diff --git a/ALTree/Nanova.pm b/ALTree/Nanova.pm
index 11502b6f52868d000b2091a2eaaa6fbd04033b78..602aa4d2c9b2cc2d66bf8e7b4af401afa49789fe 100644
--- a/ALTree/Nanova.pm
+++ b/ALTree/Nanova.pm
@@ -70,13 +70,13 @@ sub FillTableaux
my $nb_term = shift;
if ($present_node->NbChildren()==0) {
- $presentNode->GetQuantiList();
+ $present_node->GetQuantiList();
push @{$values}, @{$present_node->GetQuantiList()};
push @{$groups}, $present_node->NbQuanti();
$nb_term++;
} else {
for my $child ($present_node->GetChildrenList()) {
- FillTableaux($child, $value, $groups, $nb_term);
+ FillTableaux($child, $values, $groups, $nb_term);
}
}
diff --git a/altree b/altree
index 06ae6bf5e395ed35a310045b4905751ac0f0f5d0..09cd18ac175371a49c7c7f0448779808cf181ebb 100755
--- a/altree
+++ b/altree
@@ -1039,7 +1039,7 @@ sub SwitchRoot {
}
################################################################
-###################### ASSOCIATION TEST ########################
+#################### TRAITE PLS FICHIERS #######################
################################################################
sub TraiteSeveralFiles
@@ -1058,7 +1058,7 @@ sub TraiteSeveralFiles
$pmin_min = $res_files->[$i]->{"pmin"};
}
}
- print "La pmin minimale est $pmin_min\n";
+ print "La pmin minimale est $pmin_min, la taille de la distrib pmin est ", scalar(@distrib), "\n";
# sort {$a <=> $b} @distrib; # trie du plus petit au plus grand
my $compte=0;
@@ -1516,16 +1516,18 @@ sub main
my $racine=$tree->GetRoot();
my @children=$racine->GetChildrenList();
- {
- my $mat;
- print "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n";
- $mat=ALTree::Nanova::Tree2mat($tree->GetRoot());
- ALTree::Nanova::WriteMat($mat);
- my $values = [];
- my $groups = [];
- my $nb_term=0;
- FillTableaux($tree->GetRoot(), $values, $groups, $nb_term);
- }
+
+# EN DEVELOPPEMENT: NANOVA
+# {
+# my $mat;
+# print "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n";
+# $mat=ALTree::Nanova::Tree2mat($tree->GetRoot());
+# ALTree::Nanova::WriteMat($mat);
+# my $values = [];
+# my $groups = [];
+# my $nb_term=0;
+# FillTableaux($tree->GetRoot(), $values, $groups, $nb_term);
+# }
$option_require->("permutations",
"The number of permutations used to calculate".
@@ -1596,65 +1598,72 @@ sub main
}
}
}
- }
- if ($nb_files>1) {
- my $p_finale = TraiteSeveralFiles(\@res_files, $nb_files);
- print "\n############################################\n";
- print "p_value for the $nb_files files = $p_finale\n";
- }
+ print "tab_trees @trees\n";
+
+
###########################################################
# Let's go. Et pour la localisation
###########################################################
- if ($s_loc==1) {
- #$option_require->("splitmode");
- #my($splitmode)=$option_value->("splitmode");
- print "Localisation method using S-character\n";
- $option_require->("s-site-number");
- my($s_site_nb)=$option_value->("s-site-number");
- $option_require->("s-site-characters");
- my($s_char_state)=$option_value->("s-site-characters");
- $option_require->("co-evo");
- my($co_evo_type)=$option_value->("co-evo");
+ print "tabtrees @trees\n";
+ if ($s_loc==1) {
+ #$option_require->("splitmode");
+ #my($splitmode)=$option_value->("splitmode");
+ print "Localisation method using S-character\n";
+ $option_require->("s-site-number");
+ my($s_site_nb)=$option_value->("s-site-number");
+ $option_require->("s-site-characters");
+ my($s_char_state)=$option_value->("s-site-characters");
+ $option_require->("co-evo");
+ my($co_evo_type)=$option_value->("co-evo");
# print "co_evo_type=$co_evo_type\n";
-
-#DEBUG print "s_char_state=$s_char_state\n";
- if (not ($s_char_state =~
- m/([A-Za-z0-9]+)\s*[-=_]*[>]\s*([A-Za-z0-9]+)/)) {
- erreur("Invalid character change for character".
