| AddOneInput(const string seq, const string ct, const string constraint="", const string shape="") | Multilign_object | |
| aliFiles | Multilign_object | private |
| AverageLength() const | Multilign_object | |
| CleanupIntermediateFiles() const | Multilign_object | |
| 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 |
| energies | Multilign_object | protected |
| ErrorCode | Multilign_object | protected |
| get_dGIndex() | Multilign_object | inline |
| get_energies() | Multilign_object | inline |
| 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 |
| instance | Multilign_object | private |
| iterations | Multilign_object | private |
| maxDsv | Multilign_object | private |
| maxPairs | Multilign_object | private |
| 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 |
| output_multifind | Multilign_object | protected |
| pair_alignments | Multilign_object | mutableprotected |
| PairMultifindSeq1() | Multilign_object | private |
| PairSeq1() | Multilign_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 |
| StopProgress() | Multilign_object | |
| thermo | Multilign_object | private |
| ToHead(vvs_it first, vvs_it middle) | Multilign_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 | |
1.8.11 
