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 <[email protected]> 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 <[email protected]>" + ], + "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 <[email protected]> -license: unknown -distribution_type: module -configure_requires: - ExtUtils::MakeMaker: 0 + - 'Laszlo Kajan <[email protected]>' 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'); } } -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/libfreecontact-perl.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
