opts_t Struct Reference

#include <clustal-omega.h>

Data Fields
bool	bAutoOptions
char *	pcDistmatInfile
char *	pcDistmatOutfile
int	iClusteringType
int	iPairDistType
bool	bUseMbed
bool	bUseMbedForIteration
char *	pcGuidetreeOutfile
char *	pcGuidetreeInfile
char **	ppcHMMInput
int	iHMMInputFiles
int	iNumIterations
bool	bIterationsAuto
int	iMaxHMMIterations
int	iMaxGuidetreeIterations
hhalign_para	rHhalignPara

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Detailed Description

user/commandline options

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

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Field Documentation

bool opts_t::bAutoOptions

bool opts_t::bIterationsAuto

determine number of iterations automatically

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::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

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::ppcHMMInput

HMM input files. index range: 0..iHMMInputFiles

hhalign_para opts_t::rHhalignPara

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

• src/clustal-omega.h