Package pal.alignment
Class SitePattern
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.SitePattern
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public class SitePattern extends AbstractAlignment
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:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields Modifier and Type Field Description int[]
alias
site -> site patternint
numPatterns
number of site patternsbyte[][]
pattern
site patterns [sequence][site pattern]int[]
weight
weights of each site pattern-
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor Description SitePattern(Alignment a)
infer 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
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description char
getData(int seq, int site)
sequence alignment at (sequence, site)int
getNumberOfPatterns()
Accessor method for numPatternschar
getPatternData(int seq, int patternSite)
int
getPatternState(int seq, int patternSite)
static SitePattern
getSitePattern(Alignment a)
int[]
getSiteWeights()
Accessor method for weight-
Methods 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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Constructor Detail
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SitePattern
public SitePattern(Alignment a)
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 Detail
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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)
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getPatternState
public final int getPatternState(int seq, int patternSite)
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getSiteWeights
public int[] getSiteWeights()
Accessor method for weight
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getNumberOfPatterns
public int getNumberOfPatterns()
Accessor method for numPatterns
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getSitePattern
public static final SitePattern getSitePattern(Alignment a)
- 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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