Franck Giacomoni
and 1 contributors

NAME

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

VERSION

Version 0.1

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::Banks

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

CeCILL Copyright (C) 2019 by Franck Giacomoni

Initiated by Franck Giacomoni

followed by INRA PFEM team

Web Site = INRA PFEM