Metabolomics::Banks::PeakForest(3)

NAME
Metabolomics::Banks::PeakForest - Perl extension for PeakForest bank

VERSION
Version 0.2 - supporting/integrating REST API V2 methods Version 0.3 - Completing object properties + GCMS bank generation Version 0.4 - Integration of deltaType

SYNOPSIS
    use Metabolomics::Banks::PeakForest;

DESCRIPTION
        Metabolomics::Banks::PeakForest is a full package for Perl allowing to build a generic Perl bank object from PeakForest bank resource.

EXPORT
        use Metabolomics::Banks::PeakForest qw( :all ) ;

PUBLIC METHODS

  Metabolomics::Banks::PeakForest

new
            ## Description : new
            ## Input : $self
            ## Ouput : bless $self ;
            ## Usage : new() ;

PRIVATE_ONLY __refpeakforestcompound__
            ## Description : PRIVATE method __refpeakforestcompound__ object
            ## Input : void
            ## Output : __refpeakforestcompound__
            ## Usage : $self->__refpeakforestcompound__ ;

PRIVATE_ONLY __refpeakforestspectra__
            ## Description : PRIVATE method __refpeakforestspectra__ object
            ## Input : void
            ## Output : __refpeakforestspectra__
            ## Usage : $self->__refpeakforestspectra__ ;

buildSpectralBankFromPeakForest
            ## Description : build a spectra bank from PeakForest matching REST API
            ## Input :
            ## Output : $oBank
            ## Usage : $oBank->buildSpectralBankFromPeakForest ( ) ;

_getCompoundFromId
            ## Description : get a peakforest compound by Id, based on REST API V2
            ## Input : $cpdId
            ## Output : $oCpd
            ## Usage : my ( $oCpd ) = $self->_getCompoundFromId ($cpdId) ;

_getGcmsSpectraFromIds
            ## Description : match a GC-MS spectra from a list of peaks, based on REST API V2
            ## Input : $cpdId
            ## Output : $oSpectra
            ## Usage : my ( $oSpectra ) = $self->_getGcmsSpectraFromIds () ;

_getGcmsSpectraByMatchingPeaks
            ## Description : match a GC-MS spectra from a list of peaks, based on REST API V2
            ## Input : $cpdId
            ## Output : $oSpectra
            ## Usage : my ( $oSpectra ) = $self->_getGcmsSpectraByMatchingPeaks () ;

initPeakForestQuery
            ## Description : Deprecated - initiate a peakforest query based on REST API V1
            ## Input : $peakforestInstance
            ## Output : $query
            ## Usage : my ( $entriesNb ) = $self->initPeakForestQuery () ;

getCleanRangeSpectraFromSource
            ## Description : get the list of spectra entries from a peakforest instance and a mz range (min/max) based on REST API V1
            ## Input : $oPeakForestQuery, $minMass, $maxMass
            ## Output : $Spectra
            ## Usage : my ( $Spectra ) = $oPeakForestQuery->getCleanRangeSpectraFromSource ( $minMass, $maxMass ) ;

METHOD buildTheoPeakBankFromEntries
            ## Description : Deprecated - building from a Metabolomics::Banks::PhytoHub object, a bank integrating each potential entry in a metabolomics format (POSITIVE or NEGATIVE forms)
            ## Input : $queryMode [POS|NEG]
            ## Output : int as $entryNb
            ## Usage : my $nb = $oBank->buildTheoPeakBankFromEntries() ;

PRIVATE METHODS

  Metabolomics::Banks::peakForest

PRIVATE_ONLY __refPeakForestSpectralEntry__
            ## Description : init a new peakforest spectral entry
            ## Input : void
            ## Output : refEntry
            ## Usage : $self->__refPeakForestSpectralEntry__() ;

PRIVATE_ONLY _getEntry_INCHIKEY
            ## Description : PRIVATE method _getEntry_INCHIKEY on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_INCHIKEY () ;

PRIVATE_ONLY _getEntry_SMILES
            ## Description : PRIVATE method _getEntry_SMILES on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_SMILES () ;

PRIVATE_ONLY _getEntry_MOLECULAR_FORMULA
            ## Description : PRIVATE method _getEntry_MOLECULAR_FORMULA on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_MOLECULAR_FORMULA () ;

PRIVATE_ONLY _getEntry_THEO_EXACT_MASS
            ## Description : PRIVATE method _getEntry_EXACT_MASS on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_THEO_EXACT_MASS () ;

PRIVATE_ONLY _getEntry_EXACT_MASS
            ## Description : PRIVATE method _getEntry_EXACT_MASS on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_EXACT_MASS () ;

