/ 
Metabolomics-Fragment-Annotation-0.6.2_01
River stage zero No dependents
/ Metabolomics::Banks

NAME

Metabolomics::Banks - Perl extension to build metabolite banks for metabolomics

VERSION

Version 0.1

SYNOPSIS

use Metabolomics::Banks

DESCRIPTION

Metabolomics::Banks is a meta class for bank objects.

EXPORT

use Metabolomics::Banks qw( :all ) ;

PUBLIC METHODS

Metabolomics::Fragment::Annotation

new
## Description : set a new bank object
## Input : NA
## Output : $oBank
## Usage : my ( $oBank ) = Metabolomics::Banks->new ( ) ;
computeNeutralCpdMz_To_PositiveIonMz
## Description : compute the mz of a neutral cpd into the positive ion form mz
## Input : $initMz, $charge
## Output : $positiveMz
## Usage : my ( $positiveMz ) = computeNeutralCpdMz_To_PositiveIonMz ( $initMz, $charge ) ;
computeNeutralCpdMz_To_NegativeIonMz
## Description : compute the mz of a neutral cpd into the positive ion form mz
## Input : $initMz, $chargeNumber
## Output : $negativeMz
## Usage : my ( $negativeMz ) = computeNeutralCpdMz_To_NegativeIonMz ( $initMz, $chargeNumber ) ;
parsingMsFragments
## Description : get a list of Ms fragment from a experimental mesureament.
## Input : $oBank, $Xfile, $is_header, $column
## Output : $msFragBank
## Usage : $oBank->parsingMsFragments ( $Xfile, $is_header, $column ) ;

