BitwiseChromosome (Jenes)

java.lang.Object
- jenes.chromosome.BitwiseChromosome

All Implemented Interfaces:

java.lang.Cloneable, Chromosome<BitwiseChromosome>
```
public final class BitwiseChromosome
extends java.lang.Object
implements Chromosome<BitwiseChromosome>
```
This class provides chromosomes made of bits. Its genome contains objects coded according to a specified BitwiseChromosome.BitCoding. Typically objects coded by this chromosome are numeric values. The default integer representation is used when no BitCoding is specified.
A BitwiseChromosome has size and length attributes. The size is the number of coded value contained by its genoma; the length is the number of bits. The length depends on which coding is used for translating objects into bits. The relation between size and length is shown below:
```
  aBitwiseChromosome.length() = aBitwiseChromosome.getSize() *  aCoding.SIZE.BITS
 
```
where aCoding.SIZE.BITS is the number of bits required for coding one object.
This Chromosome performs genetic operations at bit level, processing an array of integer, thus ensuring a high throughput and minimal memory occupation. Using a 16 bit representation, a chromosome holding 4 objects (size) will be represented by 32 bits (length), thus by 2 integers (as each of integer is represented by 32 bit)
Since:

1.0

Version:

2.0

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`BitwiseChromosome.BitCoding<T>` Represents the coding used by a `BitwiseChromosome`.
`static class`	`BitwiseChromosome.BitSize` Definition of the number bit length and mask to use in the coding operations.

Nested classes/interfaces inherited from interface jenes.chromosome.Chromosome
Chromosome.Util

Constructor Summary

Constructors
Constructor and Description
`BitwiseChromosome(BitwiseChromosome chromosome)` Creates a new BitwiseChromosome using the specified one as prototype
`BitwiseChromosome(int size)` Creates a new BitwiseChromosome with the specified number of objects.
`BitwiseChromosome(int size, BitwiseChromosome.BitCoding coding)` Creates a new BitwiseChromosome with the specified number of objects and coding.

Method Summary

Methods
Modifier and Type	Method and Description
`BitwiseChromosome`	`clone()` Makes a chromosome copy
`void`	`cross(BitwiseChromosome chromosome, int from)` Exchanges the chromosome bits from the specified cross site to the final position
`void`	`cross(BitwiseChromosome chromosome, int from, int to)` Exchanges the chromosome bits in the range [from,to].
`void`	`difference(BitwiseChromosome chromosome, double[] diff)` Computes the genetic difference between two chromosomes.
`boolean`	`equals(BitwiseChromosome chromosome)` Compares the chromosome with another.
`int`	`getBitValueAt(int index)` Returns the bit value at the specified position.
`int`	`getIntLength()` Returns the chromosome length expressed in integers
`int`	`getIntSize()` Returns the number of integer used by the chromosome for coding the objects
`int`	`getIntValueAt(int index)` Returns the int value at the specified position
`int`	`getSize()` Returns the number of coded objects contained by this chromosome.
`BitwiseChromosome.BitCoding`	`getType()` Returns the `BitwiseChromosome.BitCoding` used by this chromosome
`java.lang.Object`	`getValueAt(int index)` Returns the object value at the specified position in the chromosome.
`void`	`leftShift(int from, int to)` Executes the left shift of bits within the specified range.
`int`	`length()` Returns the chromosome length expressed in bits.
`void`	`randomize()` Randomizes each chromosome bit
`void`	`randomize(int pos)` Randomizes the bit at the given position
`void`	`rightShift(int from, int to)` Executes the right shift of bits within the specified range.
`void`	`setAs(BitwiseChromosome chromosome)` Sets this chromosome as a copy of another.
`void`	`setBitValueAt(int index, int bit)` Sets the bit at a given position.
`void`	`setDefaultValueAt(int pos)` Sets the default bit value at the a given position
`void`	`setIntValueAt(int index, int value)` Sets the int value at the specified position
`void`	`setValue(int index, java.lang.Object value)` Sets the specified object value at the given position.
`void`	`swap(int pos1, int pos2)` Swaps two bits at given positions
`java.lang.Object[]`	`toArray()` Returns an array containing all of the genes in chromosome.

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - BitwiseChromosome
```
public BitwiseChromosome(int size)
```
    Creates a new BitwiseChromosome with the specified number of objects. The chromosome is made of a bit string encoding objects.
    
    Parameters:
    size - the number of objects the chromosone represents
  - BitwiseChromosome
```
public BitwiseChromosome(int size,
                 BitwiseChromosome.BitCoding coding)
```
    Creates a new BitwiseChromosome with the specified number of objects and coding.
    
    Parameters:
    size - the number of chromosome coded objects
    coding - the coding to use
  - BitwiseChromosome
```
public BitwiseChromosome(BitwiseChromosome chromosome)
```
    Creates a new BitwiseChromosome using the specified one as prototype
    
    Parameters:
    chromosome - the chromosome to copy
- Method Detail
  - getType
```
public final BitwiseChromosome.BitCoding getType()
```
    Returns the BitwiseChromosome.BitCoding used by this chromosome
    
    Returns:
    the bit coding used
  - getSize
```
public final int getSize()
```
    Returns the number of coded objects contained by this chromosome.
    
    Returns:
    the number of coded objects
  - getIntValueAt
```
public final int getIntValueAt(int index)
```
    Returns the int value at the specified position
    
    Parameters:
    index - the index of the value to return
    
    Returns:
    the int value at the specified position
  - setIntValueAt
```
public final void setIntValueAt(int index,
                 int value)
```
    Sets the int value at the specified position
    
    Parameters:
    index - the index of the element to be modify
    value - the value to set
  - getIntSize
```
public final int getIntSize()
```
    Returns the number of integer used by the chromosome for coding the objects
    
    Returns:
    the number of integers
  - getValueAt
```
public final java.lang.Object getValueAt(int index)
```
    Returns the object value at the specified position in the chromosome. The value is decoded and returned.
    
