From ecbb7e0f0bb52e84c02208a5608051fd73aeeda7 Mon Sep 17 00:00:00 2001
From: Vincent Danjean <Vincent.Danjean@ens-lyon.org>
Date: Thu, 22 Jun 2006 14:47:12 +0000
Subject: [PATCH] git-svn-id:
svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@203
cf695345-040a-0410-a956-b889e835fe2e
---
ALTree/Nanova.pm | 23 ++++++++
ALTree/Node.pm | 10 ++++
altree | 6 +-
.../ancestor_present/association/1_caco.asso | 57 +++++++++++++++++++
4 files changed, 94 insertions(+), 2 deletions(-)
diff --git a/ALTree/Nanova.pm b/ALTree/Nanova.pm
index 503ee6e..11502b6 100644
--- a/ALTree/Nanova.pm
+++ b/ALTree/Nanova.pm
@@ -60,6 +60,29 @@ sub Tree2mat
return \@mat;
}
+# Fille the various tabular necessary for NAnaova
+sub FillTableaux
+{
+
+ my $present_node = shift;
+ my $values = shift;
+ my $groups = shift;
+ my $nb_term = shift;
+
+ if ($present_node->NbChildren()==0) {
+ $presentNode->GetQuantiList();
+ push @{$values}, @{$present_node->GetQuantiList()};
+ push @{$groups}, $present_node->NbQuanti();
+ $nb_term++;
+ } else {
+ for my $child ($present_node->GetChildrenList()) {
+ FillTableaux($child, $value, $groups, $nb_term);
+ }
+ }
+
+
+}
+
sub WriteMat
{
diff --git a/ALTree/Node.pm b/ALTree/Node.pm
index fce213e..f8cf43a 100644
--- a/ALTree/Node.pm
+++ b/ALTree/Node.pm
@@ -239,6 +239,16 @@ sub Name {
}
}
+sub GetQuantiList {
+ my $self=shift;
+ return @{$self->{"quanti"}};
+}
+
+sub NbQuanti {
+ my $self=shift;
+ return scalar(@{$self->{"quanti"}});
+}
+
#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 25e2957..06ae6bf 100755
--- a/altree
+++ b/altree
@@ -1521,8 +1521,10 @@ sub main
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",
diff --git a/test/paup/ancestor_present/association/1_caco.asso b/test/paup/ancestor_present/association/1_caco.asso
index 2eea4ff..ce8d9aa 100644
--- a/test/paup/ancestor_present/association/1_caco.asso
+++ b/test/paup/ancestor_present/association/1_caco.asso
@@ -1,2 +1,59 @@
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+ /----* H002 (LEVEL: 4) case/control:8/6
+ | /----* H007 (LEVEL: 5) case/control:7/13
+ | | Site: 12 Sens: 2-->1
+ | |----* H012 (LEVEL: 5) case/control:1/4
+ | | Site: 11 Sens: 2-->1
+ |----* 15 (LEVEL: 4) case/control:13/18
+ | | Site: 1 Sens: 1-->2
+ | | Site: 2 Sens: 1-->2
+ | \----* H011 (LEVEL: 5) case/control:5/1
+ /----* 17 (LEVEL: 3) case/control:66/41
+ | | Site: 10 Sens: 2-->1
+ | | Site: 9 Sens: 2-->1
+ | | /----* H008 (LEVEL: 5) case/control:9/2
+ | | | Site: 9 Sens: 1-->2
+ | |----* 16 (LEVEL: 4) case/control:37/15
+ | | | Site: 11 Sens: 2-->1
+ | | \----* H006 (LEVEL: 5) case/control:28/13
+ | \----* H009 (LEVEL: 4) case/control:8/2
+ | Site: 12 Sens: 2-->1
+ /----* 18 (LEVEL: 2) case/control:70/43
+ | | Site: 8 Sens: 2-->1
+ | | Site: 1 Sens: 2-->1
+ | | Site: 2 Sens: 2-->1
+ | \----* H014 (LEVEL: 3) case/control:4/2
+ /----* 19 (LEVEL: 1) case/control:72/47
+ | | Site: 6 Sens: 2-->1
+ | | Site: 7 Sens: 2-->1
+ | \----* H013 (LEVEL: 2) case/control:2/4
+ |----* H001 (LEVEL: 1) case/control:11/9
+ | Site: 1 Sens: 2-->1
+ | Site: 2 Sens: 2-->1
+ | /----* H003 (LEVEL: 2) case/control:5/6
+ | | Site: 4 Sens: 2-->1
+ |----* 20 (LEVEL: 1) case/control:12/13
+ | | Site: 3 Sens: 2-->1
+ | \----* H005 (LEVEL: 2) case/control:7/7
+ | Site: 12 Sens: 2-->1
+-----* 22+(21) (LEVEL: 0) case/control:200/200
+ |
+ | [0] ddl=4 chi2=9.33 p_value_chi2=0.0535
+ | [1] ddl=6 chi2=11.24 p_value_chi2=0.07
+ | [2] ddl=7 chi2=11.30 p_value_chi2=0.112
+ | [3] ddl=10 chi2=19.46 p_value_chi2=0.029
+ | [4] ddl=13 chi2=25.55 p_value_chi2=0.015
+ |----* H000 (LEVEL: 1) case/control:98/126
+ \----* H010 (LEVEL: 1) case/control:7/5
+ Site: 5 Sens: 2-->1
+
+ Number of permutation: 1
+
+p_val for each level:
+level 1 p-value (non corrected) 0
+level 2 p-value (non corrected) 0
+level 3 p-value (non corrected) 0
+level 4 p-value (non corrected) 0
+level 5 p-value (non corrected) 0
+corrected minimal p_value in the tree: 0
--
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