Package picard.analysis

Class CounterManager

java.lang.Object
picard.analysis.CounterManager
public class CounterManager extends 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
    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
    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
    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 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 Details

    • 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 Details

    • 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 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