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Alexandre Masselot > InSilicoSpectro > InSilicoSpectro::Spectra::MSMSSpectra

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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

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