Uses of Interface jebl.evolution.sequences.SequenceType (JEBL2 lib API)

Packages that use SequenceType
Package Description

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
Modifier and Type	Method	Description
`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
Modifier and Type	Method	Description
`void`	ImportHelper.`readSequence(java.lang.StringBuilder sequence, SequenceType sequenceType, java.lang.String delimiters, int maxSites, java.lang.String gapCharacters, java.lang.String missingCharacters, java.lang.String matchCharacters, java.lang.String matchSequence)`
`void`	ImportHelper.`readSequence(java.lang.StringBuilder sequence, SequenceType sequenceType, java.lang.String delimiters, int maxSites, java.lang.String gapCharacters, java.lang.String missingCharacters, java.lang.String matchCharacters, java.lang.String matchSequence, boolean stopAtDoubleNewLine)`
`void`	ImportHelper.`readSequence(java.lang.StringBuilder sequence, SequenceType sequenceType, java.lang.String delimiters, int maxSites, java.lang.String gapCharacters, java.lang.String missingCharacters, java.lang.String matchCharacters, java.lang.String matchSequence, ProgressListener progress)`
`void`	ImportHelper.`readSequence(java.lang.StringBuilder sequence, SequenceType sequenceType, java.lang.String delimiters, int maxSites, java.lang.String gapCharacters, java.lang.String missingCharacters, java.lang.String matchCharacters, java.lang.String matchSequence, ProgressListener progress, boolean stopAtDoubleNewLine)`	Reads sequence, skipping over any comments and filtering using sequenceType.
`void`	ImportHelper.`readSequenceLine(java.lang.StringBuffer sequence, SequenceType sequenceType, java.lang.String delimiters, java.lang.String gapCharacters, java.lang.String missingCharacters, java.lang.String matchCharacters, java.lang.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
Constructor	Description
`FastaImporter(java.io.File file, SequenceType sequenceType)`	Use this constructor if you are reading from a file.
`FastaImporter(java.io.Reader reader, SequenceType sequenceType)`	This constuctor takes a reader.
`PhylipSequentialImporter(java.io.Reader reader, SequenceType sequenceType, int maxNameLength)`	Constructor

Uses of SequenceType in jebl.evolution.sequences

Fields in jebl.evolution.sequences declared as SequenceType
Modifier and Type	Field	Description
`static SequenceType`	SequenceType.`AMINO_ACID`
`static SequenceType`	SequenceType.`CODON`
`static SequenceType`	SequenceType.`NUCLEOTIDE`

Methods in jebl.evolution.sequences that return SequenceType
Modifier and Type	Method	Description
`SequenceType`	BasicSequence.`getSequenceType()`
`SequenceType`	CanonicalSequence.`getSequenceType()`
`SequenceType`	CodonSequence.`getSequenceType()`
`SequenceType`	FilteredSequence.`getSequenceType()`
`SequenceType`	Sequence.`getSequenceType()`
`SequenceType`	TranslatedSequence.`getSequenceType()`
`SequenceType`	AminoAcidState.`getType()`
`SequenceType`	CodonState.`getType()`
`SequenceType`	NucleotideState.`getType()`
`abstract SequenceType`	State.`getType()`
`static SequenceType`	Utils.`guessSequenceType(java.lang.CharSequence seq)`	Guess type of sequence from contents.

Methods in jebl.evolution.sequences with parameters of type SequenceType
Modifier and Type	Method	Description
`static State[]`	Utils.`cleanSequence(java.lang.CharSequence seq, SequenceType type)`	Produce a clean sequence filtered of spaces and digits.
`static java.lang.String`	SequenceType.Utils.`getAlphabet(SequenceType sequenceType)`

Constructors in jebl.evolution.sequences with parameters of type SequenceType
Constructor	Description
`BasicSequence(SequenceType sequenceType, Taxon taxon, java.lang.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
`CanonicalSequence(SequenceType sequenceType, Taxon taxon, java.lang.CharSequence sequenceString)`	Creates a sequence with a name corresponding to the taxon name.
`CanonicalSequence(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
Modifier and Type	Method	Description
`SequenceType`	AbstractRateMatrix.`getSequenceType()`
`SequenceType`	RateMatrix.`getSequenceType()`	Get the data type of this rate matrix