org.gersteinlab.act
Class SaturationPlotsCreator
java.lang.Object
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.
Field Summary |
protected static int |
DEF_MAX_COM
Default maximum number of combinations. |
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 |
DEF_MAX_COM
protected static final int DEF_MAX_COM
- Default maximum number of combinations.
- See Also:
- Constant Field Values
SaturationPlotsCreator
public SaturationPlotsCreator()
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 totalr
- 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