Package jebl.evolution.alignments
Class ResampledAlignment
- java.lang.Object
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- jebl.evolution.alignments.ResampledAlignment
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- 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
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Constructor Summary
Constructors Constructor Description ResampledAlignment()
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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 patternsSequence
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.
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Method Detail
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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
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getSequenceList
public java.util.List<Sequence> getSequenceList()
- Specified by:
getSequenceList
in interfaceAlignment
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getPatternCount
public int getPatternCount()
- Specified by:
getPatternCount
in interfacePatterns
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getPatternLength
public int getPatternLength()
- Specified by:
getPatternLength
in interfacePatterns
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getPatterns
public java.util.List<Pattern> getPatterns()
Description copied from interface:Patterns
Get a list of all the patterns- Specified by:
getPatterns
in interfacePatterns
- Returns:
- the list
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getTaxa
public java.util.List<Taxon> getTaxa()
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getSequenceType
public SequenceType getSequenceType()
- Specified by:
getSequenceType
in interfacePatterns
- Returns:
- the data type of the states in these site patterns.
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getSiteCount
public int getSiteCount()
- Specified by:
getSiteCount
in interfaceAlignment
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getSequences
public java.util.Set<Sequence> getSequences()
- Specified by:
getSequences
in interfaceSequences
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getSequence
public Sequence getSequence(Taxon taxon)
- Specified by:
getSequence
in interfaceSequences
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