From fd84b4e54618ee6840ed2437ff2d15c78f072ad2 Mon Sep 17 00:00:00 2001
From: Vincent Danjean <Vincent.Danjean@ens-lyon.org>
Date: Sun, 19 Apr 2009 07:18:38 +0000
Subject: [PATCH] git-svn-id:
svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@433
cf695345-040a-0410-a956-b889e835fe2e
---
ALTree/Nanova.pm | 11 ++++++----
ALTree/Node.pm | 35 +++++++++++++++++++++++++++++-
altree | 56 +++++++++++++++++++++++++++---------------------
to_rewrite.pm | 2 +-
4 files changed, 74 insertions(+), 30 deletions(-)
diff --git a/ALTree/Nanova.pm b/ALTree/Nanova.pm
index 602aa4d..47772d0 100644
--- a/ALTree/Nanova.pm
+++ b/ALTree/Nanova.pm
@@ -68,10 +68,13 @@ sub FillTableaux
my $values = shift;
my $groups = shift;
my $nb_term = shift;
+
+ print "Node: ", $present_node->Name(), " ", Dumper($values);
+ print "\n";
if ($present_node->NbChildren()==0) {
- $present_node->GetQuantiList();
- push @{$values}, @{$present_node->GetQuantiList()};
+ print "list: ", Dumper($present_node->GetQuantiList()), "\n";
+ push @{$values}, @{$present_node->GetQuantiListValues()};
push @{$groups}, $present_node->NbQuanti();
$nb_term++;
} else {
@@ -88,9 +91,9 @@ sub WriteMat
my $mat = shift;
- print STDERR Dumper($mat);
+ #print STDERR Dumper($mat);
- return;
+ #return;
for (my $i=0; $i<=$#$mat; $i++) {
foreach my $elem (@{$mat->[$i]}) {
print $elem, "\t";
diff --git a/ALTree/Node.pm b/ALTree/Node.pm
index f8cf43a..fd9f18e 100644
--- a/ALTree/Node.pm
+++ b/ALTree/Node.pm
@@ -239,9 +239,23 @@ sub Name {
}
}
+sub AddQuanti {
+ my $self=shift;
+ my $value=shift;
+ my $num_haplo=shift;
+ delete($self->{"moyenne"});
+ push @{$self->{"quanti"}}, [$value, $num_haplo];
+}
+
sub GetQuantiList {
my $self=shift;
- return @{$self->{"quanti"}};
+ return $self->{"quanti"};
+}
+
+sub GetQuantiListValues {
+ my $self=shift;
+ my @t=map {$_->[0] } @{$self->{"quanti"}};
+ return \@t;
}
sub NbQuanti {
@@ -249,6 +263,25 @@ sub NbQuanti {
return scalar(@{$self->{"quanti"}});
}
+sub GetQuantiMean {
+ my $self=shift;
+
+ if (defined($self->{"moyenne"})) {
+ return $self->{"moyenne"};
+ }
+
+ my $tab = $self->GetQuantiListValues();
+ my $sum;
+ my $i;
+ for ($i=0; $i < scalar (@{$tab}) ; $i++) {
+ $sum+=$tab->[$i];
+ }
+ my $moy=$sum/($i);
+ $self->{"moyenne"}=$moy;
+
+ return $moy;
+}
+
#Faire meme chose pour case, control et br_len (HasBrLen), level, high, sequence, label, oldfather
#Faire oldchildren (GetOldChildren, SetOldChildren, )
diff --git a/altree b/altree
index 7bb8a7e..54d4c40 100755
--- a/altree
+++ b/altree
@@ -31,7 +31,7 @@ use ALTree::Utils qw(erreur);
use ALTree::Input qw(PrepareTree);
#use Newchi2treeUtils;
use TamuAnova;
-
+#use NAnova;
use ALTree::Nanova;
###########################################
@@ -270,18 +270,6 @@ sub FillCaseControl
}
######## QUANTITATIF ########
-sub Moyenne
-{
- my $tab = shift;
- my $sum;
