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JAL-1270 missing 'alwaysRun=true' added to setup/teardown
[jalview.git]
/
test
/
jalview
/
analysis
/
CrossRefTest.java
diff --git
a/test/jalview/analysis/CrossRefTest.java
b/test/jalview/analysis/CrossRefTest.java
index
a85dcef
..
81ec443
100644
(file)
--- a/
test/jalview/analysis/CrossRefTest.java
+++ b/
test/jalview/analysis/CrossRefTest.java
@@
-37,6
+37,7
@@
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.ws.SequenceFetcher;
import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.ws.SequenceFetcher;
@@
-46,10
+47,19
@@
import java.util.ArrayList;
import java.util.List;
import org.testng.annotations.AfterClass;
import java.util.List;
import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class CrossRefTest
{
import org.testng.annotations.Test;
public class CrossRefTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testFindXDbRefs()
{
@Test(groups = { "Functional" })
public void testFindXDbRefs()
{
@@
-96,7
+106,7
@@
public class CrossRefTest
public void testFindXrefSourcesForSequence_proteinToDna()
{
SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
public void testFindXrefSourcesForSequence_proteinToDna()
{
SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
- List<String> sources = new ArrayList<String>();
+ List<String> sources = new ArrayList<>();
AlignmentI al = new Alignment(new SequenceI[] {});
/*
AlignmentI al = new Alignment(new SequenceI[] {});
/*
@@
-122,8
+132,9
@@
public class CrossRefTest
sources = new CrossRef(new SequenceI[] { seq }, al)
.findXrefSourcesForSequences(false);
// method is patched to remove EMBL from the sources to match
sources = new CrossRef(new SequenceI[] { seq }, al)
.findXrefSourcesForSequences(false);
// method is patched to remove EMBL from the sources to match
- assertEquals(3, sources.size());
- assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+ assertEquals(4, sources.size());
+ assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]",
+ sources.toString());
/*
* add a sequence to the alignment which has a dbref to UNIPROT|A1234
/*
* add a sequence to the alignment which has a dbref to UNIPROT|A1234
@@
-260,7
+271,7
@@
public class CrossRefTest
pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
- List<SequenceI> result = new ArrayList<SequenceI>();
+ List<SequenceI> result = new ArrayList<>();
/*
* first search for a dbref nowhere on the alignment:
/*
* first search for a dbref nowhere on the alignment:
@@
-416,7
+427,7
@@
public class CrossRefTest
* argument false suppresses adding DAS sources
* todo: define an interface type SequenceFetcherI and mock that
*/
* argument false suppresses adding DAS sources
* todo: define an interface type SequenceFetcherI and mock that
*/
- SequenceFetcher mockFetcher = new SequenceFetcher(false)
+ SequenceFetcher mockFetcher = new SequenceFetcher()
{
@Override
public boolean isFetchable(String source)
{
@Override
public boolean isFetchable(String source)
@@
-443,7
+454,7
@@
public class CrossRefTest
assertSame(pep2, xrefs.getSequenceAt(1));
}
assertSame(pep2, xrefs.getSequenceAt(1));
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceFetcherFactory.setSequenceFetcher(null);
public void tearDown()
{
SequenceFetcherFactory.setSequenceFetcher(null);
@@
-494,7
+505,7
@@
public class CrossRefTest
* argument false suppresses adding DAS sources
* todo: define an interface type SequenceFetcherI and mock that
*/
* argument false suppresses adding DAS sources
* todo: define an interface type SequenceFetcherI and mock that
*/
- SequenceFetcher mockFetcher = new SequenceFetcher(false)
+ SequenceFetcher mockFetcher = new SequenceFetcher()
{
@Override
public boolean isFetchable(String source)
{
@Override
public boolean isFetchable(String source)
@@
-640,7
+651,7
@@
public class CrossRefTest
* passed in calls to getSequences() - important to verify that
* duplicate sequence fetches are not requested
*/
* passed in calls to getSequences() - important to verify that
* duplicate sequence fetches are not requested
*/
- SequenceFetcher mockFetcher = new SequenceFetcher(false)
+ SequenceFetcher mockFetcher = new SequenceFetcher()
{
int call = 0;
{
int call = 0;