public void sortRows(AlignmentTrack.SortOption option, double location) {
        if (alignmentRows == null) {
            return;
        }
        for (AlignmentInterval.Row row : alignmentRows) {
            if (option == AlignmentTrack.SortOption.NUCELOTIDE) {
                // TODO -- why is this here?
            }
            row.updateScore(option, location, this);
        }
        Collections.sort(alignmentRows, new Comparator<Row>() {
            public int compare(AlignmentInterval.Row arg0, AlignmentInterval.Row arg1) {
                if (arg0.getScore() > arg1.getScore()) {
                    return 1;
                } else if (arg0.getScore() > arg1.getScore()) {
                    return -1;
                }
                return 0;
            }
        });
    }
public void sortRows(AlignmentTrack.SortOption option, double location) {
        if (alignmentRows == null) {
            return;
        }
        for (AlignmentInterval.Row row : alignmentRows) {
            if (option == AlignmentTrack.SortOption.NUCELOTIDE) {
               
            }
            row.updateScore(option, location, this);
        }
        Collections.sort(alignmentRows, new Comparator<Row>() {
            public int compare(AlignmentInterval.Row arg0, AlignmentInterval.Row arg1) {
                if (arg0.getScore() > arg1.getScore()) {
                    return 1;
                } else if (arg0.getScore() > arg1.getScore()) {
                    return -1;
                }
                return 0;
            }
        });
    }
public void sortrows(alignmenttrack.sortoption option, double location) { if (alignmentrows == null) { return; } for (alignmentinterval.row row : alignmentrows) { if (option == alignmenttrack.sortoption.nucelotide) { } row.updatescore(option, location, this); } collections.sort(alignmentrows, new comparator<row>() { public int compare(alignmentinterval.row arg0, alignmentinterval.row arg1) { if (arg0.getscore() > arg1.getscore()) { return 1; } else if (arg0.getscore() > arg1.getscore()) { return -1; } return 0; } }); }