pal.alignment
Interface AnnotationAlignment

All Superinterfaces:
Alignment, IdGroup, Report, java.io.Serializable
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

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
 
Field Summary
 
Fields inherited from interface pal.alignment.Alignment
GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA
 
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 a specific site, which could differ by site in complex alignments
 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 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
 
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
 

Method Detail

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

java.lang.String getLocusName(int site)
Returns the name of the locus


getDataType

DataType getDataType(int site)
Returns the datatype for a specific site, which could differ by site in complex alignments


report

void report(java.io.PrintWriter out)
Returns a report for the alignment

Specified by:
report in interface Report
Parameters:
out - output stream