X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblCdsTest.java;h=a44ab7f0ca58030bc9e0cdcb731a16638d322dee;hb=05c12ef9626200844bf5067056f03e84090565b3;hp=02ce2b202d425e5b5d50097758ab0c2f23185550;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git
diff --git a/test/jalview/ext/ensembl/EnsemblCdsTest.java b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index 02ce2b2..a44ab7f 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 .
+ * 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()
{
@@ -101,11 +131,12 @@ public class EnsemblCdsTest
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
@@ -122,34 +153,50 @@ 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", "transcript: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", "transcript:" + 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", "transcript:" + 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", "transcript:" + 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", "transcript:" + accId);
+ seq.addSequenceFeature(sf6);
+
+ List 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")