NAME

MS::Reader::MzIdentML::SpectrumIdentificationResult - mzIdentML result object

SYNOPSIS

    my $result = $search->next_spectrum_result;

    print $result->id;
    print $result->name;
    print $result->spectrum_id;
    print $result->data_ref;

    for my $hit ( @{ $result->hits } ) {
        # do something
    }

DESCRIPTION

The MS::Reader::MzIdentML::SpectrumIdentificationResult class represents the primary result object from a database search.

METHODS

id

Returns the unique element identifier

name =head2 spectrum_id

Return spectrum identifiers. Typically the spectrum_id return value is the "native ID" and the name may be a different identifier used by the software to reference the spectrum. These values will not always be the same depending on which software generated the results file.

data_ref

Returns an identifier which can be used to look up a SpectraData element, which in turns holds information about the original peaks file used as input to the search.

hits

Returns a reference to an array of SpectrumIdentificationItem elements, which represent individual spectra/peptide matches. These are currently returned as nested hash structures but will eventually be returned as objects.

CAVEATS AND BUGS

The API is in alpha stage and is not guaranteed to be stable.

Please reports bugs or feature requests through the issue tracker at https://github.com/jvolkening/p5-MS/issues.

AUTHOR

Jeremy Volkening <jdv@base2bio.com>

COPYRIGHT AND LICENSE

Copyright 2015-2016 Jeremy Volkening

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.