Package jebl.evolution.alignments
Class ResampledAlignment
java.lang.Object
jebl.evolution.alignments.ResampledAlignment
- Direct Known Subclasses:
BootstrappedAlignment
,JackknifedAlignment
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 -
Method Summary
Modifier and TypeMethodDescriptionint
int
Get a list of all the patternsgetSequence
(Taxon taxon) int
getTaxa()
void
Setup resampled alignment.
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Constructor Details
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ResampledAlignment
public ResampledAlignment()
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Method Details
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init
Setup resampled alignment.- Parameters:
srcAlignment
- sample sites from this alignmentsiteIndices
- Use this set to construct the resampled alignment
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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
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
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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
- Specified by:
getSequences
in interfaceSequences
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getSequence
- Specified by:
getSequence
in interfaceSequences
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