Package pal.alignment
Class AlignmentBuilder
java.lang.Object
pal.alignment.AlignmentBuilder
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
addSequence
(int[] states, String name) Add sequence data to storevoid
clearAll()
Remove all currently stored sequences.Build an alignment based on sequences stored.
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Constructor Details
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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)
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Method Details
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clearAll
public void clearAll()Remove all currently stored sequences. -
generateAlignment
Build an alignment based on sequences stored.- Parameters:
dt
- The datatype of the sequence data- Returns:
- The generated alignment
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addSequence
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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