Package pal.alignment

Class MultiLocusAnnotatedAlignment

  • All Implemented Interfaces:
    java.io.Serializable, Alignment, AnnotationAlignment, IdGroup, Report
    public class MultiLocusAnnotatedAlignment
extends SimpleAlignment
implements AnnotationAlignment
    MultiLocusAnnotatedAlignment is an extension of the SimpleAlignment that includes Annotation, and is designed for multiple loci. Separate annotation information is stored from each sites. This would be good SNP SSR type of data, but it would be inefficient for single gene data.
    Version:
    $Id:
    Author:
    Ed Buckler
    See Also:
    Serialized Form

    • Field Detail

      • chromosomePosition

        public float[] chromosomePosition
        used to designate position along chromosome

      • chromosome

        public int[] chromosome
        used to designate chromosome

      • weightedPosition

        public float[] weightedPosition
        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 java.lang.String[] locusName
        used to designate locus name

      • siteDataType

        public DataType[] siteDataType
        provides datatype for each locus separately

    • Constructor Detail

      • MultiLocusAnnotatedAlignment

        public MultiLocusAnnotatedAlignment​(Alignment a)
        Basic constructor.

      • MultiLocusAnnotatedAlignment

        public MultiLocusAnnotatedAlignment()
        null constructor.

      • MultiLocusAnnotatedAlignment

        public MultiLocusAnnotatedAlignment​(AnnotationAlignment a)
        Clone constructor for Annotated alignment

      • MultiLocusAnnotatedAlignment

        public MultiLocusAnnotatedAlignment​(Identifier[] ids,
                                    java.lang.String[] sequences,
                                    java.lang.String gaps,
                                    DataType dt)

      • MultiLocusAnnotatedAlignment

        public MultiLocusAnnotatedAlignment​(IdGroup group,
                                    java.lang.String[] sequences,
                                    DataType dt)

      • MultiLocusAnnotatedAlignment

        public MultiLocusAnnotatedAlignment​(IdGroup group,
                                    java.lang.String[] sequences,
                                    java.lang.String gaps,
                                    DataType dt)

      • MultiLocusAnnotatedAlignment

        public MultiLocusAnnotatedAlignment​(AnnotationAlignment a,
                                    IdGroup newGroup)
        This constructor will subset the alignment based on the taxa in IdGroup

    • Method Detail

      • initMatrices

        protected void initMatrices()

      • init

        protected void init​(IdGroup group,
                    java.lang.String[] sequences)

      • setChromosomePosition

        public void setChromosomePosition​(float position,
                                  int site)
        Set the position along chromosome

      • setChromosome

        public void setChromosome​(int chromosome,
                          int site)
        Sets chromosome

      • setWeightedLocusPosition

        public void setWeightedLocusPosition​(int site,
                                     float weightedPos)
        Sets the weighted position along the gene (handles gaps)

      • getLocusPosition

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

      • setLocusPosition

        public void setLocusPosition​(int position,
                             int site)
        Set the position within the locus

      • 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

      • setPositionType

        public void setPositionType​(int site,
                            char posType)
        Set thes 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
        Specified by:
        getLocusName in interface AnnotationAlignment

      • setLocusName

        public void setLocusName​(java.lang.String locusName,
                         int site)
        Sets the name of the locus