Metabolomics::Banks::MaConDa(3)

NAME
Metabolomics::Banks::MaConDa - Perl extension for contaminants bank building

VERSION
Version 0.2 - Adding POD

SYNOPSIS
    use Metabolomics::Banks::MaConDa;

DESCRIPTION
        Metabolomics::Banks::MaConDa is a full package for Perl allowing to build a generic Perl bank object from MaConDa resource.

EXPORT
        use Metabolomics::Banks::MaConDa qw( :all ) ;

PUBLIC METHODS

  Metabolomics::Banks::MaConDa

new
            ## Description : new
            ## Input : $self
            ## Ouput : bless $self ;
            ## Usage : new() ;

__refContaminant__
            ## Description : set a new contaminant object
            ## Input : NA
            ## Output : $refContaminant
            ## Usage : my ( $refContaminant ) = __refContaminant__() ;

__refContaminantExtensive__
            ## Description : set a new contaminant object in extensive version
            ## Input : NA
            ## Output : $refContaminantExtensive
            ## Usage : my ( $refContaminantExtensive ) = __refContaminantExtensive__() ;

getContaminantsFromSource
            ## Description : get all contaminants information from the MaConDa resources v01
            ## Input : $source
            ## Output : $oBank
            ## Usage : my ( $oBank ) = getContaminantsFromSource ( $source ) ;

getContaminantsExtensiveFromSource
            ## Description : get all contaminants information from the MaConDa extensive resources v01
            ## Input : $source
            ## Output : $oBank
            ## Usage : my ( $oBank ) = getContaminantsFromSource ( $source ) ;

buildTheoPeakBankFromContaminants
            ## Description : building a bank integrating each potential ion from contaminants
            ## Input : $refBank, $oContaminants, $queryMode
            ## Output : $ionBank
            ## Usage : my ( $ionBank ) = buildTheoPeakBankFromContaminants ( $refBank, $oContaminants, $queryMode ) ;

extractContaminantTypes
            ## Description : extract contaminant types listing from contaminants object
            ## Input : $oContaminants
            ## Output : $contaminantTypes
            ## Usage : my ( $contaminantTypes ) = extractContaminantTypes ( $oContaminants ) ;

extractContaminantInstruments
            ## Description : extract instruments listing from contaminants object
            ## Input : $oContaminants
            ## Output : $contaminantInstruments
            ## Usage : my ( $contaminantInstruments ) = extractContaminantInstruments ( $oContaminants ) ;

extractContaminantInstrumentTypes
            ## Description : extract instrument types listing from contaminants object
            ## Input : $oContaminants
            ## Output : $contaminantInstrumentTypes
            ## Usage : my ( $contaminantInstrumentTypes ) = extractContaminantInstrumentTypes ( $oContaminants ) ;

filterContaminantIonMode
            ## Description : filtering contaminants by their ion mode (POS|NEG|BOTH)
            ## Input : $oBank, $ionMode
            ## Output : $oFilteredBank
            ## Usage : my ( $oFilteredBank ) = filterContaminantIonMode ( $oBank, $ionMode ) ;

filterContaminantInstruments
            ## Description : filtering contaminants by their instrument (array)
            ## Input : $oBank, $instruments
            ## Output : $oFilteredBank, $totalEntryNum, $fiteredEntryNum
            ## Usage : my ( $oFilteredBank ) = filterContaminantInstruments ( $oBank, $instruments ) ;

filterContaminantInstrumentTypes
            ## Description : filtering contaminants by their instrument types (array)
            ## Input : $oBank, $instrumentTypes
            ## Output : $oFilteredBank
            ## Usage : my ( $oFilteredBank ) = filterContaminantInstrumentTypes ( $oBank, $instrumentTypes ) ;

_setContaminantExtREFERENCE
            ## Description : _setContaminantExtREFERENCE
            ## Input : $REFERENCE
            ## Output : TRUE
            ## Usage : _setContaminantExtREFERENCE ( $ION_FORM ) ;

_getContaminantExtION_MODE
            ## Description : _getContaminantExtION_MODE
            ## Input : void
            ## Output : $ION_MODE
            ## Usage : my ( $ION_MODE ) = _getContaminantExtION_MODE () ;

