From ad189d71b36cd981cd11396105f4534162a52062 Mon Sep 17 00:00:00 2001
From: Vincent Danjean <Vincent.Danjean@ens-lyon.org>
Date: Tue, 2 Aug 2005 19:17:12 +0000
Subject: [PATCH] Switching Alphy to ALTree
git-svn-id: svn+ssh://imag/users/huron/danjean/svnroot/claire/altree/trunk@45 cf695345-040a-0410-a956-b889e835fe2e
---
{Alphy => ALTree}/Base.pm | 2 +-
{Alphy => ALTree}/Chi2.pm | 6 +-
{Alphy => ALTree}/Foret.pm | 6 +-
{Alphy => ALTree}/Import.pm | 16 ++---
{Alphy => ALTree}/Node.pm | 4 +-
{Alphy => ALTree}/Sens.pm | 4 +-
{Alphy => ALTree}/Site.pm | 10 +--
{Alphy => ALTree}/SiteCollection.pm | 4 +-
{Alphy => ALTree}/SitePerForet.pm | 6 +-
{Alphy => ALTree}/SitePerTree.pm | 8 +--
{Alphy => ALTree}/SiteSens.pm | 4 +-
{Alphy => ALTree}/SiteSensPerForet.pm | 4 +-
{Alphy => ALTree}/SiteSensPerTree.pm | 4 +-
{Alphy => ALTree}/Tree.pm | 4 +-
CUtils/CUtils.xs | 2 +-
CUtils/Makefile.PL | 10 +--
CUtils/c_sources/Makefile.PL | 12 ++--
CUtils/const-c.inc | 4 +-
CUtils/const-xs.inc | 6 +-
CUtils/fallback/const-c.inc | 4 +-
CUtils/fallback/const-xs.inc | 6 +-
CUtils/lib/{Alphy => ALTree}/CUtils.pm | 14 ++--
CUtils/t/{Alphy-CUtils.t => ALTree-CUtils.t} | 4 +-
CUtils/t/double_permutation.t | 6 +-
Changes | 3 +
.../case_control/association/test.tree | 2 +-
.../case_control/localisation/test.tree | 2 +-
Documentation/manual.tex | 24 +++----
MANIFEST | 44 ++++++------
MANIFEST.SKIP | 3 +-
Makefile.PL | 10 +--
README | 4 +-
alphy => altree | 68 +++++++++----------
alphy-add-S => altree-add-S | 4 +-
alphy-convert => altree-convert | 4 +-
t/{Alphy-Utils.t => ALTree.t} | 4 +-
36 files changed, 165 insertions(+), 157 deletions(-)
rename {Alphy => ALTree}/Base.pm (93%)
rename {Alphy => ALTree}/Chi2.pm (98%)
rename {Alphy => ALTree}/Foret.pm (95%)
rename {Alphy => ALTree}/Import.pm (91%)
rename {Alphy => ALTree}/Node.pm (99%)
rename {Alphy => ALTree}/Sens.pm (96%)
rename {Alphy => ALTree}/Site.pm (90%)
rename {Alphy => ALTree}/SiteCollection.pm (94%)
rename {Alphy => ALTree}/SitePerForet.pm (96%)
rename {Alphy => ALTree}/SitePerTree.pm (88%)
rename {Alphy => ALTree}/SiteSens.pm (96%)
rename {Alphy => ALTree}/SiteSensPerForet.pm (91%)
rename {Alphy => ALTree}/SiteSensPerTree.pm (97%)
rename {Alphy => ALTree}/Tree.pm (97%)
rename CUtils/lib/{Alphy => ALTree}/CUtils.pm (88%)
rename CUtils/t/{Alphy-CUtils.t => ALTree-CUtils.t} (76%)
rename alphy => altree (96%)
rename alphy-add-S => altree-add-S (99%)
rename alphy-convert => altree-convert (99%)
rename t/{Alphy-Utils.t => ALTree.t} (76%)
diff --git a/Alphy/Base.pm b/ALTree/Base.pm
similarity index 93%
rename from Alphy/Base.pm
rename to ALTree/Base.pm
index e51258a..601c268 100644
--- a/Alphy/Base.pm
+++ b/ALTree/Base.pm
@@ -1,4 +1,4 @@
-package Alphy::Base;
+package ALTree::Base;
###########################################
######## MAIN DATA STRUCTURES #########
diff --git a/Alphy/Chi2.pm b/ALTree/Chi2.pm
similarity index 98%
rename from Alphy/Chi2.pm
rename to ALTree/Chi2.pm
index d84657e..13468b3 100644
--- a/Alphy/Chi2.pm
+++ b/ALTree/Chi2.pm
@@ -1,7 +1,7 @@
-package Alphy::Chi2;
+package ALTree::Chi2;
use strict;
-use Alphy::CUtils;
+use ALTree::CUtils;
BEGIN {
use Exporter ();
@@ -88,7 +88,7 @@ sub chi2_significatif {
if (not defined($chi2_seuil->[$ddl])) {
#my $c=`critchi2 $chi2_p $ddl`+0; # Verif que les 2 appels sont équivalents
- $chi2_seuil->[$ddl]=Alphy::CUtils::critchi($chi2_p, $ddl);
+ $chi2_seuil->[$ddl]=ALTree::CUtils::critchi($chi2_p, $ddl);
#if ($c != $$chi2_seuil[$ddl]) {
# print STDERR "Critchi2 : $c != $$chi2_seuil[$ddl]\n";
#}
diff --git a/Alphy/Foret.pm b/ALTree/Foret.pm
similarity index 95%
rename from Alphy/Foret.pm
rename to ALTree/Foret.pm
index 958f9ef..d5936c6 100644
--- a/Alphy/Foret.pm
+++ b/ALTree/Foret.pm
@@ -1,4 +1,4 @@
-package Alphy::Foret;
+package ALTree::Foret;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::Foret;
################################################################
################################################################
-use base qw(Alphy::Base Alphy::SiteCollection);
+use base qw(ALTree::Base ALTree::SiteCollection);
sub New { # [classe]
my $class=shift;
@@ -37,7 +37,7 @@ sub ProvideSite {
my $site_nb=shift;
if (not $self->HasSiteIndex($site_nb)) {
- $self->AddSite(Alphy::SitePerForet->New($site_nb));
+ $self->AddSite(ALTree::SitePerForet->New($site_nb));
}
return $self->GetSite($site_nb);
}
diff --git a/Alphy/Import.pm b/ALTree/Import.pm
similarity index 91%
rename from Alphy/Import.pm
rename to ALTree/Import.pm
index 2cf1488..ca67d02 100644
--- a/Alphy/Import.pm
+++ b/ALTree/Import.pm
@@ -1,13 +1,13 @@
-package Alphy::Import;
