MultiLocusAnnotatedAlignment

java.lang.Object
- pal.alignment.AbstractAlignment
- - pal.alignment.SimpleAlignment
  - - pal.alignment.MultiLocusAnnotatedAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, AnnotationAlignment, IdGroup, Report
```
public class MultiLocusAnnotatedAlignment
extends SimpleAlignment
implements AnnotationAlignment
```
MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci. Separate annotation information is stored from each sites. This would be good SNP SSR type of data, but it would be inefficient for single gene data.

Version:

$Id:

Author:

Ed Buckler

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[]`	`chromosome`	used to designate chromosome
`float[]`	`chromosomePosition`	used to designate position along chromosome
`java.lang.String[]`	`locusName`	used to designate locus name
`int[]`	`locusPosition`	used to designate position; do not account for gaps
`char[]`	`positionType`	used to designate position Type
`DataType[]`	`siteDataType`	provides datatype for each locus separately
`float[]`	`weightedPosition`	used to designate weighted position; accounts for gaps

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
`MultiLocusAnnotatedAlignment()`	null constructor.
`MultiLocusAnnotatedAlignment(Alignment a)`	Basic constructor.
`MultiLocusAnnotatedAlignment(AnnotationAlignment a)`	Clone constructor for Annotated alignment
`MultiLocusAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)`	This constructor will subset the alignment based on the taxa in IdGroup
`MultiLocusAnnotatedAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)`
`MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)`
`MultiLocusAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`getChromosome(int site)`	Returns chromosome
`float`	`getChromosomePosition(int site)`	Return the position along chromosome
`DataType`	`getDataType(int site)`	Returns the datatype
`java.lang.String`	`getLocusName(int site)`	Returns the name of the locus
`int`	`getLocusPosition(int site)`	Return the position along the locus (ignores gaps)
`char`	`getPositionType(int site)`	Returns position type (eg.
`float`	`getWeightedLocusPosition(int site)`	Return the weighted position along the gene (handles gaps)
`protected void`	`init(IdGroup group, java.lang.String[] sequences)`
`protected void`	`initMatrices()`
`void`	`setChromosome(int chromosome, int site)`	Sets chromosome
`void`	`setChromosomePosition(float position, int site)`	Set the position along chromosome
`void`	`setLocusName(java.lang.String locusName, int site)`	Sets the name of the locus
`void`	`setLocusPosition(int position, int site)`	Set the position within the locus
`void`	`setPositionType(int site, char posType)`	Set thes position type (eg.
`void`	`setWeightedLocusPosition(int site, float weightedPos)`	Sets the weighted position along the gene (handles gaps)

Methods inherited from class pal.alignment.AbstractAlignment
getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber

Methods inherited from interface pal.alignment.Alignment
getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount

Methods inherited from interface pal.alignment.AnnotationAlignment
report

Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from class pal.alignment.SimpleAlignment
getAlignedSequenceString, getData

Field Detail
- chromosomePosition
```
public float[] chromosomePosition
```
  used to designate position along chromosome
- chromosome
```
public int[] chromosome
```
  used to designate chromosome
- weightedPosition
```
public float[] weightedPosition
```
  used to designate weighted position; accounts for gaps
- locusPosition
```
public int[] locusPosition
```
  used to designate position; do not account for gaps
- positionType
```
public char[] positionType
```
  used to designate position Type
- locusName
```
public java.lang.String[] locusName
```
  used to designate locus name
- siteDataType
```
public DataType[] siteDataType
```
  provides datatype for each locus separately

Constructor Detail

MultiLocusAnnotatedAlignment

public MultiLocusAnnotatedAlignment(Alignment a)

Basic constructor.

MultiLocusAnnotatedAlignment
```
public MultiLocusAnnotatedAlignment()
```
null constructor.

