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::MaConDaRT: CPAN's request tracker (report bugs here)
https://rt.cpan.org/Public/Dist/Display.html?Name=Metabolomics-Fragment-Annotation
AnnoCPAN: Annotated CPAN documentation
CPAN Ratings
https://cpanratings.perl.org/d/Metabolomics-Fragment-Annotation
Search CPAN
https://metacpan.org/release/Metabolomics-Fragment-Annotation
ACKNOWLEDGEMENTS
LICENSE AND COPYRIGHT
CeCILL Copyright (C) 2019 by Franck Giacomoni
Initiated by Franck Giacomoni
followed by INRA PFEM team
Web Site = INRA PFEM