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_DNASTAT_MSA_PROFILE_DIALOG_H_
23 #define _U2_DNASTAT_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_DNAStatMSAProfileDialog.h"
33 
34 namespace U2 {
35 
36 class MSAEditor;
37 class SaveDocumentController;
38 
39 class DNAStatMSAProfileDialog : public QDialog, public Ui_DNAStatMSAProfileDialog {
40     Q_OBJECT
41 
42 public:
43     DNAStatMSAProfileDialog(QWidget *p, MSAEditor *ctx);
44 
45     void accept();
46     /*Notify user about problems with big report, and disable opening report in UGENE*/
47     void showAlignmentIsTooBigWarning();
48 private slots:
49     void sl_formatSelected();
50     void sl_formatChanged(const QString &newFormat);
51 
52 private:
53     void initSaveController();
54 
55     MSAEditor *ctx;
56     SaveDocumentController *saveController;
57 
58     static const QString HTML;
59     static const QString CSV;
60 };
61 
62 enum DNAStatMSAProfileOutputFormat {
63     DNAStatMSAProfileOutputFormat_Show,
64     DNAStatMSAProfileOutputFormat_CSV,
65     DNAStatMSAProfileOutputFormat_HTML
66 };
67 
68 class DNAStatMSAProfileTaskSettings {
69 public:
DNAStatMSAProfileTaskSettings()70     DNAStatMSAProfileTaskSettings() {
71         outFormat = DNAStatMSAProfileOutputFormat_Show;
72         usePercents = false;
73         reportGaps = false;
74         stripUnused = false;
75         countGapsInConsensusNumbering = true;
76     }
77 
78     QString profileName;  // usually object name
79     QString profileURL;  // document url
80     MultipleSequenceAlignment ma;
81     bool usePercents;  // report percents but not counts
82     DNAStatMSAProfileOutputFormat outFormat;
83     QString outURL;
84     bool reportGaps;  // report GAPS statistics
85     bool stripUnused;  // do not include into report chars unused in alignment
86     bool countGapsInConsensusNumbering;  // affects html output only
87 };
88 
89 class DNAStatMSAProfileTask : public Task {
90     Q_OBJECT
91 public:
92     DNAStatMSAProfileTask(const DNAStatMSAProfileTaskSettings &s);
93 
94     void run();
95     QString generateReport() const;
96     virtual bool isReportingEnabled() const;
97 
98     ReportResult report();
99 
100 private:
101     void computeStats();
102 
103     DNAStatMSAProfileTaskSettings s;
104 
105     // fields to keep statistics
106     struct ColumnStat {
107         char consChar;
108         QVector<int> charFreqs;
109     };
110 
111     QStringList verticalColumnNames;
112     QVector<ColumnStat> columns;
113     QVector<char> consenusChars;
114     QHash<char, int> char2index;  // char 2 index in 'ColumnStat'
115     QSet<char> unusedChars;
116     QString resultText;
117 };
118 
119 }  // namespace U2
120 
121 #endif
122