Alexandre Masselot
and 1 contributors

NAME

InSilicoSpectro::Spectra::MSRun

SYNOPSIS

DESCRIPTION

A MSRun is a collection of MSSpectra (either ms or ms/ms)

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

my $run=InSilicoSpectro::Spectra::MSRun->new()

$run->addSpectra($sp)

Add an InSilicoSpectro::Spectra::MSSpectra (either ms or msms)

$run->getNbSpectra()

Returns the number of spectra

$run->getSpectra($i)

Returns the spectra number $i

$run->msms2pmfRelation([msmskey, [pmfkey]]);

Set or get (if second parameter is not defined) the relation between msmskey and pmf

return the ref to hash if no param is given

$run->msms2pmfKeyBuildRelation( %hash )

Build the relation between msms key and pmf key for the current run.

%hash can contain different parameters :

1) %hash = ( textfile => filePath )

File structure : the first column contains msms keys and the second column pmf keys.

2) %hash = ( title_msmsregexp => string, title_msmsregexp => string )

The regexps have to contain a pattern wich can allow to create a relation between msms and pmf spectra. This pattern must be unique for a given msms key.

Example : use of the spot ID as a mapping key

        %hash =( title_msmsregexp => Spot_Id: (\d+), Peak_List_Id,
        title_pmfregexp => Spot Id: (\d+), Peak List Id );

$run->key2spectrum(key[, $sp]);

Return (or set) the spectrum (either pmf or an msms coumpond) associated with a given key;

$run->readIDJ($file [, indexxml=>1])

indexxml runs an index in the idj file...(??)

$run->readMascotXml($file);

Read data from a mascot xml exported file

$run->write($format, [$fname|fh]);

$run->writePLE($shift)

Writes the run into a ple format ($shift is typically a string with some space char to have something correctly indented)

$run->write($format, [$fname|fh])

Write the run on the given format.

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

Ex: $u->set('date', 'today')

$se->get($name)

Ex: $u->get('date')

EXAMPLES

SEE ALSO

InSilicoSpectro::Spectra::MSSpectra

COPYRIGHT

Copyright (C) 2004-2006 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, www.genebio.com

guessFormat(sourcefile)

Try to guess the spectra format (if it is not yet defined) based on the file extension stores in the argument {source}. However, if you wish to load for example .dta file from a directory, it will not determine it automatically.

get($name)