/ 
Metabolomics-Fragment-Annotation-0.6.3
River stage zero No dependents
/ Metabolomics::Banks::PhytoHub

NAME

Metabolomics::Banks::PhytoHub - Perl extension for PhytoHub bank

VERSION

Version 0.1 - init

SYNOPSIS

use Metabolomics::Banks::PhytoHub;

DESCRIPTION

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

EXPORT

use Metabolomics::Banks::PhytoHub qw( :all ) ;

PUBLIC METHODS

Metabolomics::Banks::PhytoHub

new
## Description : new
## Input : $self
## Ouput : bless $self ;
## Usage : new() ;
getMetabolitesFromSource
## Description : get the list of metabolite entries from $source file and set the Metabolomics::Banks::PhytoHub object
## Input : $source (file from the metabolomics-references project)
## Output : an int as $entriesNb
## Usage : my ( $entriesNb ) = $self->getMetabolitesFromSource ( $source ) ;
METHOD buildTheoPeakBankFromEntries
## Description : building from a Metabolomics::Banks::PhytoHub object, a bank integrating each potential entry in a metabolomics format (POSITIVE or NEGATIVE forms)
## Input : $queryMode [POS|NEG]
## Output : int as $entryNb
## Usage : my $nb = $oBank->buildTheoPeakBankFromEntries() ;

PRIVATE METHODS

Metabolomics::Banks::PhytoHub

PRIVATE_ONLY __refPhytoHubEntry__
## Description : init a new blood exposome entry
## Input : void	
## Output : refEntry
## Usage : $self->__refPhytoHubEntry__() ;
PRIVATE_ONLY _getEntry_IS_A_METABOLITE
## Description : PRIVATE method _getEntry_IS_A_METABOLITE on a refPhytoHubEntry object
## Input : void
## Output : $IS_A_METABOLITE
## Usage : my ( $IS_A_PRECURSOR ) = $entry->_getEntry_IS_A_METABOLITE () ;
PRIVATE_ONLY _getEntry_IS_A_PRECURSOR
## Description : PRIVATE method _getEntry_IS_A_PRECURSOR on a refPhytoHubEntry object
## Input : void
## Output : $IS_A_PRECURSOR
## Usage : my ( $IS_A_PRECURSOR ) = $entry->_getEntry_IS_A_PRECURSOR () ;
PRIVATE_ONLY _getEntry_INCHIKEY
## Description : PRIVATE method _getEntry_INCHIKEY on a refPhytoHubEntry object
## Input : void
## Output : $INCHIKEY
## Usage : my ( $INCHIKEY ) = $entry->_getEntry_INCHIKEY () ;
PRIVATE_ONLY _getEntry_EXACT_MASS
## Description : PRIVATE method _getEntry_EXACT_MASS on a refPhytoHubEntry object
## Input : void
## Output : $EXACT_MASS
## Usage : my ( $EXACT_MASS ) = $entry->_getEntry_EXACT_MASS () ;
PRIVATE_ONLY _getEntry_PHYTOHUB_ID
## Description : PRIVATE method _getEntry_PHYTOHUB_ID on a refPhytoHubEntry object
## Input : void
## Output : $PhytoHub_ID
## Usage : my ( $PhytoHub_ID ) = $entry->_getEntry_PHYTOHUB_ID () ;
PRIVATE_ONLY _getEntry_SMILES
## Description : PRIVATE method _getEntry_SMILES on a refPhytoHubEntry object
## Input : void
## Output : $SMILES
## Usage : my ( $SMILES ) = $entry->_getEntry_SMILES () ;
PRIVATE_ONLY _getEntry_MOLECULAR_FORMULA
## Description : PRIVATE method _getEntry_MOLECULAR_FORMULA on a refPhytoHubEntry object
## Input : void
## Output : $COMPOUND_FORMULA
## Usage : my ( $COMPOUND_FORMULA ) = $entry->_getEntry_MOLECULAR_FORMULA () ;
PRIVATE_ONLY _getEntry_COMPOUND_NAME
## Description : PRIVATE method _getEntry_COMPOUND_NAME on a refPhytoHubEntry object
## Input : void
## Output : $COMPOUND_NAME
## Usage : my ( $COMPOUND_NAME ) = $entry->_getEntry_COMPOUND_NAME () ;

AUTHOR

Franck Giacomoni, <franck.giacomoni at inrae.fr>

SEE ALSO

All information about Metabolomics::Banks::PhytoHub 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::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 INRA PFEM team

Web Site = INRA PFEM