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  1. Apr 08, 2024
  2. Nov 17, 2023
  3. Jul 24, 2020
  4. Mar 16, 2020
    • Théotime Grohens's avatar
      Remove formatting warning in Mutation files · 1fec1f62
      Théotime Grohens authored
      This commit fixes the formatting warning in the Mutation classes.
      
      - For mut_type() and sense() calls, we changed the PRId8 format specification
        to PRId32
      - For the -1 constants, we explicitly cast them to the right size
        (int8_t or int16_t) to reflect the format specification
      1fec1f62
    • Théotime Grohens's avatar
      Delete copy operator in Mutation classes · 791d48bb
      Théotime Grohens authored
      This commit gets rid of the -Wdefaulted-function-deleted warning
      that popped up in Mutation-derived classes.
      
      It came from the fact that Mutation.h had these definitions:
      
                     |     copy      |      move
      ----------------------------------------------------
      constructor    |   default     |    default
      ----------------------------------------------------
      operator       |   delete      |    delete
      
      whereas the derived classes had the following:
      
                     |     copy      |      move
      ----------------------------------------------------
      constructor    |   default     |    delete
      ----------------------------------------------------
      operator       |   default     |    delete
      
      This meant that the move operator was defaulted in the base class
      but deleted in the derived classes, producing the warning (the
      discrepancy was introduced in 6615dbb4).
      
      This commit deletes all copy operators, leaving only copy constructors,
      which are used in the Clone() method shared by Mutation classes.
      
      Note that in *HT classes, the copy constructor is defaulted but
      the classes contain pointers, so there might be a memory issue when
      calling the constructor.
      791d48bb
  5. Feb 12, 2020
  6. Oct 29, 2015
    • Vincent Liard's avatar
      rename remaining get_xxx() to xxx() · 3244d2e1
      Vincent Liard authored
      Magic command for reference:
      find ! -path '*test*' ! -path './libaevol/SFMT-src-1.4/*' \( -name '*.cpp' -o -name '*.h' \) -print0 | xargs -0 sed -i -r 's/\bget_(\w+)\b/\1/g'
      3244d2e1
  7. Oct 28, 2015
    • Vincent Liard's avatar
      shorten safe getter names · e10a4e7a
      Vincent Liard authored
      Looking forward to honour Google Style guide, the purpose is to rename getters
      from get_var() to var(). Many of such renames cause conflicts, though. In this
      commit, only the safe names were changed.
      
      grep -rEo '\bget_\w+\(' --include '*.h' --no-filename --exclude-dir tests \
       | sed -e 's/get_//' -e 's/($//' \
       | sort -u \
       | xargs -n 1 -I% sh -c "grep -roq '\b%\b' --include '*.cpp' --include '*.h' --exclude-dir tests || echo %" \
       | xargs -n1 -I% sh -c "find ! -path '*test*' ! -path './libaevol/SFMT-src-1.4/*' \( -name '*.cpp' -o -name '*.h' \) -print0 \
       | xargs -0 sed -i -r 's/\bget_%\(/%\(/g'"
      
      Yes. I know...
      
      http://google-styleguide.googlecode.com/svn/trunk/cppguide.html#Function_Names
      e10a4e7a
  8. Oct 27, 2015
    • Vincent Liard's avatar
      uniformize headers · c4cac25a
      Vincent Liard authored
      Took aevol_run.cpp's header as reference header and set it for all Aevol source files.
      c4cac25a
  9. Aug 12, 2015
  10. Jul 10, 2015
  11. Jul 06, 2015
    • David Parsons's avatar
      aevol-2 Create mutation class hierarchy · 6615dbb4
      David Parsons authored
      Instead of a single class with switches everywhere, mutations are now
      handled through a proper polymorphism.
      
      Here is the class hierarchy:
      Mutation
        <-- LocalMutation
              <-- PointMutation
              <-- SmallInsertion
              <-- SmallDeletion
        <-- Rearrangement
              <-- Duplication
              <-- Deletion
              <-- Translocation
              <-- Inversion
        <-- HT
              <-- InsertionHT
              <-- ReplacementHT
      6615dbb4
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