X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdsTest.java;h=b0a6a2d5f162b0003a6546329867bb03446994d2;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=5344575f0bd62e7e869dd49435199c7e9a848a9b;hpb=cbc07eab0291f023f89b2554c488ae9e4587ae2a;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index 5344575..b0a6a2d 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()
   {
@@ -44,25 +74,25 @@ public class EnsemblCdsTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // CDS at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
             null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // CDS (sub-type) at (start + 10500) length 101
     sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     // CDS belonging to a different transcript doesn't count
     sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
-    sf.setValue("Parent", "transcript:anotherOne");
+    sf.setValue("Parent", "anotherOne");
     genomic.addSequenceFeature(sf);
-  
+
     // exon feature doesn't count
     sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
     genomic.addSequenceFeature(sf);
@@ -70,7 +100,7 @@ public class EnsemblCdsTest
     // mRNA_region feature doesn't count (parent of CDS)
     sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     List<int[]> fromRanges = ranges.getFromRanges();
@@ -96,24 +126,24 @@ public class EnsemblCdsTest
   {
     String accId = "ABC123";
     EnsemblCds testee = new EnsemblCds();
-  
-    SequenceFeature sf = new SequenceFeature("CDS", "", 20000,
-            20500, 0f, null);
+
+    SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
+            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("anotherType", "", 20000, 20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
-  
+
     // other feature with desired parent is retained
-    sf.setValue("Parent", "transcript:" + accId);
+    sf.setValue("Parent", accId);
     assertTrue(testee.retainFeature(sf, accId));
-  
+
     // feature with wrong parent is not retained
-    sf.setValue("Parent", "transcript:XYZ");
+    sf.setValue("Parent", "XYZ");
     assertFalse(testee.retainFeature(sf, accId));
   }
 
@@ -122,34 +152,50 @@ 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", "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", 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", 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", 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", 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")