This is an automated email from the git hooks/post-receive script. lkajan pushed a commit to branch master in repository libfreecontact-perl.
commit 2b0a3868703ac383f6fcc8cbc5329ab85ec36bb4 Author: Laszlo Kajan <[email protected]> Date: Fri Jun 7 15:02:32 2013 +0200 Imported Upstream version 0.03 --- FreeContact.xs | 4 ++-- FreeContact.xsp | 13 +++++++++---- META.yml | 2 +- lib/FreeContact.pm | 9 ++++++--- t/01FreeContact.t | 2 +- 5 files changed, 19 insertions(+), 11 deletions(-) diff --git a/FreeContact.xs b/FreeContact.xs index cc4121b..74009a7 100644 --- a/FreeContact.xs +++ b/FreeContact.xs @@ -21,8 +21,8 @@ typedef freecontact::predictor::time_res_t time_res_t; #define _XPUSHS_GET_PS(__ps) \ XPUSHs(sv_2mortal(newSVpvn("clustpc", 7)));\ XPUSHs(sv_2mortal(newSVnv((__ps).clustpc)));\ - XPUSHs(sv_2mortal(newSVpvn("sparsity", 8)));\ - XPUSHs(sv_2mortal(newSVnv((__ps).sparsity)));\ + XPUSHs(sv_2mortal(newSVpvn("density", 8)));\ + XPUSHs(sv_2mortal(newSVnv((__ps).density)));\ XPUSHs(sv_2mortal(newSVpvn("gapth", 5)));\ XPUSHs(sv_2mortal(newSVnv((__ps).gapth)));\ XPUSHs(sv_2mortal(newSVpvn("mincontsep", 10)));\ diff --git a/FreeContact.xsp b/FreeContact.xsp index f116681..791a6a6 100644 --- a/FreeContact.xsp +++ b/FreeContact.xsp @@ -18,6 +18,11 @@ void get_ps_psicov() PPCODE: _XPUSHS_GET_PS(ps_psicov); + +void +get_ps_psicov_sd() + PPCODE: + _XPUSHS_GET_PS(ps_psicov_sd); %} // Example: /usr/share/doc/libextutils-xspp-perl/examples/Object-WithIntAndString/Object-WithIntAndString.xsp @@ -27,7 +32,7 @@ get_ps_psicov() ~predictor(); // lkajan: I apparently can not use this to add an INIT: block to the XS -/* cont_res_t _run( ali_t& __ali, double __cp, double __spar, double __gapth, U16 __mincontsep, +/* cont_res_t _run( ali_t& __ali, double __cp, double __dens, double __gapth, U16 __mincontsep, double __pseudocnt, double __pscnt_weight, bool __estimate_ivcov, double __shrink_lambda, bool __cov20, bool __gap_incovm, bool __vecw, double __rho, int __num_threads = 0, time_res_t *__timing = NULL @@ -36,10 +41,10 @@ get_ps_psicov() %{ cont_res_t -predictor::_run( __ali, __cp, __spar, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __gap_incovm, __vecw, __rho, __num_threads = 0, __timing = NULL ) +predictor::_run( __ali, __cp, __dens, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __gap_incovm, __vecw, __rho, __num_threads = 0, __timing = NULL ) ali_t& __ali double __cp - double __spar + double __dens double __gapth U16 __mincontsep double __pseudocnt @@ -57,7 +62,7 @@ predictor::_run( __ali, __cp, __spar, __gapth, __mincontsep, __pseudocnt, __pscn CODE: try { if(items>=16 && SvROK(ST(15)) && SvTYPE(SvRV(ST(15))) == SVt_PVHV) __timing = &timing; - RETVAL = THIS->run( __ali, __cp, __spar, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __gap_incovm, __vecw, __rho, __num_threads, __timing ); + RETVAL = THIS->run( __ali, __cp, __dens, __gapth, __mincontsep, __pseudocnt, __pscnt_weight, __estimate_ivcov, __shrink_lambda, __cov20, __gap_incovm, __vecw, __rho, __num_threads, __timing ); } catch (std::exception& e) { croak("Caught C++ exception of type or derived from 'std::exception': %s", e.what()); diff --git a/META.yml b/META.yml index 8dd3041..559a1a5 100644 --- a/META.yml +++ b/META.yml @@ -1,6 +1,6 @@ --- #YAML:1.0 name: FreeContact -version: 0.02 +version: 0.03 abstract: fast protein contact predictor author: - Laszlo Kajan <[email protected]> diff --git a/lib/FreeContact.pm b/lib/FreeContact.pm index a4e113f..582e35f 100644 --- a/lib/FreeContact.pm +++ b/lib/FreeContact.pm @@ -26,6 +26,7 @@ our @ISA = qw(Exporter); our %EXPORT_TAGS = ( 'all' => [ qw( get_ps_evfold get_ps_psicov + get_ps_psicov_sd ) ] ); our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } ); @@ -34,7 +35,7 @@ our @EXPORT = qw( ); -our $VERSION = '0.02'; +our $VERSION = '0.03'; require XSLoader; XSLoader::load('FreeContact', $VERSION); @@ -56,7 +57,7 @@ sub FreeContact::Predictor::run if(scalar(@_)%2){ confess("Odd number of arguments"); } my %args = (get_ps_evfold(), @_); return $self->_run($args{ali}, - $args{clustpc}, $args{sparsity}, $args{gapth}, $args{mincontsep}, + $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{veczw}, $args{rho}, $args{num_threads} || 0, $args{timing} @@ -115,6 +116,8 @@ can be used to generate the alignments, for example. =item get_ps_psicov() +=item get_ps_psicov_sd() + These functions return a hash of arguments (clustpc => I<num>,...,rho => I<num>) that can be used with run(). The arguments correspond to the published parametrization of the respective method. @@ -137,7 +140,7 @@ Creates an "FreeContact::Predictor". =over -=item run( ali => I<[]>, clustpc => dbl, sparsity => 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, gap_incovm => bool, veczw => bool, rho => dbl, [num_threads => int], [timing => I<{}>] ) diff --git a/t/01FreeContact.t b/t/01FreeContact.t index d6b7336..4d365c6 100644 --- a/t/01FreeContact.t +++ b/t/01FreeContact.t @@ -14,7 +14,7 @@ BEGIN { use_ok('FreeContact') }; # its man page ( perldoc Test::More ) for help writing this test script. { - can_ok('FreeContact', qw(get_ps_evfold get_ps_psicov)); + can_ok('FreeContact', qw(get_ps_evfold get_ps_psicov get_ps_psicov_sd)); can_ok('FreeContact::Predictor', qw(new _run run)); } # vim:et:ts=4:ai: -- 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
