Merge branch 'feature/JAL-3143ensemblJSON' into

[jalview.git] / src / jalview / ext / ensembl / Species.java

diff --git a/src/jalview/ext/ensembl/Species.java b/src/jalview/ext/ensembl/Species.java
index d8a00a5..cc5465e 100644 (file)
--- a/src/jalview/ext/ensembl/Species.java
+++ b/src/jalview/ext/ensembl/Species.java
@@ -1,5 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
+import java.util.HashSet;
+import java.util.Set;
+
 /**
  * Selected species identifiers used by Ensembl
  * 
@@ -14,10 +37,22 @@ enum Species
    */
   human(true), mouse(true), s_cerevisiae(true), cow(false), pig(false),
   rat(true), celegans(true), sheep(false), horse(false), gorilla(false),
-  rabbit(false), gibbon(false), dog(false), orangutan(false),
-  xenopus(true), chimpanzee(false), cat(false), zebrafish(true), chicken(
-          true), dmelanogaster(true);
+  rabbit(false), gibbon(false), dog(false), orangutan(false), xenopus(true),
+  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)
@@ -29,4 +64,9 @@ enum Species
   {
     return modelOrganism;
   }
+
+  public static Set<Species> getModelOrganisms()
+  {
+    return modelOrganisms;
+  }
 }