baobab.exec.trace
Class enumerateTraces
java.lang.Object
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
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 |
enumerateTraces
public enumerateTraces()
main
public static void main(java.lang.String[] argv)