Uses of Interface
jebl.evolution.sequences.SequenceType

Packages that use SequenceType

jebl.evolution.alignments
jebl.evolution.io
jebl.evolution.sequences
jebl.evolution.substmodel

Uses of SequenceType in jebl.evolution.alignments

Methods in jebl.evolution.alignments that return SequenceType

SequenceType	BasicAlignment.getSequenceType()
SequenceType	ConsensusSequence.getSequenceType()
SequenceType	Pattern.getSequenceType()
SequenceType	Patterns.getSequenceType()
SequenceType	ResampledAlignment.getSequenceType()

Uses of SequenceType in jebl.evolution.io

Methods in jebl.evolution.io with parameters of type SequenceType

void	ImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence)
void	ImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress) Reads sequence, skipping over any comments and filtering using sequenceType.
void	ImportHelper.readSequenceLine(StringBuffer sequence, SequenceType sequenceType, String delimiters, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence) Reads a line of sequence, skipping over any comments and filtering using sequenceType.

Constructors in jebl.evolution.io with parameters of type SequenceType

FastaImporter(File file, SequenceType sequenceType)
Use this constructor if you are reading from a file.

FastaImporter(Reader reader, SequenceType sequenceType)
Deprecated.

PhylipSequentialImporter(Reader reader, SequenceType sequenceType, int maxNameLength)
Constructor

Uses of SequenceType in jebl.evolution.sequences

Fields in jebl.evolution.sequences declared as SequenceType

static SequenceType	SequenceType.AMINO_ACID
static SequenceType	SequenceType.CODON
static SequenceType	SequenceType.NUCLEOTIDE

Methods in jebl.evolution.sequences that return SequenceType

SequenceType	BasicSequence.getSequenceType()
SequenceType	FilteredSequence.getSequenceType()
SequenceType	Sequence.getSequenceType()
SequenceType	TranslatedSequence.getSequenceType()
static SequenceType	Utils.guessSequenceType(CharSequence seq) Guess type of sequence from contents

Methods in jebl.evolution.sequences with parameters of type SequenceType

static String

SequenceType.Utils.getAlphabet(SequenceType sequenceType)

Constructors in jebl.evolution.sequences with parameters of type SequenceType

BasicSequence(SequenceType sequenceType, Taxon taxon, CharSequence sequenceString)
Creates a sequence with a name corresponding to the taxon name.

BasicSequence(SequenceType sequenceType, Taxon taxon, State[] states)
Creates a sequence with a name corresponding to the taxon name

Uses of SequenceType in jebl.evolution.substmodel

Methods in jebl.evolution.substmodel that return SequenceType

SequenceType	AbstractRateMatrix.getSequenceType()
SequenceType	RateMatrix.getSequenceType() Get the data type of this rate matrix

Methods in jebl.evolution.substmodel with parameters of type SequenceType

protected void

AbstractRateMatrix.setSequenceType(SequenceType dt)