+package ALTree::Import;
use strict;
-use Alphy::Sens;
-use Alphy::Tree;
-use Alphy::Foret;
-use Alphy::Node;
-use Alphy::SitePerTree;
-use Alphy::SitePerForet;
-use Alphy::SiteSensPerForet;
+use ALTree::Sens;
+use ALTree::Tree;
+use ALTree::Foret;
+use ALTree::Node;
+use ALTree::SitePerTree;
+use ALTree::SitePerForet;
+use ALTree::SiteSensPerForet;
BEGIN {
use Exporter ();
diff --git a/Alphy/Node.pm b/ALTree/Node.pm
similarity index 99%
rename from Alphy/Node.pm
rename to ALTree/Node.pm
index bc63aa2..ba47461 100644
--- a/Alphy/Node.pm
+++ b/ALTree/Node.pm
@@ -1,4 +1,4 @@
-package Alphy::Node;
+package ALTree::Node;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::Node;
################################################################
################################################################
-use base 'Alphy::Base';
+use base 'ALTree::Base';
# Structure Node
# "id" -> String
diff --git a/Alphy/Sens.pm b/ALTree/Sens.pm
similarity index 96%
rename from Alphy/Sens.pm
rename to ALTree/Sens.pm
index 446110b..3621755 100644
--- a/Alphy/Sens.pm
+++ b/ALTree/Sens.pm
@@ -1,4 +1,4 @@
-package Alphy::Sens;
+package ALTree::Sens;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::Sens;
################################################################
################################################################
-use base 'Alphy::Base';
+use base 'ALTree::Base';
#Creation d'une structure
sub New { # [classe] sens
diff --git a/Alphy/Site.pm b/ALTree/Site.pm
similarity index 90%
rename from Alphy/Site.pm
rename to ALTree/Site.pm
index 5af1edb..205e646 100644
--- a/Alphy/Site.pm
+++ b/ALTree/Site.pm
@@ -1,4 +1,4 @@
-package Alphy::Site;
+package ALTree::Site;
################################################################
################################################################
@@ -6,8 +6,8 @@ package Alphy::Site;
################################################################
################################################################
-use base 'Alphy::Base';
-use Alphy::Sens;
+use base 'ALTree::Base';
+use ALTree::Sens;
# Structure Site
# "site_nb" -> Integer
@@ -37,10 +37,10 @@ sub AddSens {
my($ref_site_sens)=$self->NewSens($sens);
$self->{"sens_struct"}->{$sens->GetLabel()}=$ref_site_sens;
- my $sensRev=Alphy::Sens->NewRev($sens);
+ my $sensRev=ALTree::Sens->NewRev($sens);
my($ref_site_sens_rev)=$self->NewSens($sensRev);
$self->{"sens_struct"}->{$sensRev->GetLabel()}=$ref_site_sens_rev;
- Alphy::SiteSens::LinkRev($ref_site_sens, $ref_site_sens_rev);
+ ALTree::SiteSens::LinkRev($ref_site_sens, $ref_site_sens_rev);
}
sub GetSens {
my $self=shift;
diff --git a/Alphy/SiteCollection.pm b/ALTree/SiteCollection.pm
similarity index 94%
rename from Alphy/SiteCollection.pm
rename to ALTree/SiteCollection.pm
index 63b7ab4..3d9b83d 100644
--- a/Alphy/SiteCollection.pm
+++ b/ALTree/SiteCollection.pm
@@ -1,4 +1,4 @@
-package Alphy::SiteCollection;
+package ALTree::SiteCollection;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::SiteCollection;
################################################################
################################################################
-use base 'Alphy::Base';
+use base 'ALTree::Base';
sub InitSiteCollection {
my $self=shift;
diff --git a/Alphy/SitePerForet.pm b/ALTree/SitePerForet.pm
similarity index 96%
rename from Alphy/SitePerForet.pm
rename to ALTree/SitePerForet.pm
index 0518fcd..bbfbb4d 100644
--- a/Alphy/SitePerForet.pm
+++ b/ALTree/SitePerForet.pm
@@ -1,4 +1,4 @@
-package Alphy::SitePerForet;
+package ALTree::SitePerForet;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::SitePerForet;
################################################################
################################################################
-use base qw(Alphy::Base Alphy::Site);
+use base qw(ALTree::Base ALTree::Site);
use sort '_quicksort';
sub New { # [classe] site_nb
@@ -22,7 +22,7 @@ sub New { # [classe] site_nb
sub NewSens {
my $self=shift;
my $sens=shift;
- return Alphy::SiteSensPerForet->New($sens, $self);
+ return ALTree::SiteSensPerForet->New($sens, $self);
}
sub mysort {
diff --git a/Alphy/SitePerTree.pm b/ALTree/SitePerTree.pm
similarity index 88%
rename from Alphy/SitePerTree.pm
rename to ALTree/SitePerTree.pm
index 6918fdb..5f54838 100644
--- a/Alphy/SitePerTree.pm
+++ b/ALTree/SitePerTree.pm
@@ -1,4 +1,4 @@
-package Alphy::SitePerTree;
+package ALTree::SitePerTree;
################################################################
################################################################
@@ -6,8 +6,8 @@ package Alphy::SitePerTree;