MultiLocusAnnotatedAlignment
```
public MultiLocusAnnotatedAlignment(AnnotationAlignment a)
```
Clone constructor for Annotated alignment

MultiLocusAnnotatedAlignment

public MultiLocusAnnotatedAlignment(Identifier[] ids,
                                    java.lang.String[] sequences,
                                    java.lang.String gaps,
                                    DataType dt)

MultiLocusAnnotatedAlignment

public MultiLocusAnnotatedAlignment(IdGroup group,
                                    java.lang.String[] sequences,
                                    DataType dt)

MultiLocusAnnotatedAlignment

public MultiLocusAnnotatedAlignment(IdGroup group,
                                    java.lang.String[] sequences,
                                    java.lang.String gaps,
                                    DataType dt)

MultiLocusAnnotatedAlignment

public MultiLocusAnnotatedAlignment(AnnotationAlignment a,
                                    IdGroup newGroup)

This constructor will subset the alignment based on the taxa in IdGroup

Method Detail
- initMatrices
```
protected void initMatrices()
```
- init
```
protected void init(IdGroup group,
                    java.lang.String[] sequences)
```
- getChromosomePosition
```
public float getChromosomePosition(int site)
```
  Return the position along chromosome
  
  Specified by:
  
  getChromosomePosition in interface AnnotationAlignment
- setChromosomePosition
```
public void setChromosomePosition(float position,
                                  int site)
```
  Set the position along chromosome
- getChromosome
```
public int getChromosome(int site)
```
  Returns chromosome
  
  Specified by:
  
  getChromosome in interface AnnotationAlignment
- setChromosome
```
public void setChromosome(int chromosome,
                          int site)
```
  Sets chromosome
- getWeightedLocusPosition
```
public float getWeightedLocusPosition(int site)
```
  Return the weighted position along the gene (handles gaps)
  
  Specified by:
  
  getWeightedLocusPosition in interface AnnotationAlignment
- setWeightedLocusPosition
```
public void setWeightedLocusPosition(int site,
                                     float weightedPos)
```
  Sets the weighted position along the gene (handles gaps)
- getLocusPosition
```
public int getLocusPosition(int site)
```
  Return the position along the locus (ignores gaps)
  
  Specified by:
  
  getLocusPosition in interface AnnotationAlignment
- setLocusPosition
```
public void setLocusPosition(int position,
                             int site)
```
  Set the position within the locus
- getPositionType
```
public char getPositionType(int site)
```
  Returns position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.
  
  Specified by:
  
  getPositionType in interface AnnotationAlignment
- setPositionType
```
public void setPositionType(int site,
                            char posType)
```
  Set thes position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.
- getLocusName
```
public java.lang.String getLocusName(int site)
```
  Returns the name of the locus
  
  Specified by:
  
  getLocusName in interface AnnotationAlignment
- setLocusName
```
public void setLocusName(java.lang.String locusName,
                         int site)
```
  Sets the name of the locus
- getDataType
```
public DataType getDataType(int site)
```
  Returns the datatype
  
  Specified by:
  
  getDataType in interface AnnotationAlignment

Class MultiLocusAnnotatedAlignment

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 interface pal.alignment.Alignment

Methods inherited from interface pal.alignment.AnnotationAlignment

Methods inherited from interface pal.misc.IdGroup

Methods inherited from class java.lang.Object

Methods inherited from class pal.alignment.SimpleAlignment

Field Detail

chromosomePosition

chromosome

weightedPosition

locusPosition

positionType

locusName

siteDataType

Constructor Detail

MultiLocusAnnotatedAlignment

MultiLocusAnnotatedAlignment

MultiLocusAnnotatedAlignment

MultiLocusAnnotatedAlignment

MultiLocusAnnotatedAlignment

MultiLocusAnnotatedAlignment

MultiLocusAnnotatedAlignment

Method Detail

initMatrices

init

getChromosomePosition

setChromosomePosition

getChromosome

setChromosome

getWeightedLocusPosition

setWeightedLocusPosition

getLocusPosition

setLocusPosition

getPositionType

setPositionType

getLocusName

setLocusName

getDataType