    Parameters:
    index - the position
    
    Returns:
    the object
  - setValue
```
public final void setValue(int index,
            java.lang.Object value)
```
    Sets the specified object value at the given position. The object value is encoded and then placed in the chromosome.
    
    Parameters:
    index - the position
    value - the object value to be placed
  - getBitValueAt
```
public final int getBitValueAt(int index)
```
    Returns the bit value at the specified position. This position takes into account the usage of integers made by the coding specification. For instance, if the coding requires 5 bits for each value, index 31 does not point to the last bit of the first integer, but to the second bit of the second integer, as described below [01101 01110 00011 11011 10101 10010 --] [01100 11010 ...
    
    Parameters:
    index - the position
    
    Returns:
    the bit value
  - setBitValueAt
```
public final void setBitValueAt(int index,
                 int bit)
```
    Sets the bit at a given position. Position is related to the bits actually used and not to those occupied by the chromosome data structure.
    
    Parameters:
    index - the position
    bit - the bit value
  - cross
```
public final void cross(BitwiseChromosome chromosome,
         int from,
         int to)
```
    Exchanges the chromosome bits in the range [from,to]. The range is referred to positions of bits effectively used by the chromosome and not to thoae occupied by the underlying data structure.
    
    Specified by:
    
    cross in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    chromosome - the chromosome to cross with
    from - the initial cross site
    to - the final cross site
  - cross
```
public final void cross(BitwiseChromosome chromosome,
         int from)
```
    Exchanges the chromosome bits from the specified cross site to the final position
    
    Specified by:
    
    cross in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    chromosome - the chromosome to cross with
    from - the initial cross site
  - equals
```
public final boolean equals(BitwiseChromosome chromosome)
```
    Compares the chromosome with another.
    
    Specified by:
    
    equals in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    chromosome - the chromosome to compare to.
    
    Returns:
    true, if the two chromosome are equal.
  - length
```
public final int length()
```
    Returns the chromosome length expressed in bits. This value can be different from the effective chromosome length (the latter can contain bits used to make the former multiple of Integer.SIZE)
    
    Specified by:
    
    length in interface Chromosome<BitwiseChromosome>
    
    Returns:
    the chromosome length
  - getIntLength
```
public final int getIntLength()
```
    Returns the chromosome length expressed in integers
    
    Returns:
    the number of integers
  - randomize
```
public final void randomize(int pos)
```
    Randomizes the bit at the given position
    
    Specified by:
    
    randomize in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    pos - the position of bit to alter
  - randomize
```
public final void randomize()
```
    Randomizes each chromosome bit
    
    Specified by:
    
    randomize in interface Chromosome<BitwiseChromosome>
  - leftShift
```
public final void leftShift(int from,
             int to)
```
    Executes the left shift of bits within the specified range. The shift is circular, so the most right-side bit becomes the first bit on left.
    
    Specified by:
    
    leftShift in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    from - the lower range limit
    to - the upper range limit
  - rightShift
```
public final void rightShift(int from,
              int to)
```
    Executes the right shift of bits within the specified range. The shift is circular, so the most left-side bit becomes the last bit on right.
    
    Specified by:
    
    rightShift in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    from - the lower range limit
    to - the upper range limit
  - setAs
```
public final void setAs(BitwiseChromosome chromosome)
```
    Sets this chromosome as a copy of another.
    
    Specified by:
    
    setAs in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    chromosome - the chromosome to copy
  - setDefaultValueAt
```
public final void setDefaultValueAt(int pos)
```
    Sets the default bit value at the a given position
    
    Specified by:
    
    setDefaultValueAt in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    pos - bit position
  - swap
```
public final void swap(int pos1,
        int pos2)
```
    Swaps two bits at given positions
    
    Specified by:
    
    swap in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    pos1 - first bit position
    pos2 - second bit position
  - clone
```
public final BitwiseChromosome clone()
```
    Makes a chromosome copy
    
    Specified by:
    
    clone in interface Chromosome<BitwiseChromosome>
    
    Overrides:
    
    clone in class java.lang.Object
    
    Returns:
    the chromsome clone
  - difference
```
public void difference(BitwiseChromosome chromosome,
              double[] diff)
```
    Description copied from interface: Chromosome
    
    Computes the genetic difference between two chromosomes. NOTICE: This should not be invoked directly. Please, use #getDifference instead.
    
    Specified by:
    
    difference in interface Chromosome<BitwiseChromosome>
    
    Parameters:
    chromosome - - the chromosome to quantify the minus from
    diff - - the variable to be filled by the minus values
  - toArray
```
public java.lang.Object[] toArray()
```
    Description copied from interface: Chromosome
    
    Returns an array containing all of the genes in chromosome.
    
    Specified by:
    
    toArray in interface Chromosome<BitwiseChromosome>
    
    Returns:
    an array containing all of the genes in chromosome.

Class BitwiseChromosome

Nested Class Summary

Nested classes/interfaces inherited from interface jenes.chromosome.Chromosome

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BitwiseChromosome

BitwiseChromosome

BitwiseChromosome

Method Detail

getType

getSize

getIntValueAt

setIntValueAt

getIntSize

getValueAt

setValue

getBitValueAt

setBitValueAt

cross

cross

equals

length

getIntLength

randomize

randomize

leftShift

rightShift

setAs

setDefaultValueAt

swap

clone

difference

toArray