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JAL-2777 release notes
[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
..
6611e05
100644
(file)
--- a/
test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/
test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@
-28,6
+28,7
@@
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
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 jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;
@@
-41,6
+42,14
@@
import org.testng.annotations.Test;
public class EnsemblCdnaTest
{
public class EnsemblCdnaTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@BeforeClass(alwaysRun = true)
public void setUp()
{
@BeforeClass(alwaysRun = true)
public void setUp()
{
@@
-203,14
+212,16
@@
public class EnsemblCdnaTest
20500, 0f, null);
assertFalse(testee.retainFeature(sf, accId));
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));
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
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
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
@@
-245,15
+256,18
@@
public class EnsemblCdnaTest
assertTrue(testee.identifiesSequence(sf, accId));
// exon sub-type with right parent is valid
assertTrue(testee.identifiesSequence(sf, accId));
// exon sub-type with right parent is valid
- sf.setType("coding_exon");
+ sf = new SequenceFeature("coding_exon", "", 1, 2, 0f, null);
+ sf.setValue("Parent", "transcript:" + accId);
assertTrue(testee.identifiesSequence(sf, accId));
// transcript not valid:
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));
// CDS not valid:
assertFalse(testee.identifiesSequence(sf, accId));
// CDS not valid:
- sf.setType("CDS");
+ sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
+ sf.setValue("Parent", "transcript:" + accId);
assertFalse(testee.identifiesSequence(sf, accId));
}
assertFalse(testee.identifiesSequence(sf, accId));
}