NAME

InSilicoSpectro::InSilico::AASequence - Elementary protein sequence.

SYNOPSIS

use InSilicoSpectro::InSilico::AASequence;

DESCRIPTION

Inherits from InSilicoSpectro::InSilico::Sequence. The AASequence class is intended to store protein sequence data.

ATTRIBUTES

readingFrame

Set to -3, -2, -1, 1, 2, or 3 in case the sequence was obtained by RNA/DNA translation.

METHODS

new([%h|$bpSeq|$Sequence|$AASequence])

Constructor. %h is a hash of attribute=>value pairs, $bpSeq is a BioPerl Bio::seq object, from which the attributes are copied, $Sequence and $AASequence are InSilicoSpectro::InSilico::Sequence and InSilicoSpectro::InSilico::AASequence respectively.

sequence([$val])

sequence accessor/modifier: sets sequence attribute if $val is given, returns the sequence attribute.

readingFrame([$val])

readingFrame accessor/modifier: sets readingFrame attribute if $val is given, returns the readingFrame attribute.

modif([$modif])

Modifications accessor/modifier: sets modifications if $modif, a reference to vector of modification names or a string is given (see Pheny::InSilico::MassCalculator::variablePeptide function for instance), returns a reference to a vector of modifications. This vector can be converted into a string for display purpose by the Pheny::InSilico::MassCalculator::modifToString function.

modifAt($pos, [$modif])

Accessor/modifier for modification at position $pos. Sets the modification if $modif, a string, is provided.

$pos = 0 is the N-terminal site, $pos = protein length +1 is the C-terminal site, and 1 <= $pos <= protein length correspond to amino acids.

To remove a modification set it to an empty string ''.

getMass

Returns the protein mass or undefined in case either the protein sequence is not set or there are variable modifications.

EXAMPLES

See t/InSilico/testAASequence.pl.

AUTHORS

Alexandre Masselot, www.genebio.com

Jacques Colinge, Upper Austria University of Applied Science at Hagenberg