import jalview.datamodel.AlignmentI;
import jalview.gui.Jalview2XML;
import jalview.io.AnnotationFile;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.JPred301Client;
System.out.println("State of jpredws: " + jpredws);
Assert.assertNotNull(jpredws, "jpredws is null!");
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
// again what format would be appropriate?
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
- FormatAdapter.PASTE, "PFAM");
+ DataSourceType.PASTE, FileFormat.Fasta);
assertTrue(
"Test "
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
- FormatAdapter.PASTE));
+ DataSourceType.PASTE));
// test for consistency in io
StockholmFileTest.testAlignmentEquivalence(al, al_new, false);