Class Individual

java.lang.Object
org.snpsift.pedigree.Individual
All Implemented Interfaces:
Comparable<Individual>

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

    • Individual

      public Individual(org.snpeff.ped.TfamEntry tfamEntry)
  • Method Details

    • 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 Comparable<Individual>
    • getAffected

      public Boolean getAffected()
    • getChilds

      public Collection<Individual> getChilds()
    • getChilds

      public ArrayList<Individual> getChilds(Individual spouse)
      Get only childs from this spouse
      Parameters:
      spouse -
      Returns:
    • getColor

      public String getColor()
    • getDepth

      public int getDepth()
    • getFamilyId

      public String getFamilyId()
    • getFather

      public Individual getFather()
    • getId

      public String getId()
    • getLabel

      public String getLabel()
    • getMother

      public Individual getMother()
    • getOrder

      public int getOrder()
    • getPosition

      public 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(Boolean affected)
    • setColor

      public void setColor(String color)
    • setDepth

      public void setDepth(int depth)
    • setFather

      public void setFather(Individual father)
    • setId

      public void setId(String id)
    • setLabel

      public void setLabel(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 String toString()
      Overrides:
      toString in class Object
    • toStringTree

      public String toStringTree()