/ 
Metabolomics-Fragment-Annotation-0.6.9
River stage zero No dependents
/ Metabolomics::Banks::AbInitioFragments

NAME

Metabolomics::Banks::AbInitioFragments - Perl extension for Ab Initio Fragments generator

VERSION

Version 0.3 - Adding POD Version 0.4 - Updating Fragments/Adducts/isotopes listing Version 0.5 - Completing object properties

SYNOPSIS

use Metabolomics::Banks::AbInitioFragments;

DESCRIPTION

Metabolomics::Banks::AbInitioFragments is a full package for Perl allowing to build a generic Perl bank object from Ab Initio fragments resource.

EXPORT

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

PUBLIC METHODS

Metabolomics::Banks::AbInitioFragments

new
## Description : new
## Input : $self
## Ouput : bless $self ;
## Usage : new() ;
METHOD getFragmentsFromSource
## Description : get the list of theorical fragments from $source file
## Input : $source
## Output : $theoFragments
## Usage : my ( $theoFragments ) = getFragmentsFromSource ( $source ) ;
METHOD buildTheoPeakBankFromFragments
## Description : building a bank integrating each potential fragments from a parent ion
## Input : $refBank, $mzParent, $mode (POSITIVE, NEGATIVE, NEUTRAL), $stateMolecule (POS, NEG, NEU)
## Output : $ionBank
## Usage : my ( $ionBank ) = buildTheoPeakBankFromFragments ( $refBank, $mzParent ) ;
METHOD buildTheoDimerFromMz
## Description : build potential dimers/trimers in NEG/POS mode
## Input : $Mz, $mode
## Output : $oBank
## Usage : my ( $oBank ) = buildTheoDimerFromMz ( $Mz, $mode ) ;
METHOD isotopicAdvancedCalculation
## Description : if a fragment is present in theorical bank, compute its isotopic couple.
## Input : $refBank
## Output : $ionBank
## Usage : my ( $ionBank ) = isotopicAdvancedCalculation ( $refBank ) ;

PRIVATE METHODS

Metabolomics::Banks::AbInitioFragments

PRIVATE_ONLY __refBloodExposomeEntry__
## Description : init a new ab initio fragment entry
## Input : void	
## Output : refEntry
## Usage : $self->__refAbInitioFragment__() ;
PRIVATE_ONLY _getANNOTATION_IN_NEG_MODE
## Description : _getANNOTATION_IN_NEG_MODE
## Input : void
## Output : $ANNOTATION_IN_NEG_MODE
## Usage : my ( $ANNOTATION_IN_NEG_MODE ) = _getANNOTATION_IN_NEG_MODE () ;
PRIVATE_ONLY _getANNOTATION_IN_POS_MODE
## Description : _getANNOTATION_IN_POS_MODE
## Input : void
## Output : $ANNOTATION_IN_POS_MODE
## Usage : my ( $ANNOTATION_IN_POS_MODE ) = _getANNOTATION_IN_POS_MODE () ;
PRIVATE_ONLY _getDELTA_MASS
## Description : _getDELTA_MASS
## Input : void
## Output : $DELTA_MASS
## Usage : my ( $DELTA_MASS ) = _getDELTA_MASS () ;
PRIVATE_ONLY _getFragment_TYPE
## Description : _getFragment_TYPE
## Input : void
## Output : $TYPE
## Usage : my ( $TYPE ) = _getFragment_TYPE () ;
PRIVATE_ONLY _getLOSSES_OR_GAINS
## Description : _getLOSSES_OR_GAINS
## Input : void
## Output : $LOSSES_OR_GAINS
## Usage : my ( $LOSSES_OR_GAINS ) = _getLOSSES_OR_GAINS () ;

AUTHOR

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

SEE ALSO

All information about Metabolomics::Fragment::Annotation 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::AbInitioFragments

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