Package pal.alignment
Interface AnnotationAlignment
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- All Known Implementing Classes:
ConcatenatedAnnotatedAlignment
,IndelAnnotatedAlignment
,MultiLocusAnnotatedAlignment
,SimpleAnnotatedAlignment
,StrippedAnnotatedAlignment
public interface AnnotationAlignment extends Alignment, Report
The AnnotationAlignment interface is designed to provide annotation for an alignment. This annotation can include information on chromosomal location, site positions, names of loci, and the type of position (exon, intron, etc.) This interface also permits multiple datatypes per alignment.- Version:
- $Id: AnnotationAlignment.java,v 1.2 2001/09/02 13:19:41 korbinian Exp $
- Author:
- Ed Buckler
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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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Method Summary
All Methods Instance Methods Abstract 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 a specific site, which could differ by site in complex alignmentsjava.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 locus (handles gaps)void
report(java.io.PrintWriter out)
Returns a report for the alignment-
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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Method Detail
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getChromosomePosition
float getChromosomePosition(int site)
Return the position along chromosome
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getChromosome
int getChromosome(int site)
Returns chromosome
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getWeightedLocusPosition
float getWeightedLocusPosition(int site)
Return the weighted position along the locus (handles gaps)
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getLocusPosition
int getLocusPosition(int site)
Return the position along the locus (ignores gaps)
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getPositionType
char getPositionType(int site)
Returns position type (eg. I=intron, E=exon, P=promoter, 1=first, 2=second, 3=third, etc.
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getLocusName
java.lang.String getLocusName(int site)
Returns the name of the locus
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getDataType
DataType getDataType(int site)
Returns the datatype for a specific site, which could differ by site in complex alignments
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