June 2006: v0.3 XNA/PRO libraries


These libraries are preliminary versions and are subject to frequent changes.

xna.h is a generic extendable class for nucleic acids and handles fasta and insd xml i/o.  It relies upon xmlparser.h and xmlparser.cpp.  exampleXNAuse.cpp gives a brief sample of using xna.h.  insd_m12345.xml is a typical GenBank insd xml file.  cr25s.fsa is a typical fasta file which adheres to the fasta defline format shown below.  
 GenBank gi|gi-number|gb|accession|locus
EMBL Data Library gi|gi-number|emb|accession|locus
DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus
NBRF PIR pir||entry
Protein Research Foundation prf||name
SWISS-PROT sp|accession|name
Brookhaven Protein Data Bank (1) pdb|entry|chain
Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE
Patents pat|country|number
GenInfo Backbone Id bbs|number
General database identifier gnl|database|identifier
NCBI Reference Sequence ref|accession|locus
Local Sequence identifier lcl|identifier

pro.h is a generic extendable class for amino acids and handles fasta and pdb i/o.  examplePROuse.cpp gives a brief sample of using pro.h.  4pti.pdb is a typical PDB file.
Primary library testing occurs via g++ (GCC) 4.0.3 (linux x86).  For windows use, we test only with msvc8; visual c++ 2005 express edition, which is available free of charge.  Note that the default installation of this compiler / ide requires the ms platform sdk (psdk), mainly to include windows.h.

For more information, see the documentation.


2006: BioC++