Franck Giacomoni
and 1 contributors

NAME

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

VERSION

Version 0.1

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

SUBROUTINES/METHODS

METHOD new

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

METHOD __refContaminant__

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

METHOD __refContaminantExtensive__

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

METHOD getContaminantsFromSource

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

METHOD getContaminantsExtensiveFromSource

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

METHOD buildTheoPeakBankFromContaminants

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

METHOD extractContaminantTypes

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

METHOD extractContaminantInstruments

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

METHOD extractContaminantInstrumentTypes

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

METHOD filterContaminantIonMode

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

METHOD filterContaminantInstruments

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

METHOD filterContaminantInstrumentTypes

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

METHOD _setContaminantExtREFERENCE

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

METHOD _getContaminantExtION_MODE

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

METHOD _setContaminantExtION_MODE

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

METHOD _setContaminantExtEXACT_ADDUCT_MASS

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

METHOD _getContaminantExtEXACT_ADDUCT_MASS

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

METHOD _getContaminantExtION_FORM

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

METHOD _setContaminantExtION_FORM

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

METHOD _getContaminantExtMZ

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

METHOD _setContaminantExtMZ

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

METHOD _getContaminantExtINSTRUMENT_TYPES

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

METHOD _setContaminantExtINSTRUMENT_TYPE

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

METHOD _getContaminantExtINSTRUMENTS

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

METHOD _setContaminantExtINSTRUMENT

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

METHOD _setContaminantExtCHROMATOGRAPHY

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

METHOD _setContaminantExtION_SOURCE_TYPE

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

METHOD _getContaminantExtTYPE_OF_CONTAMINANT

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

METHOD _setContaminantTYPE_OF_CONTAMINANT

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

METHOD _setContaminantPUBCHEM_CID

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

METHOD _setContaminantSTD_INCHI_KEY

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

METHOD _setContaminantSTD_INCHI

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

METHOD _getContaminantEXACT_MASS

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

METHOD _setContaminantEXACT_MASS

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

METHOD _setContaminantFORMULA

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

METHOD _getContaminantNAME

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

METHOD _setContaminantNAME

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

METHOD _getContaminantID

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

METHOD _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

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

CeCILL Copyright (C) 2019 by Franck Giacomoni

Initiated by Franck Giacomoni

followed by INRA PFEM team

Web Site = INRA PFEM