JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...

[jalview.git] / test / jalview / ext / ensembl / EnsemblCdnaTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index 95d371a..c927f04 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -20,14 +20,18 @@
  */
 package jalview.ext.ensembl;
 
+import java.util.Locale;
+
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
 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;
@@ -41,6 +45,14 @@ import org.testng.annotations.Test;
 
 public class EnsemblCdnaTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
@@ -69,19 +81,19 @@ public class EnsemblCdnaTest
     // exon at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("-");
     genomic.addSequenceFeature(sf);
 
     // exon (sub-type) at (start + exon_variant) length 101
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("-");
     genomic.addSequenceFeature(sf);
 
     // exon belonging to a different transcript doesn't count
     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
-    sf.setValue("Parent", "transcript:anotherOne");
+    sf.setValue("Parent", "anotherOne");
     genomic.addSequenceFeature(sf);
 
     // transcript feature doesn't count
@@ -124,19 +136,19 @@ public class EnsemblCdnaTest
     // exon at (start+10000) length 501
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // exon (sub-type) at (start + exon_variant) length 101
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
-    sf.setValue("Parent", "transcript:" + transcriptId);
+    sf.setValue("Parent", transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
     // exon belonging to a different transcript doesn't count
     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
-    sf.setValue("Parent", "transcript:anotherOne");
+    sf.setValue("Parent", "anotherOne");
     genomic.addSequenceFeature(sf);
 
     // transcript feature doesn't count
@@ -203,22 +215,27 @@ public class EnsemblCdnaTest
             20500, 0f, null);
     assertFalse(testee.retainFeature(sf, accId));
 
-    sf.setType("aberrant_processed_transcript");
+    sf = new SequenceFeature("aberrant_processed_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 retained
-    sf.setType("sequence_variant");
+    sf = new SequenceFeature("sequence_variant", "", 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));
 
+    // test is not case-sensitive
+    assertTrue(testee.retainFeature(sf, accId.toLowerCase(Locale.ROOT)));
+
     // feature with wrong parent is not retained
-    sf.setValue("Parent", "transcript:XYZ");
+    sf.setValue("Parent", "XYZ");
     assertFalse(testee.retainFeature(sf, accId));
   }
 
@@ -227,34 +244,51 @@ public class EnsemblCdnaTest
    * accession id as parent
    */
   @Test(groups = "Functional")
-  public void testIdentifiesSequence()
+  public void testGetIdentifyingFeatures()
   {
     String accId = "ABC123";
-    EnsemblCdna testee = new EnsemblCdna();
+    SequenceI seq = new Sequence(accId, "MKLNFRQIE");
 
-    // exon with no parent not valid
-    SequenceFeature sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
-    assertFalse(testee.identifiesSequence(sf, accId));
+    // exon with no parent: not valid
+    SequenceFeature sf1 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    seq.addSequenceFeature(sf1);
 
-    // exon with wrong parent not valid
-    sf.setValue("Parent", "transcript:XYZ");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    // exon with wrong parent: not valid
+    SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf2.setValue("Parent", "XYZ");
+    seq.addSequenceFeature(sf2);
 
     // exon with right parent is valid
-    sf.setValue("Parent", "transcript:" + accId);
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf3.setValue("Parent", accId);
+    seq.addSequenceFeature(sf3);
 
     // exon sub-type with right parent is valid
-    sf.setType("coding_exon");
-    assertTrue(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 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);
 
     // CDS not valid:
-    sf.setType("CDS");
-    assertFalse(testee.identifiesSequence(sf, accId));
+    SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
+            null);
+    sf6.setValue("Parent", accId);
+    seq.addSequenceFeature(sf6);
+
+    List<SequenceFeature> sfs = new EnsemblCdna()
+            .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")