pal.alignment
Class AlignmentBuilder

java.lang.Object
  pal.alignment.AlignmentBuilder

public class AlignmentBuilder
extends java.lang.Object

A class for the gradual construction of an alignment. To supersede simular classes hidden away in PAL History

• 25/11/2003 - Created

Version:

$Id: AlignmentBuilder.java,v 1.1 2003/11/25 01:06:21 matt Exp $

Author:

Matthew Goode

Constructor Summary

AlignmentBuilder(int initialCapacity)
The constructor

Method Summary

void	addSequence(int[] states, java.lang.String name) Add sequence data to store
void	clearAll() Remove all currently stored sequences.
Alignment	generateAlignment(DataType dt) Build an alignment based on sequences stored.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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