Uses of Interface
jebl.evolution.sequences.SequenceType
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Packages that use SequenceType Package Description jebl.evolution.alignments jebl.evolution.io jebl.evolution.sequences jebl.evolution.substmodel -
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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()
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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)
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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()
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 nameCanonicalSequence(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
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