... and use sstreams instead of sprintf

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.

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

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

=> local, rear or HT

In the process of simplifying ae_dna_replic_report::get_nb_etc(),
symbols were needed to describe composite mutations. Would have been
nice to create a separate type extending ae_mutation_type but it's not
supported by C++ as of C++11 or 14. Alternatives like encapsulating the
enums in classes felt too heavy for this task.

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...

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.

Removed all obsolete _HT_... attributes (and the corresponding 
accessors) in the ae_replication_report class, because
they were moved in the ae_dna_replic_report class a few months
ago. They record the events of transfer by insertion or 
replacement.

This modification just makes the code cleaner and does not 
affect the simulation results in any way. 

 - They are managed in ae_dna and ae_mutation and no more in ae_selection
 - They are saved in ae_dna_replic_report with the transferred sequence (to simplify the post-treatments)

Updated all the file headers

BUGFIX
  Fixed bug #267: Won't compile with zlib-1.2.7

  * Implementation of two plugins for population and environment changes (change_pop.cpp and change_env.cpp). 
  They takes one parameter file with the parameter to change and a population or an environment backup to change.
  Actually, only overall mutation/rearrangement rate change, addition of gaussian and change in environmental variation are implemented. 
  
BUGFIX
  * We fixed some segmentation faults due to tree 

  * 3 dynamic files, printed at each BACKUP_STEP :
    + Population (unchanged)
    + Environment
    + Spatial Structure
  * 2 static files containing constant parameters
    + Ouput Profile
    + Experimental Setup

The output profile and the experimental setup (latter not yet implemented) will be loadable either from a gzipped file (old format) or from a plain text file.

++
D.

Modified compilation chain:

  --with-regul changed to --with-raevol
  --without-xlib changed to the (standard) without-x

  lib-aevol was changed to libaevol for a more intuitive use with -laevol.
  Libraries generated with different compilation options are no longer differentiated by postfixes (save for the RAEVOL option) => if --with-raevol is used, the generated lib will be called libraevol (whether X and/or DEBUG are used or not). if --without-raevol (default), the generated lib will be called libaevol.
  make clean is called automatically at the end of ./configure to avoid compatibility issues.

Ported feature TRANSFER

Log overview (see previous logs for more details)
------------------------------------------------------------------------
NEW
  * Added 2 parameters TRANSFER_INS_RATE and TRANSFER_REPL_RATE to set the rate of insertion (resp. replacement) transfer.
    Default: 0.0 => No transfer.
    Both rates are per replication rates and trigger a transfer attempt (the actual occurrence of a transfer event will depend on whether an alignment is found). There can be at most one transfer of each type per replication.
  * Every possible ae_mutation now has a _length
  * Added method ae_dna::copy_into_new_GU( int32_t pos_1, int32_t pos_2 ) const
  * Added method inline void ae_genetic_unit::copy_promoters_included_in( int32_t pos_1, int32_t pos_2, ae_list** new_promoter_lists )
  * An ae_vis_a_vis now contains its score
  * Added a header for R in the output file of fixed_mutations
  * Added a new post-treatment "mutagenesis"
  * Added checking options (NO_CHECK / LIGHT_CHECK / FULL_CHECK) to the "fixed_mutations" post-treatment
  * Added a log file for transfer. Keyword TRANSFER, file name log_transfer.out
  * Added a test case for transfer.
  * New file ae_enums.h
  
MODIFIED
  * Moved the replication procedure to ae_population.
  * Deported the genome size barrier checks one level up ( e.g. from do_deletion( pos_1, pos_2 ) to do_deletion() and do_rearrangements_with_align() ).
  * Method void ae_genetic_unit::copy_lagging_promoters_starting_between( int32_t pos_1, int32_t pos_2, ae_list* new_promoter_list ) no longer has the ( pos_1 > pos_2 ) prerequisite
  * Renamed class utils to ae_utils
  
BUGFIX
  * Replaying a translocation when alignments are on could cause an error
  * The -c (or --fullcheck) option in lineage was not declared hence didn't work...
  * ae_individual::reevaluate( ae_environment* envir ) didn't reset the (new) attributes _transcribed, _translated and _folded yielding a flat fitness.
  * In post-treatments that deleted ae_common::sim, ae_dna::undergo_this_mutation( ae_mutation * mut ) could check whether it had to write in the BARRIER log. It hence tried to access a member of ae_common::sim that was NULL.
  * LOADS and BARRIER logs now work correctly
  * There were some inconsistencies with Whole Genome Events (i.e. Whole Genome Duplications)
------------------------------------------------------------------------

* Organized the repository to manage branches. *
************************************************

Everything you already know has been moved to "trunk"
Added a "branches" directory with 2 subdirectories "releases" and "features"
  * "releases" will be used for branches related to a given release, e.g. when a change to post-treatments are needed for the analysis of data generated using that release.
    For example: I am analysing data that I generated using versions 2.1.2 of the code. I hence created the branch "releases/aevol-2.1.2" so that I can code my post-treatments in a properly versionned way. These development may (depending on the level of specificity) be added to the trunk eventually (using svn merge)
  * "features" is meant to be used when developing a new feature that takes time developing. This will enable us to use svn feature more thouroughly, e.g. commit more often (even "unstable" versions) in a personal branch of the svn.

If you don't want to use branches or if you just want to be able to update regularly, you need not change your habits, just add "/trunk" when you check out
=> "svn checkout svn+ssh://username@svn.gforge.liris.cnrs.fr/svnroot/aevol/trunk"

Questions/remarks are welcome!
David