Introduces new macro TIMESTEP_FORMAT that expands to "%09" PRId64

This was mostly achieved by removing
StatRecord dependency to ExpManager

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'

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

Took aevol_run.cpp's header as reference header and set it for all Aevol source files.

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

For C++ 11 compatibility.

In the process of transforming containers to STL, some methods were
temporarily renamed "_std". This should have been removed since ae_lists
are fully removed.

Remove forgotten "_std" from
ae_individual::get_genetic_unit_list_std(),
ae_individual::get_genetic_unit_list_std_nonconst(),
ae_exp_manager::get_indivs_std(),
ae_protein::get_rna_list_std(),
World::get_indivs_std().

Vincent Liard authored 9 years ago and David Parsons committed 9 years ago

Conflicts:
	src/libaevol/ae_dna.cpp
	src/libaevol/ae_dna.h
	src/libaevol/ae_individual.cpp
	src/libaevol/ae_individual.h
	src/libaevol/ae_individual_X11.cpp
	src/libaevol/genetic_unit.cpp
	src/libaevol/genetic_unit.h
	src/libaevol/param_loader.cpp

In a classical aevol experiment it will only mean that generation
number is now called time.

In a different setup where individuals actually have a life span,
this means that a generation may correspond to several time steps.
This means that we can e.g. let molecules of public good diffuse/degrade
through several time steps btw each generation and of course makes the
whole thing more R-Aevol compliant.

And fix #includes and libaevol/Makefile.am.

In the process, got to add constness to functions in many other
files. Could have dropped constness from declarations, but since I was
at it...

Has to be tested thoroughly, still...

And a bit of other ae_lists removal.

The name convention ae_* for aevol-related classes and functions comes
from C language lacking namespaces. It was meant to prevent name
clashes. Since C++ provides namespaces, this commit wraps everything
inside an "aevol" namespace.

This means that there is no need anylonger to name classes according to
ae_*. But any new class needs to be within the aevol namespace if it is
part of aevol or to start with a "using" clause if it relies on aevol.