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lib/MS/Reader/MzIdentML/Peptide.pm  view on Meta::CPAN

package MS::Reader::MzIdentML::Peptide;

use strict;
use warnings;

use parent qw/MS::Reader::MzIdentML::SequenceItem/;

sub id         { return $_[0]->{id}         } 
sub seq        { return $_[0]->{PeptideSequence}->{pcdata} }
sub mods       { return $_[0]->{Modification} }

1;

__END__

=pod

=encoding UTF-8

lib/MS/Reader/MzML.pm  view on Meta::CPAN

sub _load_new {

    my ($self) = @_;

    $self->SUPER::_load_new();

    if (
           defined $self->{indexedmzML}->{fileChecksum}
        && defined $self->{indexedmzML}->{fileChecksum}->{pcdata}
        && length $self->{indexedmzML}->{fileChecksum}->{pcdata}
        && $self->{indexedmzML}->{fileChecksum}->{pcdata} ne '0'
    ) {

        # compare supplied and calculated SHA1 sums to validate
        my $sha1_given = $self->{indexedmzML}->{fileChecksum}->{pcdata};
        croak "ERROR: SHA1 digest mismatch\n"
            if ($sha1_given ne $self->_calc_sha1);

    }

    # Outer <mzML> may optionally be wrapped in <indexedmxML> tags. For
    # consistent downstream handling, everything outside <mzML> should be
    # discarded before returning.
    if (defined $self->{indexedmzML}) {
        $self->{mzML}->{$_} = $self->{indexedmzML}->{mzML}->{$_}

lib/MS/Reader/MzML/Record.pm  view on Meta::CPAN

        selectedIon
        scanWindow
        scan
    / };

}

sub _get_raw {

    my ($self, $array) = @_;
    return decode_base64( $array->{binary}->{pcdata} );

}

sub _get_code {

    my ($self, $array) = @_;

    return defined $self->param(MS_32_BIT_FLOAT,   ref => $array) ? 'f<'
         : defined $self->param(MS_64_BIT_FLOAT,   ref => $array) ? 'd<'
         : defined $self->param(MS_32_BIT_INTEGER, ref => $array) ? 'l<'

lib/MS/Reader/MzXML.pm  view on Meta::CPAN

sub _load_new {

    my ($self) = @_;

    $self->SUPER::_load_new();

    if (defined $self->{mzXML}->{sha1}) {

        # compare supplied and calculated SHA1 sums to validate
        my $sha1_given = $self->{mzXML}->{sha1}->{pcdata};
        croak "ERROR: SHA1 digest mismatch\n"
            if ($sha1_given ne $self->_calc_sha1);

    }

    # Outer <msRun> may optionally be wrapped in <mzXML> tags. For
    # consistent downstream handling, everything outside <msRun> should be
    # discarded before returning.
    if (defined $self->{mzXML}) {
        $self->{msRun} = $self->{mzXML}->{msRun};

lib/MS/Reader/MzXML/Spectrum.pm  view on Meta::CPAN

sub precursor {

    my ($self) = @_;
    croak "precursor() only valid for MS2 spectra"
        if ($self->{msLevel} < 2);
    croak "precursor() only valid for single precursor spectra, use direct access.\n"
        if (scalar @{$self->{precursorMz}} != 1);

    my $pre       = $self->{precursorMz}->[0];
    my $id        = $pre->{precursorScanNum};
    my $mono_mz   = $pre->{pcdata};
    my $iso_mz    = $mono_mz;
    my $iso_lower = $iso_mz - $pre->{windowWideness}/2;
    my $iso_upper = $iso_mz + $pre->{windowWideness}/2;
    my $charge    = $pre->{precursorCharge};
    my $int       = $pre->{precursorIntensity};

    croak "missing monoisotopic m/z" if (! defined $mono_mz);
    return {
        scan_id   => $id,
        iso_mz    => $iso_mz,

lib/MS/Reader/MzXML/Spectrum.pm  view on Meta::CPAN

}

sub get_array {

    my ($self, $type) = @_;

    my $ref = $self->{peaks}->{$type};
    croak "Undefined array type $type" if (! defined $ref);

    my $data = decode_base64( $ref->{pcdata} );
    $data    = uncompress($data) if ($ref->{compressionType} eq 'zlib');
    my $code = $ref->{precision} eq '64' ? 'd>' : 'f>';
    return [ unpack "$code*", $data ];

}

sub scan_window {

    my ($self) = @_; 
    

lib/MS/Reader/XML.pm  view on Meta::CPAN

    delete $self->{_curr_ref}->{_back};
    $self->{_curr_ref} = $last_ref;

    return;

}

sub _handle_char {

    my ($self, $p, $data) = @_;
    $self->{_curr_ref}->{pcdata} .= $data
        if ($data =~ /\S/);
    return;

}

sub goto {

    my ($self, $ref, $idx) = @_;
    croak "Bad list ref" if (! exists $ref->{__pos});
    croak "$idx not an integer" if ($idx =~ /\D/);

lib/MS/Reader/XML/Record.pm  view on Meta::CPAN

    delete $self->{_curr_ref}->{back}; # avoid memory leak!
    $self->{_curr_ref} = $last_ref;

    return;

}

sub _handle_char {

    my ($self, $p, $data) = @_;
    $self->{_curr_ref}->{pcdata} .= $data
        if ($data =~ /\S/);
    return;

}

sub dump {

    my ($self) = @_;
    my $copy = {};
    %$copy = %$self;