Interface SequenceType


public interface SequenceType
Interface for sequences data types.
Version:
$Id: SequenceType.java 849 2007-12-06 00:10:14Z twobeers $
Author:
Andrew Rambaut, Alexei Drummond
  • Field Details

  • Method Details

    • getStateCount

      int getStateCount()
      Get number of states including ambiguous states
      Returns:
      number of states
    • getStates

      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

      List<? extends State> getCanonicalStates()
      Get a list of canonical states ordered by their indices.
      Returns:
      a list of states
    • getState

      State getState(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

      String getName()
      name of data type
      Returns:
      string describing the data type
    • getNexusDataType

      String getNexusDataType()
      Returns:
      datatype inside a nexus characters block, if any.
    • toStateArray

      State[] toStateArray(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