mseq_t Struct Reference

structure for storing multiple sequences More...

#include <seq.h>

Data Fields

int nseqs
int seqtype
char * filename
bool aligned
char ** seq
char ** orig_seq
SQINFO * sqinfo
 Squid's sequence info structure. Index range: 0--nseq-1.

Detailed Description

structure for storing multiple sequences


Field Documentation

true if all seqs are same length

input file / source of sequences

number of sequences

original sequence residues as char pointer. range for first index: 0--nseq-1. only set during input

char** mseq_t::seq

(working) sequence residues as char pointer. range for first index: 0--nseq-1. changes during alignment.

sequence type

SQINFO* mseq_t::sqinfo

Squid's sequence info structure. Index range: 0--nseq-1.

extra data are available: int flags;

name: char name[SQINFO_NAMELEN];

database identifier: char id[SQINFO_NAMELEN];

database accession no: char acc[SQINFO_NAMELEN];

description: char desc[SQINFO_DESCLEN];

length of this seq, incl gaps in our case!: int len;

start position on source seq (valid range: 1..len): int start;

end position on source seq (valid range: 1..len): int stop;

original length of source seq: int olen;

kRNA, kDNA, kAmino, or kOther: int type;

secondary structure string (index range: 0..len-1): char *ss;

percent side chain surface access (index range: 0..len-1): char *sa;

See also:
squid.h
LogSqInfo()

The documentation for this struct was generated from the following file:
Generated on Fri Aug 31 05:32:52 2012 for Clustal Omega by  doxygen 1.6.3