import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeGroups;
import org.testng.annotations.Test;
import compbio.metadata.Argument;
public class JpredJabaStructExportImport
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static String testseqs = "examples/uniref50.fa";
public static Jws2Discoverer disc;
public static jalview.gui.AlignFrame af = null;
- @BeforeClass(alwaysRun = true)
+ @BeforeGroups(groups = { "Network" })
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
}
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" }, enabled = false)
public void testJPredStructOneSeqOnly()
{
af.selectAllSequenceMenuItem_actionPerformed(null);
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" }, enabled = false)
public void testJPredStructExport()
{
try
{
// what format would be appropriate for RNAalifold annotations?
- String aligfileout = new FormatAdapter().formatSequences("PFAM",
- al.getSequencesArray());
+ String aligfileout = FileFormat.Pfam.getWriter(null).print(
+ al.getSequencesArray(), true);
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+ false);
return;
} catch (Exception e)
{
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
- @Test(groups = { "Functional" })
+ @Test(groups = { "Network" }, enabled = false)
public void testJpredwsSettingsRecovery()
{
Assert.fail("not implemnented");