I just wrote the first alpha version of a C++ class for FASTA format reader
with a slight extension.
Basic feature of the class is this:
o To read a sequence is as simple as this:
Sequence s;
cin >> s;
To read multiple sequence, just iterate.
o No line length limit.
o It recognize identifier as the first word (non-space sequence of char)
of '>' line.
o Identifier, comments and sequence can be assessed through three
methods:
id(), rem() and seq(),
where range can be passed to seq().
o A single site can be access by index s[i] (where s is Sequence
instance).
o It allows ';' on the first column as comment line indicator. Comments
are
accessible through method rem() as a concatenated string separated
by
newline (\n).
o It comes with a function 'complement()' to obtain compliment strand of
DNA
or RNA.
This class requires string template library from standard template library
(STL).
It also includes header <iostream> which is described in STL definition.
This class is accessible with included README at
ftp://toshi-pc.fas.harvard.edu/pub/ReadFasta/ReadFasta-0.1.tgz
Although I made every effort to avoid problems, but as it's just an alpha
version,
it may have problems, so I reserve all rights and there is no warranty.
However, if anybody want to use it, I guarantee for free use.
I am still working on adding some features.
I would appreciate your comments, suggestions and bug report.
==========================================
Toshinori Endo, Ph.D.
Harvard University Biological Laboratories
16 Divinity Avenue, Cambridge MA02138-2092, USA
tendo at fas.harvard.ed
