is ignored)
     ml = new MapList(new int[] { 2, 2, 11, 5, 13, 14 },
             new int[] { 20, 11 }, 1, 1);
     assertFalse(ml.isFromForwardStrand());
 
+    // all single position ranges - defaults to forward strand
     ml = new MapList(new int[] { 2, 2, 4, 4, 6, 6 }, new int[] { 3, 1 }, 1,
             1);
     assertTrue(ml.isFromForwardStrand());