################################################################
################################################################
-use base qw(Alphy::Base Alphy::Site);
-use Alphy::SiteSensPerTree;
+use base qw(ALTree::Base ALTree::Site);
+use ALTree::SiteSensPerTree;
# Structure SitePerTree
# "site_nb" -> Integer
@@ -28,7 +28,7 @@ sub New { # [classe] site_nb
sub NewSens {
my $self=shift;
my $sens=shift;
- return Alphy::SiteSensPerTree->New($sens, $self);
+ return ALTree::SiteSensPerTree->New($sens, $self);
}
sub SetCI {
diff --git a/Alphy/SiteSens.pm b/ALTree/SiteSens.pm
similarity index 96%
rename from Alphy/SiteSens.pm
rename to ALTree/SiteSens.pm
index c09c4e1..ace170c 100644
--- a/Alphy/SiteSens.pm
+++ b/ALTree/SiteSens.pm
@@ -1,4 +1,4 @@
-package Alphy::SiteSens;
+package ALTree::SiteSens;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::SiteSens;
################################################################
################################################################
-use base 'Alphy::Base';
+use base 'ALTree::Base';
# Structure SiteSens
# "site_struct" -> Site
diff --git a/Alphy/SiteSensPerForet.pm b/ALTree/SiteSensPerForet.pm
similarity index 91%
rename from Alphy/SiteSensPerForet.pm
rename to ALTree/SiteSensPerForet.pm
index f9c1c5d..84e33c1 100644
--- a/Alphy/SiteSensPerForet.pm
+++ b/ALTree/SiteSensPerForet.pm
@@ -1,4 +1,4 @@
-package Alphy::SiteSensPerForet;
+package ALTree::SiteSensPerForet;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::SiteSensPerForet;
################################################################
################################################################
-use base qw(Alphy::Base Alphy::SiteSens);
+use base qw(ALTree::Base ALTree::SiteSens);
# Structure SiteSensPerForet
# "site_struct" -> Site
diff --git a/Alphy/SiteSensPerTree.pm b/ALTree/SiteSensPerTree.pm
similarity index 97%
rename from Alphy/SiteSensPerTree.pm
rename to ALTree/SiteSensPerTree.pm
index 06558e6..fd74c53 100644
--- a/Alphy/SiteSensPerTree.pm
+++ b/ALTree/SiteSensPerTree.pm
@@ -1,4 +1,4 @@
-package Alphy::SiteSensPerTree;
+package ALTree::SiteSensPerTree;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::SiteSensPerTree;
################################################################
################################################################
-use base qw(Alphy::Base Alphy::SiteSens);
+use base qw(ALTree::Base ALTree::SiteSens);
# Structure SiteSens
# "site_struct" -> Site
diff --git a/Alphy/Tree.pm b/ALTree/Tree.pm
similarity index 97%
rename from Alphy/Tree.pm
rename to ALTree/Tree.pm
index a112f20..3c5a802 100644
--- a/Alphy/Tree.pm
+++ b/ALTree/Tree.pm
@@ -1,4 +1,4 @@
-package Alphy::Tree;
+package ALTree::Tree;
################################################################
################################################################
@@ -6,7 +6,7 @@ package Alphy::Tree;
################################################################
################################################################
-use base qw(Alphy::Base Alphy::SiteCollection);
+use base qw(ALTree::Base ALTree::SiteCollection);
# "nodes" -> Hash of ('id' -> Node)
# "sites" -> Hash of ('site_nb' -> SitePerTree)
diff --git a/CUtils/CUtils.xs b/CUtils/CUtils.xs
index eb5668c..2cbfd78 100644
--- a/CUtils/CUtils.xs
+++ b/CUtils/CUtils.xs
@@ -10,7 +10,7 @@
#include "const-c.inc"
-MODULE = Alphy::CUtils PACKAGE = Alphy::CUtils
+MODULE = ALTree::CUtils PACKAGE = ALTree::CUtils
INCLUDE: const-xs.inc
diff --git a/CUtils/Makefile.PL b/CUtils/Makefile.PL
index f1c6ce7..1933dda 100644
--- a/CUtils/Makefile.PL
+++ b/CUtils/Makefile.PL
@@ -3,18 +3,18 @@ use ExtUtils::MakeMaker;
# See lib/ExtUtils/MakeMaker.pm for details of how to influence
# the contents of the Makefile that is written.
WriteMakefile(
- NAME => 'Alphy::CUtils',
- VERSION_FROM => 'lib/Alphy/CUtils.pm', # finds $VERSION
+ NAME => 'ALTree::CUtils',
+ VERSION_FROM => 'lib/ALTree/CUtils.pm', # finds $VERSION
PREREQ_PM => {}, # e.g., Module::Name => 1.1
($] >= 5.005 ? ## Add these new keywords supported since 5.005
- (ABSTRACT_FROM => 'lib/Alphy/CUtils.pm', # retrieve abstract from module
+ (ABSTRACT_FROM => 'lib/ALTree/CUtils.pm', # retrieve abstract from module
AUTHOR => 'Claire Bardel <bardel@vjf.inserm.fr>') : ()),
LIBS => ['-lm '], # e.g., '-lm'
DEFINE => '', # e.g., '-DHAVE_SOMETHING'
INC => '-I.', # e.g., '-I. -I/usr/include/other'
# Un-comment this if you add C files to link with later:
# OBJECT => '$(O_FILES)', # link all the C files too
- MYEXTLIB => 'c_sources/libalphy-cutils$(LIB_EXT)',
+ MYEXTLIB => 'c_sources/libaltree-cutils$(LIB_EXT)',
);
