[Biojava-l] Order MSF alignment

[Fox, Richard]

In order to keep the order of the sequence parsed by the MSFAlignmentFormat we're proposing the following change:

old code:

            //now parse through them and create gapped symbol lists
            HashMap sequenceDataMap = new HashMap();

new code:

            //now parse through them and create gapped symbol lists
            final ArrayList comparatorNames = new ArrayList(sequenceNames);
            Comparator sequenceComparator = new Comparator () {
                public int compare(Object o1, Object o2) {
                    int index1 = comparatorNames.indexOf(o1);
                    int index2 = comparatorNames.indexOf(o2);
                    if (index1 > index2) return 1;
                    else if (index1 < index2) return -1;
                    else return 0;
                }
            };
            Map sequenceDataMap = new TreeMap(sequenceComparator);

Richard J. Fox, Ph.D.
Software Engineer - Bioinformatics
MAXYGEN
515 Galveston Drive
Redwood City, CA 94063
Tel. 650.980.5616
http://www.maxygen.com