import jalview.gui.CrossRefAction;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import java.io.File;
import java.io.IOException;
import java.util.List;
import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
public class CrossRef2xmlTests extends Jalview2xmlBase
{
+ @Override
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* test store and recovery of all reachable cross refs from all reachable
* crossrefs for one or more fetched db refs. Currently, this test has a known
// perform crossref action, or retrieve stored project
List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
CrossRefAction cra = null;
-
+
if (pass2 == 0)
{ // retrieve and show cross-refs in this thread
cra = new CrossRefAction(af, seqs, dna, db);
: new CrossRef(xrseqs, dataset)
.findXrefSourcesForSequences(avp
.getAlignViewport().isNucleotide());
-
+
stringify(dbtoviewBit, savedProjects, nextxref, avp);
xrptypes.put(nextxref, _xrptypes);
{
List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
int q = 0;
- String nextnextxref = nextxref
- + " -> " + xrefdb + "{" + q + "}";
+ String nextnextxref = nextxref + " -> " + xrefdb + "{"
+ + q + "}";
if (pass3 == 0)
{
{
failedXrefMenuItems
.add("No crossrefs retrieved for '"
- + nextxref + "' to " + xrefdb + " via '"
- + nextaf.getTitle() + "'");
+ + nextxref + "' to " + xrefdb
+ + " via '" + nextaf.getTitle() + "'");
continue;
}
cra_views2 = cra.getXrefViews();
for (AlignmentViewPanel nextavp : cra_views2)
{
- nextnextxref = nextxref
- + " -> " + xrefdb + "{" + q++ + "}";
+ nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
+ + "}";
// verify references for this panel
AlignmentTest.assertAlignmentDatasetRefs(
{
List<SequenceI> nonType = new ArrayList<SequenceI>();
for (SequenceI sq : alignmentViewPanel.getAlignViewport()
- .getAlignment()
- .getSequences())
+ .getAlignment().getSequences())
{
if (sq.isProtein() != expectProtein)
{
{
Assert.fail(message + " [ "
+ (expectProtein ? "nucleotides were " : "proteins were ")
- + nonType.toString()
- + " ]");
+ + nonType.toString() + " ]");
}
}