3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org/forester
27 package org.forester.surfacing;
29 import java.util.List;
31 public interface Protein {
33 public void addProteinDomain( final Domain protein_domain );
36 * If in_nc_order is set to true, this should return true only and only if
37 * the order in List 'domains' and this protein (as determined by the start positions
38 * of the domains of this proteins, _not_ by their index) are the same
39 * (interspersing, 'other', domains in this are ignored).
40 * If in_nc_order is set to false, this should return true only and only if
41 * this contains all domains listed in 'domains' (order and count do not matter).
43 * @param domains a list of domain ids in a certain order.
44 * @param in_nc_order to consider order
47 public boolean contains( final List<DomainId> domains, final boolean in_nc_order );
49 public String getAccession();
51 public String getDescription();
53 public String getName();
55 public int getNumberOfProteinDomains();
57 public Domain getProteinDomain( final int index );
59 public int getProteinDomainCount( final DomainId domain_id );
61 public List<Domain> getProteinDomains();
63 public List<Domain> getProteinDomains( final DomainId domain_id );
65 public ProteinId getProteinId();
67 public Species getSpecies();