1 /**
2 * UGENE - Integrated Bioinformatics Tools.
3 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru>
4 * http://ugene.net
5 *
6 * This program is free software; you can redistribute it and/or
7 * modify it under the terms of the GNU General Public License
8 * as published by the Free Software Foundation; either version 2
9 * of the License, or (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with this program; if not, write to the Free Software
18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
19 * MA 02110-1301, USA.
20 */
21
22 #include "DNAFlexGraph.h"
23
24 #include <U2Core/DNAAlphabet.h>
25 #include <U2Core/DNASequenceObject.h>
26 #include <U2Core/TextUtils.h>
27
28 #include "DNAFlexGraphAlgorithm.h"
29
30 namespace U2 {
31
32 const qint64 DNAFlexGraphFactory::DEFAULT_WINDOW_SIZE = 100;
33
34 const int DNAFlexGraphFactory::DEFAULT_WINDOW_STEP = 1;
35
36 /**
37 * Name of the graph (shown to a user)
38 */
nameByType()39 static QString nameByType() {
40 return DNAFlexGraphFactory::tr("DNA Flexibility");
41 }
42
43 /**
44 * Constructor of the DNA Flexibility graph
45 */
DNAFlexGraphFactory(QObject * parent)46 DNAFlexGraphFactory::DNAFlexGraphFactory(QObject *parent)
47 : GSequenceGraphFactory(nameByType(), parent) {
48 }
49
50 /**
51 * Verifies that the sequence alphabet is standard DNA alphabet
52 */
isEnabled(const U2SequenceObject * sequenceObject) const53 bool DNAFlexGraphFactory::isEnabled(const U2SequenceObject *sequenceObject) const {
54 const DNAAlphabet *alphabet = sequenceObject->getAlphabet();
55 return alphabet->getId() == BaseDNAAlphabetIds::NUCL_DNA_DEFAULT();
56 }
57
58 /**
59 * Initializes graph data
60 */
createGraphs(GSequenceGraphView * view)61 QList<QSharedPointer<GSequenceGraphData>> DNAFlexGraphFactory::createGraphs(GSequenceGraphView *view) {
62 assert(isEnabled(view->getSequenceObject()));
63 return {QSharedPointer<GSequenceGraphData>(new GSequenceGraphData(view, getGraphName(), new DNAFlexGraphAlgorithm()))};
64 }
65
66 /**
67 * Initializes the graph drawer
68 */
getDrawer(GSequenceGraphView * view)69 GSequenceGraphDrawer *DNAFlexGraphFactory::getDrawer(GSequenceGraphView *view) {
70 qint64 window = qMin(DEFAULT_WINDOW_SIZE, view->getSequenceLength());
71 return new GSequenceGraphDrawer(view, window, DEFAULT_WINDOW_STEP);
72 }
73
74 } // namespace U2
75