, including all inherited members.
| AddOneInput(const string seq, const string ct, const string constraint="", const string shape="") | Multilign_object | |
| 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] |
| 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] |
| 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 | |
| GetNucType() 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] |
| Multifind_object(const string &outputmultifind, const vector< string > &ctfiles, const vector< string > &inputalignment, const vector< string > &inputsequences, const int &processors, TProgressDialog *progress=NULL) | Multifind_object | |
| Multifind_Predict() | Multifind_object | |
| Multilign_object() | Multilign_object | |
| Multilign_object(const vector< vector< string > > &inputlist, const bool isrna=true, TProgressDialog *progress=NULL) | Multilign_object | |
| Multilign_object(const bool Multifind, const string &outputmultifind, const vector< string > &ctfiles, TProgressDialog *progress=NULL, const bool isrna=true) | Multilign_object | |
| MultiTempMultilign() | Multilign_object | |
| normalized_ensemble_defect(RNA *rna) | Multifind_object | [private] |
| num_processors | Multifind_object | [private] |
| output_multifind | Multilign_object | [protected] |
| pair_alignments | Multilign_object | [mutable, protected] |
| predict_ncRNA_probabilities(double sci, double entropy, double single_z, double ensemble_defect_z) | Multifind_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 | |
| 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 | |
| SetNucType(const bool isrna=true) | Multilign_object | |
| SetProgress(TProgressDialog *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_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] |
| variation_multifind(vector< double > &series) | Multifind_object | [private] |
| variation_multifind(vector< float > &series) | Multifind_object | [private] |
| variation_multifind(vector< int > &series) | Multifind_object | [private] |
| WriteAlignment(const string allali="all.ali") const | Multilign_object | |
| ~Multilign_object() | Multilign_object | |
