Interface Sequence

All Superinterfaces:
Attributable, Comparable
All Known Implementing Classes:
BasicSequence, CanonicalSequence, CodonSequence, ConsensusSequence, FilteredSequence, GaplessSequence, TranslatedSequence
public interface Sequence extends Attributable, Comparable
A biomolecular sequence.
Version:
$Id: Sequence.java 365 2006-06-28 07:34:56Z pepster $
Author:
Andrew Rambaut, Alexei Drummond

  • Method Details

    • getTaxon

      Taxon getTaxon()
      Returns:
      the taxon that this sequence represents (primarily used to match sequences with tree nodes)

    • getSequenceType

      SequenceType getSequenceType()
      Returns:
      the type of symbols that this sequence is made up of.

    • getString

      String getString()
      Returns:
      a string representing the sequence of symbols.

    • getStates

      State[] getStates()
      Returns:
      an array of state objects.

    • getStateIndices

      byte[] getStateIndices()
      Returns:
      an array of state indices.

    • getState

      State getState(int site)
      Returns:
      the state at site.

    • getLength

      int getLength()
      Get the length of the sequence
      Returns:
      the length

    • appendSequences

      static Sequence appendSequences(Sequence sequence1, Sequence sequence2)
      Append two sequences together to create a new sequence object. New sequence has the taxon of the first sequence.
      Parameters:
      sequence1 -
      sequence2 -
      Returns:

    • getSubSequence

      static Sequence getSubSequence(Sequence sequence, int from, int to)
      Returns a sub-sequence for states from, to (inclusive).
      Parameters:
      sequence -
      from -
      to -
      Returns:

    • trimSequence

      static Sequence trimSequence(Sequence sequence, List<State> trimStates)

    • stripGaps

      static Sequence stripGaps(Sequence sequence)
      Strips a sequence of gaps
      Parameters:
      sequence - the sequence
      Returns:
      the stripped sequence

    • stripStates

      static Sequence stripStates(Sequence sequence, List<State> stripStates)
      Strips a sequence of any states given
      Parameters:
      sequence - the sequence
      stripStates - the states to strip
      Returns:
      an array of states

    • replaceStates

      static Sequence replaceStates(Sequence sequence, List<State> searchStates, State replaceState)
      Searchers and replaces a sequence of any states given
      Parameters:
      sequence - the sequence
      searchStates - the states to search for
      Returns:
      an array of states

    • getStateCount

      static int getStateCount(Sequence sequence, State state)
      Counts the number of occurances of a state
      Parameters:
      sequence - the sequence string to count
      state - the state
      Returns:
      the number of occurances