RNAstructure Classes  Version 6.1
Dynalign_object Member List

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

alignDynalign_objectprivate
AllocateForceAlign()Dynalign_objectprivate
arrayDynalign_objectprivate
CommonConstructor()Dynalign_objectprivate
compoundmessageTwoRNA
ct_templatedDynalign_objectprivate
dataDynalign_objectprivate
dsv_templatedDynalign_objectprivate
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 RNAInputType type1, const char filename2[], const RNAInputType type2, const bool IsRNA=true)Dynalign_object
Dynalign_object(const char filename1[], const RNAInputType type1, const char filename2[], const RNAInputType type2, const Thermodynamics *thermo1)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
ErrorCodeTwoTwoRNAprotected
forcealignDynalign_objectprivate
ForceAlignment(const int i, const int k)Dynalign_object
gapDynalign_objectprivate
GetBestPairEnergy(const int sequence, const int i, const int j)Dynalign_object
GetErrorCode() const TwoRNA
GetErrorDetails() const 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() const TwoRNA
highendDynalign_objectprivate
lowendDynalign_objectprivate
lowestDynalign_objectprivate
MAXDSVDynalign_objectprivate
MaxtraceDynalign_objectprivate
modificationflagDynalign_objectprivate
ReadAlignmentConstraints(const char filename[])Dynalign_object
ResetError()TwoRNA
savefilereadDynalign_objectprivate
SetErrorDetails(const string &details)TwoRNA
SetProgress(ProgressHandler &Progress)Dynalign_object
SetTemperature(double temperature)TwoRNA
StopProgress()Dynalign_object
storetemplatefilename(const char *name)Dynalign_objectprivate
templatefilenameDynalign_objectprivate
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 RNAInputType type1, const char filename2[], const RNAInputType type2, bool IsRNA=true)TwoRNA
TwoRNA(const char filename1[], const RNAInputType type1, const char filename2[], const RNAInputType type2, const Thermodynamics *copyThermo)TwoRNA
TwoRNA()TwoRNA
vDynalign_objectprivate
vmodDynalign_objectprivate
wDynalign_objectprivate
w3Dynalign_objectprivate
w5Dynalign_objectprivate
WriteAlignment(const char filename[])Dynalign_object
~Dynalign_object()Dynalign_object
~TwoRNA()TwoRNA