Package pal.alignment

Interface AnnotationAlignment

All Superinterfaces:
Alignment, IdGroup, Report, 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
  • Method Details

    • 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

      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(PrintWriter out)
      Returns a report for the alignment
      Specified by:
      report in interface Report
      Parameters:
      out - output stream