Package pal.alignment
Class SitePattern
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.SitePattern
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
takes an Alignment and determines its site patterns
- Version:
- $Id: SitePattern.java,v 1.11 2002/10/14 06:54:24 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
FieldsModifier and TypeFieldDescriptionint[]
site -> site patternint
number of site patternsbyte[][]
site patterns [sequence][site pattern]int[]
weights of each site patternFields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
ConstructorsConstructorDescriptioninfer site patterns for a given alignmentSitePattern
(DataType dataType, int numSites, int numSeqs, IdGroup idGroup, int numPatterns, int[] alias, int[] weight, byte[][] pattern) construct SitePattern from scratch -
Method Summary
Modifier and TypeMethodDescriptionchar
getData
(int seq, int site) sequence alignment at (sequence, site)int
Accessor method for numPatternsfinal char
getPatternData
(int seq, int patternSite) final int
getPatternState
(int seq, int patternSite) static final SitePattern
int[]
Accessor method for weightMethods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
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Field Details
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numPatterns
public int numPatternsnumber of site patterns -
alias
public int[] aliassite -> site pattern -
weight
public int[] weightweights of each site pattern -
pattern
public byte[][] patternsite patterns [sequence][site pattern]
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Constructor Details
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SitePattern
infer site patterns for a given alignment- Parameters:
a
- alignment
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SitePattern
public SitePattern(DataType dataType, int numSites, int numSeqs, IdGroup idGroup, int numPatterns, int[] alias, int[] weight, byte[][] pattern) construct SitePattern from scratch- Parameters:
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 patterns
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Method Details
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getData
public char getData(int seq, int site) sequence alignment at (sequence, site)- Specified by:
getData
in interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
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getPatternData
public final char getPatternData(int seq, int patternSite) -
getPatternState
public final int getPatternState(int seq, int patternSite) -
getSiteWeights
public int[] getSiteWeights()Accessor method for weight -
getNumberOfPatterns
public int getNumberOfPatterns()Accessor method for numPatterns -
getSitePattern
- Parameters:
a
- An alignment- Returns:
- alignment as a site pattern if it isn't already one (other wise just returns alighnment)
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