NAME
Metabolomics::Banks - Perl extension to build metabolite banks for metabolomics
VERSION
Version 0.01
SYNOPSIS
use Metabolomics::Fragment::Annotation;DESCRIPTION
Metabolomics::Fragment::Annotation is a full package for Perl dev allowing full annotation of fragments.EXPORT
SUBROUTINES/METHODS
METHOD new
## Description : set a new bank object
## Input : NA
## Output : $oBank
## Usage : my ( $oBank ) = Metabolomics::Banks->new ( ) ;METHOD set_DATABASE_ENTRIES_NB
## Description : set_DATABASE_ENTRIES_NB
## Input : $DATABASE_ENTRIES_NB
## Output : TRUE
## Usage : $self->set_DATABASE_ENTRIES_NB ( $DATABASE_ENTRIES_NB ) ;METHOD _addEntry
## Description : _addEntry
## Input : $self, $Entry ;
## Ouput : NA
## Usage : _addEntry($Entry);METHOD _addFragment
## Description : _addFragment
## Input : $self, $fragment ;
## Ouput : NA
## Usage : _addFragment($fragment);METHOD _addContaminant
## Description : _addContaminant
## Input : $self, $contaminant ;
## Ouput : NA
## Usage : _addContaminant($contaminant);METHOD _getContaminants
## Description : get the list of contaminants from the bank object
## Input : $self
## Output : $contaminants
## Usage : my ( $contaminants ) = $obank->_getContaminants () ;METHOD _getEntries
## Description : get the list of entries from the bank object
## Input : $self
## Output : $Entries
## Usage : my ( $Entries ) = $obank->_getEntries () ;METHOD _getFragments
## Description : get the list of fragments from the bank object
## Input : $self
## Output : $fragments
## Usage : my ( $fragments ) = $obank->_getFragments () ;METHOD _getTheoricalPeaks
## Description : get the list of theorical peaks from the bank object
## Input : $self
## Output : $theoPeaks
## Usage : my ( $theoPeaks ) = $obank->_getTheoricalPeaks () ;METHOD __refPeak__
## Description : set a new theorical peak
## Input : NA
## Output : refPeak
## Usage : my ( refPeak ) = __refPeak__() ;METHOD _addPeakList
## Description : _addPeakList
## Input : $self, $type, $peakList ;
## Ouput : NA;
## Usage : _addPeakList($type, $peakList);METHOD _getPeakList
## Description : get the list of fragments from the bank object
## Input : $self, $type
## Output : $peakList
## Usage : my ( $peakList ) = $obank->_getPeakList ($type) ;METHOD _setPeak_COMPUTED_MONOISOTOPIC_MASS
## Description : _setPeak_COMPUTED_MONOISOTOPIC_MASS
## Input : $COMPUTED_MONOISOTOPIC_MASS
## Output : TRUE
## Usage : _setPeak_COMPUTED_MONOISOTOPIC_MASS ( $COMPUTED_MONOISOTOPIC_MASS ) ;METHOD _getPeakCOMPUTED_MONOISOTOPIC_MASS
## Description : _getPeakCOMPUTED_MONOISOTOPIC_MASS
## Input : void
## Output : $COMPUTED_MONOISOTOPIC_MASS
## Usage : my ( $COMPUTED_MONOISOTOPIC_MASS ) = _getPeakCOMPUTED_MONOISOTOPIC_MASS () ;METHOD _setPeakMESURED_MONOISOTOPIC_MASS
## Description : _setPeakMESURED_MONOISOTOPIC_MASS
## Input : $MESURED_MONOISOTOPIC_MASS
## Output : TRUE
## Usage : _setPeakMESURED_MONOISOTOPIC_MASS ( $MESURED_MONOISOTOPIC_MASS ) ;METHOD _getPeakMESURED_MONOISOTOPIC_MASS
## Description : _getPeakMESURED_MONOISOTOPIC_MASS
## Input : void
## Output : $MESURED_MONOISOTOPIC_MASS
## Usage : my ( $MESURED_MONOISOTOPIC_MASS ) = _getPeakMESURED_MONOISOTOPIC_MASS () ;METHOD _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 ) ;METHOD _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 () ;METHOD _setANNOTATION_DA_ERROR
## Description : _setANNOTATION_DA_ERROR
## Input : $MMU_ERROR
## Output : TRUE
## Usage : _setANNOTATION_DA_ERROR ( $MMU_ERROR ) ;METHOD _setANNOTATION_PPM_ERROR
## Description : _setANNOTATION_PPM_ERROR
## Input : $PPM_ERROR
## Output : TRUE
## Usage : _setANNOTATION_PPM_ERROR ( $PPM_ERROR ) ;METHOD _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 ) ;METHOD _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 () ;METHOD _setPeak_ANNOTATION_TYPE
## Description : _setPeak_ANNOTATION_TYPE
## Input : $ANNOTATION_TYPE
## Output : TRUE
## Usage : _setPeak_ANNOTATION_TYPE ( $ANNOTATION_TYPE ) ;METHOD _getPeak_ANNOTATION_TYPE
## Description : _getPeak_ANNOTATION_TYPE
## Input : void
## Output : $ANNOTATION_TYPE
## Usage : my ( $TYPE ) = _getPeak_ANNOTATION_TYPE () ;METHOD _setANNOTATION_NAME
## Description : _setANNOTATION_NAME
## Input : $ANNOTATION_NAME
## Output : TRUE
## Usage : _setANNOTATION_NAME ( $ANNOTATION_NAME ) ;METHOD _getPeak_ANNOTATION_NAME
## Description : _getPeak_ANNOTATION_NAME
## Input : void
## Output : $ANNOTATION_NAME
## Usage : my ( $ANNOTATION_NAME ) = _getPeak_ANNOTATION_NAME () ;METHOD _getPeak_ANNOTATION_ID
## Description : _getPeak_ANNOTATION_ID
## Input : void
## Output : $ANNOTATION_ID
## Usage : my ( $ANNOTATION_ID ) = _getPeak_ANNOTATION_ID () ;METHOD _setANNOTATION_ID
## Description : _setANNOTATION_ID
## Input : $ANNOTATION_ID
## Output : TRUE
## Usage : _setANNOTATION_ID ( $ANNOTATION_ID ) ;METHOD _setPeak_ANNOTATION_ONLY_IN
## Description : _setPeak_ANNOTATION_ONLY_IN
## Input : $ANNOTATION_ONLY_IN
## Output : TRUE
## Usage : _setPeak_ANNOTATION_ONLY_IN ( $ANNOTATION_ONLY_IN ) ;METHOD 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 ) ;METHOD 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 ) ;METHOD 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 ) ;AUTHOR
Franck Giacomoni, <franck.giacomoni at inra.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::BanksRT: 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