[med-svn] [libfreecontact-perl] 44/46: Imported Upstream version 0.08
Laszlo Kajan
lkajan at alioth.debian.org
Thu Sep 19 15:55:06 UTC 2013
This is an automated email from the git hooks/post-receive script.
lkajan pushed a commit to branch master
in repository libfreecontact-perl.
commit e220e9a474f5209ce6d03df52e8fcb2e38f2dc17
Author: Laszlo Kajan <lkajan at debian.org>
Date: Thu Sep 19 15:44:31 2013 +0200
Imported Upstream version 0.08
---
Changes | 4 ++++
FreeContact.xsp | 4 ++--
MANIFEST | 3 ++-
META.json | 41 +++++++++++++++++++++++++++++++++++++++++
META.yml | 38 +++++++++++++++++++-------------------
lib/FreeContact.pm | 23 ++++++++++++-----------
t/02test.t | 8 ++++----
7 files changed, 84 insertions(+), 37 deletions(-)
diff --git a/Changes b/Changes
index 88c72f9..f66cc75 100644
--- a/Changes
+++ b/Changes
@@ -1,5 +1,9 @@
Revision history for Perl extension FreeContact.
+0.08 Mon Jul 15 16:11:26 CEST 2013
+ - Edited module documentation.
+ - Raised test precision threshold.
+
0.07 Mon Jun 17 16:27:46 CEST 2013
- Corrected 'fro' test to check for precision < 1e-5.
- Renamed "gap_incovm" to "apply_gapth".
diff --git a/FreeContact.xsp b/FreeContact.xsp
index 943312c..b0c2497 100644
--- a/FreeContact.xsp
+++ b/FreeContact.xsp
@@ -42,11 +42,11 @@ void
predictor::_get_seq_weights( freq_vec_t* __aliw, double* __wtot, ali_t& __ali, double __clustpc, bool __veczw = true, int __num_threads = 0 )
PREINIT:
freq_vec_t aliw;
- double wtot;
+ double wtot = 0;
CODE:
__aliw = &aliw; __wtot = &wtot;
try {
- THIS->get_seq_weights( *( __aliw ), *( __wtot ), __ali, __clustpc, __veczw, __num_threads );
+ THIS->get_seq_weights(*__aliw, *__wtot, __ali, __clustpc, __veczw, __num_threads);
}
catch (std::exception& e) {
croak("Caught C++ exception of type or derived from 'std::exception': %s", e.what());
diff --git a/MANIFEST b/MANIFEST
index eedeae9..49c3a4f 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -12,4 +12,5 @@ t/01FreeContact.t
t/02test.t
typemap
typemap.xsp
-META.yml Module meta-data (added by MakeMaker)
+META.yml Module YAML meta-data (added by MakeMaker)
+META.json Module JSON meta-data (added by MakeMaker)
diff --git a/META.json b/META.json
new file mode 100644
index 0000000..6c5d868
--- /dev/null
+++ b/META.json
@@ -0,0 +1,41 @@
+{
+ "abstract" : "fast protein contact predictor",
+ "author" : [
+ "Laszlo Kajan <lkajan at rostlab.org>"
+ ],
+ "dynamic_config" : 1,
+ "generated_by" : "ExtUtils::MakeMaker version 6.66, CPAN::Meta::Converter version 2.120921",
+ "license" : [
+ "unknown"
+ ],
+ "meta-spec" : {
+ "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
+ "version" : "2"
+ },
+ "name" : "FreeContact",
+ "no_index" : {
+ "directory" : [
+ "t",
+ "inc"
+ ]
+ },
+ "prereqs" : {
+ "build" : {
+ "requires" : {
+ "ExtUtils::MakeMaker" : "0"
+ }
+ },
+ "configure" : {
+ "requires" : {
+ "ExtUtils::MakeMaker" : "0"
+ }
+ },
+ "runtime" : {
+ "requires" : {
+ "ExtUtils::XSpp" : "0.01"
+ }
+ }
+ },
+ "release_status" : "stable",
+ "version" : "0.08"
+}
diff --git a/META.yml b/META.yml
index fc17db3..2364dd4 100644
--- a/META.yml
+++ b/META.yml
@@ -1,22 +1,22 @@
---- #YAML:1.0
-name: FreeContact
-version: 0.07
-abstract: fast protein contact predictor
+---
+abstract: 'fast protein contact predictor'
author:
- - Laszlo Kajan <lkajan at rostlab.org>
-license: unknown
-distribution_type: module
-configure_requires:
- ExtUtils::MakeMaker: 0
+ - 'Laszlo Kajan <lkajan at rostlab.org>'
build_requires:
- ExtUtils::MakeMaker: 0
-requires:
- ExtUtils::XSpp: 0.01
-no_index:
- directory:
- - t
- - inc
-generated_by: ExtUtils::MakeMaker version 6.57_05
+ ExtUtils::MakeMaker: 0
+configure_requires:
+ ExtUtils::MakeMaker: 0
+dynamic_config: 1
+generated_by: 'ExtUtils::MakeMaker version 6.66, CPAN::Meta::Converter version 2.120921'
+license: unknown
meta-spec:
- url: http://module-build.sourceforge.net/META-spec-v1.4.html
- version: 1.4
+ url: http://module-build.sourceforge.net/META-spec-v1.4.html
+ version: 1.4
+name: FreeContact
+no_index:
+ directory:
+ - t
+ - inc
+requires:
+ ExtUtils::XSpp: 0.01
+version: 0.08
diff --git a/lib/FreeContact.pm b/lib/FreeContact.pm
index 0eeface..50a0e37 100644
--- a/lib/FreeContact.pm
+++ b/lib/FreeContact.pm
@@ -1,3 +1,4 @@
+# FreeContact - program to predict protein residue contacts from a sufficiently large multiple alignment
# Copyright (C) 2013 by Laszlo Kajan, Technical University of Munich, Germany
#
# This program is free software; you can redistribute it and/or modify
@@ -35,7 +36,7 @@ our @EXPORT = qw(
);
-our $VERSION = '0.07';
+our $VERSION = '0.08';
require XSLoader;
XSLoader::load('FreeContact', $VERSION);
@@ -73,7 +74,8 @@ sub FreeContact::Predictor::run
$args{density}, $args{gapth}, $args{mincontsep},
$args{pseudocnt}, $args{pscnt_weight}, $args{estimate_ivcov}, $args{shrink_lambda},
$args{cov20}, $args{apply_gapth}, $args{rho},
- defined($args{veczw}) ? $args{veczw} : 1, $args{num_threads} || 0, defined($args{icme_timeout}) ? $args{icme_timeout} : 1800, $args{timing}
+ defined($args{veczw}) ? $args{veczw} : 1,
+ $args{num_threads} || 0, defined($args{icme_timeout}) ? $args{icme_timeout} : 1800, $args{timing}
);
}
@@ -148,11 +150,11 @@ Get parameters for EVfold-mfDCA operating mode.
