From d3d566fbf876a3511c06fecec695b2f59eb71169 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 22 Mar 2016 13:57:29 +0000
Subject: [PATCH] JAL-1191 isolated SequenceOntology (BioJava wrapper) to
 /ext/so folder

---
 build.xml                                                 |    2 +-
 src/jalview/{io/gff => ext/so}/SequenceOntology.java      |    8 +++++---
 src/jalview/io/gff/Gff3Helper.java                        |    6 +++---
 test/jalview/{io/gff => ext/so}/SequenceOntologyTest.java |    6 +++++-
 4 files changed, 14 insertions(+), 8 deletions(-)
 rename src/jalview/{io/gff => ext/so}/SequenceOntology.java (98%)
 rename test/jalview/{io/gff => ext/so}/SequenceOntologyTest.java (94%)

diff --git a/build.xml b/build.xml
index 43bab6f..b23293f 100755
--- a/build.xml
+++ b/build.xml
@@ -570,7 +570,7 @@
 
 <target name="compileApplet" depends="init,clean">
   <mkdir dir="${outputDir}" />
-  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
diff --git a/src/jalview/io/gff/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
similarity index 98%
rename from src/jalview/io/gff/SequenceOntology.java
rename to src/jalview/ext/so/SequenceOntology.java
index b069eef..af80b7a 100644
--- a/src/jalview/io/gff/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -1,4 +1,6 @@
-package jalview.io.gff;
+package jalview.ext.so;
+
+import jalview.io.gff.SequenceOntologyI;
 
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
@@ -26,7 +28,7 @@ import org.biojava.nbio.ontology.utils.Annotation;
  * A wrapper class that parses the Sequence Ontology and exposes useful access
  * methods. This version uses the BioJava parser.
  */
-class SequenceOntology implements SequenceOntologyI
+public class SequenceOntology implements SequenceOntologyI
 {
   /*
    * the parsed Ontology data as modelled by BioJava
@@ -58,7 +60,7 @@ class SequenceOntology implements SequenceOntologyI
    * Package private constructor to enforce use of singleton. Parses and caches
    * the SO OBO data file.
    */
-  SequenceOntology()
+  public SequenceOntology()
   {
     termsFound = new ArrayList<String>();
     termsNotFound = new ArrayList<String>();
diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index bd34d3c..031900d 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -5,7 +5,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.MappingType;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.ext.ensembl.EnsemblSeqProxy;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
 
@@ -388,8 +387,9 @@ public class Gff3Helper extends GffHelperBase
      * extract 'Name' for a transcript (to show gene name)
      * or an exon (so 'colour by label' shows exon boundaries) 
      */
-    if (EnsemblSeqProxy.isTranscript(type)
-            || so.isA(type, SequenceOntology.EXON))
+    if (SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(type)
+            || so.isA(type, SequenceOntologyI.TRANSCRIPT)
+            || so.isA(type, SequenceOntologyI.EXON))
     {
       desc = StringUtils.listToDelimitedString(attributes.get("Name"), ",");
     }
diff --git a/test/jalview/io/gff/SequenceOntologyTest.java b/test/jalview/ext/so/SequenceOntologyTest.java
similarity index 94%
rename from test/jalview/io/gff/SequenceOntologyTest.java
rename to test/jalview/ext/so/SequenceOntologyTest.java
index 0b72515..be07485 100644
--- a/test/jalview/io/gff/SequenceOntologyTest.java
+++ b/test/jalview/ext/so/SequenceOntologyTest.java
@@ -1,8 +1,12 @@
-package jalview.io.gff;
+package jalview.ext.so;
 
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.ext.so.SequenceOntology;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
-- 
1.7.10.2