NAME

InSilicoSpectro::Spectra::Filter::MSFilterCollection

SYNOPSIS

my $file= "a.idj.xml"; my $sr=InSilicoSpectro::Spectra::MSRun->new(); $sr->readIDJ($file);

my $fc = new InSilicoSpectro::Spectra::Filter::MSFilterCollection(); $fc->readXml('a_filter_list.xml'); $fc->filterSpectra($sr);

my $file_out; open ($file_out, ">another.idj.xml"); $sr->write('idj', $file_out); close $file_out;

DESCRIPTION

This class allows you to filter your spectra with a list of filters in a xml-entry. The spectra is succesively filtered one after each other.

METHODS

my $sf=InSilicoSpectro::Spectra::Filter::MSFilterCollection->new()

create a new object.

$sf->readXml($filename)

opens the provided XML-file containing the information the filters and its parameters.

$sf->filterSpectra($Spectra, [$filter_nr])

apply all or only a selected XML-filter previously loaded on the Spectra (can be MS, MSMS, MSCmpd-Spectra or MSRun).

$sf->checkValidity();

checks if the different values provided by the xml are valid.

$sf->xmlFilter([$filter_nr]);

returns the filter chosen or a list containing all the filters.

$sf->addXmlFilter($filter_twig_el);

adds a xml-filter-twig-el to the actual filter-list.

EXAMPLES

see the the MSFilterCollection.t for an example.

SEE ALSO

search.cpan.org

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

AUTHORS

Roman Mylonas, www.genebio.com