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

Constructors
Constructor Description

AlignmentBuilder(int initialCapacity)
The constructor

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`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