BootstrappedAlignment
, JackknifedAlignment
public class ResampledAlignment extends java.lang.Object implements Alignment
Constructor | Description |
---|---|
ResampledAlignment() |
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.
|
public void init(Alignment srcAlignment, int[] siteIndices)
srcAlignment
- sample sites from this alignmentsiteIndices
- Use this set to construct the resampled alignmentpublic java.util.List<Sequence> getSequenceList()
getSequenceList
in interface Alignment
public int getPatternCount()
getPatternCount
in interface Patterns
public int getPatternLength()
getPatternLength
in interface Patterns
public java.util.List<Pattern> getPatterns()
Patterns
getPatterns
in interface Patterns
public java.util.List<Taxon> getTaxa()
public SequenceType getSequenceType()
getSequenceType
in interface Patterns
public int getSiteCount()
getSiteCount
in interface Alignment
public java.util.Set<Sequence> getSequences()
getSequences
in interface Sequences
public Sequence getSequence(Taxon taxon)
getSequence
in interface Sequences
http://code.google.com/p/jebl2/