Clustal Omega 1.2.4
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
 
int * tree_order
 
SQINFO * sqinfo
 Squid's sequence info structure. Index range: 0–nseq-1.
 
char *** pppcHMMBNames
 
int ** ppiHMMBindex
 

Detailed Description

structure for storing multiple sequences

Field Documentation

◆ aligned

bool mseq_t::aligned

true if all seqs are same length

◆ filename

char* mseq_t::filename

input file / source of sequences

◆ nseqs

int mseq_t::nseqs

number of sequences

◆ orig_seq

char** mseq_t::orig_seq

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

◆ ppiHMMBindex

int** mseq_t::ppiHMMBindex

◆ pppcHMMBNames

char*** mseq_t::pppcHMMBNames

◆ seq

char** mseq_t::seq

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

◆ seqtype

int mseq_t::seqtype

sequence type

◆ sqinfo

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()

◆ tree_order

int* mseq_t::tree_order

order in which sequences appear in guide-tree


The documentation for this struct was generated from the following file: