This is an automated email from the git hooks/post-receive script. lkajan pushed a commit to branch master in repository libfreecontact-perl.
commit d7a93140c9ca85f49d5ec20a1fc9e31e75304e8f Author: Laszlo Kajan <[email protected]> Date: Fri May 10 18:41:07 2013 +0200 Imported Upstream version 0.01 --- FreeContact.c | 410 --------------------------------------------------------- MANIFEST | 2 - MANIFEST.SKIP | 4 +- 3 files changed, 2 insertions(+), 414 deletions(-) diff --git a/FreeContact.bs b/FreeContact.bs deleted file mode 100644 index e69de29..0000000 diff --git a/FreeContact.c b/FreeContact.c deleted file mode 100644 index 086904e..0000000 --- a/FreeContact.c +++ /dev/null @@ -1,410 +0,0 @@ -/* - * This file was generated automatically by ExtUtils::ParseXS version 2.2206 from the - * contents of FreeContact.xs. Do not edit this file, edit FreeContact.xs instead. - * - * ANY CHANGES MADE HERE WILL BE LOST! - * - */ - -#line 1 "FreeContact.xs" -/* Copyright (C) 2013 by Laszlo Kajan, Technical University of Munich, Germany - - This program is free software; you can redistribute it and/or modify - it under the same terms as Perl itself, either Perl version 5.10.1 or, - at your option, any later version of Perl 5 you may have available. -*/ -#include <freecontact.h> - -#ifdef __cplusplus -extern "C" { -#include "EXTERN.h" -#include "perl.h" -#include "XSUB.h" -} -#endif - -using namespace freecontact; -typedef freecontact::predictor::cont_res_t cont_res_t; -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("gapth", 5)));\ - XPUSHs(sv_2mortal(newSVnv((__ps).gapth)));\ - XPUSHs(sv_2mortal(newSVpvn("mincontsep", 10)));\ - XPUSHs(sv_2mortal(newSVuv((__ps).mincontsep)));\ -\ - XPUSHs(sv_2mortal(newSVpvn("pseudocnt", 9)));\ - XPUSHs(sv_2mortal(newSVnv((__ps).pseudocnt)));\ - XPUSHs(sv_2mortal(newSVpvn("pscnt_weight", 12)));\ - XPUSHs(sv_2mortal(newSVnv((__ps).pscnt_weight)));\ - XPUSHs(sv_2mortal(newSVpvn("estimate_ivcov", 14)));\ - XPUSHs(sv_2mortal(newSViv((__ps).estimate_ivcov)));\ - XPUSHs(sv_2mortal(newSVpvn("shrink_lambda", 13)));\ - XPUSHs(sv_2mortal(newSVnv((__ps).shrink_lambda)));\ -\ - 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("veczw", 5)));\ - XPUSHs(sv_2mortal(newSViv((__ps).veczw)));\ - XPUSHs(sv_2mortal(newSVpvn("rho", 3)));\ - XPUSHs(sv_2mortal(newSVnv((__ps).rho))); - -#line 59 "FreeContact.c" -#ifndef PERL_UNUSED_VAR -# define PERL_UNUSED_VAR(var) if (0) var = var -#endif - -#ifndef PERL_ARGS_ASSERT_CROAK_XS_USAGE -#define PERL_ARGS_ASSERT_CROAK_XS_USAGE assert(cv); assert(params) - -/* prototype to pass -Wmissing-prototypes */ -STATIC void -S_croak_xs_usage(pTHX_ const CV *const cv, const char *const params); - -STATIC void -S_croak_xs_usage(pTHX_ const CV *const cv, const char *const params) -{ - const GV *const gv = CvGV(cv); - - PERL_ARGS_ASSERT_CROAK_XS_USAGE; - - if (gv) { - const char *const gvname = GvNAME(gv); - const HV *const stash = GvSTASH(gv); - const char *const hvname = stash ? HvNAME(stash) : NULL; - - if (hvname) - Perl_croak(aTHX_ "Usage: %s::%s(%s)", hvname, gvname, params); - else - Perl_croak(aTHX_ "Usage: %s(%s)", gvname, params); - } else { - /* Pants. I don't think that it should be possible to get here. */ - Perl_croak(aTHX_ "Usage: CODE(0x%"UVxf")(%s)", PTR2UV(cv), params); - } -} -#undef PERL_ARGS_ASSERT_CROAK_XS_USAGE - -#ifdef PERL_IMPLICIT_CONTEXT -#define croak_xs_usage(a,b) S_croak_xs_usage(aTHX_ a,b) -#else -#define croak_xs_usage S_croak_xs_usage -#endif - -#endif - -/* NOTE: the prototype of newXSproto() is different in versions of perls, - * so we define a portable version of newXSproto() - */ -#ifdef newXS_flags -#define newXSproto_portable(name, c_impl, file, proto) newXS_flags(name, c_impl, file, proto, 0) -#else -#define newXSproto_portable(name, c_impl, file, proto) (PL_Sv=(SV*)newXS(name, c_impl, file), sv_setpv(PL_Sv, proto), (CV*)PL_Sv) -#endif /* !defined(newXS_flags) */ - -#line 111 "FreeContact.c" - -/* INCLUDE_COMMAND: Including output of '/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp' from 'FreeContact.xs' */ - -#include <exception> - - -XS(XS_FreeContact_get_ps_evfold); /* prototype to pass -Wmissing-prototypes */ -XS(XS_FreeContact_get_ps_evfold) -{ -#ifdef dVAR - dVAR; dXSARGS; -#else - dXSARGS; -#endif - if (items != 0) - croak_xs_usage(cv, ""); - PERL_UNUSED_VAR(ax); /* -Wall */ - SP -= items; - { -#line 12 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp" - _XPUSHS_GET_PS(ps_evfold); -#line 133 "FreeContact.c" - PUTBACK; - return; - } -} - - -XS(XS_FreeContact_get_ps_psicov); /* prototype to pass -Wmissing-prototypes */ -XS(XS_FreeContact_get_ps_psicov) -{ -#ifdef dVAR - dVAR; dXSARGS; -#else - dXSARGS; -#endif - if (items != 0) - croak_xs_usage(cv, ""); - PERL_UNUSED_VAR(ax); /* -Wall */ - SP -= items; - { -#line 17 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp" - _XPUSHS_GET_PS(ps_psicov); -#line 155 "FreeContact.c" - PUTBACK; - return; - } -} - - -XS(XS_FreeContact__Predictor_new); /* prototype to pass -Wmissing-prototypes */ -XS(XS_FreeContact__Predictor_new) -{ -#ifdef dVAR - dVAR; dXSARGS; -#else - dXSARGS; -#endif - if (items < 1 || items > 2) - croak_xs_usage(cv, "CLASS, __dbg = false"); - { - bool __dbg; - char * CLASS = (char *)SvPV_nolen(ST(0)); - predictor * RETVAL; - - if (items < 2) - __dbg = false; - else { - __dbg = (bool)SvTRUE(ST(1)); - } -#line 28 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp" - try { - RETVAL = new predictor( __dbg ); - } - catch (std::exception& e) { - croak("Caught C++ exception of type or derived from 'std::exception': %s", e.what()); - } - catch (...) { - croak("Caught C++ exception of unknown type"); - } -#line 192 "FreeContact.c" - ST(0) = sv_newmortal(); - sv_setref_pv( ST(0), CLASS, (void*)RETVAL ); - - } - XSRETURN(1); -} - - -XS(XS_FreeContact__Predictor_DESTROY); /* prototype to pass -Wmissing-prototypes */ -XS(XS_FreeContact__Predictor_DESTROY) -{ -#ifdef dVAR - dVAR; dXSARGS; -#else - dXSARGS; -#endif - if (items != 1) - croak_xs_usage(cv, "THIS"); - { - predictor * THIS; - - if( sv_isobject(ST(0)) && (SvTYPE(SvRV(ST(0))) == SVt_PVMG) ) - THIS = (predictor *)SvIV((SV*)SvRV( ST(0) )); - else{ - warn( "FreeContact::Predictor::DESTROY() -- THIS is not a blessed SV reference" ); - XSRETURN_UNDEF; - }; -#line 42 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp" - try { - delete THIS; - } - catch (std::exception& e) { - croak("Caught C++ exception of type or derived from 'std::exception': %s", e.what()); - } - catch (...) { - croak("Caught C++ exception of unknown type"); - } -#line 230 "FreeContact.c" - } - XSRETURN_EMPTY; -} - - -XS(XS_FreeContact__Predictor__run); /* prototype to pass -Wmissing-prototypes */ -XS(XS_FreeContact__Predictor__run) -{ -#ifdef dVAR - dVAR; dXSARGS; -#else - dXSARGS; -#endif - if (items < 14 || items > 16) - croak_xs_usage(cv, "THIS, __ali, __cp, __spar, __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)SvNV(ST(2)); - double __spar = (double)SvNV(ST(3)); - double __gapth = (double)SvNV(ST(4)); - U16 __mincontsep = (unsigned short)SvUV(ST(5)); - double __pseudocnt = (double)SvNV(ST(6)); - double __pscnt_weight = (double)SvNV(ST(7)); - bool __estimate_ivcov = (bool)SvTRUE(ST(8)); - double __shrink_lambda = (double)SvNV(ST(9)); - bool __cov20 = (bool)SvTRUE(ST(10)); - bool __gap_incovm = (bool)SvTRUE(ST(11)); - bool __vecw = (bool)SvTRUE(ST(12)); - double __rho = (double)SvNV(ST(13)); - int __num_threads; - time_res_t* __timing; -#line 73 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp" - time_res_t timing; -#line 264 "FreeContact.c" - predictor * THIS; - cont_res_t RETVAL; - - { - if(SvROK(ST(1)) && SvTYPE(SvRV(ST(1))) == SVt_PVAV) - { - // ST(1) is an array reference to strings - the sequences in the alignment - AV *arr = (AV*)SvRV(ST(1)); - I32 seqcnt = av_len(arr)+1; // av_len returns highest index - if(seqcnt > 0) - { - SV** lineptr = av_fetch(arr, 0, false); - if(lineptr != NULL && SvPOK(*lineptr)) - { - STRLEN alilen = SvCUR(*lineptr); - if(alilen <= 0xFFFF) - { - __ali = ali_t(alilen); - - for(I32 k = 0; k < seqcnt; ++k) - { - SV** lineptr = av_fetch(arr, k, false); - if(lineptr != NULL && SvPOK(*lineptr)) - { - STRLEN alilen = SvCUR(*lineptr); - if(alilen <= 0xFFFF) - { - const char *al = SvPVbyte(*lineptr, alilen); - __ali.push(std::string(al, alilen)); - } - } - } - } - else croak("FreeContact::Predictor::_run() -- __ali->[0] is too long"); - } - else croak("FreeContact::Predictor::_run() -- __ali->[0] is not a character string"); - } - } - else croak("FreeContact::Predictor::_run() -- __ali is not an AV reference"); - }; - - if (items < 15) - __num_threads = 0; - else { - __num_threads = (int)SvIV(ST(14)); - } - - if (items < 16) - __timing = NULL; - else { - __timing = (time_res_t*)~NULL; - } - - if( sv_isobject(ST(0)) && (SvTYPE(SvRV(ST(0))) == SVt_PVMG) ) - THIS = (predictor *)SvIV((SV*)SvRV( ST(0) )); - else{ - warn( "FreeContact::Predictor::_run() -- THIS is not a blessed SV reference" ); - XSRETURN_UNDEF; - }; -#line 75 "/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp" - try { - if(__timing) __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 ); - } - catch (std::exception& e) { - croak("Caught C++ exception of type or derived from 