[med-svn] [libfreecontact-perl] 36/46: Imported Upstream version 0.07
Laszlo Kajan
lkajan at alioth.debian.org
Thu Sep 19 15:55:05 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 b5d66043f5352b573709c1443467089d6c63538b
Author: Laszlo Kajan <lkajan at debian.org>
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 <lkajan at rostlab.org>
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+- ]
}
}
--
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