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lib/InSilicoSpectro/Databanks/DBEntry.pm  view on Meta::CPAN

use strict;

package InSilicoSpectro::Databanks::DBEntry;
require Exporter;
use Carp;

=head1 NAME

InSilico::Databanks::DBEntry - fasta databank entry + header's annotated info

=head1 SYNOPSIS


=head1 DESCRIPTION

describes an databnk entry (header + sequence)

=head1 FUNCTIONS


=head1 METHODS


=head3 my $dbe=InSilico::Databanks::DBEntry->new([\%h]);

=head2 Accessors/Setters

=head3 $dbe->AC([val])

get/set accession code

=head3 $dbe->ID([val])

get/set accession ID

=head3 $dbe->dbName([val])

[GS]et databank name

=head3 $dbe->taxoID([val])

[GS]et taxonomy if (typically NCBI taxid

=head3 $dbe->description([val])

=head3 $dbe->sequence([val])

Get/Set AC, ID, ...

=head3 $dbe->seqType(["AA"|"DNA"])

Get or set the sequence type

=head3 $dbe->annotatedModRes(string|[[pos1, mod1], [pos2, mod2]]);

get or set annotated PTM from a string (e.g. (1|ACET_nterm)(2|ACET_nterm)(185|PHOS)) or an array. All previously set TPM are removed

=head3 $dbe->add_annotatedModRes(pos, modkey)

add an annotated PTM

=head3 $dbe->clear_annotatedModRes()

remove all annotated modres

=head3 $dbe->variants(string|[[pos1, seq1a, seq1b], [pos2, seq2a, seq2b]]);

get or set variant a string (e.g. ("(9|F|Y)(30|D|N)(41|A|G)(43|Q|R)") or an array. All previously set TPM are removed

=head3 $dbe->add_variant(pos, seqa, seqb)

add a VARIANT, replacing seqa by seqb (often just one aminoacid) at pos

=head3 $dbe->clear_variants()

remove all Variants

=head2 I/O

=head3 $dbe->readFasta($fastacontent);

read info from fasta contents (fitrs line with '>' and info + remaining is sequence.

=head3 $dbe->printFasta();

print the entry under fasta format (use SelectSaver or whatever select method to redirect towards a file descriptor);

=head3 $dbe->printHtml();

Print the entry under a html format.

=head1 EXAMPLES


=head1 SEE ALSO

=head1 COPYRIGHT

Copyright (C) 2004-2005  Geneva Bioinformatics www.genebio.com

This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.

This library 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
Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

=head1 AUTHORS