jebl.evolution.alignments
Class ResampledAlignment
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
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ResampledAlignment
public ResampledAlignment()
init
public void init(Alignment srcAlignment,
int[] siteIndices)
- Setup resampled alignment.
- Parameters:
srcAlignment
- sample sites from this alignmentsiteIndices
- 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
http://code.google.com/p/jebl2/