X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdsTest.java;h=a44ab7f0ca58030bc9e0cdcb731a16638d322dee;hb=b9bde68b87a581a1f21e47cb19839791a192134a;hp=02ce2b202d425e5b5d50097758ab0c2f23185550;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index 02ce2b2..a44ab7f 100644
--- a/test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdsTest.java
@@ -1,12 +1,34 @@
+/*
+ * 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 static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyLite;
 import jalview.util.MapList;
@@ -20,6 +42,14 @@ import org.testng.annotations.Test;
 
 public class EnsemblCdsTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
@@ -101,11 +131,12 @@ public class EnsemblCdsTest
             null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("CDS_predicted");
+    sf = new SequenceFeature("CDS_predicted", "", 20000, 20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
     // other feature with no parent is retained
-    sf.setType("sequence_variant");
+    sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
+            20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with desired parent is retained
@@ -122,34 +153,50 @@ public class EnsemblCdsTest
    * accession id as parent
    */
   @Test(groups = "Functional")
-  public void testIdentifiesSequence()
+  public void testGetIdentifyingFeatures()
   {
     String accId = "ABC123";
-    EnsemblCds testee = new EnsemblCds();
+    SequenceI seq = new Sequence(accId, "MKDONS");
 
     // cds with no parent not valid
-    SequenceFeature sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf1 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+    seq.addSequenceFeature(sf1);
 
     // cds with wrong parent not valid
-    sf.setValue("Parent", "transcript:XYZ");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+    sf2.setValue("Parent", "transcript:XYZ");
+    seq.addSequenceFeature(sf2);
 
     // cds with right parent is valid
-    sf.setValue("Parent", "transcript:" + accId);
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+    sf3.setValue("Parent", "transcript:" + accId);
+    seq.addSequenceFeature(sf3);
 
     // cds sub-type with right parent is valid
-    sf.setType("CDS_predicted");
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
+            null);
+    sf4.setValue("Parent", "transcript:" + accId);
+    seq.addSequenceFeature(sf4);
 
     // transcript not valid:
-    sf.setType("transcript");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+            null);
+    sf5.setValue("Parent", "transcript:" + accId);
+    seq.addSequenceFeature(sf5);
 
     // exon not valid:
-    sf.setType("exon");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf6.setValue("Parent", "transcript:" + accId);
+    seq.addSequenceFeature(sf6);
+
+    List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,
+            accId);
+    assertFalse(sfs.contains(sf1));
+    assertFalse(sfs.contains(sf2));
+    assertTrue(sfs.contains(sf3));
+    assertTrue(sfs.contains(sf4));
+    assertFalse(sfs.contains(sf5));
+    assertFalse(sfs.contains(sf6));
   }
 
   @Test(groups = "Functional")