PRIVATE_ONLY _getEntry_DELTA_PPM
            ## Description : PRIVATE method _getEntry_DELTA_PPM on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_DELTA_PPM () ;

PRIVATE_ONLY _getEntry_RELATIVE_INTENSITY
            ## Description : PRIVATE method _getEntry_RELATIVE_INTENSITY on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_RELATIVE_INTENSITY () ;

PRIVATE_ONLY _getEntry_COMPOUND_ID
            ## Description : PRIVATE method _getEntry_COMPOUND_ID on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $PhytoHub_ID ) = $entry->_getEntry_COMPOUND_ID () ;

PRIVATE_ONLY _getEntry_SPECTRAL_ID
            ## Description : PRIVATE method _getEntry_SPECTRAL_ID on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $PhytoHub_ID ) = $entry->_getEntry_SPECTRAL_ID () ;

PRIVATE_ONLY _getEntry_COMPOUND_NAME
            ## Description : PRIVATE method _getEntry_COMPOUND_NAME on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_COMPOUND_NAME () ;

PRIVATE_ONLY _getEntry_MOLECULAR_COMPOSITION
            ## Description : PRIVATE method _getEntry_MOLECULAR_COMPOSITION on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_MOLECULAR_COMPOSITION () ;

PRIVATE_ONLY _getEntry_PEAK_ATTRIBUTION
            ## Description : PRIVATE method _getEntry_PEAK_ATTRIBUTION on a refPeakForestSpectraEntry object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $VALUE ) = $entry->_getEntry_PEAK_ATTRIBUTION () ;

PRIVATE_ONLY _getSpectra_ID
            ## Description : PRIVATE method _getSpectra_ID on a __refpeakforestspectra__ object
            ## Input : void
            ## Output : $VALUE
            ## Usage : my ( $ID ) = $spectrum->_getSpectra_ID () ;

PRIVATE_ONLY _getSpectra_PEAKS
            ## Description : PRIVATE method _getSpectra_PEAKS on a refPeakForestSpectra object
            ## Input : void
            ## Output : $VALUES
            ## Usage : my ( $VALUES ) = $spectrum->_getSpectra_PEAKS () ;

PRIVATE_ONLY _getSpectra_COMPOUNDS
            ## Description : PRIVATE method _getSpectra_COMPOUNDS on a refPeakForestSpectra object
            ## Input : void
            ## Output : $VALUES
            ## Usage : my ( $VALUES ) = $spectrum->_getSpectra_COMPOUNDS () ;

PRIVATE_ONLY _getSpectra_SPECTRUM_NAME
            ## Description : PRIVATE method _getSpectra_SPECTRUM_NAME on a refPeakForestSpectra object
            ## Input : void
            ## Output : $VALUES
            ## Usage : my ( $VALUES ) = $spectrum->_getSpectra_SPECTRUM_NAME () ;

PRIVATE_ONLY _getCpd_NAME
            ## Description : PRIVATE method _getCpd_NAME on a refPeakForestCompound object
            ## Input : void
            ## Output : $VALUES
            ## Usage : my ( $VALUES ) = $spectrum->_getCpd_NAME () ;

PRIVATE_ONLY _getCpd_INCHIKEY
            ## Description : PRIVATE method _getCpd_INCHIKEY on a refPeakForestCompound object
            ## Input : void
            ## Output : $VALUES
            ## Usage : my ( $VALUES ) = $spectrum->_getCpd_INCHIKEY () ;

PRIVATE_ONLY _getCpd_CAN_SMILES
            ## Description : PRIVATE method _getCpd_CAN_SMILES on a refPeakForestCompound object
            ## Input : void
            ## Output : $VALUES
            ## Usage : my ( $VALUES ) = $spectrum->_getCpd_CAN_SMILES () ;

PRIVATE_ONLY _getCpd_FORMULA
            ## Description : PRIVATE method _getCpd_FORMULA on a refPeakForestCompound object
            ## Input : void
            ## Output : $VALUES
            ## Usage : my ( $VALUES ) = $spectrum->_getCpd_FORMULA () ;

PRIVATE_ONLY _launchGenericRestQuery
            ## Description : PRIVATE method _launchGenericRestQuery launch Rest queries and return json object
            ## Input : $QUERY
            ## Output : $JSON
            ## Usage : my ( $JSON ) = $self->_launchGenericRestQuery ($QUERY) ;

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

SEE ALSO
All information about Metabolomics::Banks::PeakForest 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::Fragment::Annotation

•   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 INRA PFEM team

Web Site = INRA PFEM