pal.alignment
Class SitePattern

java.lang.Object
  pal.alignment.AbstractAlignment
      pal.alignment.SitePattern

All Implemented Interfaces:

java.io.Serializable, Alignment, IdGroup, Report

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

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Field Summary

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

idGroup, numSeqs, numSites

Fields inherited from interface pal.alignment.Alignment

GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA

Constructor Summary

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

Method Summary

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

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

numPatterns

public int numPatterns

number of site patterns

alias

public int[] alias

site -> site pattern

weight

public int[] weight

weights of each site pattern

pattern

public byte[][] pattern

site patterns [sequence][site pattern]

Constructor Detail

SitePattern

public SitePattern(Alignment a)

infer site patterns for a given alignment

Parameters:

a - alignment

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 type

numSites - number of sites

numSeqs - number of sequences

idGroup - sequence identifiers

numPatterns - number of site patterns

alias - link site -> site pattern

weight - frequency of a site pattern

pattern - site patterns

Method Detail

getData

public char getData(int seq,
                    int site)

sequence alignment at (sequence, site)

Specified by:

getData in interface Alignment

Specified by:

getData in class AbstractAlignment

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

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)