, including all inherited members.
| align | Dynalign_object | [private] |
| AllocateForceAlign() | Dynalign_object | [private] |
| array | Dynalign_object | [private] |
| CommonConstructor() | Dynalign_object | [private] |
| compoundmessage | TwoRNA | |
| ct_templated | Dynalign_object | [private] |
| data | Dynalign_object | [private] |
| dsv_templated | Dynalign_object | [private] |
| Dynalign(const short int maxtrace=20, const short int bpwin=5, 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 char savefile[]=NULL, const bool optimalonly=false, const short int singlefold_subopt_percent=30, const bool local=false, const short int numProcessors=1, const int maxpairs=-1) | Dynalign_object | |
| Dynalign_object() | Dynalign_object | |
| Dynalign_object(const char sequence1[], const char sequence2[], const bool IsRNA=true) | Dynalign_object | |
| Dynalign_object(const char filename1[], const int type1, const char filename2[], const int type2, const bool IsRNA=true) | Dynalign_object | |
| Dynalign_object(const char filename[]) | Dynalign_object | |
| Dynalign_object(const char *filename, const short maxtrace, const short bpwin, const short awin, const short percent) | Dynalign_object | |
| ErrorCodeTwo | TwoRNA | [protected] |
| forcealign | Dynalign_object | [private] |
| ForceAlignment(const int i, const int k) | Dynalign_object | |
| gap | Dynalign_object | [private] |
| GetBestPairEnergy(const int sequence, const int i, const int j) | Dynalign_object | |
| GetErrorCode() | TwoRNA | |
| GetErrorMessage(const int error) | Dynalign_object | |
| GetErrorMessageString(const int error) | TwoRNA | |
| GetForcedAlignment(const int i, const int seq) | Dynalign_object | |
| GetLowestEnergy() | Dynalign_object | |
| GetRNA1() | TwoRNA | |
| GetRNA2() | TwoRNA | |
| GetTemperature() | TwoRNA | |
| highend | Dynalign_object | [private] |
| lowend | Dynalign_object | [private] |
| lowest | Dynalign_object | [private] |
| MAXDSV | Dynalign_object | [private] |
| Maxtrace | Dynalign_object | [private] |
| modificationflag | Dynalign_object | [private] |
| ReadAlignmentConstraints(const char filename[]) | Dynalign_object | |
| ResetError() | TwoRNA | |
| savefileread | Dynalign_object | [private] |
| SetProgress(TProgressDialog &Progress) | Dynalign_object | |
| SetTemperature(double temperature) | TwoRNA | |
| StopProgress() | Dynalign_object | |
| storetemplatefilename(const char *name) | Dynalign_object | [private] |
| templatefilename | Dynalign_object | [private] |
| Templatefromct(const char ctfilename[]) | Dynalign_object | |
| Templatefromdsv(const char dsvfilename[], const float maxdsvchange) | Dynalign_object | |
| TwoRNA(const char sequence1[], const char sequence2[], bool IsRNA=true) | TwoRNA | |
| TwoRNA(const char filename1[], const int type1, const char filename2[], const int type2, bool IsRNA=true) | TwoRNA | |
| TwoRNA() | TwoRNA | |
| v | Dynalign_object | [private] |
| vmod | Dynalign_object | [private] |
| w | Dynalign_object | [private] |
| w3 | Dynalign_object | [private] |
| w5 | Dynalign_object | [private] |
| WriteAlignment(const char filename[]) | Dynalign_object | |
| ~Dynalign_object() | Dynalign_object | |
| ~TwoRNA() | TwoRNA | |
