libpappsomspp
Library for mass spectrometry
utils.h
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1 /*******************************************************************************
2  * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
3  *
4  * This file is part of the PAPPSOms++ library.
5  *
6  * PAPPSOms++ is free software: you can redistribute it and/or modify
7  * it under the terms of the GNU General Public License as published by
8  * the Free Software Foundation, either version 3 of the License, or
9  * (at your option) any later version.
10  *
11  * PAPPSOms++ 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 PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
18  *
19  * Contributors:
20  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
21  *implementation
22  ******************************************************************************/
23 
24 
25 #pragma once
26 
27 
28 /////////////////////// StdLib includes
29 #include <chrono>
30 
31 /////////////////////// Qt includes
32 #include <QString>
33 #include <QByteArray>
34 #include <QRegularExpression>
35 #include <QTextStream>
36 
37 
38 /////////////////////// Local includes
39 #include "types.h"
40 #include "exportinmportconfig.h"
41 
42 
43 namespace pappso
44 {
45 
46 class Trace;
47 
49 {
50  public:
51  //! Regular expression matching <numerical value><non-numerical*><numerical
52  //! value>
53  static QRegularExpression xyMassDataFormatRegExp;
54 
55  //! Regular expression matching <m/z value><non-numerical*>
56  static QRegularExpression mzListDataFormatRegExp;
57 
58  //! Regular expression matching <size_t><non-numerical*>
59  static QRegularExpression sizetListDataFormatRegExp;
60 
61  //! Regular expression that tracks the end of line in text files.
62  static QRegularExpression endOfLineRegExp;
63 
64  static const QString getLexicalOrderedString(unsigned int num);
65  static void writeLexicalOrderedString(QTextStream *p_out, unsigned int num);
66 
67  static int zeroDecimalsInValue(pappso_double value);
68  static pappso_double roundToDecimals(pappso_double value, int decimal_places);
69  static long long int
70  roundToDecimal32bitsAsLongLongInt(pappso::pappso_double input);
71 
72  static std::string toUtf8StandardString(const QString &text);
73 
74  static bool writeToFile(const QString &text, const QString &file_name);
75  static bool appendToFile(const QString &text, const QString &file_name);
76  static std::size_t
77  extractScanNumberFromMzmlNativeId(const QString &spectrum_native_id);
78 
79  static QString pointerToString(const void *const pointer);
80 
81  static bool almostEqual(double value1, double value2, int decimalPlaces = 10);
82 
83  static double nearestGreater(double value);
84 
85  static QString
86  chronoTimePointDebugString(const QString &msg,
87  std::chrono::system_clock::time_point chrono_time =
88  std::chrono::system_clock::now());
89 
90  static QString chronoIntervalDebugString(
91  const QString &msg,
92  std::chrono::system_clock::time_point chrono_start,
93  std::chrono::system_clock::time_point chrono_finish =
94  std::chrono::system_clock::now());
95 
96  static std::vector<double>
97  splitMzStringToDoubleVectorWithSpaces(const QString &text,
98  std::size_t &error_count);
99 
100  static std::vector<std::size_t>
101  splitSizetStringToSizetVectorWithSpaces(const QString &text,
102  std::size_t &error_count);
103 
104  /** @brief convenient function to transform a boolean to QString "TRUE" or
105  * "FALSE" QString returned is readable by R
106  * @return QString "TRUE" or "FALSE"
107  */
108  static QString booleanToString(bool value);
109 
110  /** @brief Convenience function to return a string describing the MzFormat of
111  * a file
112  * @return QString like "brukerTims" for enum value MzFormat::brukerTims.
113  */
114  static QString mzFormatAsString(MzFormat mz_format);
115 };
116 
117 } // namespace pappso
static QRegularExpression xyMassDataFormatRegExp
Definition: utils.h:53
static QRegularExpression mzListDataFormatRegExp
Regular expression matching <m/z value><non-numerical*>
Definition: utils.h:56
static QRegularExpression sizetListDataFormatRegExp
Regular expression matching <size_t><non-numerical*>
Definition: utils.h:59
static QRegularExpression endOfLineRegExp
Regular expression that tracks the end of line in text files.
Definition: utils.h:62
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
MzFormat
Definition: types.h:108
double pappso_double
A type definition for doubles.
Definition: types.h:49
This header contains all the type re-definitions and all the global variables definitions used in the...