if (eval {require ExtUtils::Constant; 1}) {
# If you edit these definitions to change the constants used by this module,
@@ -23,7 +23,7 @@ if (eval {require ExtUtils::Constant; 1}) {
# changes.
my @names = (qw());
ExtUtils::Constant::WriteConstants(
- NAME => 'Alphy::CUtils',
+ NAME => 'ALTree::CUtils',
NAMES => \@names,
DEFAULT_TYPE => 'IV',
C_FILE => 'const-c.inc',
diff --git a/CUtils/c_sources/Makefile.PL b/CUtils/c_sources/Makefile.PL
index 877c840..37300aa 100644
--- a/CUtils/c_sources/Makefile.PL
+++ b/CUtils/c_sources/Makefile.PL
@@ -2,9 +2,9 @@
use ExtUtils::MakeMaker;
$Verbose = 1;
WriteMakefile(
- NAME => 'Alphy::CUtils',
+ NAME => 'ALTree::CUtils',
SKIP => [qw(all static static_lib dynamic dynamic_lib)],
- clean => {'FILES' => 'libalphy-cutils$(LIB_EXT)'},
+ clean => {'FILES' => 'libaltree-cutils$(LIB_EXT)'},
);
sub MY::top_targets {
@@ -13,11 +13,11 @@ all :: static
pure_all :: static
-static :: libalphy-cutils$(LIB_EXT)
+static :: libaltree-cutils$(LIB_EXT)
-libalphy-cutils$(LIB_EXT): $(O_FILES)
- $(AR) cr libalphy-cutils$(LIB_EXT) $(O_FILES)
- $(RANLIB) libalphy-cutils$(LIB_EXT)
+libaltree-cutils$(LIB_EXT): $(O_FILES)
+ $(AR) cr libaltree-cutils$(LIB_EXT) $(O_FILES)
+ $(RANLIB) libaltree-cutils$(LIB_EXT)
';
}
diff --git a/CUtils/const-c.inc b/CUtils/const-c.inc
index 55caf8d..88ec417 100644
--- a/CUtils/const-c.inc
+++ b/CUtils/const-c.inc
@@ -40,11 +40,11 @@ my $types = {map {($_, 1)} qw()};
my @names = (qw());
print constant_types(); # macro defs
-foreach (C_constant ("Alphy::CUtils", 'constant', 'IV', $types, undef, 3, @names) ) {
+foreach (C_constant ("ALTree::CUtils", 'constant', 'IV', $types, undef, 3, @names) ) {
print $_, "\n"; # C constant subs
}
print "#### XS Section:\n";
-print XS_constant ("Alphy::CUtils", $types);
+print XS_constant ("ALTree::CUtils", $types);
__END__
*/
diff --git a/CUtils/const-xs.inc b/CUtils/const-xs.inc
index 297750c..1945c56 100644
--- a/CUtils/const-xs.inc
+++ b/CUtils/const-xs.inc
@@ -20,12 +20,12 @@ constant(sv)
Second, if present, is found value */
switch (type) {
case PERL_constant_NOTFOUND:
- sv = sv_2mortal(newSVpvf("%s is not a valid Alphy::CUtils macro", s));
+ sv = sv_2mortal(newSVpvf("%s is not a valid ALTree::CUtils macro", s));
PUSHs(sv);
break;
case PERL_constant_NOTDEF:
sv = sv_2mortal(newSVpvf(
- "Your vendor has not defined Alphy::CUtils macro %s, used", s));
+ "Your vendor has not defined ALTree::CUtils macro %s, used", s));
PUSHs(sv);
break;
/* Uncomment this if you need to return IVs
@@ -81,7 +81,7 @@ constant(sv)
break; */
default:
sv = sv_2mortal(newSVpvf(
- "Unexpected return type %d while processing Alphy::CUtils macro %s, used",
+ "Unexpected return type %d while processing ALTree::CUtils macro %s, used",
type, s));
PUSHs(sv);
}
diff --git a/CUtils/fallback/const-c.inc b/CUtils/fallback/const-c.inc
index 55caf8d..88ec417 100644
--- a/CUtils/fallback/const-c.inc
+++ b/CUtils/fallback/const-c.inc
@@ -40,11 +40,11 @@ my $types = {map {($_, 1)} qw()};
my @names = (qw());
print constant_types(); # macro defs
-foreach (C_constant ("Alphy::CUtils", 'constant', 'IV', $types, undef, 3, @names) ) {
+foreach (C_constant ("ALTree::CUtils", 'constant', 'IV', $types, undef, 3, @names) ) {
print $_, "\n"; # C constant subs
}
print "#### XS Section:\n";
-print XS_constant ("Alphy::CUtils", $types);
+print XS_constant ("ALTree::CUtils", $types);
__END__
*/
diff --git a/CUtils/fallback/const-xs.inc b/CUtils/fallback/const-xs.inc
index 297750c..1945c56 100644
--- a/CUtils/fallback/const-xs.inc
+++ b/CUtils/fallback/const-xs.inc
@@ -20,12 +20,12 @@ constant(sv)
Second, if present, is found value */
switch (type) {
case PERL_constant_NOTFOUND:
- sv = sv_2mortal(newSVpvf("%s is not a valid Alphy::CUtils macro", s));
+ sv = sv_2mortal(newSVpvf("%s is not a valid ALTree::CUtils macro", s));
PUSHs(sv);
break;
case PERL_constant_NOTDEF:
sv = sv_2mortal(newSVpvf(
- "Your vendor has not defined Alphy::CUtils macro %s, used", s));
+ "Your vendor has not defined ALTree::CUtils macro %s, used", s));
PUSHs(sv);
break;
/* Uncomment this if you need to return IVs
@@ -81,7 +81,7 @@ constant(sv)
break; */
default:
sv = sv_2mortal(newSVpvf(
- "Unexpected return type %d while processing Alphy::CUtils macro %s, used",
+ "Unexpected return type %d while processing ALTree::CUtils macro %s, used",
type, s));
PUSHs(sv);
}
diff --git a/CUtils/lib/Alphy/CUtils.pm b/CUtils/lib/ALTree/CUtils.pm
similarity index 88%
rename from CUtils/lib/Alphy/CUtils.pm
rename to CUtils/lib/ALTree/CUtils.pm
index a94d233..c99756a 100644
--- a/CUtils/lib/Alphy/CUtils.pm
+++ b/CUtils/lib/ALTree/CUtils.pm
@@ -1,4 +1,4 @@
-package Alphy::CUtils;
+package ALTree::CUtils;
use 5.008;
use strict;
@@ -14,7 +14,7 @@ our @ISA = qw(Exporter);
# names by default without a very good reason. Use EXPORT_OK instead.
# Do not simply export all your public functions/methods/constants.
-# This allows declaration use Alphy::CUtils ':all';
+# This allows declaration use ALTree::CUtils ':all';
# If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
# will save memory.
our %EXPORT_TAGS = ( 'all' => [ qw(
@@ -40,7 +40,7 @@ sub AUTOLOAD {
my $constname;
our $AUTOLOAD;
($constname = $AUTOLOAD) =~ s/.*:://;
- croak "&Alphy::CUtils::constant not defined" if $constname eq 'constant';
+ croak "&ALTree::CUtils::constant not defined" if $constname eq 'constant';
my ($error, $val) = constant($constname);
if ($error) { croak $error; }
{
@@ -57,7 +57,7 @@ sub AUTOLOAD {
}
require XSLoader;
-XSLoader::load('Alphy::CUtils', $VERSION);
+XSLoader::load('ALTree::CUtils', $VERSION);
# Preloaded methods go here.
@@ -69,16 +69,16 @@ __END__
=head1 NAME
-Alphy::CUtils - Perl extension for blah blah blah
+ALTree::CUtils - Perl extension for blah blah blah
=head1 SYNOPSIS
- use Alphy::CUtils;
+ use ALTree::CUtils;
blah blah blah
=head1 DESCRIPTION
-Stub documentation for Alphy::CUtils, created by h2xs. It looks like the
+Stub documentation for ALTree::CUtils, created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.
