Package pal.alignment
Interface AnnotationAlignment
- All Superinterfaces:
Alignment
,IdGroup
,Report
,Serializable
- All Known Implementing Classes:
ConcatenatedAnnotatedAlignment
,IndelAnnotatedAlignment
,MultiLocusAnnotatedAlignment
,SimpleAnnotatedAlignment
,StrippedAnnotatedAlignment
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
-
Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
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Method Summary
Modifier and TypeMethodDescriptionint
getChromosome
(int site) Returns chromosomefloat
getChromosomePosition
(int site) Return the position along chromosomegetDataType
(int site) Returns the datatype for a specific site, which could differ by site in complex alignmentsgetLocusName
(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
(PrintWriter out) Returns a report for the alignmentMethods inherited from interface pal.alignment.Alignment
getAlignedSequenceString, getData, getDataType, getSequenceCount, getSiteCount
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
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Method Details
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getChromosomePosition
float getChromosomePosition(int site) Return the position along chromosome -
getChromosome
int getChromosome(int site) Returns chromosome -
getWeightedLocusPosition
float getWeightedLocusPosition(int site) Return the weighted position along the locus (handles gaps) -
getLocusPosition
int getLocusPosition(int site) Return the position along the locus (ignores gaps) -
getPositionType
char getPositionType(int site) Returns position type (eg. I=intron, E=exon, P=promoter, 1=first, 2=second, 3=third, etc. -
getLocusName
Returns the name of the locus -
getDataType
Returns the datatype for a specific site, which could differ by site in complex alignments -
report
Returns a report for the alignment
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