Metabolomics::Banks(3)

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_FORMULA
        ## Description : _setPeak_ANNOTATION_FORMULA
        ## Input : $ANNOTATION_FORMULA
        ## Output : TRUE
        ## Usage : $self->_setPeak_ANNOTATION_FORMULA ( $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

•   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

LICENSE AND COPYRIGHT
CeCILL Copyright (C) 2019 by Franck Giacomoni

Initiated by Franck Giacomoni

followed by INRA PFEM team

Web Site = INRA PFEM