baobab.exec.trace
Class enumerateTraces

java.lang.Object
  extended by baobab.exec.trace.enumerateTraces

public class enumerateTraces
extends java.lang.Object

Enumerates all the traces (classes of solutions) of sorting a signed permutation (or genome) into another, by enumerating all solutions.

To get help, run the program without parameters.

How traces are represented

A reversal in a trace is represented by the sorted set of the absolute values of the markers that are affected by the reversal (see REF). Example:

   01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13.
 :: +01 +03 -02 -11 +05 -09 -10 +08 +06 -07 -04 +12  ::
                    -----------                         (reversal from [05.] +05 to -10 [08.])
 :: +01 +03 -02 -11 +10 +09 -05 +08 +06 -07 -04 +12  ::
 
This reversal is represented by {5.9.10} A trace is represented as follows:
 [normal form of the trace] : h=N [SIZE] 
 
where N is the height (the number of parts that are separated by "<" in the normal form) of the trace and SIZE is the number of elements in the trace. The normal form of a trace is described in REF.

Example of a trace:

 {2.3}{3}{4.-.11}{5.-.10}{6}{6.-.8.10}{6.8} < {6.-.9}{7.8} : h=2 [90720]
 

Reference: Marília D. V. Braga, Marie-France Sagot, Celine Scornavacca and Eric Tannier. Exploring The Solution Space of Sorting by Reversals With Experiments and an Application to Evolution, to appear in Transactions on Computational Biology and Bioinformatics, 2008.

Author:
Marilia Dias Vieira Braga

Constructor Summary
enumerateTraces()
           
 
Method Summary
static void main(java.lang.String[] argv)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

enumerateTraces

public enumerateTraces()
Method Detail

main

public static void main(java.lang.String[] argv)