Package org.snpsift.pedigree
Class PedigreeDraw
- java.lang.Object
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- org.snpsift.pedigree.PedigreeDraw
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public class PedigreeDraw extends java.lang.Object
Draws a pedigree using SVG- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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Constructor Summary
Constructors Constructor Description PedigreeDraw(java.lang.String tfamFileName)
PedigreeDraw(org.snpeff.ped.PedPedigree pedigree)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
assignOrder()
Assign orderint
calcDepth()
Max depth in this pedigreevoid
circle(int x, int y, int r, java.lang.String strokeColor, int strokeWidth, java.lang.String fillColor)
void
colorAffected()
Color individuals by affected statusvoid
diamond(int x, int y, int width, int height, java.lang.String strokeColor, int strokeWidth, java.lang.String fillColor)
Draw a diamond (unknown sex)java.lang.String
drawSvg()
Draw the full pedigree as an SVG graphvoid
drawSvgByFamily(java.lang.String outdir, java.lang.String info)
Draw each familyvoid
female(Individual ind)
java.util.List<Individual>
findSpouses(Individual ind)
Individual
get(java.lang.String id)
java.util.ArrayList<Individual>
getIndividuals()
int
getSizeX()
int
getSizeY()
void
label(java.awt.Point p, java.lang.String label)
void
line(java.awt.Point p1, java.awt.Point p2)
void
line(java.awt.Point p1, java.awt.Point p2, java.lang.String color)
void
line(Individual parent1, Individual parent2, Individual child)
Line between Mother-Father and Childvoid
lineDashed(java.awt.Point p1, java.awt.Point p2, java.lang.String color)
void
male(Individual ind)
protected void
moveIfLeft(int posX, int deltaX, java.util.Set<Individual> except)
Move if the object is located to the left of posXprotected void
moveIfRight(int posX, int deltaX, java.util.Set<Individual> except)
Move if the object is located to the right of posXvoid
square(int x, int y, int width, int height, java.lang.String strokeColor, int strokeWidth, java.lang.String fillColor)
void
unknown(Individual ind)
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Method Detail
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assignOrder
public int assignOrder()
Assign order- Returns:
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calcDepth
public int calcDepth()
Max depth in this pedigree- Returns:
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circle
public void circle(int x, int y, int r, java.lang.String strokeColor, int strokeWidth, java.lang.String fillColor)
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colorAffected
public void colorAffected()
Color individuals by affected status
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diamond
public void diamond(int x, int y, int width, int height, java.lang.String strokeColor, int strokeWidth, java.lang.String fillColor)
Draw a diamond (unknown sex)- Parameters:
x
-y
-width
-height
-strokeColor
-strokeWidth
-fillColor
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drawSvg
public java.lang.String drawSvg()
Draw the full pedigree as an SVG graph- Returns:
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drawSvgByFamily
public void drawSvgByFamily(java.lang.String outdir, java.lang.String info)
Draw each family
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female
public void female(Individual ind)
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findSpouses
public java.util.List<Individual> findSpouses(Individual ind)
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get
public Individual get(java.lang.String id)
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getIndividuals
public java.util.ArrayList<Individual> getIndividuals()
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getSizeX
public int getSizeX()
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getSizeY
public int getSizeY()
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label
public void label(java.awt.Point p, java.lang.String label)
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line
public void line(Individual parent1, Individual parent2, Individual child)
Line between Mother-Father and Child- Parameters:
parent1
-parent2
-child
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line
public void line(java.awt.Point p1, java.awt.Point p2)
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line
public void line(java.awt.Point p1, java.awt.Point p2, java.lang.String color)
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lineDashed
public void lineDashed(java.awt.Point p1, java.awt.Point p2, java.lang.String color)
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male
public void male(Individual ind)
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moveIfLeft
protected void moveIfLeft(int posX, int deltaX, java.util.Set<Individual> except)
Move if the object is located to the left of posX- Parameters:
xpos
-deltaX
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moveIfRight
protected void moveIfRight(int posX, int deltaX, java.util.Set<Individual> except)
Move if the object is located to the right of posX- Parameters:
xpos
-deltaX
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square
public void square(int x, int y, int width, int height, java.lang.String strokeColor, int strokeWidth, java.lang.String fillColor)
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unknown
public void unknown(Individual ind)
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