NAME

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

VERSION

Version 0.2 - Adding POD Version 0.3 - Completing object properties

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