Package org.snpsift.pedigree
Class Individual
java.lang.Object
org.snpsift.pedigree.Individual
- All Implemented Interfaces:
Comparable<Individual>
An individual in the pedigree
Individuals are like TfamEntries but have drawing info (coordinates, color, etc.)
- Author:
- pablocingolani
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addChild
(Individual ind) int
Depth in the graph.int
compareTo
(Individual ind) getChilds
(Individual spouse) Get only childs from this spousegetColor()
int
getDepth()
getId()
getLabel()
int
getOrder()
org.snpeff.ped.Sex
getSex()
protected boolean
hasOrder()
boolean
boolean
isDescendant
(Individual ind) Is 'this' descendant from 'ind' (e.g.boolean
isFemale()
boolean
isMale()
boolean
isRoot()
Is this a root node?protected void
removeChild
(Individual ind) void
setAffected
(Boolean affected) void
void
setDepth
(int depth) void
setFather
(Individual father) void
void
void
setMother
(Individual mother) void
setOrder
(int order) void
setSex
(org.snpeff.ped.Sex sex) void
sizeByDepth
(int[] sizeByLevel) Size by depthtoString()
-
Constructor Details
-
Individual
public Individual(org.snpeff.ped.TfamEntry tfamEntry)
-
-
Method Details
-
addChild
-
calcDepth
public int calcDepth()Depth in the graph. Depth is zero for root nodes- Returns:
-
compareTo
- Specified by:
compareTo
in interfaceComparable<Individual>
-
getAffected
-
getChilds
-
getChilds
Get only childs from this spouse- Parameters:
spouse
-- Returns:
-
getColor
-
getDepth
public int getDepth() -
getFamilyId
-
getFather
-
getId
-
getLabel
-
getMother
-
getOrder
public int getOrder() -
getPosition
-
getSex
public org.snpeff.ped.Sex getSex() -
hasOrder
protected boolean hasOrder() -
hasPosition
public boolean hasPosition() -
isDescendant
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
-
setAffected
-
setColor
-
setDepth
public void setDepth(int depth) -
setFather
-
setId
-
setLabel
-
setMother
-
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
-
toStringTree
-