Index
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