From 1b05277809b4cba38b6fc5607a3a8d9e8764e841 Mon Sep 17 00:00:00 2001
From: Vincent Danjean <Vincent.Danjean@ens-lyon.org>
Date: Thu, 18 Feb 2010 20:56:21 +0000
Subject: [PATCH] MacOSX does not handle files with different case For example,
altree and ALTree can not be both existing Now, altree is moved into progs/
git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@436 cf695345-040a-0410-a956-b889e835fe2e
---
MANIFEST | 6 +++---
Makefile.PL | 6 +++---
altree => progs/altree | 2 +-
altree-add-S => progs/altree-add-S | 6 +++---
altree-convert => progs/altree-convert | 2 +-
to_rewrite.pm | 3 ++-
6 files changed, 13 insertions(+), 12 deletions(-)
rename altree => progs/altree (99%)
rename altree-add-S => progs/altree-add-S (99%)
rename altree-convert => progs/altree-convert (99%)
diff --git a/MANIFEST b/MANIFEST
index a5369f6..8cd6bb9 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1,6 +1,3 @@
-altree
-altree-add-S
-altree-convert
ALTree/Base.pm
ALTree/Chi2.pm
ALTree/Foret.pm
@@ -56,6 +53,9 @@ Documentation/manual.tex
Documentation/stage.bib
Makefile.PL
MANIFEST This list of files
+progs/altree
+progs/altree-add-S
+progs/altree-convert
README
t/ALTree.t
test/create_file/paup_file/caco.phase
diff --git a/Makefile.PL b/Makefile.PL
index 1b02c60..694f309 100644
--- a/Makefile.PL
+++ b/Makefile.PL
@@ -6,11 +6,11 @@ WriteMakefile(
NAME => 'altree',
PMLIBDIRS => [ 'ALTree' ],
DIR => [ 'CUtils' ],
- VERSION => '1.1.0',
+ VERSION => '1.1.1',
LICENSE => 'perl',
PREREQ_PM => {}, # e.g., Module::Name => 1.1
($] >= 5.005 ? ## Add these new keywords supported since 5.005
- (ABSTRACT_FROM => 'altree', # retrieve abstract from module
+ (ABSTRACT_FROM => 'progs/altree', # retrieve abstract from module
AUTHOR => 'Claire Bardel <Claire.Bardel@univ-lyon1.fr>') : ()),
- EXE_FILES => [qw (altree altree-add-S altree-convert)],
+ EXE_FILES => [qw (progs/altree progs/altree-add-S progs/altree-convert)],
);
diff --git a/altree b/progs/altree
similarity index 99%
rename from altree
rename to progs/altree
index 54d4c40..3101d02 100755
--- a/altree
+++ b/progs/altree
@@ -11,7 +11,7 @@ use Data::Dumper;
srand(654321);
our $VERSION;
-$VERSION = sprintf "0.%03d", q$Revision$ =~ /(\d+)/g;
+$VERSION = sprintf "0.%03d", q$Revision: 433 $ =~ /(\d+)/g;
# Positionner la variable PERL5LIB si besoin
diff --git a/altree-add-S b/progs/altree-add-S
similarity index 99%
rename from altree-add-S
rename to progs/altree-add-S
index e8b4594..bb262ad 100755
--- a/altree-add-S
+++ b/progs/altree-add-S
@@ -14,7 +14,7 @@ our($opt_h,$opt_i, $opt_o, $opt_e, $opt_p, $opt_t, $opt_l, $opt_j,
$opt_g, $opt_q);
our $VERSION;
-$VERSION = sprintf "0.%03d", q$Revision$ =~ /(\d+)/g;
+$VERSION = sprintf "0.%03d", q$Revision: 427 $ =~ /(\d+)/g;
sub DefineAncDer {
my $data_type=shift;
@@ -177,7 +177,7 @@ sub travail
}
if ($ici==0 && $phylo_prog eq "PAUP") {
- if ($ligne =~ /dimension ntax=([0-9]+) nchar=([0-9]+);/) {
+ if ($ligne =~ /dimension ntax=([0-9]+)\s+nchar=([0-9]+);/) {
$num_car=$2+1;
print "dimension ntax=$1 nchar=", $num_car, ";\n";
}elsif ($ligne =~ /format symbols=\"([0-9ATGCU]+)\"/) {
@@ -406,7 +406,7 @@ sub main
if ($opt_i) {
open(STDIN, '<', $opt_i) or die "Impossible to open $opt_i : $!" ;
}
-
+
my $correspond_name;
if ($opt_j) {
$correspond_name=$opt_j;
diff --git a/altree-convert b/progs/altree-convert
similarity index 99%
rename from altree-convert
rename to progs/altree-convert
index 2276a08..c629480 100755
--- a/altree-convert
+++ b/progs/altree-convert
@@ -11,7 +11,7 @@ use Pod::Usage;
our($opt_h, $opt_r, $opt_i, $opt_j, $opt_o, $opt_t, $opt_p, $opt_c, $opt_q, $opt_s);
our $VERSION;
-$VERSION = sprintf "0.%03d", q$Revision$ =~ /(\d+)/g;
+$VERSION = sprintf "0.%03d", q$Revision: 290 $ =~ /(\d+)/g;
##### FONCTIONS ANNEXES GLOBALES POUR TOUS LES INPUTS ####
diff --git a/to_rewrite.pm b/to_rewrite.pm
index 197333b..e8d1828 100644
--- a/to_rewrite.pm
+++ b/to_rewrite.pm
@@ -10,6 +10,7 @@ use ALTree::Utils qw(erreur);
use ALTree::Input qw(PrepareTree);
#use Newchi2treeUtils;
use TamuAnova;
+use GSL::CDF qw(:all);
sub parcours_nosplit_chi2split
{
@@ -223,7 +224,7 @@ sub CalculChi2
}
#my $p=`pochisq $chi2 $ddl`+0; # Verif que les 2 appellent
#bien la même chose!
- $p_value=ALTree::CUtils::pochisq($chi2,$ddl);
+ $p_value=gsl_cdf_chisq_Q($chi2,$ddl);
#if ($p != $p_value) {
#print STDERR "pochisq: $p != $p_value !\n";
#}
--
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