Uses of Interface
jebl.evolution.sequences.SequenceType
Packages that use SequenceType
Package
Description
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Uses of SequenceType in jebl.evolution.alignments
Methods in jebl.evolution.alignments that return SequenceTypeModifier and TypeMethodDescriptionBasicAlignment.getSequenceType()
ConsensusSequence.getSequenceType()
Pattern.getSequenceType()
Patterns.getSequenceType()
ResampledAlignment.getSequenceType()
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Uses of SequenceType in jebl.evolution.io
Methods in jebl.evolution.io with parameters of type SequenceTypeModifier and TypeMethodDescriptionvoid
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, boolean stopAtDoubleNewLine) void
ImportHelper.readSequence
(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress) void
ImportHelper.readSequence
(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress, boolean stopAtDoubleNewLine) 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 SequenceTypeModifierConstructorDescriptionFastaImporter
(File file, SequenceType sequenceType) Use this constructor if you are reading from a file.FastaImporter
(Reader reader, SequenceType sequenceType) This constuctor takes a reader.PhylipSequentialImporter
(Reader reader, SequenceType sequenceType, int maxNameLength) Constructor -
Uses of SequenceType in jebl.evolution.sequences
Fields in jebl.evolution.sequences declared as SequenceTypeModifier and TypeFieldDescriptionstatic final SequenceType
SequenceType.AMINO_ACID
static final SequenceType
SequenceType.CODON
static final SequenceType
SequenceType.NUCLEOTIDE
Methods in jebl.evolution.sequences that return SequenceTypeModifier and TypeMethodDescriptionBasicSequence.getSequenceType()
CanonicalSequence.getSequenceType()
CodonSequence.getSequenceType()
FilteredSequence.getSequenceType()
Sequence.getSequenceType()
TranslatedSequence.getSequenceType()
AminoAcidState.getType()
CodonState.getType()
NucleotideState.getType()
abstract SequenceType
State.getType()
static SequenceType
Utils.guessSequenceType
(CharSequence seq) Guess type of sequence from contents.Methods in jebl.evolution.sequences with parameters of type SequenceTypeModifier and TypeMethodDescriptionstatic State[]
Utils.cleanSequence
(CharSequence seq, SequenceType type) Produce a clean sequence filtered of spaces and digits.static String
SequenceType.Utils.getAlphabet
(SequenceType sequenceType) Constructors in jebl.evolution.sequences with parameters of type SequenceTypeModifierConstructorDescriptionBasicSequence
(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 nameCanonicalSequence
(SequenceType sequenceType, Taxon taxon, 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 SequenceTypeModifier and TypeMethodDescriptionAbstractRateMatrix.getSequenceType()
RateMatrix.getSequenceType()
Get the data type of this rate matrix