ca.cas.painting
Class PaintFactory

java.lang.Object
  ca.cas.painting.PaintFactory

public class PaintFactory
extends java.lang.Object

Class contains static methods for building common Paints from Genomes. Currently implemented methods include mFISH and oneFISH.

Constructor Summary

PaintFactory()

Method Summary

static Paint	mFISH(Genome g) Produces a WholeChromPaint from a Genome where every chromosome with is painted with the name of the chromosome and centromeres are visible.
static Paint	mFISH(Genome g, boolean track_centromeres) Produces a WholeChromPaint from a Genome where every chromosome with is painted with the name of the chromosome and centromeres are visible, if track_centromeres == true.
static Paint	oneFISH(Genome g, java.lang.String chrom_name, java.lang.String chrom_color, java.lang.String counterstain_color) Produces a WholeChromPaint from a Genome where chromsomes with chrom_name are painted with chrom_color, all other chromosomes are counterstained with counterstain_color, and centromeres are visible.
static Paint	oneFISH(Genome g, java.lang.String chrom_name, java.lang.String chrom_color, java.lang.String counterstain_color, boolean track_centromeres) Produces a WholeChromPaint from a Genome where chromsomes with chrom_name are painted with chrom_color, all other chromosomes are counterstained with counterstain_color, and centromeres are visible, if track_centromeres == true.

Methods inherited from class java.lang.Object

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

Constructor Detail

PaintFactory

public PaintFactory()

Method Detail

mFISH

public static Paint mFISH(Genome g,
                          boolean track_centromeres)

Produces a WholeChromPaint from a Genome where every chromosome with is painted with the name of the chromosome and centromeres are visible, if track_centromeres == true.

Parameters:

g - genome

track_centromeres - with centromere probes?

Returns:

a Paint where every Chromosome in the genome is painted with its name

mFISH

public static Paint mFISH(Genome g)

Produces a WholeChromPaint from a Genome where every chromosome with is painted with the name of the chromosome and centromeres are visible.

Parameters:

g - genome

Returns:

a Paint where every Chromosome in the genome is painted with its name

oneFISH

public static Paint oneFISH(Genome g,
                            java.lang.String chrom_name,
                            java.lang.String chrom_color,
                            java.lang.String counterstain_color,
                            boolean track_centromeres)

Produces a WholeChromPaint from a Genome where chromsomes with chrom_name are painted with chrom_color, all other chromosomes are counterstained with counterstain_color, and centromeres are visible, if track_centromeres == true.

Parameters:

g - genome

chrom_name - Name of chromosome to paint

chrom_color - Color to paint chromosomes with chrom_name

counterstain_color - Color for counterstained chromosomes

track_centromeres -

Returns:

a WholeChromPaint where every chromosome with name == chrom_name and all other chromosomes are counterstained.

oneFISH

public static Paint oneFISH(Genome g,
                            java.lang.String chrom_name,
                            java.lang.String chrom_color,
                            java.lang.String counterstain_color)

Produces a WholeChromPaint from a Genome where chromsomes with chrom_name are painted with chrom_color, all other chromosomes are counterstained with counterstain_color, and centromeres are visible.

Parameters:

g - genome

chrom_name - Name of chromosome to paint

chrom_color - Color to paint chromosomes with chrom_name

counterstain_color - Color for counterstained chromosomes

Returns:

a WholeChromPaint where every chromosome with name == chrom_name and all other chromosomes are counterstained.