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

-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

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)],
 );

altree → 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
 

altree-add-S → 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;

altree-convert → 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 ####

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 mme 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";
 	    #}