/ 
MS-0.207003
River stage zero No dependents
/ MS::Reader::PepXML::Result

NAME

MS::Reader::PepXML::Result - pepXML search result object

SYNOPSIS

while (my $result = $search->next_result) {

    my $top_hit = $result->get_hit(0);
    my $peptide = $top_hit->{peptide};
    my $deltas  = $result->mod_delta_array(0);

}

DESCRIPTION

The MS::Reader::PepXML::Result class represent search query results (<<spectrum_query>> elements in the pepXML schema). mass spectrometry data. It aims to provide complete access to the data contents while not being overburdened by detailed class infrastructure. Convenience methods are provided for accessing commonly used data. Users who want to extract data not accessible through the available methods should examine the data structure of the parsed object. The dump() method provides an easy method of doing so.

METHODS

get_hit

my $first_hit = $result->get_hit(0);

Takes one optional argument (zero-based index of the hit) and returns a hash reference containing the result data for the hit. Currently most useful data is extracted directly from this hash reference. In the future additional accessors may be added for commonly accessed data. If no arguments are provided, returns the first hit.

mod_delta_array

my $deltas = $result->mod_delta_array(0);

Takes one optional argument (zero-based index of the hit) and returns an array reference containing floating point delta masses for each location on the peptide. The length of the array wil be equal to peptide length + 2 - the first and last values represent N-terminal and C-terminal modifications respectively. If no arguments are provided, returns the first hit.

dump

my $string = $result->dump;

Returns a textual serialization of the MS::Reader::PepXML::Result object as a text string. This is useful for understanding how to access information not provided directly by class methods.

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/>.