Package pal.alignment
Class AlignmentBuilder
- java.lang.Object
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- pal.alignment.AlignmentBuilder
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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
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Constructor Summary
Constructors Constructor Description AlignmentBuilder(int initialCapacity)
The constructor
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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 storevoid
clearAll()
Remove all currently stored sequences.Alignment
generateAlignment(DataType dt)
Build an alignment based on sequences stored.
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Method Detail
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clearAll
public void clearAll()
Remove all currently stored sequences.
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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
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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
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