ca.cas.painting
Class WholeChromPaint

java.lang.Object
  ca.cas.painting.WholeChromPaint

All Implemented Interfaces:

Paint

public class WholeChromPaint
extends java.lang.Object
implements Paint

A whole chromosome Paint. This class can be used to simulate any whole chromosome painting scheme (such mFISH, FISH, 2-FISH, any mapping from the set of chromosomes to a set of colors). Also includes functionality for counterstaining and centromere probes. Defaults are no counterstain and centromere probes.

Constructor Summary

WholeChromPaint(boolean track_centromeres, boolean counterstain, java.lang.String counterstain_label)
creates a whole chromosome paint.

Method Summary

Fragment	agglomerate(Fragment first, Fragment second) Determines whether the two fragments span a cryptic break.
boolean	appearsWhole(FPChrom fpchrom) Returns true if the final pattern chromosome appears whole.
boolean	counterstain() returns true if the paint uses a counterstain
boolean	hasCentromere(long source, long target, long centromere) returns true if source and target are on opposite sides of centromere.
boolean	isCounterstained(Fragment frag) Returns true if the fragment is counterstained.
boolean	isOriented() returns true if the Painting scheme is oriented.
Fragment	paint(AbEdge chrom_edge) returns the same result as paint(chrom_edge.getSource(), chrom_edge.getTarget())
Fragment	paint(AbVertex source, AbVertex target) returns the fragment associated to the chromatin edge that would span the source and target vertices.
java.lang.String	setPaint(Chromosome c, java.lang.String label) creates a whole chromosome paint with centromere probes and no counterstain.
boolean	trackCentromeres() returns true if the Paint records centromeres

Methods inherited from class java.lang.Object

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

Constructor Detail

WholeChromPaint

public WholeChromPaint(boolean track_centromeres,
                       boolean counterstain,
                       java.lang.String counterstain_label)

creates a whole chromosome paint.

Parameters:

track_centromeres - keep track of centromeres

counterstain - counterstain unpainted chromosomes.

counterstain_label - what ``paint'' to apply to counterstained chromosomes.

Method Detail

setPaint

public java.lang.String setPaint(Chromosome c,
                                 java.lang.String label)

creates a whole chromosome paint with centromere probes and no counterstain. public WholeChromPaint() { } /** sets the paint label from a chromosome.

Parameters:

c - chromosome

label - label for that chromosome

Returns:

previous label associated with c, or null if there was no label for c.

isOriented

public boolean isOriented()

Description copied from interface: Paint

returns true if the Painting scheme is oriented. For instance, FISH is unoreinted, but banding is oriented. In particular, if paint(AbVertex, AbVertex) is independent of the order then the Paint is unoriented.

Specified by:

isOriented in interface Paint

Returns:

true if the Paint is oriented, else false.

counterstain

public boolean counterstain()

Description copied from interface: Paint

returns true if the paint uses a counterstain

Specified by:

counterstain in interface Paint

Returns:

true if the paint uses a counterstain, else false.

trackCentromeres

public boolean trackCentromeres()

Description copied from interface: Paint

returns true if the Paint records centromeres

Specified by:

trackCentromeres in interface Paint

Returns:

true if the paint records centromere, else false.

paint

public Fragment paint(AbEdge chrom_edge)

Description copied from interface: Paint

returns the same result as paint(chrom_edge.getSource(), chrom_edge.getTarget())

Specified by:

paint in interface Paint

Parameters:

chrom_edge - chromatin edge

Returns:

painted version of chromatin edge

paint

public Fragment paint(AbVertex source,
                      AbVertex target)

returns the fragment associated to the chromatin edge that would span the source and target vertices. if they are not on the same chromosome, the method returns null. if they are on the same chromosome, it returns a Fragment with a label accorded by this paint to that chromosome, a length according to the difference between the source and target vertex locations, and a centromere flag according to whether these two locations fall on opposite sides of the chromosome.

Specified by:

paint in interface Paint

Parameters:

source - source vertex

target - target vertex

Returns:

Fragment label associated to the chromatin edge that would span the source and target vertices.

agglomerate

public Fragment agglomerate(Fragment first,
                            Fragment second)

Determines whether the two fragments span a cryptic break. In a whole chromosome paint, this happens when they both have the same label and there is no more than one centromere between them. If this is true, then the method returns a Fragment with the same label, a centromere if either fragment had a centromere, and a length equal to the sum of the two lengths.

Specified by:

agglomerate in interface Paint

Parameters:

first - first fragment

second - second fragment

Returns:

agglomeration of the two fragments, or if not agglomerable, null

appearsWhole

public boolean appearsWhole(FPChrom fpchrom)

Returns true if the final pattern chromosome appears whole. This is true if the chromosome is not a ring, has only one fragment and that fragment has a centromere (if we're tracking centromeres). This method will need some work before we use it to paint circular genomes.

Specified by:

appearsWhole in interface Paint

Parameters:

fpchrom - final pattern chromosome

Returns:

true if the final pattern chromosome appears whole

isCounterstained

public boolean isCounterstained(Fragment frag)

Returns true if the fragment is counterstained. In particular, if it has the counterstain as its label.

Specified by:

isCounterstained in interface Paint

Parameters:

frag - fragment

Returns:

true if the fragment is counterstained.

hasCentromere

public boolean hasCentromere(long source,
                             long target,
                             long centromere)

returns true if source and target are on opposite sides of centromere.

Parameters:

source -

target -

centromere -

Returns:

true if centromere lies between source and target, else false.