Contains all command line arguments. More...
#include <structs.h>
Public Attributes | |
char * | cfg_file |
char * | db_file |
char * | q_file |
char * | res_file |
char * | stat_file |
char * | m1_file |
char * | m2_file |
int | mD |
double | e |
int | p |
int | out |
int | split |
int | help |
int | version |
int | verbose |
float | m1_seqT |
float | m2_seqT |
float | m2_strucT |
float | m2T |
Contains all command line arguments.
gotoh_arguments contains all command line arguments or their initialized values if not set by the user. It can be initialized by gotoh_initArguments() and freed by gotoh_freeArguments().
Filename of configuration file. Format see examples/Configuration.dat.
char* gotoh_arguments::db_file |
Filename of database file containing FASTA formatted sequences.
double gotoh_arguments::e |
Evalue - only candidate alignments with lower or equal Evalue than this value are returned. Default: 1e-3
Print usage information.
char* gotoh_arguments::m1_file |
Filename of query file containing a motif as frequency matrix reformatted using scripts/reformatFasta.pl
float gotoh_arguments::m1_seqT |
Sequence threshold to be a matching pattern for single motifs. Default: 0.7
char* gotoh_arguments::m2_file |
Filename of query file containing a 2-sided motif as frequency matrices reformatted using scripts/reformatFasta.pl
float gotoh_arguments::m2_seqT |
Sequence threshold to be a matching pattern for 2-sided motifs. Default: 0.5
Structure threshold to be a matching pattern for 2-sided motifs. Default: 0.8
float gotoh_arguments::m2T |
Complete Threshold for 2-sided motifs. Default: 0.6
Maximal distance between the 2 sides of the 2-sided motif
Output format. Values are:
0
- Blast tabular output 1
- Blast tabular output + aligned sequences 2
- FASTA format. NOTE: Hit sequence only, without gaps ! 3
- MAF format. NOTE: Header truncated to 30 characters! 4
- BED + aligned sequences 5
- GFF + aligned sequencesDefault: 0
Percent identity - only candidate alignments with higher or equal percent identity than this value are returned. Default: 60
char* gotoh_arguments::q_file |
Filename of query file conatining FASTA formatted (ungapped) sequences.
filenmae of output file.
Splits value - the database is split into pieces to enhance memory usage. Default: 10000
Filename of file where to statistics on the E-value calculation, i.e. the data of the histogram, the fit parameters and the final fitted curve
Print Verbose output.
Print version information.