Adds all of the final edges found so far to the AbGraph set by setAbGraph()
To ensure that Misrejoiner has finished the process of misrejoining, call
getAllFinalEdges() before calling this method or call getAndAddFinalEdges()
does the final chromosome appear like a whole chromosome?
For instance, in mFISH, if the break restituted, or an exchange occured between homologues
the final chromosome will appear uneffected.
Each ConstantDist object represents a probability distribution for
which the probability of one particular integer is 1.0 and the value
of every other integer is 0.0
ExponentialMisrejoiner extends Misrejoiner with the rule that the probability
of two free ends joining decays exponentially with the distance between
the two free ends in the Geometry
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.
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.
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.
Interface encapsulates the behavior of the chromatin painting as a means of translating from
the chromatin edges of an AbGraph to the Fragments of a Final Pattern.
Creates a Genome object from a file which must follow a particular format
There is a separate line in the file for each Chromosome in the Genome
each line must be written in the following way:
[name]:[homologue # (0 or 1)]:[# base pairs]:[index # of centromere]:[circularity (true or false)]