java.lang.Object
- pal.alignment.AbstractAlignment
- - pal.alignment.IndelAlignment
  - - pal.alignment.IndelAnnotatedAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, AnnotationAlignment, IdGroup, Report
```
public class IndelAnnotatedAlignment
extends IndelAlignment
implements AnnotationAlignment
```
an extension of the IndelAlignment that includes annotation. This should only extract indels from a single locus.

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
`float[]`	`weightedLocusPosition`	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

IndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
Basic constructor.

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)
`void`	`setChromosome(int chromosome)`	Sets chromosome
`void`	`setChromosomePosition(float position)`	Set the position along chromosome
`void`	`setLocusName(java.lang.String locusName)`	Sets the name of the locus

Methods inherited from class pal.alignment.IndelAlignment
getData

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

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

- Field Detail
  - chromosomePosition
```
public float chromosomePosition
```
    used to designate position along chromosome
  - chromosome
```
public int chromosome
```
    used to designate chromosome
  - weightedLocusPosition
```
public float[] weightedLocusPosition
```
    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
- Constructor Detail
  - IndelAnnotatedAlignment
```
public IndelAnnotatedAlignment(AnnotationAlignment a,
                               boolean anchored)
```
    Basic constructor. All annotation is based off the first site in the AnnotationAlignment. This Alignment should not span multiple loci.
    
    Parameters:
    
    anchored - sets to score anchored indels as same position
- Method Detail
  - getChromosomePosition
```
public float getChromosomePosition(int site)
```
    Return the position along chromosome
    
    Specified by:
    
    getChromosomePosition in interface AnnotationAlignment
  - setChromosomePosition
```
public void setChromosomePosition(float position)
```
    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)
```
    Sets chromosome
  - getWeightedLocusPosition
```
public float getWeightedLocusPosition(int site)
```
    Return the weighted position along the gene (handles gaps)
    
    Specified by:
    
    getWeightedLocusPosition in interface AnnotationAlignment
  - getLocusPosition
```
public int getLocusPosition(int site)
```
    Return the position along the locus (ignores gaps)
    
    Specified by:
    
    getLocusPosition in interface AnnotationAlignment
  - 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
  - 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)
```
    Sets the name of the locus
  - getDataType
```
public DataType getDataType(int site)
```
    Returns the datatype
    
    Specified by:
    
    getDataType in interface AnnotationAlignment

Class IndelAnnotatedAlignment

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.IndelAlignment

Methods inherited from class pal.alignment.AbstractAlignment

Methods inherited from class java.lang.Object

Methods inherited from interface pal.alignment.Alignment

Methods inherited from interface pal.alignment.AnnotationAlignment

Methods inherited from interface pal.misc.IdGroup

Field Detail

chromosomePosition

chromosome

weightedLocusPosition

locusPosition

positionType

locusName

Constructor Detail

IndelAnnotatedAlignment

Method Detail

getChromosomePosition

setChromosomePosition

getChromosome

setChromosome

getWeightedLocusPosition

getLocusPosition

getPositionType

getLocusName

setLocusName

getDataType