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Alexandre Masselot > InSilicoSpectro > InSilicoSpectro::Spectra::MSRun

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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)

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