Field Detail

• NUCLEOTIDE

  static final SequenceType NUCLEOTIDE

• AMINO_ACID

  static final SequenceType AMINO_ACID

• CODON

  static final SequenceType CODON

Method Detail

• getStateCount

  int getStateCount()

  Get number of states including ambiguous states

  Returns:

  number of states

• getStates

  java.util.List<? extends State> getStates()

  Get a list of states ordered by their indices.

  Returns:

  a list of states

• getCanonicalStateCount

  int getCanonicalStateCount()

  Get number of canonical states

  Returns:

  number of states

• getCanonicalStates

  java.util.List<? extends State> getCanonicalStates()

  Get a list of canonical states ordered by their indices.

  Returns:

  a list of states

• getState

  State getState​(java.lang.String code)

  Get state corresponding to a string code

  Parameters:

  code - a string code

  Returns:

  the state with the given code, or null if there is no such state

• getState

  State getState​(char code)

  Get state whose code is the one-character string consisting only of code.

  Parameters:

  code -

  Returns:

  the state with the given code, or null if there is no such state

• getCodeLength

  int getCodeLength()

  Returns:

  the length, in characters, of a state, when encoded as a string. i.e. 1 for Nucleotides and AminoAcids and 3 for Codons.

• getState

  State getState​(int index)

  Get state corresponding to a state index

  Parameters:

  index - a state index

  Returns:

  the state

• getUnknownState

  State getUnknownState()

  Get state corresponding to an unknown

  Returns:

  the state

• getGapState

  State getGapState()

  Get state corresponding to a gap

  Returns:

  state

• isUnknown

  boolean isUnknown​(State state)

  Returns:

  true if this state is an unknown state

• isGap

  boolean isGap​(State state)

  Returns:

  true if this state is a gap

• getName

  java.lang.String getName()

  name of data type

  Returns:

  string describing the data type

• getNexusDataType

  java.lang.String getNexusDataType()

  Returns:

  datatype inside a nexus characters block, if any.

• toStateArray

  State[] toStateArray​(java.lang.String sequenceString)

  Converts a string of state codes into an array of State objects for this SequenceType

  Parameters:

  sequenceString -

  Returns:

  the State array

• toStateArray

  State[] toStateArray​(byte[] indexArray)

  Converts an array of state indices into an array of State objects for this SequenceType

  Parameters:

  indexArray -

  Returns:

  the State array