- " S. It should be Anc -> Der\n", 0);
- }
- my($s_anc)=$1;
- my($s_der)=$2;
- my($s_state)= ALTree::Sens->New($s_anc." --> ".$s_der);
- my($foret)=ALTree::Foret->New();
-
-
- #$Data::Dumper::Indent = 0;
- for my $file_tree (@trees) {
- my $tree=$file_tree->{"tree"};
-
- my ($b_t)=$tree->GetNbBrNonNulle();
- my $site=$tree->GetSite($s_site_nb);
- if (not defined($site)) {
- erreur("Invalid value ($s_site_nb) for".
- " --s-site-number\n", 0);
+#DEBUG print "s_char_state=$s_char_state\n";
+ if (not ($s_char_state =~
+ m/([A-Za-z0-9]+)\s*[-=_]*[>]\s*([A-Za-z0-9]+)/)) {
+ erreur("Invalid character change for character".
+ " S. It should be Anc -> Der\n", 0);
}
+ my($s_anc)=$1;
+ my($s_der)=$2;
+ my($s_state)= ALTree::Sens->New($s_anc." --> ".$s_der);
+ my($foret)=ALTree::Foret->New();
- my($s_t, $s_t_rev)=CalculateRit($tree, $s_site_nb, $s_state,
- $co_evo_type);
- CalculateEit($tree, $s_site_nb, $s_t, $s_t_rev, $b_t);
- $foret->AddTree($tree);
+ #$Data::Dumper::Indent = 0;
+ for my $file_tree (@trees) {
+ my $tree=$file_tree->{"tree"};
+
+ my ($b_t)=$tree->GetNbBrNonNulle();
+
+ my $site=$tree->GetSite($s_site_nb);
+ if (not defined($site)) {
+ erreur("Invalid value ($s_site_nb) for".
+ " --s-site-number\n", 0);
+ }
+
+ print "TREE1, $tree\n";
+ my($s_t, $s_t_rev)=CalculateRit($tree, $s_site_nb, $s_state,
+ $co_evo_type);
+ print "TREE2, $tree\n";
+ CalculateEit($tree, $s_site_nb, $s_t, $s_t_rev, $b_t);
+ print "TREE3, $tree\n";
+ $foret->AddTree($tree);
+ print "TREE4, $tree\n";
+ }
+ $foret->CalculVi();
+ #PrintAllVi($foret, $s_site_nb);# Non trié
+ #PrintViMax($foret, $s_site_nb); # Affiche la liste en choisissant
+ #pour chaque sit, juste le meilleur sens
+ print "\n";
+ print "Results:\n";
+ PrintViMaxSens($foret, $s_site_nb);
}
- $foret->CalculVi();
- #PrintAllVi($foret, $s_site_nb);# Non trié
- #PrintViMax($foret, $s_site_nb); # Affiche la liste en choisissant
- #pour chaque sit, juste le meilleur sens
- print "\n";
- print "Results:\n";
- PrintViMaxSens($foret, $s_site_nb);
+ }
+ if ($nb_files>1) {
+ my $p_finale = TraiteSeveralFiles(\@res_files, $nb_files);
+ print "\n############################################\n";
+ print "p_value for the $nb_files files = $p_finale\n";
}
}
}
diff --git a/altree-add-S b/altree-add-S
index e841145b1b8634a04762343f352b9f4ffeca8745..b450fa08bcaeb5993d1235269e4c8c3aaa3aeebc 100755
--- a/altree-add-S
+++ b/altree-add-S
@@ -41,9 +41,9 @@ sub ReadCorrespond
if ($ligne =~ /^$/) {
next;
}
-
- ###### Qualitative data ######
- if ($data_qual eq "qualitative") {
+
+ ####### Qualitative data ######
+ if ($data_qual eq "quali") {
@tableau=split(/\s+/, $ligne);
if ($#tableau != 2) {
die "error in $name_correspond: not 3 columns at line '$ligne'\n";
@@ -54,7 +54,8 @@ sub ReadCorrespond
die "You have probably exchanged the order of cases and controls in file $name_correspond. It should be: haplo_name m_case_number c_control_number\n";
}
$correspondance{$tableau[0]}->{"case"}=$tableau[1]+0;
- $correspondance{$tableau[0]}->{"control"}=$tableau[2]+0;
+ $correspondance{$tableau[0]}->{"control"}=$tableau[2]+0;
+
}
} else {
##### Quantitative data #######
@@ -244,7 +245,7 @@ sub travail
# print "$nom\n";
###### QUALITATIVE ######
- if ($data_qual eq "qualitative") {
+ if ($data_qual eq "quali") {
if (not exists ($correspondance->{$nom})){
print STDERR "$nom is not found in the file $name_correspond. Assuming it is the outgroup.\nThe number of cases and controls affected to this sequence is set to 0\n";
$correspondance->{$nom}->{"case"}=0;