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;
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);
- String aligfileout = new FormatAdapter().formatSequences("PFAM",
- al.getSequencesArray());
+ String aligfileout = FileFormat.Pfam.getAlignmentFile().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,
// test for consistency in io
StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
// test for consistency in io
StockholmFileTest.testAlignmentEquivalence(al, al_new, true);