RNAstructure Classes  Version 6.1
Multifind_object Class Reference

Multifind_object Class. More...

#include <Multifind_object.h>

Inheritance diagram for Multifind_object:
Multilign_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...
 
int CleanupIntermediateFiles () const
 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...
 
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
outputmultifindis the name of the Multifind output file to which the output is written to.
ctfilesis a vector of strings storing the names of the ct files to which the output structures are written to.
inputalignmentis a vector of strings storing the input sequences in the alignment (with gaps).
inputsequencesis a vector of strings storing the input sequences in the alignment (without gaps).
processorsis a interger indicating the number of processors required by Multifind in smp calculations.(only applicable in smp version)
progressis 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: