Read Me

Compile
----------
make 

Run
----------
The compilation generates three executables:
 * test: you can use it directly or through testMultiple.sh for random 
         insertions and deletions.
 * slidingWindow: index only a window of given length and slide it along the
                  text.
 * locate: index a file and locate the specified patterns using the index.

For removing object files you can use 'make clean'.
For removing object, precompiled header and excutable files you can use 
'make cleanall'


Papers
---------
The method implemented is described in the following papers:
 ------ Dynamic Sequence with Indels -----
 uses huffman shaped wavelet tree
 space: O(n H_0) time: O((log n) H_0)
 paper: V. M\"akinen, G. Navarro. 
        Dynamic Entropy-Compressed Sequences and Full-Text Indexes. 
        CPM 2006, Chapter 3.6 

        W. Gerlach. 
        Dynamic FM-Index for a collection of texts with application
        to space-efficient construction of the compressed suffix array.
        Master's thesis. Universit\"at Bielefeld, Germany.

 ------ Dynamic Suffix Array -------
 papers: M. Salson, T. Lecroq, M. L\'eonard, L. Mouchard. 
         Dynamic Burrows-Wheeler Transform.
         PSC 2008, pp. 13--25, 2008.
                        
         M. Salson, T. Lecroq, M. L\'eonard, L. Mouchard.
         A Four-Stage Algorithm for Updating a Burrows-Wheeler Transform
         Theoretical Computer Science, 410(43):4350–4359, 2009.
                                        
         M. Salson, T. Lecroq, M. L\'eonard, L. Mouchard. 
         Dynamic Extended Suffix Arrays. 
         Journal of Discrete Algorithms. doi:10.1016/j.jda.2009.02.007