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, whichIdNumberpublic 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 AlignmentgetData in class AbstractAlignmentpublic 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