_setContaminantExtION_MODE
            ## Description : _setContaminantExtION_MODE
            ## Input : $ION_MODE
            ## Output : TRUE
            ## Usage : _setContaminantExtION_MODE ( $ION_FORM ) ;

_setContaminantExtEXACT_ADDUCT_MASS
            ## Description : _setContaminantExtEXACT_ADDUCT_MASS
            ## Input : $EXACT_ADDUCT_MASS
            ## Output : TRUE
            ## Usage : _setContaminantExtEXACT_ADDUCT_MASS ( $ION_FORM ) ;

_getContaminantExtEXACT_ADDUCT_MASS
            ## Description : _getContaminantExtEXACT_ADDUCT_MASS
            ## Input : void
            ## Output : $EXACT_ADDUCT_MASS
            ## Usage : my ( $EXACT_ADDUCT_MASS ) = _getContaminantExtEXACT_ADDUCT_MASS () ;

_getContaminantExtION_FORM
            ## Description : _getContaminantExtION_FORM
            ## Input : void
            ## Output : $ION_FORM
            ## Usage : my ( $ION_FORM ) = _getContaminantExtION_FORM () ;

_setContaminantExtION_FORM
            ## Description : _setContaminantExtION_FORM
            ## Input : $ION_FORM
            ## Output : TRUE
            ## Usage : _setContaminantExtION_FORM ( $ION_FORM ) ;

_getContaminantExtMZ
            ## Description : _getContaminantExtMZ
            ## Input : void
            ## Output : $MZ
            ## Usage : my ( $EXACT_ADDUCT_MASS ) = _getContaminantExtMZ () ;

_setContaminantExtMZ
            ## Description : _setContaminantExtMZ
            ## Input : $MZ
            ## Output : TRUE
            ## Usage : _setContaminantExtMZ ( $MZ ) ;

_getContaminantExtINSTRUMENT_TYPES
            ## Description : _getContaminantExtINSTRUMENT_TYPES
            ## Input : void
            ## Output : $INSTRUMENT_TYPE
            ## Usage : my ( $INSTRUMENT_TYPE ) = _getContaminantExtINSTRUMENT_TYPES () ;

_setContaminantExtINSTRUMENT_TYPE
            ## Description : _setContaminantExtINSTRUMENT_TYPE
            ## Input : $INSTRUMENT_TYPE
            ## Output : TRUE
            ## Usage : _setContaminantExtINSTRUMENT_TYPE ( $INSTRUMENT_TYPE ) ;

_getContaminantExtINSTRUMENTS
            ## Description : _getContaminantExtINSTRUMENTS
            ## Input : void
            ## Output : $INSTRUMENT
            ## Usage : my ( $INSTRUMENT ) = _getContaminantExtINSTRUMENTS () ;

_setContaminantExtINSTRUMENT
            ## Description : _setContaminantExtINSTRUMENT
            ## Input : $INSTRUMENT
            ## Output : TRUE
            ## Usage : _setContaminantExtINSTRUMENT ( $INSTRUMENT ) ;

_setContaminantExtCHROMATOGRAPHY
            ## Description : _setContaminantExtCHROMATOGRAPHY
            ## Input : $CHROMATOGRAPHY
            ## Output : TRUE
            ## Usage : _setContaminantExtCHROMATOGRAPHY ( $CHROMATOGRAPHY ) ;

_setContaminantExtION_SOURCE_TYPE
            ## Description : _setContaminantExtION_SOURCE_TYPE
            ## Input : $ION_SOURCE_TYPE
            ## Output : TRUE
            ## Usage : _setContaminantExtION_SOURCE_TYPE ( $ION_SOURCE_TYPE ) ;

_getContaminantExtTYPE_OF_CONTAMINANT
            ## Description : _getContaminantExtTYPE_OF_CONTAMINANT
            ## Input : void
            ## Output : $TYPE_OF_CONTAMINANT
            ## Usage : my ( $TYPE_OF_CONTAMINANT ) = _getContaminantExtTYPE_OF_CONTAMINANT () ;

