From b691a827f39b1d02cd01ee2f2e0b2077c01818bd Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 9 Oct 2017 15:24:10 +0100
Subject: [PATCH] JAL-2523 convenience method to get model organisms

---
 src/jalview/ext/ensembl/Species.java      |   20 +++++++++++++++++++
 test/jalview/ext/ensembl/SpeciesTest.java |   30 +++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 test/jalview/ext/ensembl/SpeciesTest.java

diff --git a/src/jalview/ext/ensembl/Species.java b/src/jalview/ext/ensembl/Species.java
index af01225..cc5465e 100644
--- a/src/jalview/ext/ensembl/Species.java
+++ b/src/jalview/ext/ensembl/Species.java
@@ -20,6 +20,9 @@
  */
 package jalview.ext.ensembl;
 
+import java.util.HashSet;
+import java.util.Set;
+
 /**
  * Selected species identifiers used by Ensembl
  * 
@@ -38,6 +41,18 @@ enum Species
   chimpanzee(false), cat(false), zebrafish(true), chicken(true),
   dmelanogaster(true);
 
+  static Set<Species> modelOrganisms = new HashSet<>();
+
+  static
+  {
+    for (Species s : values())
+    {
+      if (s.isModelOrganism())
+      {
+        modelOrganisms.add(s);
+      }
+    }
+  }
   boolean modelOrganism;
 
   private Species(boolean model)
@@ -49,4 +64,9 @@ enum Species
   {
     return modelOrganism;
   }
+
+  public static Set<Species> getModelOrganisms()
+  {
+    return modelOrganisms;
+  }
 }
diff --git a/test/jalview/ext/ensembl/SpeciesTest.java b/test/jalview/ext/ensembl/SpeciesTest.java
new file mode 100644
index 0000000..44658e7
--- /dev/null
+++ b/test/jalview/ext/ensembl/SpeciesTest.java
@@ -0,0 +1,30 @@
+package jalview.ext.ensembl;
+
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
+public class SpeciesTest
+{
+  @Test
+  public void testGetModelOrganisms()
+  {
+    Set<Species> models = Species.getModelOrganisms();
+    assertTrue(models.contains(Species.human));
+    assertFalse(models.contains(Species.horse));
+    for (Species s : Species.values())
+    {
+      if (s.isModelOrganism())
+      {
+        assertTrue(models.contains(s));
+      }
+      else
+      {
+        assertFalse(models.contains(s));
+      }
+    }
+  }
+}
-- 
1.7.10.2