import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
import jalview.io.FastaFile;
import jalview.io.FileParse;
import jalview.io.gff.SequenceOntologyFactory;
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(),
FileParse fp = proxy.getSequenceReader(Arrays
.asList(new String[] { sq }));
SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
- FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
+ FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
SequenceI[] trueSqs = trueRes.getSeqsAsArray();
Assert.assertEquals(sqs.length, trueSqs.length,
"Different number of sequences retrieved for query " + sq);