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()