Package pal.alignment

Class StrippedAnnotatedAlignment

  • All Implemented Interfaces:
    java.io.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:
    Serialized Form

    • Field Detail

      • minimumProportion

        protected double minimumProportion

      • minimumCount

        protected int minimumCount

      • firstSite

        protected int firstSite

      • lastSite

        protected int lastSite

    • Constructor Detail

      • StrippedAnnotatedAlignment

        public StrippedAnnotatedAlignment​(AnnotationAlignment a)
        Simple constructor

    • Method Detail

      • 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 java.lang.String getLocusName​(int site)
        Returns the name of the locus
        Specified by:
        getLocusName 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​(java.io.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