pal.alignment
Interface AnnotationAlignment

All Superinterfaces:
Alignment, IdGroup, Report, java.io.Serializable
All Known Implementing Classes:
MultiLocusAnnotatedAlignment, SimpleAnnotatedAlignment, StrippedAnnotatedAlignment, IndelAnnotatedAlignment, ConcatenatedAnnotatedAlignment

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.


Fields inherited from interface pal.alignment.Alignment
GAP
 
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, getFrequency, getSequenceCount, getSiteCount, setDataType, setFrequency
 
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
 

Method Detail

getChromosomePosition

public float getChromosomePosition(int site)
Return the position along chromosome

getChromosome

public int getChromosome(int site)
Returns chromosome

getWeightedLocusPosition

public float getWeightedLocusPosition(int site)
Return the weighted position along the locus (handles gaps)

getLocusPosition

public int getLocusPosition(int site)
Return the position along the locus (ignores gaps)

getPositionType

public char getPositionType(int site)
Returns 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

getDataType

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

report

public void report(java.io.PrintWriter out)
Returns a report for the alignment
Specified by:
report in interface Report
Following copied from interface: pal.misc.Report
Parameters:
out - output stream