public void DoChromothripsis()
{
Chromothripsis chromo;
if (chromosome == "4q")
{
Chromosome chr = new Chromosome("4");
Range chr4q = chr.GetQ();
chromo = new Chromothripsis(chr, chr4q);
}
else
{
Chromosome chr = new Chromosome(chromosome);
chromo = new Chromothripsis(chr);
}
chromo.RunSimulations(runs, cuts, probability, modelDatabase, extendedOutput);
}
public void worker_ChromothripsisBatch(object sender, EventArgs e)
{
App.Log();
App.Log();
Chromothripsis chromo4q, chromo4qnull, chromo4qnull2, chromo4qnull3;
Chromosome chr4 = new Chromosome("4");
Range chr4q = chr4.GetQ();
chromo4q = new Chromothripsis(chr4, chr4q);
Chromosome chr4qnull = new Chromosome("4qnull");
chromo4qnull = new Chromothripsis(chr4qnull);
Chromosome chr4qnull2 = new Chromosome("4qnull_2");
chromo4qnull2 = new Chromothripsis(chr4qnull2);
Chromosome chr4qnull3 = new Chromosome("4qnull_3");
chromo4qnull3 = new Chromothripsis(chr4qnull3);
int i;
for (i = 0; i < 2; i++)
{
chromo4qnull.RunSimulations(100000, 400, 0.5, "chromo");
}
for (i = 0; i < 2; i++)
{
chromo4qnull2.RunSimulations(100000, 400, 0.5, "chromo");
}
for (i = 0; i < 2; i++)
{
chromo4qnull3.RunSimulations(100000, 400, 0.5, "chromo");
}
for (i = 0; i < 20; i++)
{
chromo4q.RunSimulations(100000, 200, 0.5, "chromo");
}
for (i = 0; i < 10; i++)
{
chromo4qnull.RunSimulations(100000, 200, 0.5, "chromo");
}
chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
chromo4qnull.RunSimulations(100000, 200, 0.5, "pfam-a");
chromo4qnull2.RunSimulations(100000, 200, 0.5, "pfam-a");
chromo4qnull3.RunSimulations(100000, 200, 0.5, "pfam-a");
for (i = 0; i < 20; i++)
{
chromo4q.RunSimulations(100000, 200, 0.5, "chromo");
}
for (i = 0; i < 10; i++)
{
chromo4qnull2.RunSimulations(100000, 200, 0.5, "chromo");
}
for (i = 0; i < 10; i++)
{
chromo4qnull3.RunSimulations(100000, 200, 0.5, "chromo");
}
for (i = 0; i < 10; i++)
{
chromo4qnull.RunSimulations(100000, 200, 0.5, "chromo");
}
for (i = 0; i < 100; i++)
{
chromo4q.RunSimulations(100000, 200, 0.5, "chromo");
}
/*
*
* for (i = 0; i < 5; i++) chromo4q.RunSimulations(250000, 200, 0.5, "chromo");
* for (i = 0; i < 3; i++) chromo4qnull.RunSimulations(250000, 200, 0.5, "chromo");
* for (i = 0; i < 3; i++) chromo4qnull2.RunSimulations(250000, 200, 0.5, "chromo");
* for (i = 0; i < 3; i++) chromo4qnull3.RunSimulations(250000, 200, 0.5, "chromo");
*
* for (i = 0; i < 15; i++) chromo4q.RunSimulations(100000, 100, 0.5, "chromo");
* for (i = 0; i < 7; i++) chromo4qnull.RunSimulations(100000, 100, 0.5, "chromo");
* for (i = 0; i < 7; i++) chromo4qnull2.RunSimulations(100000, 100, 0.5, "chromo");
* for (i = 0; i < 7; i++) chromo4qnull3.RunSimulations(100000, 100, 0.5, "chromo");
*
* for (i = 0; i < 12; i++) chromo4q.RunSimulations(100000, 400, 0.5, "chromo");
* for (i = 0; i < 5; i++) chromo4qnull.RunSimulations(100000, 400, 0.5, "chromo");
* for (i = 0; i < 5; i++) chromo4qnull2.RunSimulations(100000, 400, 0.5, "chromo");
* for (i = 0; i < 5; i++) chromo4qnull3.RunSimulations(100000, 400, 0.5, "chromo");
*/
// App.Log("<h3>Original chromosome vs. null models</h3>", true);
/* for (i = 0; i < 9; i++) chromo4q.RunSimulations(100000, 200, 0.5, "chromo");
* chromo4q.RunSimulations(100000, 200, 0.5, "chromo", true);
* for (i = 0; i < 9; i++) chromo4qnull.RunSimulations(100000, 200, 0.5, "chromo");
* chromo4qnull.RunSimulations(100000, 200, 0.5, "chromo", true);
* for (i = 0; i < 10; i++) chromo4qnull2.RunSimulations(100000, 200, 0.5, "chromo");
* for (i = 0; i < 10; i++) chromo4qnull3.RunSimulations(100000, 200, 0.5, "chromo");*/
/*
* App.Log("<h3>PFam-A Test</h3>", true);
* chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
* chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
* chromo4q.RunSimulations(100000, 200, 0.5, "pfam-a");
* chromo4qnull.RunSimulations(100000, 200, 0.5, "pfam-a");
* chromo4qnull.RunSimulations(100000, 200, 0.5, "pfam-a");
* chromo4qnull2.RunSimulations(100000, 200, 0.5, "pfam-a");
* chromo4qnull2.RunSimulations(100000, 200, 0.5, "pfam-a");
* chromo4qnull2.RunSimulations(100000, 200, 0.5, "pfam-a");
* chromo4qnull2.RunSimulations(100000, 200, 0.5, "pfam-a");
*/
/*
* App.Log("<h3>Run numbers</h3>", true);
* for (i = 0; i < 5; i++) chromo4q.RunSimulations(1000, 100, 0.5, "chromo");
* for (i = 0; i < 5; i++) chromo4q.RunSimulations(5000, 100, 0.5, "chromo");
* for (i = 0; i < 5; i++) chromo4q.RunSimulations(10000, 100, 0.5, "chromo");
* for (i = 0; i < 5; i++) chromo4q.RunSimulations(50000, 100, 0.5, "chromo");
* for (i = 0; i < 3; i++) chromo4q.RunSimulations(100000, 100, 0.5, "chromo");
* for (i = 0; i < 2; i++) chromo4q.RunSimulations(500000, 100, 0.5, "chromo");
* chromo4q.RunSimulations(1000000, 100, 0.5, "chromo");
* chromo4q.RunSimulations(2000000, 100, 0.5, "chromo");
*/
// for (i = 0; i < 10; i++) chromo4q.RunSimulations(100000, 200, 0.5, "chromo");
}