Bug #20427 for InSilicoSpectro:

Hi Alex, Oouf, my apologies: I'm not sure what I was looking at yesterday, but I gave you the wrong version number. I've actually got version 1.2.5. As requested, I've attached my InSilicoSpectro.pm file. Yes, I am using ActiveState Perl: Z:\>perl -v This is perl, v5.8.7 built for MSWin32-x86-multi-thread (with 14 registered patches, see perl -V for more detail) Copyright 1987-2005, Larry Wall Binary build 815 [211909] provided by ActiveState http://www.ActiveState.com ActiveState is a division of Sophos. Built Nov 2 2005 08:44:52 Thanks for looking at this (and for providing such useful tools in the first place!). -Anne Marie On Thu Jul 13 03:11:43 2006, guest wrote: Show quoted text
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=head1 NAME InSilicoSpectro - InSilico Mass Spectrometry toolkit =head1 DESCRIPTION =head1 INSTALL =head1 FUNCTIONS =head3 saveInSilicoDef([$out]) Saves all registred definitions into $out (eg insilicodef.xml) =head3 getInSilicoDefFile() returns the default insilicodeffile, from environament variable named by $InSilicoSpectro::DEF_FILENAME_ENV (default is $INSILICOSPECTRO_DEFFILE) =head1 SEE ALSO InSilicoSpectro::InSilico::CleavEnzyme, InSilicoSpectro::InSilico::ModRes, InSilicoSpectro::Spectra, InSilicoSpectro::Utils =head1 COPYRIGHT Copyright (C) 2004-2005 Geneva Bioinformatics www.genebio.com This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA =head1 AUTHORS Jacques Colinge, fh-hagenberg.at Alexandre Masselot, www.genebio.com =cut use strict; package InSilicoSpectro; require Exporter; use Carp; use InSilicoSpectro::InSilico::CleavEnzyme; use InSilicoSpectro::InSilico::ModRes; our (@ISA, @EXPORT, @EXPORT_OK, $VERSION); @ISA = qw(Exporter); @EXPORT = qw($VERSION &saveInSilicoDef &init &getInSilicoDefFile $DEF_FILENAME_ENV); @EXPORT_OK = (); $VERSION = "1.2.5"; our $DEF_FILENAME_ENV='INSILICOSPECTRO_DEFFILE'; sub saveInSilicoDef{ my $out=shift; $out=">$out" if ((defined $out) and not $out=~/^>/); my $saver=(defined $out)?(new SelectSaver(InSilicoSpectro::Utils::io->getFD($out) or die "cannot open [$out]: $!")):\*STDOUT; print <<EOT; <inSilicoDefinitions> <elements/> <aminoAcids/> <codons/> <cleavEnzymes> EOT foreach (InSilicoSpectro::InSilico::CleavEnzyme::getList()){ $_->getXMLTwigElt->print(); print "\n"; } print <<EOT; </cleavEnzymes> <fragTypeDescriptions/> <modRes> EOT foreach (InSilicoSpectro::InSilico::ModRes::getList()){ $_->getXMLTwigElt->print(); print "\n"; } print <<EOT; </modRes> </inSilicoDefinitions> EOT } sub init{ my @tmp=@_; push(@tmp, getInSilicoDefFile()) if ((not @tmp) and getInSilicoDefFile()); unless(@tmp){ print STDERR "no default found, opening config file from Phenyx::Config::GlobalParam\n" if $InSilicoSpectro::Utils::io::VERBOSE; require Phenyx::Config::GlobalParam; Phenyx::Config::GlobalParam::readParam(undef, 1); require Phenyx::Manage::User; my $tmp=Phenyx::Manage::User->new(name=>'default')->getFile('insilicodef.xml'); push @tmp, $tmp; } @tmp or croak "must provide at least one file argument"; InSilicoSpectro::InSilico::ModRes::init(@tmp); InSilicoSpectro::InSilico::CleavEnzyme::init(@tmp); InSilicoSpectro::InSilico::MassCalculator::init(@tmp); } sub getInSilicoDefFile{ return $ENV{$DEF_FILENAME_ENV}; } 1;