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

Uses of SequenceType in jebl.evolution.io
 

Methods in jebl.evolution.io with parameters of type SequenceType
 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
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
static SequenceType SequenceType.AMINO_ACID
           
static SequenceType SequenceType.CODON
           
static SequenceType SequenceType.NUCLEOTIDE
           
 

Methods in jebl.evolution.sequences that return SequenceType
 SequenceType CanonicalSequence.getSequenceType()
           
 SequenceType TranslatedSequence.getSequenceType()
           
 SequenceType BasicSequence.getSequenceType()
           
 SequenceType FilteredSequence.getSequenceType()
           
 SequenceType Sequence.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
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
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
 SequenceType AbstractRateMatrix.getSequenceType()
           
 SequenceType RateMatrix.getSequenceType()
          Get the data type of this rate matrix
 



http://code.google.com/p/jebl2/