This is an automated email from the git hooks/post-receive script. lkajan pushed a commit to branch master in repository libfreecontact-perl.
commit b5d66043f5352b573709c1443467089d6c63538b Author: Laszlo Kajan <[email protected]> Date: Mon Jul 15 16:10:40 2013 +0200 Imported Upstream version 0.07 --- Changes | 4 ++++ FreeContact.xs | 4 ++-- FreeContact.xsp | 12 ++++++------ META.yml | 2 +- lib/FreeContact.pm | 12 ++++++++---- t/02test.t | 9 +++++---- 6 files changed, 26 insertions(+), 17 deletions(-) diff --git a/Changes b/Changes index bafb435..88c72f9 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,9 @@ Revision history for Perl extension FreeContact. +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". + 0.06 Sun Jun 16 00:36:16 CEST 2013 - New method get_seq_weights() for obtaining sequence weight vector and total weight of alignment. diff --git a/FreeContact.xs b/FreeContact.xs index 09fa024..50c0df8 100644 --- a/FreeContact.xs +++ b/FreeContact.xs @@ -40,8 +40,8 @@ typedef freecontact::predictor::freq_vec_t freq_vec_t; \ XPUSHs(sv_2mortal(newSVpvn("cov20", 5)));\ XPUSHs(sv_2mortal(newSViv((__ps).cov20)));\ - XPUSHs(sv_2mortal(newSVpvn("gap_incovm", 10)));\ - XPUSHs(sv_2mortal(newSViv((__ps).gap_incovm)));\ + XPUSHs(sv_2mortal(newSVpvn("apply_gapth", 11)));\ + XPUSHs(sv_2mortal(newSViv((__ps).apply_gapth)));\ XPUSHs(sv_2mortal(newSVpvn("rho", 3)));\ XPUSHs(sv_2mortal(newSVnv((__ps).rho))); diff --git a/FreeContact.xsp b/FreeContact.xsp index 6c7e5ad..943312c 100644 --- a/FreeContact.xsp +++ b/FreeContact.xsp @@ -63,14 +63,14 @@ predictor::_get_seq_weights( freq_vec_t* __aliw, double* __wtot, ali_t& __ali, d /* cont_res_t run( ali_t& __ali, double __cp, double __density, double __gapth, U16 __mincontsep, double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda, - bool __cov20, bool __gap_incovm, double __rho, + bool __cov20, bool __apply_gapth, double __rho, bool __veczw = true, int __num_threads = 0, time_res_t *__timing = NULL );*/ }; %{ cont_res_t -predictor::_run( __ali, __cp, __density, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __gap_incovm, __rho, __veczw = true, __num_threads = 0, __icme_timeout = 1800, __timing = NULL ) +predictor::_run( __ali, __cp, __density, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __apply_gapth, __rho, __veczw = true, __num_threads = 0, __icme_timeout = 1800, __timing = NULL ) ali_t& __ali double __cp double __density @@ -81,7 +81,7 @@ predictor::_run( __ali, __cp, __density, __gapth, __mincontsep, __pseudocnt, __p bool __estimate_ivcov double __shrink_lambda bool __cov20 - bool __gap_incovm + bool __apply_gapth double __rho bool __veczw int __num_threads @@ -92,7 +92,7 @@ predictor::_run( __ali, __cp, __density, __gapth, __mincontsep, __pseudocnt, __p CODE: try { if(items>=17 && SvROK(ST(16)) && SvTYPE(SvRV(ST(16))) == SVt_PVHV) __timing = &timing; - RETVAL = THIS->run( __ali, __cp, __density, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __gap_incovm, __rho, __veczw, __num_threads, __icme_timeout, __timing ); + RETVAL = THIS->run( __ali, __cp, __density, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __apply_gapth, __rho, __veczw, __num_threads, __icme_timeout, __timing ); } catch (freecontact::icme_timeout_error& e) { @@ -111,7 +111,7 @@ predictor::_run( __ali, __cp, __density, __gapth, __mincontsep, __pseudocnt, __p %{ cont_res_t -predictor::_run_with_seq_weights(ali_t& __ali, freq_vec_t &__aliw, double __wtot, double __density, double __gapth, U16 __mincontsep, double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda, bool __cov20, bool __gap_incovm, double __rho, int __num_threads = 0, time_t __icme_timeout = 1800, time_res_t *__timing = NULL) +predictor::_run_with_seq_weights(ali_t& __ali, freq_vec_t &__aliw, double __wtot, double __density, double __gapth, U16 __mincontsep, double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda, bool __cov20, bool __apply_gapth, double __rho, int __num_threads = 0, time_t __icme_timeout = 1800, time_res_t *__timing = NULL) PREINIT: time_res_t timing; CODE: @@ -120,7 +120,7 @@ predictor::_run_with_seq_weights(ali_t& __ali, freq_vec_t &__aliw, double __wtot RETVAL = THIS->run( __ali, __aliw, __wtot, __density, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, - __cov20, __gap_incovm, __rho, + __cov20, __apply_gapth, __rho, __num_threads, __icme_timeout, __timing ); } catch (freecontact::icme_timeout_error& e) diff --git a/META.yml b/META.yml index a0bea3e..fc17db3 100644 --- a/META.yml +++ b/META.yml @@ -1,6 +1,6 @@ --- #YAML:1.0 name: FreeContact -version: 0.06 +version: 0.07 abstract: fast protein contact predictor author: - Laszlo Kajan <[email protected]> diff --git a/lib/FreeContact.pm b/lib/FreeContact.pm index 8447299..0eeface 100644 --- a/lib/FreeContact.pm +++ b/lib/FreeContact.pm @@ -35,7 +35,7 @@ our @EXPORT = qw( ); -our $VERSION = '0.06'; +our $VERSION = '0.07'; require XSLoader; XSLoader::load('FreeContact', $VERSION); @@ -72,7 +72,7 @@ sub FreeContact::Predictor::run return $self->_run($args{ali}, $args{clustpc}, $args{density}, $args{gapth}, $args{mincontsep}, $args{pseudocnt}, $args{pscnt_weight}, $args{estimate_ivcov}, $args{shrink_lambda}, - $args{cov20}, $args{gap_incovm}, $args{rho}, + $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} ); } @@ -85,7 +85,7 @@ sub FreeContact::Predictor::run_with_seq_weights return $self->_run_with_seq_weights($args{ali}, $args{aliw}, $args{wtot}, $args{density}, $args{gapth}, $args{mincontsep}, $args{pseudocnt}, $args{pscnt_weight}, $args{estimate_ivcov}, $args{shrink_lambda}, - $args{cov20}, $args{gap_incovm}, $args{rho}, + $args{cov20}, $args{apply_gapth}, $args{rho}, $args{num_threads} || 0, defined($args{icme_timeout}) ? $args{icme_timeout} : 1800, $args{timing} ); } @@ -183,7 +183,7 @@ Defaults for the arguments are obtained with get_ps_evfold(). =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, gap_incovm => bool, veczw => bool, rho => dbl, + cov20 => bool, apply_gapth => bool, veczw => bool, rho => dbl, [num_threads => int], [icme_timeout => int], [timing => I<{}>] ) Defaults for the arguments are obtained with get_ps_evfold(). @@ -197,6 +197,10 @@ row must hold the query, with no gaps. =item TODO +=item clustpc + +BLOSUM-style clustering similarity threshold [0-1]. + =item icme_timeout Inverse covariance matrix estimation timeout in seconds. Default: 1800. diff --git a/t/02test.t b/t/02test.t index f99063e..7591f76 100644 --- a/t/02test.t +++ b/t/02test.t @@ -30,11 +30,12 @@ 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 $prec_threshold = 5e-5; is(reftype($res), 'HASH'); - #use Data::Dumper; warn(Dumper($res)); - ok(abs($res->{fro}->[2741]->[2]-$evfold_24_42)/$evfold_24_42 < 1e-6, 'precision test'); # 25 K 43 N 0.230969 0.0129471 + #use Data::Dumper; warn(Dumper($res->{fro}->[2741])); + ok(abs($res->{fro}->[2741]->[2]-$evfold_24_42)/$evfold_24_42 < $prec_threshold, 'precision test'); # 25 K 43 N 0.230969 0.0129471 ok($timing->{num_threads} == $num_threads, "timing results test"); #use Data::Dumper; warn(Dumper($timing)); @@ -53,8 +54,8 @@ sub check_obj { 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 => $timing); -warn($res->{fro}->[2741]->[2]); - ok(abs($res->{fro}->[2741]->[2]-$evfold_24_42)/$evfold_24_42 < 1e-6, 'wtot precision test'); # [ 2, 3, 8.08998+- ] + + ok(abs($res->{fro}->[2741]->[2]-$evfold_24_42)/$evfold_24_42 < $prec_threshold, 'wtot precision test'); # [ 2, 3, 8.08998+- ] } } -- 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
