Package org.snpsift.pedigree

Class Individual

  • All Implemented Interfaces:
    java.lang.Comparable<Individual>
    public class Individual
extends java.lang.Object
implements java.lang.Comparable<Individual>
    An individual in the pedigree Individuals are like TfamEntries but have drawing info (coordinates, color, etc.)
    Author:
    pablocingolani

    • Constructor Detail

      • Individual

        public Individual​(org.snpeff.ped.TfamEntry tfamEntry)

    • Method Detail

      • addChild

        protected void addChild​(Individual ind)

      • calcDepth

        public int calcDepth()
        Depth in the graph. Depth is zero for root nodes
        Returns:

      • compareTo

        public int compareTo​(Individual ind)
        Specified by:
        compareTo in interface java.lang.Comparable<Individual>

      • getAffected

        public java.lang.Boolean getAffected()

      • getChilds

        public java.util.Collection<Individual> getChilds()

      • getChilds

        public java.util.ArrayList<Individual> getChilds​(Individual spouse)
        Get only childs from this spouse
        Parameters:
        spouse -
        Returns:

      • getColor

        public java.lang.String getColor()

      • getDepth

        public int getDepth()

      • getFamilyId

        public java.lang.String getFamilyId()

      • getId

        public java.lang.String getId()

      • getLabel

        public java.lang.String getLabel()

      • getOrder

        public int getOrder()

      • getPosition

        public java.awt.Point getPosition()

      • getSex

        public org.snpeff.ped.Sex getSex()

      • hasOrder

        protected boolean hasOrder()

      • hasPosition

        public boolean hasPosition()

      • isDescendant

        public boolean isDescendant​(Individual ind)
        Is 'this' descendant from 'ind' (e.g. son, grand son, etc.)
        Parameters:
        ind -
        Returns:

      • isFemale

        public boolean isFemale()

      • isMale

        public boolean isMale()

      • isRoot

        public boolean isRoot()
        Is this a root node?
        Returns:

      • removeChild

        protected void removeChild​(Individual ind)

      • setAffected

        public void setAffected​(java.lang.Boolean affected)

      • setColor

        public void setColor​(java.lang.String color)

      • setDepth

        public void setDepth​(int depth)

      • setFather

        public void setFather​(Individual father)

      • setId

        public void setId​(java.lang.String id)

      • setLabel

        public void setLabel​(java.lang.String label)

      • setMother

        public void setMother​(Individual mother)

      • setOrder

        public void setOrder​(int order)

      • setSex

        public void setSex​(org.snpeff.ped.Sex sex)

      • sizeByDepth

        public void sizeByDepth​(int[] sizeByLevel)
        Size by depth
        Parameters:
        sizeByLevel -

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • toStringTree

        public java.lang.String toStringTree()