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

Detailed Description

user/commandline options

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

Field Documentation

determine number of iterations automatically

use mbed-like clustering

use mbed-like clustering also during iteration

clustering type (from cmdline arg)

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

max number of guidetree iterations

maximum number of hmm iterations

number of iterations

pairwise distance method

distance matrix input file

distance matrix output file

guidetree input file

guidetree output file

HMM input files. index range: 0..iHMMInputFiles

hhalign_para opts_t::rHhalignPara

The documentation for this struct was generated from the following file:
Generated on Fri Aug 31 05:32:52 2012 for Clustal Omega by  doxygen 1.6.3