Clustal Omega 1.2.4
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#include <clustal-omega.h>
Data Fields | |
bool | bAutoOptions |
char * | pcDistmatInfile |
char * | pcDistmatOutfile |
int | iClusteringType |
int | iClustersizes |
char * | pcClustfile |
int | iTransitivity |
char * | pcPosteriorfile |
int | iPairDistType |
bool | bUseMbed |
bool | bUseMbedForIteration |
bool | bPileup |
char * | pcGuidetreeOutfile |
char * | pcGuidetreeInfile |
bool | bUseKimura |
bool | bPercID |
char ** | ppcHMMInput |
int | iHMMInputFiles |
char * | pcHMMBatch |
int | iNumIterations |
bool | bIterationsAuto |
int | iMaxHMMIterations |
int | iMaxGuidetreeIterations |
hhalign_para | rHhalignPara |
user/commandline options
changes here will have to be reflected in ParseCommandLine() and during setup of the default opts
bool opts_t::bAutoOptions |
bool opts_t::bIterationsAuto |
determine number of iterations automatically
bool opts_t::bPercID |
print percentage identity
bool opts_t::bPileup |
pile-up flag
bool opts_t::bUseKimura |
use Kimura corrected distance
bool opts_t::bUseMbed |
use mbed-like clustering
bool opts_t::bUseMbedForIteration |
use mbed-like clustering also during iteration
int opts_t::iClusteringType |
clustering type (from cmdline arg)
int opts_t::iClustersizes |
number of sequences in cluster
int opts_t::iHMMInputFiles |
number of provided HMM input files. not really a user option but need for ppcHMMInput
int opts_t::iMaxGuidetreeIterations |
max number of guidetree iterations
int opts_t::iMaxHMMIterations |
maximum number of hmm iterations
int opts_t::iNumIterations |
number of iterations
int opts_t::iPairDistType |
pairwise distance method
int opts_t::iTransitivity |
use transitivity
char* opts_t::pcClustfile |
file with clustering information
char* opts_t::pcDistmatInfile |
distance matrix input file
char* opts_t::pcDistmatOutfile |
distance matrix output file
char* opts_t::pcGuidetreeInfile |
guidetree input file
char* opts_t::pcGuidetreeOutfile |
guidetree output file
char* opts_t::pcHMMBatch |
HMM batch-file, specify HMMs for individual sequences. FS, r291 ->
char* opts_t::pcPosteriorfile |
file with posterior probability information
char** opts_t::ppcHMMInput |
HMM input files. index range: 0..iHMMInputFiles
hhalign_para opts_t::rHhalignPara |