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
dynobj	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
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