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Commit ac48de27 authored by David Parsons's avatar David Parsons
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Rename view_generation => view

parent 07d42e46
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......@@ -99,12 +99,10 @@ AC_SUBST(PTHREAD_LIBS)
# ************************ --without-x option *********************
#
# When this option is set, typing make will produce aevol and
# most post-treatment programs, but not aevol_X11.
# When this option is set, running make will produce aevol and
# most post-treatment programs without visualization capabilities
# This is useful if we want to run computations on a cluster where the
# X libraries are not present. If, on the contrary, we type ./configure
# without this option, then typing make will produce aevol_X11 and
# view_generation_X11 (and the other post-treatment programs).
# X libraries are not present.
AC_MSG_CHECKING([whether to enable graphical outputs])
AC_ARG_WITH(x, [ --without-x to disable graphical output], , with_x=yes)
......
......@@ -11,7 +11,7 @@ endif
dist_man1_MANS = aevol_create.1 aevol_run.1 aevol_modify.1 aevol_propagate.1
dist_man1_MANS += aevol_misc_lineage.1 aevol_misc_ancstats.1
dist_man1_MANS += aevol_misc_robustness.1 aevol_misc_compute_pop_stats.1
dist_man1_MANS += aevol_misc_view_generation.1 aevol_misc_create_eps.1
dist_man1_MANS += aevol_misc_view.1 aevol_misc_create_eps.1
dist_man1_MANS += aevol_misc_extract.1 aevol_misc_fixed_mutations.1
dist_man1_MANS += aevol_misc_gene_families.1
......
......@@ -69,4 +69,4 @@ number of single mutants to create and evaluate. Default = 1000. Note that this
.SH "SEE ALSO"
.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps, aevol_misc_robustness
.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view, aevol_misc_create_eps, aevol_misc_robustness
......@@ -48,4 +48,4 @@ specify the index (ID in current generation) of the individual for whom detailed
specify the rank of the individual for whom detailed reproduction statistics are desired
.SH "SEE ALSO"
.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps
.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view, aevol_misc_create_eps
......@@ -3,20 +3,20 @@
.SH NAME
Aevol \- an in silico experimental evolution platform
.SH SYNOPSIS
.B aevol_misc_view_generation \-h
.B aevol_misc_view \-h
|
.B \-\-help
.br
.B aevol_misc_view_generation \-V
.B aevol_misc_view \-V
|
.B \-\-version
.br
.B aevol_misc_view_generation \fB\-t\fI TIMESTEP
.B aevol_misc_view \fB\-t\fI TIMESTEP
.SH DESCRIPTION
.B Aevol
is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
.TP
.B aevol_misc_view_generation
.B aevol_misc_view
view the simulation at the provided timestep
.SH OPTIONS
.TP
......
......@@ -152,11 +152,11 @@ Please note that these tools have only been tested on simple experimental setups
\subsection{aevol\_misc\_view\_generation}
\label{sect:view-gener}
The \verb?view_generation? tool is probably the easiest and most straightforward tool provided with \aevol{}.
The \verb?view? tool is probably the easiest and most straightforward tool provided with \aevol{}.
It allows one to visualize a generation using the exact same graphical outputs used in \verb?aevol_run?.
However, since it relies on graphics, it is only available when \aevol{} is compiled with X enabled (which is the default).
Usage: \verb?aevol_misc_view_generation -g generation_number?
Usage: \verb?aevol_misc_view -g generation_number?
There must have been a backup of the population at this generation. For example, if the program is called with the option
\verb?-g 4000?, there must be a file called \verb?pop_004000.ae? in the \verb?populations? directory.
......
......@@ -115,15 +115,15 @@ done
# A set of post-treatment tools is available to help analyse the outcome.
#
# ---------- aevol_misc_view_generation ----------
# ---------- aevol_misc_view ----------
#
# The simplest miscellaneous tool is view_generation. It allows one to
# visualize a generation using the exact same graphical outputs used in
# aevol_run.
# The simplest miscellaneous tool is view. It allows one to
# visualize a simulation at a given timestep using the exact
# same graphical outputs used in aevol_run.
# However, since it relies on graphics, it is only available when aevol is
# compiled with x enabled (which is the default).
#
aevol_misc_view_generation -g 10000
aevol_misc_view -g 10000
# ---------- aevol_misc_create_eps ----------
......
......@@ -47,7 +47,7 @@ aevol_misc_fixed_mutations
# aevol_misc_transform_plasmid
if WITH_X
bin_PROGRAMS += aevol_misc_view_generation
bin_PROGRAMS += aevol_misc_view
endif # X
# noinst_PROGRAMS = aevol_misc_template
......@@ -64,4 +64,4 @@ aevol_misc_mutational_robustness_SOURCES = mutationalrobustness.cpp
# aevol_misc_robustness_SOURCES = robustness.cpp
# aevol_misc_template_SOURCES = template.cpp
# aevol_misc_transform_plasmid_SOURCES = transform_plasmid.cpp
aevol_misc_view_generation_SOURCES = view_generation.cpp
aevol_misc_view_SOURCES = view.cpp
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