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() -
Uses of SequenceType in jebl.evolution.io
Methods in jebl.evolution.io with parameters of type SequenceTypeModifier and TypeMethodDescriptionvoidImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence) voidImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, boolean stopAtDoubleNewLine) voidImportHelper.readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress) voidImportHelper.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.voidImportHelper.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 SequenceTypeSequenceType.AMINO_ACIDstatic final SequenceTypeSequenceType.CODONstatic final SequenceTypeSequenceType.NUCLEOTIDEMethods 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 SequenceTypeState.getType()static SequenceTypeUtils.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 StringSequenceType.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