# 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 |
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]`
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]`
inputList | Multilign_object | `[private]`
instance | Multilign_object | `[private]`
isRNA | 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, 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 |
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 | `[mutable, protected]`
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 |
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 |
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 |
SHAPEIntercept | Multilign_object | `[private]`
SHAPESlope | Multilign_object | `[private]`
StopProgress() | Multilign_object |
temperature | 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 |