/ 
Metabolomics-Fragment-Annotation-0.6.2
River stage zero No dependents
/ Metabolomics::Banks::AbInitioFragments

NAME

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

VERSION

Version 0.2

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

SUBROUTINES/METHODS

METHOD new

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

METHOD __refBloodExposomeEntry__

## Description : init a new ab initio fragment entry
## Input : void	
## Output : refEntry
## Usage : $self->__refAbInitioFragment__() ;

METHOD _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 () ;

METHOD _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 () ;

METHOD _getDELTA_MASS

## Description : _getDELTA_MASS
## Input : void
## Output : $DELTA_MASS
## Usage : my ( $DELTA_MASS ) = _getDELTA_MASS () ;

METHOD _getTYPE

## Description : _getTYPE
## Input : void
## Output : $TYPE
## Usage : my ( $TYPE ) = _getTYPE () ;

METHOD _getLOSSES_OR_GAINS

## Description : _getLOSSES_OR_GAINS
## Input : void
## Output : $LOSSES_OR_GAINS
## Usage : my ( $LOSSES_OR_GAINS ) = _getLOSSES_OR_GAINS () ;

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 ) ;

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::AbInitioFragments

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

CeCILL Copyright (C) 2019 by Franck Giacomoni

Initiated by Franck Giacomoni

followed by INRA PFEM team

Web Site = INRA PFEM