RNAstructure Classes  Version 6.1
Multifind_object Member List

This is the complete list of members for Multifind_object, including all inherited members.

AddOneInput(const string seq, const string ct, const string constraint="", const string shape="")Multilign_object
average_entropy()Multifind_objectprivate
average_multifind(vector< double > &series)Multifind_objectprivate
average_multifind(vector< float > &series)Multifind_objectprivate
average_multifind(vector< int > &series)Multifind_objectprivate
AverageLength() const Multilign_object
CleanupIntermediateFiles() const Multilign_object
common_energies()Multifind_objectprivate
CountBP(const int i=0, const int j=0, const double percent=0.8) const Multilign_object
ct_filesMultilign_objectprotected
dGIndexMultilign_objectprotected
energiesMultilign_objectprotected
entropy(vector< char > column)Multifind_objectprivate
ErrorCodeMultilign_objectprotected
get_dGIndex()Multilign_objectinline
get_energies()Multilign_objectinline
get_gap(string sequence)Multifind_objectprivate
get_pair_alignments()Multilign_objectinline
GetErrorCode() const Multilign_objectinline
GetErrorDetails()Multilign_objectinline
GetErrorMessage(const int error) const Multilign_object
GetIndexSeq() const Multilign_object
GetInputFilenames()Multilign_object
GetIterations() const Multilign_object
GetMaxDsv() const Multilign_object
GetMaxPairs() const Multilign_object
GetPairs()Multilign_object
GetProgress() const Multilign_object
GetSequenceNumber() const Multilign_object
GetSHAPEIntercept() const Multilign_object
GetSHAPESlope() const Multilign_object
GetTemperature() const Multilign_object
input_alignmentMultilign_objectprotected
input_sequencesMultilign_objectprotected
Multifind_object(const string &outputmultifind, const vector< string > &ctfiles, const vector< string > &inputalignment, const vector< string > &inputsequences, const int &processors, ProgressHandler *progress=NULL)Multifind_object
Multifind_Predict()Multifind_object
Multilign_object()Multilign_object
Multilign_object(const vector< vector< string > > &inputlist, const bool isrna=true, ProgressHandler *progress=NULL)Multilign_object
Multilign_object(const bool Multifind, const string &outputmultifind, const vector< string > &ctfiles, ProgressHandler *progress=NULL, const bool isrna=true)Multilign_object
MultiTempMultilign()Multilign_object
normalized_ensemble_defect(RNA *rna)Multifind_objectprivate
num_processorsMultifind_objectprivate
output_multifindMultilign_objectprotected
pair_alignmentsMultilign_objectmutableprotected
predict_ncRNA_probabilities(double sci, double entropy, double single_z, double ensemble_defect_z)Multifind_objectprivate
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)Multilign_object
Randomize()Multilign_object
RemoveOneInput(const string seq)Multilign_object
ResetError()Multilign_object
SetIndexSeq(size_t indexSeq=1)Multilign_object
SetIndexSeq(const string seqname)Multilign_object
SetIterations(const int it=2)Multilign_object
SetMaxDsv(const float maxdsvchange=1)Multilign_object
SetMaxPairs(const int maxpairs=-1)Multilign_object
SetProgress(ProgressHandler *Progress=NULL)Multilign_object
SetSHAPEIntercept(const double intercept=-0.6)Multilign_object
SetSHAPESlope(const double slope=1.8)Multilign_object
SetTemperature(const double temp=310.15)Multilign_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)Multifind_objectprivate
StopProgress()Multilign_object
sum_multifind(vector< double > &series)Multifind_objectprivate
sum_multifind(vector< float > &series)Multifind_objectprivate
sum_multifind(vector< int > &series)Multifind_objectprivate
variation_multifind(vector< double > &series)Multifind_objectprivate
variation_multifind(vector< float > &series)Multifind_objectprivate
variation_multifind(vector< int > &series)Multifind_objectprivate
WriteAlignment(const string allali="all.ali") const Multilign_object
~Multilign_object()Multilign_object