java.lang.Object
com.compomics.util.experiment.identification.protein_inference.fm_index.Rank
All Implemented Interfaces:
Serializable

public class Rank
extends Object
implements Serializable
Rank as used in the FM index.
Author:
Dominik Kopczynski
See Also:
Serialized Form
  • Field Summary

    Fields 
    Modifier and Type Field Description
    int length
    The length.
  • Constructor Summary

    Constructors 
    Constructor Description
    Rank()
    Empty default constructor.
    Rank​(byte[] text, long[] aAlphabet)
    Constructor.
    Rank​(long[] originalBitfield, int length)
    Constructor.
  • Method Summary

    Modifier and Type Method Description
    int getAllocatedBytes()
    Returns the number of bytes for the allocated arrays.
    int getRank​(int index, boolean zeros)
    Returns the rank.
    int getRankOne​(int index)
    Returns the rank of ones.
    int getRankZero​(int index)
    Returns the rank of zeros.
    int getSelect​(int index)
    Returns the position of the i-th one
    boolean isOne​(int index)
    Returns true if the value is equal to one.
    int isOneInt​(int index)
    Returns true if the value is equal to one.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Field Details

    • length

      public final int length
      The length.
  • Constructor Details

    • Rank

      public Rank()
      Empty default constructor.
    • Rank

      public Rank​(byte[] text, long[] aAlphabet)
      Constructor.
      Parameters:
      text - the text
      aAlphabet - the alphabet
    • Rank

      public Rank​(long[] originalBitfield, int length)
      Constructor.
      Parameters:
      originalBitfield - an original bitfield
      length - length of original bitfield
  • Method Details

    • getRank

      public int getRank​(int index, boolean zeros)
      Returns the rank.
      Parameters:
      index - the value
      zeros - the zeros
      Returns:
      the rank
    • getRankOne

      public final int getRankOne​(int index)
      Returns the rank of ones.
      Parameters:
      index - the value
      Returns:
      the rank
    • getRankZero

      public int getRankZero​(int index)
      Returns the rank of zeros.
      Parameters:
      index - the value
      Returns:
      the rank
    • isOne

      public boolean isOne​(int index)
      Returns true if the value is equal to one.
      Parameters:
      index - the value
      Returns:
      true if the value is equal to one
    • getSelect

      public int getSelect​(int index)
      Returns the position of the i-th one
      Parameters:
      index - of the i-th one
      Returns:
      position of the i-th one
    • isOneInt

      public int isOneInt​(int index)
      Returns true if the value is equal to one.
      Parameters:
      index - the value
      Returns:
      the bit
    • getAllocatedBytes

      public int getAllocatedBytes()
      Returns the number of bytes for the allocated arrays.
      Returns:
      the number of bytes for the allocated arrays