Uses of Class
statalign.io.RawSequences

Packages that use RawSequences

statalign.base
statalign.io
statalign.io.input.plugins
statalign.model.subst
statalign.model.subst.plugins

Uses of RawSequences in statalign.base

Fields in statalign.base declared as RawSequences

RawSequences

InputData.seqs The input sequences, optionally aligned

Methods in statalign.base that return RawSequences

RawSequences

Tree.getSeqs()

Methods in statalign.base with parameters of type RawSequences

void	Tree.setSeqs(RawSequences rs)

Uses of RawSequences in statalign.io

Fields in statalign.io declared as RawSequences

RawSequences

ProteinSkeletons.seqs

Methods in statalign.io that return RawSequences

RawSequences	RawSequences.getSeqs()
RawSequences	ProteinSkeletons.getSeqs()
RawSequences	DataType.getSeqs()

Methods in statalign.io with parameters of type RawSequences

void	RawSequences.add(RawSequences more)
void	RawSequences.setSeqs(RawSequences rs)
void	ProteinSkeletons.setSeqs(RawSequences rs)
void	DataType.setSeqs(RawSequences rs)

Uses of RawSequences in statalign.io.input.plugins

Methods in statalign.io.input.plugins that return RawSequences

RawSequences

FastaReader.read(java.io.Reader reader) Reads the contents (aligned/non-aligned sequences) of the given data source in Fasta format.

Uses of RawSequences in statalign.model.subst

Methods in statalign.model.subst with parameters of type RawSequences

abstract double

SubstitutionModel.acceptable(RawSequences r) If a model cannot accept the currently loaded sequences (for example, because the sequences contains a character that is not part of the model) then it returns a negative number.

Uses of RawSequences in statalign.model.subst.plugins

Methods in statalign.model.subst.plugins with parameters of type RawSequences

double	NucleotideModel.acceptable(RawSequences r) This function decides if this model can analyze input sequences.
double	AminoAcidModel.acceptable(RawSequences r) This function decides if the model can accept the input sequences.