diff --git a/CUtils/t/Alphy-CUtils.t b/CUtils/t/ALTree-CUtils.t
similarity index 76%
rename from CUtils/t/Alphy-CUtils.t
rename to CUtils/t/ALTree-CUtils.t
index f463dd6..b6d73c1 100644
--- a/CUtils/t/Alphy-CUtils.t
+++ b/CUtils/t/ALTree-CUtils.t
@@ -1,12 +1,12 @@
# Before `make install' is performed this script should be runnable with
-# `make test'. After `make install' it should work as `perl Alphy-CUtils.t'
+# `make test'. After `make install' it should work as `perl ALTree-CUtils.t'
#########################
# change 'tests => 1' to 'tests => last_test_to_print';
use Test::More tests => 1;
-BEGIN { use_ok('Alphy::CUtils') };
+BEGIN { use_ok('ALTree::CUtils') };
#########################
diff --git a/CUtils/t/double_permutation.t b/CUtils/t/double_permutation.t
index 0be45b1..7d0f4be 100644
--- a/CUtils/t/double_permutation.t
+++ b/CUtils/t/double_permutation.t
@@ -6,17 +6,17 @@
# change 'tests => 1' to 'tests => last_test_to_print';
use Test::More tests => 3;
-BEGIN { use_ok('Alphy::CUtils') };
+BEGIN { use_ok('ALTree::CUtils') };
#########################
# Insert your test code below, the Test::More module is use()ed here so read
# its man page ( perldoc Test::More ) for help writing this test script.
-$res=Alphy::CUtils::double_permutation(2,3, [0, 0.1]);
+$res=ALTree::CUtils::double_permutation(2,3, [0, 0.1]);
is($res, undef, "undef when bad args");
-$res=Alphy::CUtils::double_permutation(10, 2,
+$res=ALTree::CUtils::double_permutation(10, 2,
[12.1, 432.2, 123.3, 15.4, 3453.5, 34253.6, 12.7, 23.8, 23.9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20]
);
diff --git a/Changes b/Changes
index 837a061..9047d25 100644
--- a/Changes
+++ b/Changes
@@ -1,5 +1,8 @@
Revision history for Perl extension Alphy::Utils.
+0.9.2 Tue Aug 2 19:19:05 2005
+ - New name : ALTree instead of ALPhy
+
0.01 Sun Jun 5 19:04:07 2005
- original version; created by h2xs 1.23 with options
-AX -n Alphy::Utils
diff --git a/Documentation/example_files/case_control/association/test.tree b/Documentation/example_files/case_control/association/test.tree
index b0f0b04..225eef6 100644
--- a/Documentation/example_files/case_control/association/test.tree
+++ b/Documentation/example_files/case_control/association/test.tree
@@ -2,7 +2,7 @@
Begin trees; [Treefile saved Tue Jul 5 18:05:27 2005]
[!
->Data file = /home/cbardel/recherche/logiciel/alphy/Documentation/example_files/phase/association/caco.paup
+>Data file = /home/cbardel/recherche/logiciel/altree/Documentation/example_files/phase/association/caco.paup
>Heuristic search settings:
> Optimality criterion = parsimony
> Character-status summary:
diff --git a/Documentation/example_files/case_control/localisation/test.tree b/Documentation/example_files/case_control/localisation/test.tree
index 9cdb10c..edc051a 100644
--- a/Documentation/example_files/case_control/localisation/test.tree
+++ b/Documentation/example_files/case_control/localisation/test.tree
@@ -2,7 +2,7 @@
Begin trees; [Treefile saved Tue Jul 5 16:13:26 2005]
[!
->Data file = /home/cbardel/recherche/logiciel/alphy/Documentation/example_files/phase/localisation/et_caco.paup
+>Data file = /home/cbardel/recherche/logiciel/altree/Documentation/example_files/phase/localisation/et_caco.paup
>Heuristic search settings:
> Optimality criterion = parsimony
> Character-status summary:
diff --git a/Documentation/manual.tex b/Documentation/manual.tex
index 860d7c8..4598784 100644
--- a/Documentation/manual.tex
+++ b/Documentation/manual.tex
@@ -42,14 +42,14 @@
\newcommand{\paml}{\texttt{paml}\xspace}
%TODO est-ce que phyml s'écrit comme ça ?
\newcommand{\phyml}{\texttt{phyml}\xspace}
-\newcommand{\alphy}{\texttt{ALPhy}\xspace}
+\newcommand{\altree}{\texttt{ALTree}\xspace}
\renewcommand{\thetable} {\rm\Roman{table}}
\renewcommand{\thefigure} {\rm\Roman{figure}}
-\newcommand{\newchitree}{\texttt{ALPhy}\xspace}
-\newcommand{\etHTname}{alphy-add-S}
-\newcommand{\etHT}{\texttt{ALPhy-add-S}\xspace}
-\newcommand{\rechaploname}{alphy-convert}
-\newcommand{\rechaplo}{\texttt{ALPhy-convert}\xspace}
+\newcommand{\newchitree}{\texttt{ALTree}\xspace}
+\newcommand{\etHTname}{altree-add-S}
+\newcommand{\etHT}{\texttt{ALTree-add-S}\xspace}
+\newcommand{\rechaploname}{altree-convert}
+\newcommand{\rechaplo}{\texttt{ALTree-convert}\xspace}
\newcommand{\acctran}{\texttt{acctran}\xspace}
\newcommand{\deltran}{\texttt{deltran}\xspace}
\newcommand{\chisquare}{chi-square\xspace}
@@ -106,12 +106,12 @@ General Public License. The complete text of the GNU General Public
License can be found in the annexe~\ref{GPL} on page~\pageref{GPL}.
-%\section{Short description of the programs available in \alphy}
+%\section{Short description of the programs available in \altree}
\begin{figure}[htbp]
\includegraphics[width=\linewidth]{overview.fig}\centering
- \caption{\alphy softwares}
- \label{fig:alphy}
+ \caption{\altree softwares}
+ \label{fig:altree}
\end{figure}
\section{\newchitree}
\subsection{Association test}
@@ -186,7 +186,7 @@ The software can run on various linux/Unix platform and on MacOS X.
\label{sec:require}
\subsection{Phylogeny reconstruction programs}
-Before using \alphy, you must build a phylogeny of the haplotypes.
+Before using \altree, you must build a phylogeny of the haplotypes.
