RNAstructure Classes  Version 6.1
Multilign_object Member List

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

AddOneInput(const string seq, const string ct, const string constraint="", const string shape="")Multilign_object
aliFilesMultilign_objectprivate
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_filesMultilign_objectprotected
dGIndexMultilign_objectprotected
dsvFilesMultilign_objectprivate
dynobjMultilign_objectprivate
energiesMultilign_objectprotected
ErrorCodeMultilign_objectprotected
get_dGIndex()Multilign_objectinline
get_energies()Multilign_objectinline
get_pair_alignments()Multilign_objectinline
GetErrorCode() const Multilign_objectinline
GetErrorDetails()Multilign_objectinline
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_alignmentMultilign_objectprotected
input_sequencesMultilign_objectprotected
inputListMultilign_objectprivate
iterationsMultilign_objectprivate
maxDsvMultilign_objectprivate
maxPairsMultilign_objectprivate
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_objectprivate
NameDsvFiles()Multilign_objectprivate
NameMultifindAliFiles()Multilign_objectprivate
NameMultifindDsvFiles()Multilign_objectprivate
output_multifindMultilign_objectprotected
pair_alignmentsMultilign_objectmutableprotected
PairMultifindSeq1()Multilign_objectprivate
PairSeq1()Multilign_objectprivate
PrepInput()Multilign_objectprivate
PrepMultifindInput()Multilign_objectprivate
progressMultilign_objectprivate
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
seqPairMultilign_objectprivate
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
SHAPEInterceptMultilign_objectprivate
SHAPESlopeMultilign_objectprivate
StopProgress()Multilign_object
thermoMultilign_objectprivate
ToHead(vvs_it first, vvs_it middle)Multilign_objectprivate
vs_index typedefMultilign_objectprivate
vvs_cit typedefMultilign_objectprivate
vvs_it typedefMultilign_objectprivate
WriteAlignment(const string allali="all.ali") const Multilign_object
~Multilign_object()Multilign_object