Package pal.alignment

Class IndelAnnotatedAlignment

java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.IndelAlignment
pal.alignment.IndelAnnotatedAlignment
All Implemented Interfaces:
Serializable, Alignment, AnnotationAlignment, IdGroup, Report
public class IndelAnnotatedAlignment extends IndelAlignment implements AnnotationAlignment
an extension of the IndelAlignment that includes annotation. This should only extract indels from a single locus.
Version:
$Id:
Author:
Ed Buckler
See Also:

  • Field Details

    • chromosomePosition

      public float chromosomePosition
      used to designate position along chromosome

    • chromosome

      public int chromosome
      used to designate chromosome

    • weightedLocusPosition

      public float[] weightedLocusPosition
      used to designate weighted position; accounts for gaps

    • locusPosition

      public int[] locusPosition
      used to designate position; do not account for gaps

    • positionType

      public char[] positionType
      used to designate position Type

    • locusName

      public String locusName
      used to designate locus name

  • Constructor Details

    • IndelAnnotatedAlignment

      public IndelAnnotatedAlignment(AnnotationAlignment a, boolean anchored)
      Basic constructor. All annotation is based off the first site in the AnnotationAlignment. This Alignment should not span multiple loci.
      Parameters:
      anchored - sets to score anchored indels as same position

  • Method Details

    • getChromosomePosition

      public float getChromosomePosition(int site)
      Return the position along chromosome
      Specified by:
      getChromosomePosition in interface AnnotationAlignment

    • setChromosomePosition

      public void setChromosomePosition(float position)
      Set the position along chromosome

    • getChromosome

      public int getChromosome(int site)
      Returns chromosome
      Specified by:
      getChromosome in interface AnnotationAlignment

    • setChromosome

      public void setChromosome(int chromosome)
      Sets chromosome

    • getWeightedLocusPosition

      public float getWeightedLocusPosition(int site)
      Return the weighted position along the gene (handles gaps)
      Specified by:
      getWeightedLocusPosition in interface AnnotationAlignment

    • getLocusPosition

      public int getLocusPosition(int site)
      Return the position along the locus (ignores gaps)
      Specified by:
      getLocusPosition in interface AnnotationAlignment

    • getPositionType

      public char getPositionType(int site)
      Returns position type (eg. I=intron, E-exon, P=promoter, 1=first, 2=second, 3=third, etc.
      Specified by:
      getPositionType in interface AnnotationAlignment

    • getLocusName

      public String getLocusName(int site)
      Returns the name of the locus
      Specified by:
      getLocusName in interface AnnotationAlignment

    • setLocusName

      public void setLocusName(String locusName)
      Sets the name of the locus

    • getDataType

      public DataType getDataType(int site)
      Returns the datatype
      Specified by:
      getDataType in interface AnnotationAlignment