picard.analysis

Class CounterManager

java.lang.Object

picard.analysis.CounterManager

public class CounterManager
extends java.lang.Object

Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset. Each Counter represents a certain region of a processed sequence starting from offset and can accumulate some value for each locus of this sequence, for instance, read coverage.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	CounterManager.Counter Class represents an integer array with methods to increment and get the values from it with respect to offset of outer CounterManager.

Constructor Summary

Constructors

Constructor and Description
CounterManager(int arrayLength, int readLength) Constructor creates new CounterManager without any Counters, counters are added to CounterManager via newCounter() method

Method Summary

Modifier and Type	Method and Description
void	checkOutOfBounds(int locusPosition) Method checks that new locus position is not out of bounds of Counter arrays and there is enough space in them to hold information on at least one more read of length this#readLength.
void	clear() Clears all inner Counter arrays
CounterManager.Counter	newCounter() Creates a new Counter object and adds it to the list of managed Counters.

Methods inherited from class java.lang.Object

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

Constructor Detail

CounterManager

public CounterManager(int arrayLength,
                      int readLength)

Constructor creates new CounterManager without any Counters, counters are added to CounterManager via newCounter() method

Parameters:

arrayLength - length of inner Counter arrays

readLength - proposed length of processed reads

Method Detail

checkOutOfBounds

public void checkOutOfBounds(int locusPosition)

Method checks that new locus position is not out of bounds of Counter arrays and there is enough space in them to hold information on at least one more read of length this#readLength. If there is no free space, but there is accumulated information in Counter arrays after new locus position that we may need, the arrays are rebased, so that 0 index of arrays represents new locus position. In other case, we just clear the arrays.

Parameters:

locusPosition - position in the reference sequence, that will be represented by index 0 of CounterManager.Counter arrays.

clear

public void clear()

Clears all inner Counter arrays

newCounter

public CounterManager.Counter newCounter()

Creates a new Counter object and adds it to the list of managed Counters.

Returns:

CounterManager.Counter, that will be managed by current CounterManager