Metabolomics::Banks(3)

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

VERSION
Version 0.2 - Adding POD

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 _getPeak_ANNOTATION_FORMULA
            ## Description : _getPeak_ANNOTATION_FORMULA
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_FORMULA () ;

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 ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_SMILES
            ## Description : _getPeak_ANNOTATION_SMILES
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_SMILES () ;

PRIVATE_ONLY _setPeak_ANNOTATION_SMILES
            ## Description : _setPeak_ANNOTATION_SMILES
            ## Input : $VALUE
            ## Output : TRUE
            ## Usage : _setPeak_ANNOTATION_SMILES ( $VALUE ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_INCHIKEY
            ## Description : _getPeak_ANNOTATION_INCHIKEY
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_INCHIKEY () ;

PRIVATE_ONLY _setPeak_ANNOTATION_INCHIKEY
            ## Description : _setPeak_ANNOTATION_INCHIKEY
            ## Input : $VALUE
            ## Output : TRUE
            ## Usage : _setPeak_ANNOTATION_INCHIKEY ( $VALUE ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_IS_A_PRECURSOR
            ## Description : _getPeak_ANNOTATION_IS_A_PRECURSOR
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_IS_A_PRECURSOR () ;

PRIVATE_ONLY _setPeak_ANNOTATION_IS_A_PRECURSOR
            ## Description : _setPeak_ANNOTATION_IS_A_PRECURSOR
            ## Input : $VALUE
            ## Output : TRUE
            ## Usage : _setPeak_ANNOTATION_IS_A_PRECURSOR ( $VALUE ) ;

PRIVATE_ONLY _getPeak_ANNOTATION_IS_A_PRECURSOR
            ## Description : _getPeak_ANNOTATION_IS_A_PRECURSOR
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = _getPeak_ANNOTATION_IS_A_PRECURSOR () ;

PRIVATE_ONLY _setPeak_ANNOTATION_IS_A_METABOLITE
            ## Description : _setPeak_ANNOTATION_IS_A_METABOLITE
            ## Input : $VALUE
            ## Output : TRUE
            ## Usage : _setPeak_ANNOTATION_IS_A_METABOLITE ( $VALUE ) ;

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

•   RT: CPAN's request tracker (report bugs here)

    <https://rt.cpan.org/Public/Dist/Display.html?Name=Metabolomics-Fragment-Annotation>

•   AnnoCPAN: Annotated CPAN documentation

    <http://annocpan.org/dist/Metabolomics-Fragment-Annotation>

•   CPAN Ratings

    <https://cpanratings.perl.org/d/Metabolomics-Fragment-Annotation>

•   Search CPAN

    <https://metacpan.org/release/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 INRAE PFEM team

Web Site = INRAE PFEM