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

use InSilicoSpectro::InSilico::AASequence;

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

readingFrame

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

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

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

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.

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 ''.

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

See t/InSilico/testAASequence.pl.

Alexandre Masselot, www.genebio.com

Jacques Colinge, Upper Austria University of Applied Science at Hagenberg