#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

Detailed Description

user/commandline options

changes here will have to be reflected in ParseCommandLine() and during setup of the default opts

Field Documentation

◆ bAutoOptions

bool opts_t::bAutoOptions

◆ bIterationsAuto

bool opts_t::bIterationsAuto

determine number of iterations automatically

◆ bPercID

bool opts_t::bPercID

print percentage identity

◆ bPileup

bool opts_t::bPileup

pile-up flag

◆ bUseKimura

bool opts_t::bUseKimura

use Kimura corrected distance

◆ bUseMbed

bool opts_t::bUseMbed

use mbed-like clustering

◆ bUseMbedForIteration

bool opts_t::bUseMbedForIteration

use mbed-like clustering also during iteration

◆ iClusteringType

int opts_t::iClusteringType

clustering type (from cmdline arg)

◆ iClustersizes

int opts_t::iClustersizes

number of sequences in cluster

◆ iHMMInputFiles

int opts_t::iHMMInputFiles

number of provided HMM input files. not really a user option but need for ppcHMMInput

◆ iMaxGuidetreeIterations

int opts_t::iMaxGuidetreeIterations

max number of guidetree iterations

◆ iMaxHMMIterations

int opts_t::iMaxHMMIterations

maximum number of hmm iterations

◆ iNumIterations

int opts_t::iNumIterations

number of iterations

◆ iPairDistType

int opts_t::iPairDistType

pairwise distance method

◆ iTransitivity

int opts_t::iTransitivity

use transitivity

◆ pcClustfile

char* opts_t::pcClustfile

file with clustering information

◆ pcDistmatInfile

char* opts_t::pcDistmatInfile

distance matrix input file

◆ pcDistmatOutfile

char* opts_t::pcDistmatOutfile

distance matrix output file

◆ pcGuidetreeInfile

char* opts_t::pcGuidetreeInfile

guidetree input file

◆ pcGuidetreeOutfile

char* opts_t::pcGuidetreeOutfile

guidetree output file

◆ pcHMMBatch

char* opts_t::pcHMMBatch

HMM batch-file, specify HMMs for individual sequences. FS, r291 ->

◆ pcPosteriorfile

char* opts_t::pcPosteriorfile

file with posterior probability information

◆ ppcHMMInput

char** opts_t::ppcHMMInput

HMM input files. index range: 0..iHMMInputFiles

◆ rHhalignPara

hhalign_para opts_t::rHhalignPara

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

src/clustal-omega.h

Data Fields