X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGenomeTest.java;h=11140f9f86eaddbe668e2b739397bbb2fcf1c6dd;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=377c8c7b8689e9949c08bf493210ac35e20a90a2;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index 377c8c7..11140f9 100644
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.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;
@@ -19,6 +41,14 @@ import org.testng.annotations.Test;
 
 public class EnsemblGenomeTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
@@ -47,13 +77,13 @@ public class EnsemblGenomeTest
     // transcript at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
             20500, 0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    sf.setValue("id", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // transcript (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    sf.setValue("id", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
@@ -61,13 +91,13 @@ public class EnsemblGenomeTest
     // although strictly it is a sequence_variant in SO
     sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
             0f, null);
-    sf.setValue("ID", "transcript:" + transcriptId);
+    sf.setValue("id", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // transcript with a different ID doesn't count
     sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
-    sf.setValue("ID", "transcript:anotherOne");
+    sf.setValue("id", "anotherOne");
     genomic.addSequenceFeature(sf);
 
     // parent of transcript feature doesn't count
@@ -107,22 +137,24 @@ public class EnsemblGenomeTest
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("mature_transcript");
+    sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
+            null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("NMD_transcript_variant");
+    sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
+            0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
     // other feature with no parent is kept
-    sf.setType("anything");
+    sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with correct parent is kept
-    sf.setValue("Parent", "transcript:" + accId);
+    sf.setValue("Parent", accId);
     assertTrue(testee.retainFeature(sf, accId));
 
     // other feature with wrong parent is not kept
-    sf.setValue("Parent", "transcript:XYZ");
+    sf.setValue("Parent", "XYZ");
     assertFalse(testee.retainFeature(sf, accId));
   }
 
@@ -131,39 +163,59 @@ public class EnsemblGenomeTest
    * accession id as ID
    */
   @Test(groups = "Functional")
-  public void testIdentifiesSequence()
+  public void testGetIdentifyingFeatures()
   {
     String accId = "ABC123";
-    EnsemblGenome testee = new EnsemblGenome();
+    SequenceI seq = new Sequence(accId, "HEARTS");
 
     // transcript with no ID not valid
-    SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
+    SequenceFeature sf1 = new SequenceFeature("transcript", "", 1, 2, 0f,
             null);
-    assertFalse(testee.identifiesSequence(sf, accId));
+    seq.addSequenceFeature(sf1);
 
     // transcript with wrong ID not valid
-    sf.setValue("ID", "transcript");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    // NB change desc to avoid rejection of duplicate feature!
+    SequenceFeature sf2 = new SequenceFeature("transcript", "a", 1, 2, 0f,
+            null);
+    sf2.setValue("id", "transcript");
+    seq.addSequenceFeature(sf2);
 
     // transcript with right ID is valid
-    sf.setValue("ID", "transcript:" + accId);
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf3 = new SequenceFeature("transcript", "b", 1, 2, 0f,
+            null);
+    sf3.setValue("id", accId);
+    seq.addSequenceFeature(sf3);
 
     // transcript sub-type with right ID is valid
-    sf.setType("ncRNA");
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
+    sf4.setValue("id", accId);
+    seq.addSequenceFeature(sf4);
 
     // Ensembl treats NMD_transcript_variant as if a transcript
-    sf.setType("NMD_transcript_variant");
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
+            1, 2, 0f, null);
+    sf5.setValue("id", accId);
+    seq.addSequenceFeature(sf5);
 
     // gene not valid:
-    sf.setType("gene");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
+    sf6.setValue("id", accId);
+    seq.addSequenceFeature(sf6);
 
     // exon not valid:
-    sf.setType("exon");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf7.setValue("id", accId);
+    seq.addSequenceFeature(sf7);
+
+    List<SequenceFeature> sfs = new EnsemblGenome()
+            .getIdentifyingFeatures(seq, accId);
+    assertFalse(sfs.contains(sf1));
+    assertFalse(sfs.contains(sf2));
+    assertTrue(sfs.contains(sf3));
+    assertTrue(sfs.contains(sf4));
+    assertTrue(sfs.contains(sf5));
+    assertFalse(sfs.contains(sf6));
+    assertFalse(sfs.contains(sf7));
   }
 
 }