- String aligfileout = new FormatAdapter().formatSequences("PFAM",
- al.getSequencesArray());
- String anfileout = new AnnotationFile().printAnnotations(
- al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Null string",
+ String aligfileout = FileFormat.Pfam.getWriter(al)
+ .print(al.getSequencesArray(), true);
+ String anfileout = new AnnotationFile()
+ .printAnnotationsForAlignment(al);
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Null string",