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java.lang.Object | +--neobio.alignment.Factor
This class is used by FactorSequence to create a linked list of factors of a text as induced by its Lempel-Ziv (LZ78) factorisation.
Each instance of this class represent a string composed of its an ancestor factor's string plus one character, and contains:
FactorSequence| Field Summary | |
| protected  Factor | ancestorA pointer to this factor's ancestor, which represents a prefix of this factor's text. | 
| protected  int | lengthThe number of characters of the text represented by this factor. | 
| protected  char | new_charThe new character of this factor. | 
| protected  Factor | nextA pointer to the next factor. | 
| protected  int | serial_numberThis factor's serial number, which indicates the order of this factor inside the linked list of factors of a text. | 
| Constructor Summary | |
| Factor()Creates a new empty Factor. | |
| Factor(Factor ancestor,
             int serial_number,
             char new_char)Creates a new Factorinstance with the specified serial number and
 new character, and pointing to the given ancestor. | |
| Method Summary | |
|  Factor | getAncestor()Returns this factor's ancestor factor. | 
|  int | getAncestorSerialNumber()This method is a shorthand to return the serial number of this factor's ancestor. | 
|  char | getNewChar()Returns this factor's new character. | 
|  Factor | getNext()Returns this factor's next factor. | 
|  int | getSerialNumber()Returns this factor's serial number. | 
|  int | length()Returns this factor's length. | 
|  void | setNext(Factor next)Sets this factor's nextpointer to point to the specified factor. | 
|  java.lang.String | toString()Returns a string representation of the text represented by this factor. | 
| Methods inherited from class java.lang.Object | 
| clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait | 
| Field Detail | 
protected Factor ancestor
protected Factor next
protected int serial_number
protected int length
protected char new_char
| Constructor Detail | 
public Factor()
Factor. It has no ancestor and no character (both
 are set to null). Its serial number is set to zero as well as its
 length.
 This constructor is used to initiate the a linked list of factors of a text. Its
 next pointer is initially null, but it is typically set
 to point to the first factor afterwards (with the setNext method).
setNext(neobio.alignment.Factor)
public Factor(Factor ancestor,
              int serial_number,
              char new_char)
Factor instance with the specified serial number and
 new character, and pointing to the given ancestor. Its length is set to its
 ancestor's length plus 1.
 Its next pointer is initially null, but it is
 typically set to point to the next factor afterwards (with the setNext
 method).
ancestor - this factor's ancestorserial_number - this factor's serial numbernew_char - this factor's new charactersetNext(neobio.alignment.Factor)| Method Detail | 
public void setNext(Factor next)
next pointer to point to the specified factor.
 Although the next factor has typically a serial number equal to this factor's
 serial number plus 1, no attempt is made to guarantee this rule. This allows
 special constructs or a different order in the factorisation.
next - the factor that will be pointed togetNext()public Factor getAncestor()
public int getAncestorSerialNumber()
public Factor getNext()
setNext(neobio.alignment.Factor)public int getSerialNumber()
public int length()
public char getNewChar()
public java.lang.String toString()
toString in class java.lang.Object| 
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