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. | |
structure for storing multiple sequences
| bool mseq_t::aligned |
true if all seqs are same length
| char* mseq_t::filename |
input file / source of sequences
| int mseq_t::nseqs |
number of sequences
| char** mseq_t::orig_seq |
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.
| int mseq_t::seqtype |
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;
1.6.3