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

Fields
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

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

Constructors
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

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 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)

Class SitePattern

Nested Class Summary

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

Field Summary

Fields inherited from class pal.alignment.AbstractAlignment

Fields inherited from interface pal.alignment.Alignment

Constructor Summary

Method Summary

Methods inherited from class pal.alignment.AbstractAlignment

Methods inherited from class java.lang.Object

Field Detail

numPatterns

alias

weight

pattern

Constructor Detail

SitePattern

SitePattern

Method Detail

getData

getPatternData

getPatternState

getSiteWeights

getNumberOfPatterns

getSitePattern