baobab.exec.trace.benchmark
Class analyzeTracesBenchmark0

java.lang.Object
  extended by baobab.exec.trace.benchmark.analyzeTracesBenchmark0

public class analyzeTracesBenchmark0
extends java.lang.Object

Enumerates all the traces (classes of solutions) of sorting a signed permutation (or genome) into another. This program do not enumerate all solutions and construct the traces directly.

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]
 

Applying constraints to reversal selection

Possible constraints:


Subtraces

If one or more constraints are applied, then subtraces are enumerated. A subtrace is represented as follows:

 [representative of the subtrace] : [normal form of the trace] : h=N [SIZE] : score=S1;S2;...;Sn 
 
where N is the height (the number of parts that are separated by "<" in the normal form) of the trace; SIZE is the number of elements in the subtrace; scores S1,S2,...,Sn are the scores of the subtrace according to constraints 1,2,...n.

Whenever the normal form is part of the subtrace, it is chosen as its representative.

Example of a subtrace:

 {2.3}{3}{4.-.11}{5.-.10}{6}{6.-.8.10}{6.8}{6.-.9}{7.8} : {2.3}{3}{4.-.11}{5.-.10}{6}{6.-.8.10}{6.8} < {6.-.9}{7.8} : h=2 [45360] : score=2;3
 


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
analyzeTracesBenchmark0()
           
 
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

analyzeTracesBenchmark0

public analyzeTracesBenchmark0()
Method Detail

main

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