package jalview.ext.ensembl;
import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
-import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
+import static org.testng.AssertJUnit.assertSame;
import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FastaFile;
import jalview.io.FileParse;
import java.lang.reflect.Method;
import java.util.Arrays;
+import java.util.List;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
public class EnsemblSeqProxyTest
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final Object[][] allSeqs = new Object[][] {
{
new EnsemblProtein(),
}
- @Test(groups = "Functional")
- public void testIsTranscriptIdentifier()
- {
- EnsemblSeqProxy testee = new EnsemblGene();
- assertFalse(testee.isTranscriptIdentifier(null));
- assertFalse(testee.isTranscriptIdentifier(""));
- assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
- assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
- assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
- assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
- assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
- assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
- }
-
- @Test(groups = "Functional")
- public void testIsGeneIdentifier()
- {
- EnsemblSeqProxy testee = new EnsemblGene();
- assertFalse(testee.isGeneIdentifier(null));
- assertFalse(testee.isGeneIdentifier(""));
- assertFalse(testee.isGeneIdentifier("ENST00000012345"));
- assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
- assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
- assertFalse(testee.isGeneIdentifier("ensg00000012345"));
- assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
- assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
- }
-
/**
* Test the method that appends a single allele's reverse complement to a
* string buffer
SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
- SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
+ List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
+ sf2, sf3, sf4 });
// sort by start position ascending (forward strand)
// sf2 and sf3 tie and should not be reordered by sorting
- EnsemblSeqProxy.sortFeatures(sfs, true);
- assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
+ SequenceFeatures.sortFeatures(sfs, true);
+ assertSame(sfs.get(0), sf2);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf1);
+ assertSame(sfs.get(3), sf4);
// sort by end position descending (reverse strand)
- EnsemblSeqProxy.sortFeatures(sfs, false);
- assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
+ SequenceFeatures.sortFeatures(sfs, false);
+ assertSame(sfs.get(0), sf1);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf2);
+ assertSame(sfs.get(3), sf4);
}
}