Package pal.alignment
Class SimpleAnnotatedAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.SimpleAlignment
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- pal.alignment.SimpleAnnotatedAlignment
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields Modifier and Type Field Description int
chromosome
used to designate chromosomefloat
chromosomePosition
used to designate position along chromosomejava.lang.String
locusName
used to designate locus namechar[]
positionType
used to designate position Typefloat[]
weightedPosition
used to designate weighted position; accounts for gaps-
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor 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 IdGroupSimpleAnnotatedAlignment(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, 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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getChromosome(int site)
Returns chromosomefloat
getChromosomePosition(int site)
Return the position along chromosomeDataType
getDataType(int site)
Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)java.lang.String
getLocusName(int site)
Returns the name of the locusint
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 chromosomevoid
setChromosomePosition(float position)
Set the position along chromosomevoid
setLocusName(java.lang.String locusName)
Sets the name of the locusvoid
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
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Methods inherited from class pal.alignment.AbstractAlignment
getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, setDataType, setIdentifier, toString, whichIdNumber
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface pal.alignment.Alignment
getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount
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Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Field Detail
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chromosomePosition
public float chromosomePosition
used to designate position along chromosome
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chromosome
public int chromosome
used to designate chromosome
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weightedPosition
public float[] weightedPosition
used to designate weighted position; accounts for gaps
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positionType
public char[] positionType
used to designate position Type
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locusName
public java.lang.String locusName
used to designate locus name
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Constructor Detail
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SimpleAnnotatedAlignment
public SimpleAnnotatedAlignment(Alignment a)
Clone constructor from an unannotated alignment. All annotation is set to defaults
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SimpleAnnotatedAlignment
public SimpleAnnotatedAlignment(AnnotationAlignment a)
Clone constructor.
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SimpleAnnotatedAlignment
public SimpleAnnotatedAlignment(AnnotationAlignment a, IdGroup newGroup)
This constructor will subset the alignment based on the taxa in IdGroup
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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.
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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.
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Method Detail
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getChromosomePosition
public float getChromosomePosition(int site)
Return the position along chromosome- Specified by:
getChromosomePosition
in interfaceAnnotationAlignment
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setChromosomePosition
public void setChromosomePosition(float position)
Set the position along chromosome
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getChromosome
public int getChromosome(int site)
Returns chromosome- Specified by:
getChromosome
in interfaceAnnotationAlignment
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setChromosome
public void setChromosome(int chromosome)
Sets chromosome
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getWeightedLocusPosition
public float getWeightedLocusPosition(int site)
Return the weighted position along the gene (handles gaps)- Specified by:
getWeightedLocusPosition
in interfaceAnnotationAlignment
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setWeightedLocusPosition
public void setWeightedLocusPosition(int site, float weightedPos)
Sets the weighted position along the gene (handles gaps)
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getLocusPosition
public int getLocusPosition(int site)
Return the position along the locus (ignores gaps)- Specified by:
getLocusPosition
in interfaceAnnotationAlignment
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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 interfaceAnnotationAlignment
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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.
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getLocusName
public java.lang.String getLocusName(int site)
Returns the name of the locus- Specified by:
getLocusName
in interfaceAnnotationAlignment
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setLocusName
public void setLocusName(java.lang.String locusName)
Sets the name of the locus
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getDataType
public DataType getDataType(int site)
Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)- Specified by:
getDataType
in interfaceAnnotationAlignment
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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 interfaceAnnotationAlignment
- Specified by:
report
in interfaceReport
- Overrides:
report
in classAbstractAlignment
- Parameters:
out
- output stream
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