Fasta Sequence class

tendo tendo at fas.harvard.edu
Wed Dec 16 15:14:49 EST 1998


I finished the alpha version of class libraries for multiple sequence
as well as CLUSTAL formatted multiple alignment.
You can get the whole package including the revised ReadFasta class at

    ftp://toshi-pc.fas.harvard.edu/pub/ReadFasta/ReadFasta-0.2.tgz


The usage for the new classes is almost the same as ReadFasta class.

    o To read and write Fasta formatted multiple sequence is:

            #include <iostream>
            #include "MultiSeq.h"

            main () {
                MultiSeq m;
                cin >> m;
                cout << m;
            }

    o To read CLUSTAL formatted multiple alignment and write
        in FASTA format is:

            #include <iostream>
            #include "AlignedSeq.h"

            main() {
                AlignedSeq a;
                cin >> a;
                cout << a;
            }

      o Each sequence is accessible by index, i.e.


            m[0], m[1] for the first sequence.

        Each element is of Sequence class in ReadFasta, so all of its
feature
        is available.


I also fixed a couple of problems in the previous package as well as
documentation, although the attached document is incomplete yet.

I would like to hear from you.

Toshi
==========================================
Toshinori Endo, Ph.D.
Harvard University Biological Laboratories
16 Divinity Avenue, Cambridge MA02138-2092, USA
tendo at fas.harvard.ed






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