X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblGenomeTest.java;h=8687da94338b18b03bac698e28b0466ccdfe4a48;hb=d7e95f458ebcbbdcc13f8b07357542ab2d7e4547;hp=daad8b162cd65c66451b2aeff08bcd694bdc67f6;hpb=e96f5e8ce137e879dd4b4f37fb5c4d134e2778e2;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblGenomeTest.java b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index daad8b1..8687da9 100644
--- a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -7,6 +27,7 @@ import static org.testng.AssertJUnit.assertTrue;
 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;
@@ -19,13 +40,21 @@ import org.testng.annotations.Test;
 
 public class EnsemblGenomeTest
 {
-  @BeforeClass
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceOntologyFactory.setInstance(null);
@@ -43,15 +72,14 @@ public class EnsemblGenomeTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // transcript at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
-            20500, 0f,
-            null);
+            20500, 0f, null);
     sf.setValue("ID", "transcript:" + 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);
@@ -65,12 +93,12 @@ public class EnsemblGenomeTest
     sf.setValue("ID", "transcript:" + 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");
     genomic.addSequenceFeature(sf);
-  
+
     // parent of transcript feature doesn't count
     sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
             null);
@@ -107,15 +135,17 @@ public class EnsemblGenomeTest
     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
             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
@@ -136,34 +166,38 @@ public class EnsemblGenomeTest
   {
     String accId = "ABC123";
     EnsemblGenome testee = new EnsemblGenome();
-  
+
     // transcript with no ID not valid
     SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
             null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // transcript with wrong ID not valid
     sf.setValue("ID", "transcript");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // transcript with right ID is valid
     sf.setValue("ID", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript sub-type with right ID is valid
-    sf.setType("ncRNA");
+    sf = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
+    sf.setValue("ID", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
 
     // Ensembl treats NMD_transcript_variant as if a transcript
-    sf.setType("NMD_transcript_variant");
+    sf = new SequenceFeature("NMD_transcript_variant", "", 1, 2, 0f, null);
+    sf.setValue("ID", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // gene not valid:
-    sf.setType("gene");
+    sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
+    sf.setValue("ID", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
-    sf.setType("exon");
+    sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf.setValue("ID", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
   }