InSilicoSpectro::Spectra::Filter::MSFilterCollection - InSilicoSpectro::Spectra::Filter::MSFilterCollection documentation

InSilicoSpectro documentation

Contained in the InSilicoSpectro distribution.

Index

NAME
SYNOPSIS
DESCRIPTION
METHODS
EXAMPLES
SEE ALSO
COPYRIGHT
AUTHORS

Code Index:

package InSilicoSpectro::Spectra::Filter::MSFilterCollection
EOF

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

InSilicoSpectro documentation

Contained in the InSilicoSpectro distribution.

use strict;

package InSilicoSpectro::Spectra::Filter::MSFilterCollection;

use InSilicoSpectro::Spectra::MSSpectra;
use InSilicoSpectro::Spectra::Filter::MSFilter;
#use InSilicoSpectro::Spectra::MSMSSpectra;
#use InSilicoSpectro::Spectra::MSRun;

require Exporter;
our (@ISA,@EXPORT,@EXPORT_OK, $VERSION);
@ISA=qw (Exporter);
@EXPORT=qw($VERSION);
@EXPORT_OK=qw();

#use File::Basename;
use Carp;
#use List::Util qw(max min sum first);


$VERSION = "0.9";

###############################

sub new{
  
 my $pkg = shift;

 my $self = {};
 my $class = ref($pkg) || $pkg;
 bless $self, $class;
 return $self;
}

##############################
### read xml


use XML::Twig;

sub readXml{
  my ($this, $xml_file) = @_;

  $this->{xml_file}= $xml_file;
  $this->{xmlFilterList}= ();

  my $twig=XML::Twig->new(twig_handlers=>{
					  '/ExpMsMsSpectrumFilter'=> sub {twig_addSpectrumFilter($this, $_[0], $_[1])},
					 },
			  pretty_print=>'indented'
			 );
  
  #actually parse the file
  $twig->parsefile($xml_file) or croak "cannot parse [$xml_file]: $!";

}


sub twig_addSpectrumFilter{
  my ($this, $twig, $el)=@_;

  foreach my $twig_el ($el->get_xpath('*')) {
    $this->addXmlFilter($twig_el);
  }

  #free memory;
  $twig->purge if defined $twig;
}


sub readXmlString{
  my ($this, $xml_string)= @_;

  $this->{xmlFilterList}= ();

  my $twig= XML::Twig->new(twig_handlers=>{
					  '/ExpMsMsSpectrumFilter'=> sub {twig_addSpectrumFilter($this, $_[0], $_[1])},
					 },
			  pretty_print=>'indented'
			 );

  $twig->parse($xml_string) or croak "cannot parse the xml-string: $!";

}




######################################

sub addXmlFilter{
  my ($this, $filter_el)= @_;

  push @{$this->{xmlFilterList}}, $filter_el;

  return $this->{xmlFilterList};
}


#####################################


sub filterSpectra{
  my ($this, $spectra, $filter_nr) = @_;

  if(defined $filter_nr){
    my $sf = new InSilicoSpectro::Spectra::Filter::MSFilter();
    $sf->readTwigEl($this->{xmlFilterList}->[$filter_nr]);
    $sf->filterSpectra($spectra);
  }else{
    foreach(0..$#{$this->{xmlFilterList}}){
      $this->filterSpectra($spectra, $_);
    }
  }

  return $spectra;
}



#######################################


sub xmlFilter{
  my ($this, $filter_nr);

  if(defined $filter_nr){
    return $this->{xmlFilterList}->[$filter_nr];
  }

  return $this->{xmlFilterList};

}




return 1;