Three phylogeny software are compatible with our program:
\begin{itemize}
\item \paup~\cite{Swofford02}: available at
@@ -212,7 +212,7 @@ to compute the ML tree and then, to use \paml to estimate the
character states at each node.
\subsection{Required tools}
-\prog{perl} is required to run \alphy. \prog{perl} version 5.8.7 or
+\prog{perl} is required to run \altree. \prog{perl} version 5.8.7 or
higher should work. Lower version can work, but it has not been
tested.
@@ -740,7 +740,7 @@ The \phylip format file can be obtained by running the following command line:\\
This command generates the file \fn{correspond.txt} and \fn{trio.prephy}. The latter is not a valid phylip format file: you have to modify it slightly according to your data and your analysis. In this example, we choose to root the tree on a consensus ancestral sequence (see~\ref{description_paup}). So, we add this ancestral sequence in \fn{trio.prephy} to form the \fn{trio.phy} file and we build an \fn{ancestors} file, containing this sequence. \phylip is then run on \fn{trio.phy} with the options \cmd{0,37} (tree rooting), \cmd{5} (states at each node are written in the output file) and \cmd{a} (ancestral states must be used). We obtain two files: \fn{outtree} containing all the trees and \fn{outfile} containing the trees and the states at each nodes.
\subsection{Association analysis}
-alphy -i outfile -j correspond.txt -a -t SNP --root H000\_anc --rootmeth ancestor -p phylip -b -r 100 --anc-seq 11000100010 >100\_trio\_phy.asso
+altree -i outfile -j correspond.txt -a -t SNP --root H000\_anc --rootmeth ancestor -p phylip -b -r 100 --anc-seq 11000100010 >100\_trio\_phy.asso
diff --git a/MANIFEST b/MANIFEST
index 41c7ad3..83ef86c 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1,20 +1,20 @@
-alphy
-alphy-add-S
-alphy-convert
-Alphy/Base.pm
-Alphy/Chi2.pm
-Alphy/Foret.pm
-Alphy/Import.pm
-Alphy/Node.pm
-Alphy/Sens.pm
-Alphy/Site.pm
-Alphy/SiteCollection.pm
-Alphy/SitePerForet.pm
-Alphy/SitePerTree.pm
-Alphy/SiteSens.pm
-Alphy/SiteSensPerForet.pm
-Alphy/SiteSensPerTree.pm
-Alphy/Tree.pm
+altree
+altree-add-S
+altree-convert
+ALTree/Base.pm
+ALTree/Chi2.pm
+ALTree/Foret.pm
+ALTree/Import.pm
+ALTree/Node.pm
+ALTree/Sens.pm
+ALTree/Site.pm
+ALTree/SiteCollection.pm
+ALTree/SitePerForet.pm
+ALTree/SitePerTree.pm
+ALTree/SiteSens.pm
+ALTree/SiteSensPerForet.pm
+ALTree/SiteSensPerTree.pm
+ALTree/Tree.pm
Changes
CUtils/c_sources/chisq.c
CUtils/c_sources/chisq.h
@@ -30,10 +30,10 @@ CUtils/const-xs.inc
CUtils/CUtils.xs
CUtils/fallback/const-c.inc
CUtils/fallback/const-xs.inc
-CUtils/lib/Alphy/CUtils.pm
+CUtils/lib/ALTree/CUtils.pm
CUtils/Makefile.PL
CUtils/ppport.h
-CUtils/t/Alphy-CUtils.t
+CUtils/t/ALTree-CUtils.t
CUtils/t/double_permutation.t
Documentation/example_files/case_control/association/100_caco.asso
Documentation/example_files/case_control/association/caco.paup
@@ -49,6 +49,10 @@ Documentation/example_files/case_control/caco.phase.out_pairs
Documentation/example_files/case_control/caco.phase.out_recom
Documentation/example_files/case_control/caco.phy
Documentation/example_files/case_control/caco.prepaup
+Documentation/example_files/case_control/general/caco.paup
+Documentation/example_files/case_control/general/caco.phase
+Documentation/example_files/case_control/general/caco.phase.out
+Documentation/example_files/case_control/general/caco.prepaup
Documentation/example_files/case_control/localisation/caco.loc
Documentation/example_files/case_control/localisation/caco.paup
Documentation/example_files/case_control/localisation/correspond.txt
@@ -66,4 +70,4 @@ Makefile.PL
MANIFEST
META.yml Module meta-data (added by MakeMaker)
README
-t/Alphy-Utils.t
+t/ALTree.t
diff --git a/MANIFEST.SKIP b/MANIFEST.SKIP
index e11130c..9f0b7e1 100644
--- a/MANIFEST.SKIP
+++ b/MANIFEST.SKIP
@@ -2,6 +2,7 @@
\bRCS\b
\bCVS\b
,v$
+.cvsignore$
# Makemaker generated files and dirs.
^MANIFEST\.
@@ -17,7 +18,7 @@
^\.#
# Distributions
-^alphy-.*\.tar\.gz$
+^altree-.*\.tar\.gz$
# Documentation
^Documentation/fig/.*\.pdftex(_t)?$
diff --git a/Makefile.PL b/Makefile.PL
index 62b0b6c..2b419b7 100644
--- a/Makefile.PL
+++ b/Makefile.PL
@@ -3,13 +3,13 @@ use ExtUtils::MakeMaker;
