org.gersteinlab.act
Class SaturationPlotsCreator

java.lang.Object
  extended by org.gersteinlab.act.SaturationPlotsCreator

public class SaturationPlotsCreator
extends java.lang.Object

        This class produces saturation plots from a set of files, each
        containing a list of genomic regions. Each genomic region is specified
        using the following format:

        

        where
            is the identifier of the region-at-large, such as the chromosome
         is the starting position of the region
           is the ending position of the region (this position is inside
                the region)

        The y-axis could be the absolute number of nucleotides, or a fraction of
        an input total number of nucleotides, such as the total number of
        nucleotides of the coding transcripts in the example. To use the absolute
        number, input the total as 0.

        If the number of input files is no more than 31, the program can compute
        the coverage from all combinations of the input datasets. If the number
        of input files is more than 31, or if the number of combinations is more
        than a specified threshold, a random sample of the combinations will be
        considered.
        


Nested Class Summary
protected static class SaturationPlotsCreator.DefaultBoxAndWhiskerCategoryDatasetWithNoFarOuts
           
 
Field Summary
protected static int DEF_MAX_COM
          Default maximum number of combinations.
 
Constructor Summary
SaturationPlotsCreator()
           
 
Method Summary
static int choose(int n, int r)
          Get the number of ways to choose r balls from n balls.
static void main(java.lang.String[] argv)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

DEF_MAX_COM

protected static final int DEF_MAX_COM
Default maximum number of combinations.

See Also:
Constant Field Values
Constructor Detail

SaturationPlotsCreator

public SaturationPlotsCreator()
Method Detail

main

public static void main(java.lang.String[] argv)
                 throws java.lang.Exception
Throws:
java.lang.Exception

choose

public static int choose(int n,
                         int r)
                  throws java.lang.IllegalArgumentException
Get the number of ways to choose r balls from n balls.

Parameters:
n - The number of balls in total
r - The number of balls being chosen
Returns:
The number of ways
Throws:
java.lang.IllegalArgumentException - If n or r is negative, or if n is smaller than r