Multifind_object Class Reference

Multifind_object Class. More...

#include <Multifind_object.h>

Inheritance diagram for Multifind_object:

List of all members.

Public Member Functions
	Multifind_object (const string &outputmultifind, const vector< string > &ctfiles, const vector< string > &inputalignment, const vector< string > &inputsequences, const int &processors, TProgressDialog *progress=NULL)
int	Multifind_Predict ()
	The core function doing Multilign calculation and SVM prediction.
Private Member Functions
double	sum_multifind (vector< double > &series)
double	average_multifind (vector< double > &series)
double	variation_multifind (vector< double > &series)
double	sum_multifind (vector< float > &series)
double	average_multifind (vector< float > &series)
double	variation_multifind (vector< float > &series)
double	sum_multifind (vector< int > &series)
double	average_multifind (vector< int > &series)
double	variation_multifind (vector< int > &series)
double	normalized_ensemble_defect (RNA *rna)
double	entropy (vector< char > column)
double	average_entropy ()
vector< double >	single_z_predict (string sequence, svm_model *model_folding_average, svm_model *model_folding_std, svm_model *model_ensemble_average, svm_model *model_ensemble_std)
int	get_gap (string sequence)
double	common_energies ()
vector< double >	predict_ncRNA_probabilities (double sci, double entropy, double single_z, double ensemble_defect_z)
Private Attributes
int	num_processors

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Detailed Description

Multifind_object Class.

The Multifind_object class provides an entry point for the Multifind algorithm.

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Constructor & Destructor Documentation

Multifind_object::Multifind_object	(	const string &	outputmultifind,
		const vector< string > &	ctfiles,
		const vector< string > &	inputalignment,
		const vector< string > &	inputsequences,
		const int &	processors,
		TProgressDialog *	progress = NULL
	)

Constructor:

Parameters:

	outputmultifind	is the name of the Multifind output file to which the output is written to.
	ctfiles	is a vector of strings storing the names of the ct files to which the output structures are written to.
	inputalignment	is a vector of strings storing the input sequences in the alignment (with gaps).
	inputsequences	is a vector of strings storing the input sequences in the alignment (without gaps).
	processors	is a interger indicating the number of processors required by Multifind in smp calculations.(only applicable in smp version)
	progress	is a TProgressDialog for reporting progress of the calculation to the user. The default value of NULL means that no communication is provided.

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Member Function Documentation

double Multifind_object::average_entropy

(

)

[private]

double Multifind_object::average_multifind

(

vector< int > &

series

)

[private]

double Multifind_object::average_multifind

(

vector< float > &

series

)

[private]

double Multifind_object::average_multifind

(

vector< double > &

series

)

[private]

double Multifind_object::common_energies

(

)

[private]

double Multifind_object::entropy

(

vector< char >

column

)

[private]

int Multifind_object::get_gap

(

string

sequence

)

[private]

int Multifind_object::Multifind_Predict

(

)

The core function doing Multilign calculation and SVM prediction.

double Multifind_object::normalized_ensemble_defect

(

RNA *

rna

)

[private]

vector< double > Multifind_object::predict_ncRNA_probabilities	(	double	sci,
		double	entropy,
		double	single_z,
		double	ensemble_defect_z
	)			[private]

vector< double > Multifind_object::single_z_predict	(	string	sequence,
		svm_model *	model_folding_average,
		svm_model *	model_folding_std,
		svm_model *	model_ensemble_average,
		svm_model *	model_ensemble_std
	)			[private]

double Multifind_object::sum_multifind

(

vector< int > &

series

)

[private]

double Multifind_object::sum_multifind

(

vector< float > &

series

)

[private]

double Multifind_object::sum_multifind

(

vector< double > &

series

)

[private]

double Multifind_object::variation_multifind

(

vector< int > &

series

)

[private]

double Multifind_object::variation_multifind

(

vector< float > &

series

)

[private]

double Multifind_object::variation_multifind

(

vector< double > &

series

)

[private]

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Member Data Documentation

int Multifind_object::num_processors [private]

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The documentation for this class was generated from the following files:

• I:/RNAstructure/RNA_class/Multifind_object.h
• I:/RNAstructure/RNA_class/Multifind_object.cpp