# See lib/ExtUtils/MakeMaker.pm for details of how to influence
# the contents of the Makefile that is written.
WriteMakefile(
- NAME => 'alphy',
- PMLIBDIRS => [ 'Alphy' ],
+ NAME => 'altree',
+ PMLIBDIRS => [ 'ALTree' ],
DIR => [ 'CUtils' ],
- VERSION => '0.9.1d',
+ VERSION => '0.9.2',
PREREQ_PM => {}, # e.g., Module::Name => 1.1
($] >= 5.005 ? ## Add these new keywords supported since 5.005
- (ABSTRACT_FROM => 'alphy', # retrieve abstract from module
+ (ABSTRACT_FROM => 'altree', # retrieve abstract from module
AUTHOR => 'Claire Bardel <bardel@vjf.inserm.fr>') : ()),
- EXE_FILES => [qw (alphy alphy-add-S alphy-convert)],
+ EXE_FILES => [qw (altree altree-add-S altree-convert)],
);
diff --git a/README b/README
index 8880ab3..54ec5a6 100644
--- a/README
+++ b/README
@@ -1,5 +1,5 @@
-Alphy version 0.01
-==================
+ALTree version 0.92
+===================
The README is used to introduce the module and provide instructions on
how to install the module, any machine dependencies it may have (for
diff --git a/alphy b/altree
similarity index 96%
rename from alphy
rename to altree
index 3b9e421..661a825 100755
--- a/alphy
+++ b/altree
@@ -25,8 +25,8 @@ $VERSION = sprintf "%d.%03d", q$Revision$ =~ /(\d+)/g;
# Si les modules sont installés dans les emplacements standard de
# perl, c'est inutile
-use Alphy::Chi2 ();
-use Alphy::Import;
+use ALTree::Chi2 ();
+use ALTree::Import;
#use Newchi2treeUtils;
###########################################
@@ -278,7 +278,7 @@ sub ReadPAUP
}
if ($has_sens) {
$sens_chgt =~ s/=/-/g;
- $tab_infoapo[$j]->[5]=Alphy::Sens->New($sens_chgt); # direction of the change
+ $tab_infoapo[$j]->[5]=ALTree::Sens->New($sens_chgt); # direction of the change
$j++;
}
}
@@ -405,7 +405,7 @@ sub ReadPAML
#$tab_infoapo[$j]->[3]=; # CI
$tab_infoapo[$j]->[4]=1; # nb steps =1 for SNPs
my($sens_chgt)=$2."->".$3;
- $tab_infoapo[$j]->[5]=Alphy::Sens->New($sens_chgt); # direction of the change
+ $tab_infoapo[$j]->[5]=ALTree::Sens->New($sens_chgt); # direction of the change
$j++;
}
}
@@ -424,7 +424,7 @@ sub ReadPAML
sub TreeBuilding{
my($tab_longbranche)=shift;
my($i);
- my($tree)=Alphy::Tree->New();
+ my($tree)=ALTree::Tree->New();
#print "TreeBuilding\n";
for ($i=0;$i<=$#$tab_longbranche;$i++) {
@@ -439,13 +439,13 @@ sub TreeBuilding{
my $pere;
my $fils;
if (not $tree->HasNodeIndex($fils_id)) {
- $fils=Alphy::Node->New($fils_id); #creation de la structure Node
+ $fils=ALTree::Node->New($fils_id); #creation de la structure Node
$tree->AddNode($fils); # puis, on la met dans tree
} else {
$fils=$tree->GetNode($fils_id);
}
if (not $tree->HasNodeIndex($pere_id)) {
- $pere=Alphy::Node->New($pere_id); #creation de la structure Node
+ $pere=ALTree::Node->New($pere_id); #creation de la structure Node
$tree->AddNode($pere); # puis, on la met dans tree
} else {
$pere=$tree->GetNode($pere_id);
@@ -492,7 +492,7 @@ sub FillTreeApoInfoPAUP
my $site;
if (not $tree->HasSiteIndex($apo_num)) {
- $site=Alphy::SitePerTree->New($apo_num);
+ $site=ALTree::SitePerTree->New($apo_num);
$tree->AddSite($site);
if (defined $apo_CI) { # For PAML trees, CI is not defined
$site->SetCI($apo_CI);
@@ -561,10 +561,10 @@ sub FillTreeApo2Phylip
elsif ($fathersite ne $childsite) {
$br_len++;
my($apo_num)=$i+1;
- my($apo_sens)=Alphy::Sens->New($fathersite."->".$childsite);
+ my($apo_sens)=ALTree::Sens->New($fathersite."->".$childsite);
my $site;
if (not $tree->HasSiteIndex($apo_num)) {
- $site=Alphy::SitePerTree->New($apo_num);
+ $site=ALTree::SitePerTree->New($apo_num);
$tree->AddSite($site);
} else {
$site=$tree->GetSite($apo_num);
@@ -777,27 +777,27 @@ sub CalculChi2
$test_results->{"texte"}=
"No cases, ($sum_control controls)";
if ($sign_util==SignUtil::YES) {
- $significatif=Alphy::Chi2::NON_SIGNIFICATIF;
+ $significatif=ALTree::Chi2::NON_SIGNIFICATIF;
}
} elsif ($error == 2) {
$test_results->{"texte"}="No controls: only $sum_case cases";
if ($sum_case>=Seuil::ONLY_CASE) {
if ($sign_util==SignUtil::YES) {
$significatif=1;
- $test_results->{"sign"}=Alphy::Chi2::SIGNIFICATIF;
+ $test_results->{"sign"}=ALTree::Chi2::SIGNIFICATIF;
}
} else {
if ($sign_util==SignUtil::YES) {
$significatif=0;
- $test_results->{"sign"}=Alphy::Chi2::NON_SIGNIFICATIF;
+ $test_results->{"sign"}=ALTree::Chi2::NON_SIGNIFICATIF;
}
}
- #$test_results->{"sign"}=Alphy::Chi2::NON_SIGNIFICATIF;
+ #$test_results->{"sign"}=ALTree::Chi2::NON_SIGNIFICATIF;
} elsif ($error == 4) {
$test_results->{"texte"}="Only one clade";
if ($sign_util==SignUtil::YES) {
$significatif=0;
- $test_results->{"sign"}=Alphy::Chi2::NON_SIGNIFICATIF;
+ $test_results->{"sign"}=ALTree::Chi2::NON_SIGNIFICATIF;
}
# Manque plein de trucs par rapport à la fonction dans chi2tree...
} else {
@@ -808,12 +808,12 @@ sub CalculChi2
$test_results->{"warning"}="Small sample size correction used";