=item get_ps_psicov()
-Get parameters for PSICOV (best performance) operating mode.
+Get parameters for PSICOV 'improved results' operating mode.
=item get_ps_psicov_sd()
-Get parameters for PSICOV 'sensible default' operating mode. This is much faster than PSICOV for a
+Get parameters for PSICOV 'sensible default' operating mode. This is much faster than 'improved results' for a
slight loss of precision.
These get_ps_() functions return a hash of arguments (clustpc => I<num>,...,rho => I<num>) that can be used
@@ -177,14 +179,15 @@ Creates an "FreeContact::Predictor".
=over
-=item get_seq_weights() TODO
+=item get_seq_weights()
Defaults for the arguments are obtained with get_ps_evfold().
-=item run( ali => I<[]>, clustpc => dbl, density => dbl, gapth => dbl, mincontsep => uint,
+=item run(ali => I<[]>, clustpc => dbl,
+ density => dbl, gapth => dbl, mincontsep => uint,
pseudocnt => dbl, pscnt_weight => dbl, estimate_ivcov => bool, shrink_lambda => dbl,
- cov20 => bool, apply_gapth => bool, veczw => bool, rho => dbl,
- [num_threads => int], [icme_timeout => int], [timing => I<{}>] )
+ cov20 => bool, apply_gapth => bool, rho => dbl,
+ [veczw => bool], [num_threads => int], [icme_timeout => int], [timing => I<{}>])
Defaults for the arguments are obtained with get_ps_evfold().
@@ -195,8 +198,6 @@ Defaults for the arguments are obtained with get_ps_evfold().
Reference to array holding alignment rows as strings. The first
row must hold the query, with no gaps.
-=item TODO
-
=item clustpc
BLOSUM-style clustering similarity threshold [0-1].
@@ -243,7 +244,7 @@ run() returns a hash reference of contact prediction results:
l1norm => ...
}
-'fro' scores are recommended in EVfold
+Use 'fro' scores with EVfold.
=back
diff --git a/t/02test.t b/t/02test.t
index 7591f76..ff52524 100644
--- a/t/02test.t
+++ b/t/02test.t
@@ -30,7 +30,7 @@ sub check_obj {
my $res = FreeContact::Predictor->new(dbg => 1)->run(ali => \@aln, num_threads => $num_threads, timing => $timing);
my $evfold_24_42 = 0.0129471030086279; # 0-based indices
- my $prec_threshold = 5e-5;
+ my $prec_threshold = 3e-4;
is(reftype($res), 'HASH');
@@ -42,7 +42,7 @@ sub check_obj {
my %test_parset = FreeContact::get_ps_psicov();
eval {
- $res = FreeContact::Predictor->new(dbg => 1)->run(%test_parset, ali => \@aln, num_threads => $num_threads, icme_timeout => 2, timing => $timing);
+ $res = FreeContact::Predictor->new(dbg => 1)->run(%test_parset, ali => \@aln, num_threads => $num_threads, icme_timeout => 2, timing => undef);
};
like($@, qr/^Caught FreeContact timeout exception:/);
@@ -53,9 +53,9 @@ sub check_obj {
is(@$aliw, 1000);
ok(abs($wtot-620.777)/620.777 < 1e-6, 'wtot test');
- my $res = FreeContact::Predictor->new(dbg => 1)->run_with_seq_weights(ali => \@aln, aliw => $aliw, wtot => $wtot, num_threads => $num_threads, timing => $timing);
+ my $res = FreeContact::Predictor->new(dbg => 1)->run_with_seq_weights(ali => \@aln, aliw => $aliw, wtot => $wtot, num_threads => $num_threads);
- ok(abs($res->{fro}->[2741]->[2]-$evfold_24_42)/$evfold_24_42 < $prec_threshold, 'wtot precision test'); # [ 2, 3, 8.08998+- ]
+ ok(abs($res->{fro}->[2741]->[2]-$evfold_24_42)/$evfold_24_42 < $prec_threshold, 'wtot precision test');
}
}
--
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