Alexandre Masselot
and 1 contributors

NAME

InSilicoSpectro::Spectra::MSMSSpectra

SYNOPSIS

#set new spectra with source my $sp=InSilicoSpectro::Spectra::MSSpectra->new({source=>$file}); #if the format cannot (or may not) be deduced from the file name, we can set it $sp->format('dta'); $sp->open();

#convert into another format $sp->write('idj', "/tmp/a.idj.xml");

DESCRIPTION

General framework for MS/MS spectra.

This mainly means:

converting file between several kinds of usual formats.

FUNCTIONS

getReadFmtList()

returns the list of data format with available read handlers (known type for input).

getWriteFmtList()

returns the list of data format with available write handlers (known type for ouput).

METHODS

$sp=InSilicoSpectro::Spectra::MSSpectra->new(\%h);

Arguments are through a hash (see $sp->set($name, $val) method.

$sp->read()

$sp->set($name, $val)

Set an instance paramter, name can be

src

the source file (or directory, for .dta)

format

input data format such as 'mgf', 'pkl', 'dta', 'idj.xml'.

sampleInfo

sampling info. $val is either a reference to a hash, or a string such as 'tag1=value1;tag2=value' (ex='intrument=LCQ;instrumentID=xyz'). Setting sampleInfo will erase the former value (consider $sp->addSampleInfoTag($name, $value) instead;

$sp->get($name)

Get an instance parameter.

$sp->size()

Returns the number of compounds

FORMAT NOTEs

Sequest (dta):

header line format is [M+H]+ charge

rem: native dta contains only one ms/ms spectrum. dtas can be concatenated, separated by one blank line

Micromass (pkl)

header line format is m/z intensity charge

EXPORT

$MERGE_MULTIPLE_PREC_CHARGES

if true, spectra with same framgementa data and coherent precursor info but diferent charges will be merged into one multiple-charge spectrum. [default=1];

EXAMPLES

set lib/Phenyx/Spectra/test directory

SEE ALSO

InSilicoSpectro::Spectra::MSSpectra InSilicoSpectro::Spectra::MSMSCmpd, Phenyx::Config::GlobalParam

COPYRIGHT

Copyright (C) 2004-2007 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

Alexandre Masselot, Pierre-Alain Binz, www.genebio.com