PRIVATE METHODS

Metabolomics::Banks

PRIVATE_ONLY _set_DATABASE_ENTRIES_NB
## Description : _set_DATABASE_ENTRIES_NB
## Input : $DATABASE_ENTRIES_NB
## Output : TRUE
## Usage : $self->_set_DATABASE_ENTRIES_NB ( $DATABASE_ENTRIES_NB ) ;
PRIVATE_ONLY _addEntry
## Description : _addEntry
## Input : $self, $Entry ;
## Ouput :  NA
## Usage : _addEntry($Entry);
PRIVATE_ONLY _addFragment
## Description : _addFragment
## Input : $self, $fragment ;
## Ouput :  NA
## Usage : _addFragment($fragment);
PRIVATE_ONLY _addContaminant
## Description : _addContaminant
## Input : $self, $contaminant ;
## Ouput :  NA
## Usage : _addContaminant($contaminant);
PRIVATE_ONLY _getContaminants
## Description : get the list of contaminants from the bank object
## Input : $self
## Output : $contaminants
## Usage : my ( $contaminants ) = $obank->_getContaminants () ;
PRIVATE_ONLY _getEntries
## Description : get the list of entries from the bank object
## Input : $self
## Output : $Entries
## Usage : my ( $Entries ) = $obank->_getEntries () ;
PRIVATE_ONLY _getFragments
## Description : get the list of fragments from the bank object
## Input : $self
## Output : $fragments
## Usage : my ( $fragments ) = $obank->_getFragments () ;
PRIVATE_ONLY _getTheoricalPeaks
## Description : get the list of theorical peaks from the bank object
## Input : $self
## Output : $theoPeaks
## Usage : my ( $theoPeaks ) = $obank->_getTheoricalPeaks () ;
PRIVATE_ONLY __refPeak__
## Description : set a new theorical peak
## Input : NA	
## Output : refPeak
## Usage : my ( refPeak ) = __refPeak__() ;
PRIVATE_ONLY _addPeakList
## Description : _addPeakList
## Input : $self, $type, $peakList ;
## Ouput : NA;
## Usage : _addPeakList($type, $peakList);
PRIVATE_ONLY _getPeakList
## Description : get the list of fragments from the bank object
## Input : $self, $type
## Output : $peakList
## Usage : my ( $peakList ) = $obank->_getPeakList ($type) ;
PRIVATE_ONLY _setPeak_COMPUTED_MONOISOTOPIC_MASS
## Description : _setPeak_COMPUTED_MONOISOTOPIC_MASS
## Input : $COMPUTED_MONOISOTOPIC_MASS
## Output : TRUE
## Usage : _setPeak_COMPUTED_MONOISOTOPIC_MASS ( $COMPUTED_MONOISOTOPIC_MASS ) ;
PRIVATE_ONLY _getPeakCOMPUTED_MONOISOTOPIC_MASS
## Description : _getPeakCOMPUTED_MONOISOTOPIC_MASS
## Input : void
## Output : $COMPUTED_MONOISOTOPIC_MASS
## Usage : my ( $COMPUTED_MONOISOTOPIC_MASS ) = _getPeakCOMPUTED_MONOISOTOPIC_MASS () ;
PRIVATE_ONLY _setPeakMESURED_MONOISOTOPIC_MASS
## Description : _setPeakMESURED_MONOISOTOPIC_MASS
## Input : $MESURED_MONOISOTOPIC_MASS
## Output : TRUE
## Usage : _setPeakMESURED_MONOISOTOPIC_MASS ( $MESURED_MONOISOTOPIC_MASS ) ;
PRIVATE_ONLY _getPeakMESURED_MONOISOTOPIC_MASS
## Description : _getPeakMESURED_MONOISOTOPIC_MASS
## Input : void
## Output : $MESURED_MONOISOTOPIC_MASS
## Usage : my ( $MESURED_MONOISOTOPIC_MASS ) = _getPeakMESURED_MONOISOTOPIC_MASS () ;
PRIVATE_ONLY _setANNOTATION_IN_NEG_MODE
## Description : _setANNOTATION_IN_NEG_MODE
## Input : $ANNOTATION_IN_NEG_MODE
## Output : TRUE
## Usage : _setANNOTATION_IN_NEG_MODE ( $ANNOTATION_IN_NEG_MODE ) ;
PRIVATE_ONLY _getPeak_ANNOTATION_IN_NEG_MODE
## Description : _getPeak_ANNOTATION_IN_NEG_MODE
## Input : void
## Output : $ANNOTATION_IN_NEG_MODE
## Usage : my ( $ANNOTATION_IN_NEG_MODE ) = _getPeak_ANNOTATION_IN_NEG_MODE () ;
PRIVATE_ONLY _setANNOTATION_DA_ERROR
## Description : _setANNOTATION_DA_ERROR
## Input : $MMU_ERROR
## Output : TRUE
## Usage : _setANNOTATION_DA_ERROR ( $MMU_ERROR ) ;
PRIVATE_ONLY _setANNOTATION_PPM_ERROR
## Description : _setANNOTATION_PPM_ERROR
## Input : $PPM_ERROR
## Output : TRUE
## Usage : _setANNOTATION_PPM_ERROR ( $PPM_ERROR ) ;
PRIVATE_ONLY _setANNOTATION_IN_NEG_MODE
## Description : _setANNOTATION_IN_NEG_MODE
## Input : $ANNOTATION_IN_POS_MODE
## Output : TRUE
## Usage : _setANNOTATION_IN_POS_MODE ( $ANNOTATION_IN_POS_MODE ) ;
PRIVATE_ONLY _getPeak_ANNOTATION_IN_POS_MODE
## Description : _getPeak_ANNOTATION_IN_POS_MODE
## Input : void
## Output : $ANNOTATION_IN_POS_MODE
## Usage : my ( $ANNOTATION_IN_POS_MODE ) = _getPeak_ANNOTATION_IN_POS_MODE () ;
PRIVATE_ONLY _setPeak_ANNOTATION_TYPE
## Description : _setPeak_ANNOTATION_TYPE
## Input : $ANNOTATION_TYPE
## Output : TRUE
## Usage : _setPeak_ANNOTATION_TYPE ( $ANNOTATION_TYPE ) ;
PRIVATE_ONLY _getPeak_ANNOTATION_TYPE
## Description : _getPeak_ANNOTATION_TYPE
## Input : void
## Output : $ANNOTATION_TYPE
## Usage : my ( $TYPE ) = _getPeak_ANNOTATION_TYPE () ;
PRIVATE_ONLY _setANNOTATION_NAME
## Description : _setANNOTATION_NAME
## Input : $ANNOTATION_NAME
## Output : TRUE
## Usage : _setANNOTATION_NAME ( $ANNOTATION_NAME ) ;
PRIVATE_ONLY _getPeak_ANNOTATION_NAME
## Description : _getPeak_ANNOTATION_NAME
## Input : void
## Output : $ANNOTATION_NAME
## Usage : my ( $ANNOTATION_NAME ) = _getPeak_ANNOTATION_NAME () ;
PRIVATE_ONLY _getPeak_ANNOTATION_ID
## Description : _getPeak_ANNOTATION_ID
## Input : void
## Output : $ANNOTATION_ID
## Usage : my ( $ANNOTATION_ID ) = _getPeak_ANNOTATION_ID () ;
PRIVATE_ONLY _setANNOTATION_ID
## Description : _setANNOTATION_ID
## Input : $ANNOTATION_ID
## Output : TRUE
## Usage : _setANNOTATION_ID ( $ANNOTATION_ID ) ;
PRIVATE_ONLY _setPeak_ANNOTATION_FORMULA
## Description : _setPeak_ANNOTATION_FORMULA
## Input : $ANNOTATION_FORMULA
## Output : TRUE
## Usage : $self->_setPeak_ANNOTATION_FORMULA ( $ANNOTATION_ID ) ;
PRIVATE_ONLY _setPeak_ANNOTATION_ONLY_IN
## Description : _setPeak_ANNOTATION_ONLY_IN
## Input : $ANNOTATION_ONLY_IN
## Output : TRUE
## Usage : _setPeak_ANNOTATION_ONLY_IN ( $ANNOTATION_ONLY_IN ) ;

AUTHOR

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

SEE ALSO

All information about Metabolomics::Banks 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

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