import jalview.datamodel.AlignmentI;
import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.datamodel.AlignmentI;
import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.AADisorderClient;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.AADisorderClient;
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
assertTrue("Couldn't discover any IUPred services to use to test.",
iupreds.size() > 0);
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
assertTrue("Couldn't discover any IUPred services to use to test.",
iupreds.size() > 0);
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
public void testDisorderAnnotExport()
{
disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
public void testDisorderAnnotExport()
{
disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
- String aligfileout = new FormatAdapter().formatSequences("PFAM",
- al.getSequencesArray());
+ String aligfileout = FileFormat.Pfam.getWriter(al).print(
+ al.getSequencesArray(), true);
assertTrue(
"Test "
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
assertTrue(
"Test "
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
- StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
+ false);