-
- assertTrue("Test "+testname+"\nAlignment was not annotated - annotation file not imported.",new AnnotationFile().readAnnotationFile(al, af, FormatAdapter.FILE));
-
- String anfileout = new AnnotationFile().printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), al.getProperties());
- assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Null string",anfileout!=null);
- assertTrue("Test "+testname+"\nAlignment annotation file was not regenerated. Empty string",anfileout.length()>"JALVIEW_ANNOTATION".length());
-
- System.out.println("Output annotation file:\n"+anfileout+"\n<<EOF\n");
-
+ ColumnSelection cs = new ColumnSelection();
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment was not annotated - annotation file not imported.",
+ new AnnotationFile().readAnnotationFile(al, cs, af,
+ FormatAdapter.FILE));
+
+ AnnotationFile aff = new AnnotationFile();
+ ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
+ new Hashtable());
+ String anfileout = new AnnotationFile().printAnnotations(
+ al.getAlignmentAnnotation(), al.getGroups(),
+ al.getProperties(), null, al, v);
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
+ anfileout != null);
+ assertTrue(
+ "Test "
+ + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
+ anfileout.length() > "JALVIEW_ANNOTATION".length());
+
+ System.out.println("Output annotation file:\n" + anfileout
+ + "\n<<EOF\n");
+