- my $i;
- for ($i=0; $i < scalar (@{$tab}) ; $i++) {
- $sum+=$tab->[$i]->[0];
- }
- my $moy=$sum/($i);
- return $moy;
-}
-
sub FillQuanti
{
my($present_node)=shift;
@@ -289,12 +277,14 @@ sub FillQuanti
if ($present_node->NbChildren()==0) {
my($id);
$id=$present_node->{"id"};
- if (not defined $present_node->{"quanti"}) {# car sinon, pb pour H000
- $present_node->{"quanti"}=[];
- push @{$present_node->{"quanti"}}, @{$correspondance->{$id}};
- }
- my $moy=Moyenne($present_node->{"quanti"});
- $present_node->{"moyenne"}=$moy;
+ #if (not defined $present_node->{"quanti"}) {
+ # car sinon, pb pour H000
+ #$present_node->{"quanti"}=[];
+ #print "cor: ", Dumper($correspondance->{$id}), "\n";
+ foreach my $corresp (@{$correspondance->{$id}}) {
+ $present_node->AddQuanti($corresp->[0], $corresp->[1]);
+ }
+ #}
#DEBUG print STDERR $present_node->{"id"}, " " ;
#DEBUG for (my $i=0; $i< scalar (@{$present_node->{"quanti"}}); $i++) {
@@ -305,11 +295,10 @@ sub FillQuanti
my($child);
for $child ($present_node->GetChildrenList()) {
FillQuanti($child, $correspondance);
- push (@{$present_node->{"quanti"}}, @{$child->{"quanti"}});
+ foreach my $quanti (@{$child->GetQuantiList()}) {
+ $present_node->AddQuanti($quanti->[0], $quanti->[1]);
+ }
}
- my $moy=Moyenne($present_node->{"quanti"});
- $present_node->{"moyenne"}=$moy;
-
#DEBUG print STDERR $present_node->{"id"}, " " ;
#DEBUG for (my $i=0; $i< scalar (@{$present_node->{"quanti"}}); $i++) {
#DEBUG print STDERR $present_node->{"quanti"}->[$i]->[0], " (" ,$present_node->{"quanti"}->[$i]->[1], ") ";
@@ -1533,8 +1522,27 @@ sub main
# my $values = [];
# my $groups = [];
# my $nb_term=0;
-# FillTableaux($tree->GetRoot(), $values, $groups, $nb_term);
+# ALTree::Nanova::FillTableaux($tree->GetRoot(), $values, $groups, $nb_term);
+# print "Values:\n";
+# foreach my $val (@{$values}) {
+# print $val, "\t";
+# }
+# print "\n";
+# print "Groups:\n";
+# foreach my $group (@{$groups}) {
+# print $group, "\t";
+# }
+# print "\n";
+# print "*********\n";
+# my $una_results;
+# $una_results = NAnova::UnbalancedNestedANOVA($mat, $groups, $values);
+# my $i=1;
+# foreach my $res (@{$una_results}) {
+# print "Level $i\tF=",$res->{"F"}, "\tp-value=",$res->{"p_value"}, "\n";
+# $i++;
+ # }
# }
+# print "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n";
$option_require->("permutations",
"The number of permutations used to calculate".
diff --git a/to_rewrite.pm b/to_rewrite.pm
index 5d1a89f..197333b 100644
--- a/to_rewrite.pm
+++ b/to_rewrite.pm
@@ -308,7 +308,7 @@ sub InfosAffichees
$chaine.=" case/control:".$node->{"case"}."/".$node->{"control"};
}
if ($mode==3 || $mode == 4) {
- $chaine.= sprintf " mean:%.2f",$node->{"moyenne"};
+ $chaine.= sprintf " mean:%.2f",$node->GetQuantiMean();
}
if (1) { # affiche les apomorphies
$chaine.="\n";
--
GitLab