public class SitePattern extends AbstractAlignment
IdGroup.Utils
Modifier and Type | Field | Description |
---|---|---|
int[] |
alias |
site -> site pattern
|
int |
numPatterns |
number of site patterns
|
byte[][] |
pattern |
site patterns [sequence][site pattern]
|
int[] |
weight |
weights of each site pattern
|
idGroup, numSeqs, numSites
Constructor | Description |
---|---|
SitePattern(Alignment a) |
infer site patterns for a given alignment
|
SitePattern(DataType dataType,
int numSites,
int numSeqs,
IdGroup idGroup,
int numPatterns,
int[] alias,
int[] weight,
byte[][] pattern) |
construct SitePattern from scratch
|
Modifier and Type | Method | Description |
---|---|---|
char |
getData(int seq,
int site) |
sequence alignment at (sequence, site)
|
int |
getNumberOfPatterns() |
Accessor method for numPatterns
|
char |
getPatternData(int seq,
int patternSite) |
|
int |
getPatternState(int seq,
int patternSite) |
|
static SitePattern |
getSitePattern(Alignment a) |
|
int[] |
getSiteWeights() |
Accessor method for weight
|
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
public int numPatterns
public int[] alias
public int[] weight
public byte[][] pattern
public SitePattern(Alignment a)
a
- alignmentpublic SitePattern(DataType dataType, int numSites, int numSeqs, IdGroup idGroup, int numPatterns, int[] alias, int[] weight, byte[][] pattern)
dataType
- data typenumSites
- number of sitesnumSeqs
- number of sequencesidGroup
- sequence identifiersnumPatterns
- number of site patternsalias
- link site -> site patternweight
- frequency of a site patternpattern
- site patternspublic char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment
public final char getPatternData(int seq, int patternSite)
public final int getPatternState(int seq, int patternSite)
public int[] getSiteWeights()
public int getNumberOfPatterns()
public static final SitePattern getSitePattern(Alignment a)
a
- An alignment