# J'ai pas compté dans combien de branches...
if ($ddl == 1) {
- $p_value=Alphy::CUtils::bilateral($tabnodes_a_traiter->[0]->{"case"},
+ $p_value=ALTree::CUtils::bilateral($tabnodes_a_traiter->[0]->{"case"},
$tabnodes_a_traiter->[0]->{"control"},
$tabnodes_a_traiter->[1]->{"case"},
$tabnodes_a_traiter->[1]->{"control"});
if ($sign_util==SignUtil::YES) {
- $significatif=Alphy::Chi2::chi2_fisher_significatif($p_value);
+ $significatif=ALTree::Chi2::chi2_fisher_significatif($p_value);
}
} else {
my(@clades, $node);
@@ -823,34 +823,34 @@ sub CalculChi2
# totaux des différents clades à utiliser dans le
# réechantillonnage
}
- ($p_value)= Alphy::Chi2::reech_chi2($sum_case, $sum_control,
+ ($p_value)= ALTree::Chi2::reech_chi2($sum_case, $sum_control,
$ddl+1, $chi2, \@clades);
$test_results->{"warning"}.=" ($p_value)";
if ($sign_util==SignUtil::YES) {
- $significatif= Alphy::Chi2::reech_significatif ($p_value);
+ $significatif= ALTree::Chi2::reech_significatif ($p_value);
if ($significatif !=
- Alphy::Chi2::chi2_significatif($ddl, $chi2)) {
+ ALTree::Chi2::chi2_significatif($ddl, $chi2)) {
$test_results->{"warning"}.=" Result has changed !";
}
}
}
} else {
if ($sign_util==SignUtil::YES) {
- $significatif=Alphy::Chi2::chi2_significatif($ddl, $chi2);
+ $significatif=ALTree::Chi2::chi2_significatif($ddl, $chi2);
}
#my $p=`pochisq $chi2 $ddl`+0; # Verif que les 2 appellent
#bien la même chose!
- $p_value=Alphy::CUtils::pochisq($chi2,$ddl);
+ $p_value=ALTree::CUtils::pochisq($chi2,$ddl);
#if ($p != $p_value) {
#print STDERR "pochisq: $p != $p_value !\n";
#}
}
if ($sign_util==SignUtil::YES) {
if ($significatif) {
- $test_results->{"sign"}=Alphy::Chi2::SIGNIFICATIF;
+ $test_results->{"sign"}=ALTree::Chi2::SIGNIFICATIF;
#$test_results->{"texte"}.="significatif";
} else {
- $test_results->{"sign"}=Alphy::Chi2::NON_SIGNIFICATIF;
+ $test_results->{"sign"}=ALTree::Chi2::NON_SIGNIFICATIF;
# $test_results->{"texte"}.="non significatif";
}
}
@@ -1205,9 +1205,9 @@ sub InfosAffichees
}
if ($mode ==2) {
if (defined($test->{"sign"})) {
- if ($test->{"sign"} == Alphy::Chi2::NON_SIGNIFICATIF) {
+ if ($test->{"sign"} == ALTree::Chi2::NON_SIGNIFICATIF) {
$chaine .= " (non significatif)";
- } elsif ($test->{"sign"} == Alphy::Chi2::SIGNIFICATIF) {
+ } elsif ($test->{"sign"} == ALTree::Chi2::SIGNIFICATIF) {
$chaine .= " (significatif)";
} else {
die "Internal error : unknown value ".
@@ -1779,8 +1779,8 @@ sub manage_options
) or pod2usage(2);
if (defined($options{"version"})) {
print $0, " version ", $VERSION, "\n";
- print "(CUtils version ", $Alphy::CUtils::VERSION,
- "; chi2.pm version ", $Alphy::Chi2::VERSION,
+ print "(CUtils version ", $ALTree::CUtils::VERSION,
+ "; chi2.pm version ", $ALTree::Chi2::VERSION,
"; Perl version ", $], ")\n";
exit 0;
}
@@ -1955,7 +1955,7 @@ sub main
if ($permutation==0) {
my($seuil_chi2)=$option_value->("chi2-threshold", 0.01,
"Using default chi2 threshold 0.01");
- Alphy::Chi2::definition_p_chi2($seuil_chi2, 0.01); # mettre une option
+ ALTree::Chi2::definition_p_chi2($seuil_chi2, 0.01); # mettre une option
# pour seuil test_prop
$sign_util = SignUtil::YES # on a besoin de la significativité
} elsif ($permutation>0) {
@@ -1974,7 +1974,7 @@ sub main
($value_per_line, $ligne_chi2)=RepeatAssociation
($tree, $correspondance, $prolonge,$permutation, $sign_util);
my($corrected_values);
- $corrected_values=Alphy::CUtils::double_permutation
+ $corrected_values=ALTree::CUtils::double_permutation
($permutation+1, $value_per_line, $ligne_chi2);
print "\n";
@@ -2018,8 +2018,8 @@ sub main
}
my($s_anc)=$1;
my($s_der)=$2;
- my($s_state)= Alphy::Sens->New($s_anc." --> ".$s_der);
- my($foret)=Alphy::Foret->New();
+ my($s_state)= ALTree::Sens->New($s_anc." --> ".$s_der);
+ my($foret)=ALTree::Foret->New();
#$Data::Dumper::Indent = 0;
for (my($i)=0; $i<$trees_to_analyse; $i++) {
@@ -2105,11 +2105,11 @@ __END__
=head1 NAME
-alphy - Analysing phylogeny trees
+altree - Analysing phylogeny trees
=head1 SYNOPSIS
-alphy [options]
+altree [options]
Options:
--version program version
diff --git a/alphy-add-S b/altree-add-S
similarity index 99%
rename from alphy-add-S
rename to altree-add-S
index accc47b..cfdfdc0 100755
--- a/alphy-add-S
+++ b/altree-add-S
@@ -294,11 +294,11 @@ __END__
=head1 NAME
-alphy-add-S - Title...
+altree-add-S - Title...
=head1 SYNOPSIS
-alphy-add-S [options]
+altree-add-S [options]
Options:
--version program version
diff --git a/alphy-convert b/altree-convert
similarity index 99%
rename from alphy-convert
rename to altree-convert
index bb92d86..a47760f 100755
--- a/alphy-convert
+++ b/altree-convert
@@ -558,11 +558,11 @@ __END__
=head1 NAME
-alphy-convert - Title...
+altree-convert - Title...
=head1 SYNOPSIS
-alphy-convert [options]
+altree-convert [options]
Options:
--version program version
diff --git a/t/Alphy-Utils.t b/t/ALTree.t
similarity index 76%
rename from t/Alphy-Utils.t
rename to t/ALTree.t
index bd8d67d..6a96ae3 100644
--- a/t/Alphy-Utils.t
+++ b/t/ALTree.t
@@ -1,12 +1,12 @@
# Before `make install' is performed this script should be runnable with
-# `make test'. After `make install' it should work as `perl Alphy-Utils.t'
+# `make test'. After `make install' it should work as `perl ALTree.t'
#########################
# change 'tests => 1' to 'tests => last_test_to_print';
use Test::More tests => 1;
-BEGIN { use_ok('Alphy::Import') };
+BEGIN { use_ok('ALTree::Import') };
#########################
--
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