_setContaminantTYPE_OF_CONTAMINANT
            ## Description : _setContaminantTYPE_OF_CONTAMINANT
            ## Input : $TYPE_OF_CONTAMINANT
            ## Output : TRUE
            ## Usage : _setContaminantTYPE_OF_CONTAMINANT ( $TYPE_OF_CONTAMINANT ) ;

_setContaminantPUBCHEM_CID
            ## Description : _setContaminantPUBCHEM_CID
            ## Input : $PUBCHEM_CID
            ## Output : TRUE
            ## Usage : _setContaminantPUBCHEM_CID ( $PUBCHEM_CID ) ;

_setContaminantSTD_INCHI_KEY
            ## Description : _setContaminantSTD_INCHI_KEY
            ## Input : $STD_INCHI_KEY
            ## Output : TRUE
            ## Usage : _setContaminantSTD_INCHI_KEY ( $STD_INCHI_KEY ) ;

_setContaminantSTD_INCHI
            ## Description : _setContaminantSTD_INCHI
            ## Input : $STD_INCHI
            ## Output : TRUE
            ## Usage : _setContaminantSTD_INCHI ( $STD_INCHI ) ;

_getContaminantEXACT_MASS
            ## Description : _getContaminantEXACT_MASS
            ## Input : void
            ## Output : $EXACT_MASS
            ## Usage : my ( $EXACT_MASS ) = _getContaminantEXACT_MASS () ;

_setContaminantEXACT_MASS
            ## Description : _setContaminantEXACT_MASS
            ## Input : $EXACT_MASS
            ## Output : TRUE
            ## Usage : _setContaminantEXACT_MASS ( $EXACT_MASS ) ;

_setContaminantFORMULA
            ## Description : _setContaminantFORMULA
            ## Input : $FORMULA
            ## Output : TRUE
            ## Usage : _setContaminantFORMULA ( $FORMULA ) ;

_getContaminantNAME
            ## Description : _getContaminantNAME
            ## Input : void
            ## Output : $NAME
            ## Usage : my ( $NAME ) = _getContaminantNAME () ;

_setContaminantNAME
            ## Description : _setContaminantNAME
            ## Input : $NAME
            ## Output : TRUE
            ## Usage : _setContaminantNAME ( $NAME ) ;

_getContaminantID
            ## Description : _getContaminantID
            ## Input : void
            ## Output : $ID
            ## Usage : my ( $ID ) = _getContaminantID () ;

_setContaminantID
            ## Description : _setContaminantID
            ## Input : $ID
            ## Output : TRUE
            ## Usage : _setContaminantID ( $ID ) ;

AUTHOR
Franck Giacomoni, "<franck.giacomoni at inra.fr>"

SEE ALSO
All information about Metabolomics::Fragment would be find here: https://services.pfem.clermont.inra.fr/gitlab/fgiacomoni/metabolomics-fragnot

BUGS
Please report any bugs or feature requests to "bug-Metabolomics-Fragment-Annotation at rt.cpan.org", or through the web interface at <https://rt.cpan.org/Public/Dist/Display.html?Name=Metabolomics-Fragment-Annotation>. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT
You can find documentation for this module with the perldoc command.

    perldoc Metabolomics::Banks::MaConDa

•   RT: CPAN's request tracker (report bugs here)

    <https://rt.cpan.org/Public/Dist/Display.html?Name=Metabolomics-Fragment-Annotation>

•   AnnoCPAN: Annotated CPAN documentation

    <http://annocpan.org/dist/Metabolomics-Fragment-Annotation>

•   CPAN Ratings

    <https://cpanratings.perl.org/d/Metabolomics-Fragment-Annotation>

•   Search CPAN

    <https://metacpan.org/release/Metabolomics-Fragment-Annotation>

ACKNOWLEDGEMENTS
Thank you to INRAE and All metabolomics colleagues.

LICENSE AND COPYRIGHT
CeCILL Copyright (C) 2019 by Franck Giacomoni

Initiated by Franck Giacomoni

followed by INRAE PFEM team

Web Site = INRAE PFEM