[med-svn] [libfreecontact-perl] 19/46: Imported Upstream version 0.03
Laszlo Kajan
lkajan at alioth.debian.org
Thu Sep 19 15:55:01 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 2b0a3868703ac383f6fcc8cbc5329ab85ec36bb4
Author: Laszlo Kajan <lkajan at debian.org>
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 <lkajan at rostlab.org>
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
More information about the debian-med-commit
mailing list