Package org.snpsift.pedigree

Class PedigreeDraw

  • public class PedigreeDraw
extends java.lang.Object
    Draws a pedigree using SVG
    Author:
    pablocingolani

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static boolean debug  

    • Constructor Summary

      Constructors 
      Constructor Description
      PedigreeDraw​(java.lang.String tfamFileName)  
      PedigreeDraw​(org.snpeff.ped.PedPedigree pedigree)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int assignOrder()
      Assign order
      int calcDepth()
      Max depth in this pedigree
      void circle​(int x, int y, int r, java.lang.String strokeColor, int strokeWidth, java.lang.String fillColor)  
      void colorAffected()
      Color individuals by affected status
      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)
      java.lang.String drawSvg()
      Draw the full pedigree as an SVG graph
      void drawSvgByFamily​(java.lang.String outdir, java.lang.String info)
      Draw each family
      void 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 Child
      void 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 posX
      protected void moveIfRight​(int posX, int deltaX, java.util.Set<Individual> except)
      Move if the object is located to the right of posX
      void square​(int x, int y, int width, int height, java.lang.String strokeColor, int strokeWidth, java.lang.String fillColor)  
      void unknown​(Individual ind)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • debug

        public static boolean debug

    • Constructor Detail

      • PedigreeDraw

        public PedigreeDraw​(org.snpeff.ped.PedPedigree pedigree)

      • PedigreeDraw

        public PedigreeDraw​(java.lang.String tfamFileName)

    • Method Detail

      • assignOrder

        public int assignOrder()
        Assign order
        Returns:

      • calcDepth

        public int calcDepth()
        Max depth in this pedigree
        Returns:

      • circle

        public void circle​(int x,
                   int y,
                   int r,
                   java.lang.String strokeColor,
                   int strokeWidth,
                   java.lang.String fillColor)

      • colorAffected

        public void colorAffected()
        Color individuals by affected status

      • 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 -

      • drawSvg

        public java.lang.String drawSvg()
        Draw the full pedigree as an SVG graph
        Returns:

      • drawSvgByFamily

        public void drawSvgByFamily​(java.lang.String outdir,
                            java.lang.String info)
        Draw each family

      • get

        public Individual get​(java.lang.String id)

      • getIndividuals

        public java.util.ArrayList<Individual> getIndividuals()

      • getSizeX

        public int getSizeX()

      • getSizeY

        public int getSizeY()

      • label

        public void label​(java.awt.Point p,
                  java.lang.String label)

      • line

        public void line​(Individual parent1,
                 Individual parent2,
                 Individual child)
        Line between Mother-Father and Child
        Parameters:
        parent1 -
        parent2 -
        child -

      • line

        public void line​(java.awt.Point p1,
                 java.awt.Point p2)

      • line

        public void line​(java.awt.Point p1,
                 java.awt.Point p2,
                 java.lang.String color)

      • lineDashed

        public void lineDashed​(java.awt.Point p1,
                       java.awt.Point p2,
                       java.lang.String color)

      • 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 -

      • 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 -

      • square

        public void square​(int x,
                   int y,
                   int width,
                   int height,
                   java.lang.String strokeColor,
                   int strokeWidth,
                   java.lang.String fillColor)

      • unknown

        public void unknown​(Individual ind)