Package pal.alignment

Class StrippedAnnotatedAlignment

java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.StrippedAlignment
pal.alignment.StrippedAnnotatedAlignment
All Implemented Interfaces:
Serializable, Alignment, AnnotationAlignment, IdGroup, Report
public class StrippedAnnotatedAlignment extends StrippedAlignment implements AnnotationAlignment
This is the stripped implementation of the Annotation interface, which is designed to provide stripped and annotated alignments. This annotation can include information on chromosomal location, site positions, locus name, and the type of position (exon, intron, etc.) This class also add some methods for stripping sites based on frequency, count, and a range of positions.
Version:
$Id: StrippedAnnotatedAlignment.java,v 1
Author:
Ed Buckler
See Also:

  • Field Details

    • minimumProportion

      protected double minimumProportion

    • minimumCount

      protected int minimumCount

    • firstSite

      protected int firstSite

    • lastSite

      protected int lastSite

  • Constructor Details

    • StrippedAnnotatedAlignment

      public StrippedAnnotatedAlignment(AnnotationAlignment a)
      Simple constructor

  • Method Details

    • getChromosomePosition

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

    • getChromosome

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

    • 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

    • getDataType

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

    • removeSitesOutsideRange

      public void removeSitesOutsideRange(int firstSite, int lastSite)
      Remove sites based on site position (excluded sites are lastSite) This not effect any prior exclusions.
      Parameters:
      firstSite - first site to keep in the range
      lastSite - last site to keep in the range

    • removeConstantSitesIgnoreGapsMissing

      public void removeConstantSitesIgnoreGapsMissing()
      remove constant sites but ignore gaps and missing data (- and ?)

    • removeSitesBasedOnFreqIgnoreGapsMissing

      public void removeSitesBasedOnFreqIgnoreGapsMissing(double minimumProportion, int minimumCount)
      remove sites based on minimum frequency (the count of good bases) and based on the proportion of good sites different from consensus
      Parameters:
      minimumProportion - minimum proportion of sites different from the consensus
      minimumCount - minimum number of sequences with a good bases (not - or ?)

    • report

      public void report(PrintWriter out)
      Description copied from interface: Report
      print human readable report (e.g., on parameters and associated model)
      Specified by:
      report in interface AnnotationAlignment
      Specified by:
      report in interface Report
      Overrides:
      report in class AbstractAlignment
      Parameters:
      out - output stream