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Commits on Apr 27, 2010
  1. fixes to report

    hrkm committed Apr 27, 2010
Commits on Apr 26, 2010
  1. Modify sbh negative

    doriath committed Apr 26, 2010
  2. Modify SBH positive section

    doriath committed Apr 26, 2010
  3. Changes in introduction

    doriath committed Apr 26, 2010
  4. Fix generator description.

    doriath committed Apr 26, 2010
  5. graph pictures in report

    hrkm committed Apr 26, 2010
  6. graph pictures

    hrkm committed Apr 26, 2010
  7. Small fix

    doriath committed Apr 26, 2010
  8. Add definitions TODO.

    doriath committed Apr 26, 2010
  9. small fix

    hrkm committed Apr 26, 2010
  10. analysis actualization

    hrkm committed Apr 26, 2010
  11. larger charts

    hrkm committed Apr 26, 2010
  12. Merge commit

    doriath committed Apr 26, 2010
  13. Small changes in report

    doriath committed Apr 26, 2010
  14. Add itemize and enumerate.

    doriath committed Apr 26, 2010
  15. Add new rake task

    doriath committed Apr 26, 2010
    $ rake report - generates the pdf report
    Modify the template of report file
  16. added negative algorithm

    hrkm committed Apr 26, 2010
    added 3 new charts for negative algorithm
    added new chapters for report
    output file for negative algorithm
Commits on Apr 25, 2010
  1. time measure for rake

    hrkm committed Apr 25, 2010
    added general_negative_no_trunc - run general algorith with no constraint on the length of output
    added general_no_trunc algorithm
    added 5 charts to include in report
    added "results" chapter to report
    added computational complexities to algorithms in report
    added excel file with analysis of output files
    
    warning: tex compilation not tested !
    
    output files:
    output_gn - output of rake general_negative
    output_gnnt - output of rake general_negative_no_trunc
    output_gp - output of rake general_positive
    output_gp2 - output of rake general_positive (second run)
    output p - output of rake positive
Commits on Apr 24, 2010
Commits on Apr 23, 2010
Commits on Apr 21, 2010
  1. fix with statistics from sbh_check

    hrkm committed Apr 21, 2010
Commits on Apr 17, 2010
  1. update with new rake commands

    hrkm committed Apr 17, 2010
  2. sbh_check prints out:

    hrkm committed Apr 17, 2010
    - length of sequence
    - number of used words from instance
    - number of additionaly made words
    - number of repeats (this words were made during the merge of arcs with length larger than 1)
    also fixed bug - now function doesn't create 9 additional words when cutting result sequence into set of oligonucleotids (of lengths 9,8,7,...,2,1)
    
    added simple cut-off for sbh_general (if last merged sequence is too long we cut it to the maximum allowed length and stop algorithm, this is our result)
    
    changed script to include following stats:
    File - the name of file
    Words - words included in file
    N - number of words that should be included in file without errors)
    Length - length of the result sequence (should be N + 9 for words with length equal to 10)
    Used w - number of words used from instance file to create result sequence
    Made w - number of words made to connect the gaps
    Repeats - number of duplicate words that were made during merge of sequences
    Error - difference between "Words" and "Used w"
    
    note that sum of "Used w", "Made w" and "Repeats" should be N
    
    in case we will conform the special algorithm for negative errors, the "Used w" should be equal to "Words" and still "Length" should be equal to N + 9 ("Made w" = "Repeats" = "Error" = 0)
  3. Fix sbh_check

    doriath committed Apr 17, 2010
  4. rake script update

    hrkm committed Apr 17, 2010
    larger number as basic minimum (previous led to infinite loops)
    moved algorithm from negative to general
    fixed sbh_print_graph