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 #ifndef _U2_DISTANCE_MATRIX_MSA_PROFILE_DIALOG_H_
23 #define _U2_DISTANCE_MATRIX_MSA_PROFILE_DIALOG_H_
24 
25 #include <QHash>
26 #include <QSet>
27 
28 #include <U2Core/MultipleSequenceAlignment.h>
29 #include <U2Core/Task.h>
30 #include <U2Core/global.h>
31 
32 #include "ui_DistanceMatrixMSAProfileDialog.h"
33 
34 class QFile;
35 
36 namespace U2 {
37 
38 class MSAEditor;
39 class MSADistanceAlgorithm;
40 class SaveDocumentController;
41 
42 class DistanceMatrixMSAProfileDialog : public QDialog, public Ui_DistanceMatrixMSAProfileDialog {
43     Q_OBJECT
44 
45 public:
46     DistanceMatrixMSAProfileDialog(QWidget *p, MSAEditor *ctx);
47 
48     void accept();
49 
50 private slots:
51     void sl_formatSelected();
52     void sl_formatChanged(const QString &newFormatId);
53 
54 private:
55     void initSaveController();
56 
57     MSAEditor *ctx;
58     SaveDocumentController *saveController;
59 
60     static const QString HTML;
61     static const QString CSV;
62 };
63 
64 enum DistanceMatrixMSAProfileOutputFormat {
65     DistanceMatrixMSAProfileOutputFormat_Show,
66     DistanceMatrixMSAProfileOutputFormat_CSV,
67     DistanceMatrixMSAProfileOutputFormat_HTML
68 };
69 
70 class DistanceMatrixMSAProfileTaskSettings {
71 public:
72     DistanceMatrixMSAProfileTaskSettings();
73 
74     QString algoId;  // selected algorithm id
75     QString profileName;  // usually object name
76     QString profileURL;  // document url
77     MultipleSequenceAlignment ma;
78     bool usePercents;  // report percents but not counts
79     bool excludeGaps;  // exclude gaps when calculate distance
80     bool showGroupStatistic;
81     DistanceMatrixMSAProfileOutputFormat outFormat;
82     QString outURL;
83     MSAEditor *ctx;
84 };
85 
86 class DistanceMatrixMSAProfileTask : public Task {
87     Q_OBJECT
88 public:
89     DistanceMatrixMSAProfileTask(const DistanceMatrixMSAProfileTaskSettings &s);
90 
91     virtual void prepare();
92     QString generateReport() const;
93     virtual bool isReportingEnabled() const;
94 
95     void createDistanceTable(MSADistanceAlgorithm *algo, const QList<MultipleSequenceAlignmentRow> &rows, QFile *f);
96 
97     QList<Task *> createStatisticsDocument(Task *subTask);
98 
99     QList<Task *> onSubTaskFinished(Task *subTask);
100     // void run();
101     ReportResult report();
102 
103 private:
104     DistanceMatrixMSAProfileTaskSettings s;
105     QString resultText;
106 };
107 
108 }  // namespace U2
109 
110 #endif
111