SimpleAnnotatedAlignment

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

All Implemented Interfaces:

java.io.Serializable, Alignment, AnnotationAlignment, IdGroup, Report
```
public class SimpleAnnotatedAlignment
extends SimpleAlignment
implements AnnotationAlignment
```
This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment. This annotation can include information on chromosomal location, site positions, locus name, and the type of position (exon, intron, etc.) This class is designed for alignments with a single locus but multiple sites within the locus. This class does not permit multiple datatypes per alignment.

Version:

$Id: SimpleAnnotatedAlignment.java,v 1

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 and Description
`int`	`chromosome` used to designate chromosome
`float`	`chromosomePosition` used to designate position along chromosome
`java.lang.String`	`locusName` used to designate locus name
`char[]`	`positionType` used to designate position Type
`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 and Description
`SimpleAnnotatedAlignment(Alignment a)` Clone constructor from an unannotated alignment.
`SimpleAnnotatedAlignment(AnnotationAlignment a)` Clone constructor.
`SimpleAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)` This constructor will subset the alignment based on the taxa in IdGroup
`SimpleAnnotatedAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)` This constructor creates a basic SimpleAnnotatedAlignment.
`SimpleAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, DataType dt)` This constructor creates a basic SimpleAnnotatedAlignment.
`SimpleAnnotatedAlignment(IdGroup group, java.lang.String[] sequences, java.lang.String gaps, DataType dt)` This constructor creates a basic SimpleAnnotatedAlignment.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`getChromosome(int site)` Returns chromosome
`float`	`getChromosomePosition(int site)` Return the position along chromosome
`DataType`	`getDataType(int site)` Returns the datatype (for SimpleAnnotatedAlignment there is only one 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`	`report(java.io.PrintWriter out)` print human readable report (e.g., on parameters and associated model)
`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
`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.SimpleAlignment
getAlignedSequenceString, getData

Methods inherited from class pal.alignment.AbstractAlignment
getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, 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.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
  - weightedPosition
```
public float[] weightedPosition
```
    used to designate weighted position; accounts for gaps
  - positionType
```
public char[] positionType
```
    used to designate position Type
  - locusName
```
public java.lang.String locusName
```
    used to designate locus name
- Constructor Detail
  - SimpleAnnotatedAlignment
```
public SimpleAnnotatedAlignment(Alignment a)
```
    Clone constructor from an unannotated alignment. All annotation is set to defaults
  - SimpleAnnotatedAlignment
```
public SimpleAnnotatedAlignment(AnnotationAlignment a)
```
    Clone constructor.
  - SimpleAnnotatedAlignment
```
public SimpleAnnotatedAlignment(AnnotationAlignment a,
                                IdGroup newGroup)
```
    This constructor will subset the alignment based on the taxa in IdGroup
  - SimpleAnnotatedAlignment
```
public SimpleAnnotatedAlignment(Identifier[] ids,
                                java.lang.String[] sequences,
                                java.lang.String gaps,
                                DataType dt)
```
    This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.
  - SimpleAnnotatedAlignment
```
public SimpleAnnotatedAlignment(IdGroup group,
                                java.lang.String[] sequences,
                                DataType dt)
```
    This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.
  - SimpleAnnotatedAlignment
```
public SimpleAnnotatedAlignment(IdGroup group,
                                java.lang.String[] sequences,
                                java.lang.String gaps,
                                DataType dt)
```
    This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.
- 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
  - 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
  - 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)
```
    Sets the name of the locus
  - getDataType
```
public DataType getDataType(int site)
```
    Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)
    
    Specified by:
    
    getDataType in interface AnnotationAlignment
  - report
```
public void report(java.io.PrintWriter out)
```
    Description copied from interface: Report
    
    print human readable report (e.g., on parameters and associated model)
    
    Specified by:
    
    report in interface AnnotationAlignment
    
    Specified by:
    
    report in interface Report
    
    Overrides:
    
    report in class AbstractAlignment
    
    Parameters:
    
    out - output stream

Class SimpleAnnotatedAlignment

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.SimpleAlignment

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.misc.IdGroup

Field Detail

chromosomePosition

chromosome

weightedPosition

positionType

locusName

Constructor Detail

SimpleAnnotatedAlignment

SimpleAnnotatedAlignment

SimpleAnnotatedAlignment

SimpleAnnotatedAlignment

SimpleAnnotatedAlignment

SimpleAnnotatedAlignment

Method Detail

getChromosomePosition

setChromosomePosition

getChromosome

setChromosome

getWeightedLocusPosition

setWeightedLocusPosition

getLocusPosition

getPositionType

setPositionType

getLocusName

setLocusName

getDataType

report