X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdsTest.java;h=8482c903e4238bcb379e1d8ec554641566e52686;hb=c4a72d18f6a7b2cf3de4a46b7a35cbfd0d76438f;hp=fb17845c0ec73c0d982f444d03840c350e7b31ce;hpb=e96f5e8ce137e879dd4b4f37fb5c4d134e2778e2;p=jalview.git

diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index fb17845..8482c90 100644
--- a/test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdsTest.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;
@@ -7,25 +27,35 @@ 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;
 
 import java.util.List;
 
+import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class EnsemblCdsTest
 {
-  @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);
@@ -43,25 +73,25 @@ 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.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.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");
     genomic.addSequenceFeature(sf);
-  
+
     // exon feature doesn't count
     sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
     genomic.addSequenceFeature(sf);
@@ -69,7 +99,7 @@ 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();
@@ -95,22 +125,23 @@ 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("CDS_psequence_variantredicted", "", 20000,
+            20500, 0f, null);
     assertTrue(testee.retainFeature(sf, accId));
-  
+
     // other feature with desired parent is retained
     sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.retainFeature(sf, accId));
-  
+
     // feature with wrong parent is not retained
     sf.setValue("Parent", "transcript:XYZ");
     assertFalse(testee.retainFeature(sf, accId));
@@ -125,30 +156,46 @@ public class EnsemblCdsTest
   {
     String accId = "ABC123";
     EnsemblCds testee = new EnsemblCds();
-  
+
     // cds with no parent not valid
     SequenceFeature sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // cds with wrong parent not valid
     sf.setValue("Parent", "transcript:XYZ");
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // cds with right parent is valid
     sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // cds sub-type with right parent is valid
-    sf.setType("CDS_predicted");
+    sf = new SequenceFeature("CDS_predicted", "", 1, 2, 0f, null);
+    sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
-  
+
     // transcript not valid:
-    sf.setType("transcript");
+    sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+    sf.setValue("Parent", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
-  
+
     // exon not valid:
-    sf.setType("exon");
+    sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
+    sf.setValue("Parent", "transcript:" + accId);
     assertFalse(testee.identifiesSequence(sf, accId));
   }
 
+  @Test(groups = "Functional")
+  public void testIsValidReference() throws Exception
+  {
+    EnsemblSequenceFetcher esq = new EnsemblCds();
+    Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
+    Assert.assertTrue(esq.isValidReference("ENST00000288602"));
+    Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
+    Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
+    Assert.assertFalse(esq.isValidReference("ENST0000288602"));
+    // non-human species have a 3 character identifier included:
+    Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
+  }
+
 }