Package org.snpsift.pedigree

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()