#include <Multifind_object.h>

Inheritance diagram for Multifind_object:

Public Member Functions
	Multifind_object (const string &outputmultifind, const vector< string > &ctfiles, const vector< string > &inputalignment, const vector< string > &inputsequences, const int &processors, ProgressHandler *progress=NULL)

int	Multifind_Predict ()
	The core function doing Multilign calculation and SVM prediction. More...

Public Member Functions inherited from Multilign_object
	Multilign_object ()
	Default constructor: More...

	Multilign_object (const vector< vector< string > > &inputlist, const bool isrna=true, ProgressHandler *progress=NULL)

	Multilign_object (const bool Multifind, const string &outputmultifind, const vector< string > &ctfiles, ProgressHandler *progress=NULL, const bool isrna=true)

	~Multilign_object ()

int	CountBP (const int i=0, const int j=0, const double percent=0.8) const
	count the number of basepairs with the lowest free energies below the percent of the miminal free energy. Dsv file is used for the counting. By default, the first dsv file in the progressive dynalign calculations is used, i.e. i = 0 and j = 0. More...

int	ProgressiveMultilign (const short int numProcessors=1, const bool Dsv=1, const bool Ali=1, const short int maxtrace=750, const short int bpwin=2, const short int awin=1, const short int percent=20, const short int imaxseparation=-99, const float gap=0.4, const bool singleinsert=true, const short int singlefold_subopt_percent=30, const bool local=false)

int	MultiTempMultilign ()

int	WriteAlignment (const string allali="all.ali") const
	calculate and output multiple alignment More...

int	GetErrorCode () const
	Return an error code, where a return of zero is no error. More...

string	GetErrorMessage (const int error) const

const string	GetErrorDetails ()

void	ResetError ()
	Reset the underlying RNA objects internal error code, after an error is handled. More...

int	SetMaxPairs (const int maxpairs=-1)

int	GetMaxPairs () const
	get the value of MaxPairs More...

int	AverageLength () const
	get the average length of the input sequences More...

int	SetIterations (const int it=2)
	set the value of iterations More...

int	GetIterations () const
	get the value of iterations More...

int	SetMaxDsv (const float maxdsvchange=1)
	set the value of MaxDsv/maxdsvchange More...

float	GetMaxDsv () const
	get the value of MaxDsv/maxdsvchange More...

int	GetSequenceNumber () const
	get the sequence number More...

int	SetIndexSeq (size_t indexSeq=1)
	set the Index Sequence for Multilign calculation. More...

int	SetIndexSeq (const string seqname)
	an overloaded function accepting a string as its parameter. More...

string	GetIndexSeq () const
	return the filename of the index seq. More...

void	Randomize ()
	randomize the order of inputList. More...

int	AddOneInput (const string seq, const string ct, const string constraint="", const string shape="")
	add one entry into inputList. More...

int	RemoveOneInput (const string seq)
	remove one entry from inputList. More...

void	SetSHAPESlope (const double slope=1.8)
	set the slope parameter for SHAPE More...

double	GetSHAPESlope () const
	get the SHAPESlope More...

void	SetSHAPEIntercept (const double intercept=-0.6)
	set the intercept parameter for SHAPE. More...

double	GetSHAPEIntercept () const
	get the SHAPEIntercept. More...

void	SetTemperature (const double temp=310.15)
	set the temperature to fold the sequences. More...

double	GetTemperature () const
	get the temperature to fold the sequences More...

void	SetNucType (const bool isrna=true)
	set the flag isRNA to be true or false. By default it is true. When it is true, RNA nearest neighbor parameters are used. More...

bool	GetNucType () const
	get the type fo nucleic acid More...

int	CleanupIntermediateFiles () const
	delete intermediate pairwise dsv and aout files More...

void	SetProgress (ProgressHandler *Progress=NULL)
	Provide a TProgressDialog for following calculation progress. More...

void	StopProgress ()
	Provide a means to stop using a TProgressDialog by assigning NULL to progress pointer. More...

ProgressHandler *	GetProgress () const
	get the progress More...

void	GetInputFilenames ()
	For diagnostic purpose only. Output the input sequence, ct, constraints, and SHAPE filenames to stdout. More...

void	GetPairs ()
	For diagnostic purpose only. Output the paired sequence filenames to stdout. More...

vector< float >	get_energies ()

vector< float >	get_dGIndex ()

vector< vector< string > >	get_pair_alignments ()

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

Additional Inherited Members
Protected Attributes inherited from Multilign_object
int	ErrorCode

vector< string >	input_alignment

vector< string >	input_sequences

vector< string >	ct_files

string	output_multifind

vector< float >	energies

vector< float >	dGIndex

vector< vector< string > >	pair_alignments

Detailed Description

Multifind_object Class.

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

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,
		ProgressHandler *	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.

Member Function Documentation

double Multifind_object::average_entropy ( )

private

double Multifind_object::average_multifind ( vector< double > & series )

private

double Multifind_object::average_multifind ( vector< float > & series )

private

double Multifind_object::average_multifind ( vector< int > & 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< double > & series )

private

double Multifind_object::sum_multifind ( vector< float > & series )

private

double Multifind_object::sum_multifind ( vector< int > & series )

private

double Multifind_object::variation_multifind ( vector< double > & series )

private

double Multifind_object::variation_multifind ( vector< float > & series )

private

double Multifind_object::variation_multifind ( vector< int > & series )

private

Member Data Documentation

int Multifind_object::num_processors

private

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

RNA_class/Multifind_object.h
RNA_class/Multifind_object.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation