pal.alignment
Class 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

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

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

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