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

cpanm Metabolomics::Fragment::Annotation

perl -MCPAN -e shell
install Metabolomics::Fragment::Annotation