X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdnaTest.java;h=c927f0464629147d245ef2dd572d4d2d1130574a;hb=41b0e9331ac71787c1280aa1d809f54c575fbf97;hp=90c38d4a4d070adf8155b80fc766f1c9a77b610d;hpb=e24933a537e0f640c75d4685c468615872bc77fc;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index 90c38d4..c927f04 100644
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -1,13 +1,37 @@
+/*
+ * 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 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;
@@ -21,17 +45,26 @@ import org.testng.annotations.Test;
 
 public class EnsemblCdnaTest
 {
-  @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);
   }
+
   /**
    * Test that the cdna part of genomic sequence is correctly identified by
    * 'exon' features (or subtypes) - reverse strand case.
@@ -48,19 +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
@@ -99,30 +132,30 @@ public class EnsemblCdnaTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     // 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
     sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
     sf.setStrand("-"); // weird but ignored
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     List<int[]> fromRanges = ranges.getFromRanges();
@@ -151,18 +184,18 @@ public class EnsemblCdnaTest
     genomic.setStart(10000);
     genomic.setEnd(50000);
     String transcriptId = "ABC123";
-  
+
     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
             null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("-");
     genomic.addSequenceFeature(sf);
-  
+
     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
     sf.setValue("Parent", "transcript:" + transcriptId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
-  
+
     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
             transcriptId, 23);
     assertNull(ranges);
@@ -182,22 +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));
   }
 
@@ -206,34 +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")