| RNAstructure Classes Version 6.2

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 |
aliFiles | Multilign_object | private
average_entropy() | Multifind_object | private
average_multifind(vector< double > &series) | Multifind_object | private
average_multifind(vector< float > &series) | Multifind_object | private
average_multifind(vector< int > &series) | Multifind_object | private
AverageLength() const | Multilign_object |
CleanupIntermediateFiles() const | Multilign_object |
common_energies() | Multifind_object | private
CountBP(const int i=0, const int j=0, const double percent=0.8) const | Multilign_object |
ct_files | Multilign_object | protected
dGIndex | Multilign_object | protected
dsvFiles | Multilign_object | private
dynobj | Multilign_object | private
energies | Multilign_object | protected
entropy(vector< char > column) | Multifind_object | private
ErrorCode | Multilign_object | protected
get_dGIndex() | Multilign_object | inline
get_energies() | Multilign_object | inline
get_gap(string sequence) | Multifind_object | private
get_pair_alignments() | Multilign_object | inline
GetErrorCode() const | Multilign_object | inline
GetErrorDetails() | Multilign_object | inline
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_alignment | Multilign_object | protected
input_sequences | Multilign_object | protected
inputList | Multilign_object | private
iterations | Multilign_object | private
maxDsv | Multilign_object | private
maxPairs | Multilign_object | private
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 |
NameAliFiles() | Multilign_object | private
NameDsvFiles() | Multilign_object | private
NameMultifindAliFiles() | Multilign_object | private
NameMultifindDsvFiles() | Multilign_object | private
normalized_ensemble_defect(RNA *rna) | Multifind_object | private
num_processors | Multifind_object | private
output_multifind | Multilign_object | protected
pair_alignments | Multilign_object | mutable protected
PairMultifindSeq1() | Multilign_object | private
PairSeq1() | Multilign_object | private
predict_ncRNA_probabilities(double sci, double entropy, double single_z, double ensemble_defect_z) | Multifind_object | private
PrepInput() | Multilign_object | private
PrepMultifindInput() | Multilign_object | private
progress | Multilign_object | private
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 |
seqPair | Multilign_object | private
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 |
SHAPEIntercept | Multilign_object | private
SHAPESlope | Multilign_object | private
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_object | private
StopProgress() | Multilign_object |
sum_multifind(vector< double > &series) | Multifind_object | private
sum_multifind(vector< float > &series) | Multifind_object | private
sum_multifind(vector< int > &series) | Multifind_object | private
thermo | Multilign_object | private
ToHead(vvs_it first, vvs_it middle) | Multilign_object | private
variation_multifind(vector< double > &series) | Multifind_object | private
variation_multifind(vector< float > &series) | Multifind_object | private
variation_multifind(vector< int > &series) | Multifind_object | private
vs_index typedef | Multilign_object | private
vvs_cit typedef | Multilign_object | private
vvs_it typedef | Multilign_object | private
WriteAlignment(const string allali="all.ali") const | Multilign_object |
~Multilign_object() | Multilign_object |