ResampledAlignment (JEBL2 lib API)

java.lang.Object
- jebl.evolution.alignments.ResampledAlignment

All Implemented Interfaces:

Alignment, Patterns, Sequences

Direct Known Subclasses:

BootstrappedAlignment, JackknifedAlignment
```
public class ResampledAlignment
extends java.lang.Object
implements Alignment
```
Date: 17/01/2006 Time: 08:08:44

Version:

$Id: ResampledAlignment.java 482 2006-10-25 06:30:57Z twobeers $ Provide a re-sampled alignment. This means an alignment constructed by choosing a set of sites from the source alignment and concataneting them. The set may be of any length and may contain duplications (sampling with replacment). Due to Java restrictions on constructors, class is implemented using delegation.

Author:

Joseph Heled

Constructor Summary

Constructors
Constructor Description

ResampledAlignment()

Constructors
Constructor	Description
`ResampledAlignment()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getPatternCount()`
`int`	`getPatternLength()`
`java.util.List<Pattern>`	`getPatterns()`	Get a list of all the patterns
`Sequence`	`getSequence(Taxon taxon)`
`java.util.List<Sequence>`	`getSequenceList()`
`java.util.Set<Sequence>`	`getSequences()`
`SequenceType`	`getSequenceType()`
`int`	`getSiteCount()`
`java.util.List<Taxon>`	`getTaxa()`
`void`	`init(Alignment srcAlignment, int[] siteIndices)`	Setup resampled alignment.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - ResampledAlignment
```
public ResampledAlignment()
```
- Method Detail
  - init
```
public void init(Alignment srcAlignment,
                 int[] siteIndices)
```
    Setup resampled alignment.
    
    Parameters:
    
    srcAlignment - sample sites from this alignment
    
    siteIndices - Use this set to construct the resampled alignment
  - getSequenceList
```
public java.util.List<Sequence> getSequenceList()
```
    Specified by:
    
    getSequenceList in interface Alignment
  - getPatternCount
```
public int getPatternCount()
```
    Specified by:
    
    getPatternCount in interface Patterns
  - getPatternLength
```
public int getPatternLength()
```
    Specified by:
    
    getPatternLength in interface Patterns
  - getPatterns
```
public java.util.List<Pattern> getPatterns()
```
    Description copied from interface: Patterns
    
    Get a list of all the patterns
    
    Specified by:
    
    getPatterns in interface Patterns
    
    Returns:
    
    the list
  - getTaxa
```
public java.util.List<Taxon> getTaxa()
```
    Specified by:
    
    getTaxa in interface Patterns
    
    Returns:
    
    the list of taxa that the state values correspond to.
  - getSequenceType
```
public SequenceType getSequenceType()
```
    Specified by:
    
    getSequenceType in interface Patterns
    
    Returns:
    
    the data type of the states in these site patterns.
  - getSiteCount
```
public int getSiteCount()
```
    Specified by:
    
    getSiteCount in interface Alignment
  - getSequences
```
public java.util.Set<Sequence> getSequences()
```
    Specified by:
    
    getSequences in interface Sequences
  - getSequence
```
public Sequence getSequence(Taxon taxon)
```
    Specified by:
    
    getSequence in interface Sequences

Class ResampledAlignment

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ResampledAlignment

Method Detail

init

getSequenceList

getPatternCount

getPatternLength

getPatterns

getTaxa

getSequenceType

getSiteCount

getSequences

getSequence