Package pal.alignment

Class SimpleAnnotatedAlignment

  • All Implemented Interfaces:
    java.io.Serializable, Alignment, AnnotationAlignment, IdGroup, Report

    public class SimpleAnnotatedAlignment
    extends SimpleAlignment
    implements AnnotationAlignment
    This is the basic implementation of the Annotation interface, which is designed to provide annotation for an alignment. This annotation can include information on chromosomal location, site positions, locus name, and the type of position (exon, intron, etc.) This class is designed for alignments with a single locus but multiple sites within the locus. This class does not permit multiple datatypes per alignment.
    Version:
    $Id: SimpleAnnotatedAlignment.java,v 1
    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
      • positionType

        public char[] positionType
        used to designate position Type
      • locusName

        public java.lang.String locusName
        used to designate locus name
    • Constructor Detail

      • SimpleAnnotatedAlignment

        public SimpleAnnotatedAlignment​(Alignment a)
        Clone constructor from an unannotated alignment. All annotation is set to defaults
      • SimpleAnnotatedAlignment

        public SimpleAnnotatedAlignment​(AnnotationAlignment a)
        Clone constructor.
      • SimpleAnnotatedAlignment

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

        public SimpleAnnotatedAlignment​(Identifier[] ids,
                                        java.lang.String[] sequences,
                                        java.lang.String gaps,
                                        DataType dt)
        This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.
      • SimpleAnnotatedAlignment

        public SimpleAnnotatedAlignment​(IdGroup group,
                                        java.lang.String[] sequences,
                                        DataType dt)
        This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.
      • SimpleAnnotatedAlignment

        public SimpleAnnotatedAlignment​(IdGroup group,
                                        java.lang.String[] sequences,
                                        java.lang.String gaps,
                                        DataType dt)
        This constructor creates a basic SimpleAnnotatedAlignment. The annotation should be added with the set commands.
    • Method Detail

      • setChromosomePosition

        public void setChromosomePosition​(float position)
        Set the position along chromosome
      • setChromosome

        public void setChromosome​(int chromosome)
        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
      • 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)
        Sets the name of the locus
      • getDataType

        public DataType getDataType​(int site)
        Returns the datatype (for SimpleAnnotatedAlignment there is only one datatype)
        Specified by:
        getDataType in interface AnnotationAlignment
      • 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