- AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0], newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
- AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1], newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
- for (AlignmentAnnotation alan:newAl.getAlignmentAnnotation())
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
+ newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
+ newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
+ for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())