Constructor Detail

• AlignmentBuilder

  public AlignmentBuilder(int initialCapacity)

  The constructor

  Parameters:

  initialCapacity - The initial amount of space to allocate for sequence storage (dynamically adjusts if number of sequences exceeds capacity)

Method Detail

• clearAll

  public void clearAll()

  Remove all currently stored sequences.

• generateAlignment

  public Alignment generateAlignment(DataType dt)

  Build an alignment based on sequences stored.

  Parameters:

  dt - The datatype of the sequence data

  Returns:

  The generated alignment

• addSequence

  public void addSequence(int[] states,
                          java.lang.String name)

  Add sequence data to store

  Parameters:

  states - The states of the sequence (builder assumes all state arrays are equal length)

  name - The name of the sequence