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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.SitePattern
public class SitePattern
takes an Alignment and determines its site patterns
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary | |
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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 |
Fields inherited from class pal.alignment.AbstractAlignment |
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idGroup, numSeqs, numSites |
Fields inherited from interface pal.alignment.Alignment |
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GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA |
Constructor Summary | |
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SitePattern(Alignment a)
infer site patterns for a given alignment |
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SitePattern(DataType dataType,
int numSites,
int numSeqs,
IdGroup idGroup,
int numPatterns,
int[] alias,
int[] weight,
byte[][] pattern)
construct SitePattern from scratch |
Method Summary | |
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char |
getData(int seq,
int site)
sequence alignment at (sequence, site) |
int |
getNumberOfPatterns()
Accessor method for numPatterns |
char |
getPatternData(int seq,
int patternSite)
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int |
getPatternState(int seq,
int patternSite)
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static SitePattern |
getSitePattern(Alignment a)
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int[] |
getSiteWeights()
Accessor method for weight |
Methods inherited from class pal.alignment.AbstractAlignment |
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getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public int numPatterns
public int[] alias
public int[] weight
public byte[][] pattern
Constructor Detail |
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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 patternsMethod Detail |
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public 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
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