'std::exception': %s", e.what()); - } - catch (...) { - croak("Caught C++ exception of unknown type"); - } -#line 335 "FreeContact.c" - if(__timing && SvROK(ST(15)) && SvTYPE(SvRV(ST(15))) == SVt_PVHV) - { - // return { 'key' => 0.0, ... } - HV* res = (HV*)SvRV(ST(15)); - for(time_res_t::const_iterator tr_i = __timing->begin(), tr_e = __timing->end(); tr_i != tr_e; ++tr_i) - hv_store(res, tr_i->first.c_str(), tr_i->first.length(), newSVnv(tr_i->second), 0); - } - - SvSETMAGIC(ST(15)); - ST(0) = sv_newmortal(); - if(RETVAL.empty()) ST(0) = &PL_sv_undef; - else - { - - // return { 'l1norm' => [ [ 0, 1, 45.786 ], [ 0, 2, 7.993 ], ... ], ... } - HV* res = (HV*)sv_2mortal((SV*)newHV()); - for(cont_res_t::const_iterator cr_i = RETVAL.begin(), cr_e = RETVAL.end(); cr_i != cr_e; ++cr_i) - { - AV* contacts = (AV*)sv_2mortal((SV*)newAV()); av_extend(contacts, cr_i->second.size()-1); // extend to index - - for(std::vector<contact_t>::const_iterator ct_i = cr_i->second.begin(), ct_e = cr_i->second.end(); ct_i != ct_e; ++ct_i) - { - AV* ijscore = (AV*)sv_2mortal((SV*)newAV()); av_extend(ijscore, 2); // extend to index - - av_push(ijscore, newSVuv(ct_i->i)); - av_push(ijscore, newSVuv(ct_i->j)); - av_push(ijscore, newSVnv(ct_i->score)); - // - av_push(contacts, newRV((SV*)ijscore)); - } - - hv_store(res, cr_i->first.c_str(), cr_i->first.length(), newRV((SV*)contacts), 0); - } - - sv_setsv(ST(0), newRV((SV*)res)); - } - } - XSRETURN(1); -} - - -/* INCLUDE: Returning to 'FreeContact.xs' from '/usr/bin/perl -MExtUtils::XSpp::Cmd -e xspp -- --typemap=typemap.xsp FreeContact.xsp' */ - -#ifdef __cplusplus -extern "C" -#endif -XS(boot_FreeContact); /* prototype to pass -Wmissing-prototypes */ -XS(boot_FreeContact) -{ -#ifdef dVAR - dVAR; dXSARGS; -#else - dXSARGS; -#endif -#if (PERL_REVISION == 5 && PERL_VERSION < 9) - char* file = __FILE__; -#else - const char* file = __FILE__; -#endif - - PERL_UNUSED_VAR(cv); /* -W */ - PERL_UNUSED_VAR(items); /* -W */ - XS_VERSION_BOOTCHECK ; - - newXS("FreeContact::get_ps_evfold", XS_FreeContact_get_ps_evfold, file); - newXS("FreeContact::get_ps_psicov", XS_FreeContact_get_ps_psicov, file); - newXS("FreeContact::Predictor::new", XS_FreeContact__Predictor_new, file); - newXS("FreeContact::Predictor::DESTROY", XS_FreeContact__Predictor_DESTROY, file); - newXS("FreeContact::Predictor::_run", XS_FreeContact__Predictor__run, file); -#if (PERL_REVISION == 5 && PERL_VERSION >= 9) - if (PL_unitcheckav) - call_list(PL_scopestack_ix, PL_unitcheckav); -#endif - XSRETURN_YES; -} - diff --git a/MANIFEST b/MANIFEST index 408dd5d..eedeae9 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1,7 +1,5 @@ Changes examples/demo_1000.aln -FreeContact.bs -FreeContact.c FreeContact.xs FreeContact.xsp lib/FreeContact.pm diff --git a/MANIFEST.SKIP b/MANIFEST.SKIP index 0c34b60..0e81c31 100644 --- a/MANIFEST.SKIP +++ b/MANIFEST.SKIP @@ -23,6 +23,8 @@ \b_build/ \.o$ \.tar\.gz$ +FreeContact.bs +FreeContact.c # Avoid temp and backup files. ~$ @@ -37,5 +39,3 @@ .swp$ .vim$ -debian -zergtest -- 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
