MikkelSchubert / adapterremoval / #39

Committed 20 Aug 2024 01:31PM UTC coverage: 79.602% (-3.8%) from 83.365%

Build # #39

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push

travis-ci

Committed by

MikkelSchubert

Commit Message

update schema URL to use github pages

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76.32

/src/strutils.hpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com           *
 *                                                                       *
 * This program is free software: you can redistribute it and/or modify  *
 * it under the terms of the GNU General Public License as published by  *
 * the Free Software Foundation, either version 3 of the License, or     *
 * (at your option) any later version.                                   *
 *                                                                       *
 * This program is distributed in the hope that it will be useful,       *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 * GNU General Public License for more details.                          *
 *                                                                       *
 * You should have received a copy of the GNU General Public License     *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>. *
\*************************************************************************/
#pragma once

#include <cstddef>     // for size_t
#include <cstdint>     // for uint64_t
#include <ostream>     // for ostream
#include <sstream>     // for ostringstream
#include <string>      // for string
#include <string_view> // for string_view
#include <vector>      // for vector

namespace adapterremoval {

using string_vec = std::vector<std::string>;

const size_t DEFAULT_MAX_COLUMNS = 78;
const size_t DEFAULT_INDENTATION = 4;

/** Computes the Levenshtein distance between two strings. */
size_t
levenshtein(std::string_view s, std::string_view t);

/**
 * Returns a timestamp in the specified format, see
 * https://en.cppreference.com/w/cpp/io/manip/put_time
 */
std::string
timestamp(const char* format, bool milliseconds = false);

/**
 * Convert a string to an unsigned integer.
 *
 * Throws std::invalid_argument if the string does not contain a proper number,
 * if it contains more than just a number, or if the number overflows a
 * unsigned integer.
 */
unsigned
str_to_unsigned(const std::string& s);

/** Lowercases letters in the range a-z */
constexpr char
to_lower(char c)
{
  return (c >= 'A' && c <= 'Z') ? static_cast<char>(c + 32) : c;
}

/** Lowercases letters in the range a-z */
std::string
to_lower(std::string str);

/** Uppercase letters in the range a-z */
constexpr char
to_upper(char c)
{
  return (c >= 'a' && c <= 'z') ? static_cast<char>(c - 32) : c;
}

/** Uppercase letters in the range a-z */
std::string
to_upper(std::string str);

/** Returns true if str1 ends with str2 (case sensitive) */
bool
starts_with(std::string_view str1, std::string_view str2);

/** Returns true if str1 ends with str2 (case sensitive) */
bool
ends_with(std::string_view str1, std::string_view str2);

string_vec
split_text(std::string_view text, char separator);

/** Split text by newlines */
inline string_vec
split_lines(std::string_view text)
{
  return split_text(text, '\n');
}

/** Split text by newlines and add fixed indentation following newlines. */
std::string
indent_lines(std::string_view lines, size_t indentation = DEFAULT_INDENTATION);

/**
 * Formats text into fixed-width columns.
 *
 * @param value Text representing a single paragraph to be formatted.
 * @param max_width Maximum width of output lines in characters.
 * @param ljust Indent lines after the first line by this amount of characters.
 *
 * Note that all whitespace in the input string is consumed; output words are
 * separated by a single space, and the terminal line does not end with a
 * newline.
 */
string_vec
wrap_text(const std::string& value,
          size_t max_width = DEFAULT_MAX_COLUMNS,
          size_t ljust = 0);

template<typename T>
std::string
join_text(const std::vector<T>& values,
          std::string_view sep,
          std::string_view final_sep)
{
  std::ostringstream stream;
  for (auto it = values.begin(); it != values.end(); ++it) {
    if (it != values.begin()) {
      if (it + 1 == values.end()) {
        stream << final_sep;
      } else {
        stream << sep;
      }
    }

    stream << *it;
  }

  return stream.str();
}

template<typename T>
std::string
join_text(const std::vector<T>& values, std::string_view sep)
{
  return join_text(values, sep, sep);
}

/**
 * Wrapper around 'indent_lines' and 'wrap_text'.
 *
 * Defaults to 78 character columns, with 4 character indentation, and no ljust,
 * corresponding to function defaults. Unlike simply combining 'indent_lines'
 * and 'wrap_text', the 'format' function preserves newlines, allowing
 * paragraphs to be printed easily.
 */
class cli_formatter
{
public:
  /** Creates formatter using default parameters (see above). */
  cli_formatter();

  /** Include (or not) indentation on the first line of output. */
  cli_formatter& set_indent_first_line(bool value);
  /** Maximum number of columns in each line in output. */
  cli_formatter& set_column_width(size_t value);
  /** Number of spaces to indent line 2+ in each paragraph. */
  cli_formatter& set_ljust(size_t value);
  /** Fixed indentation for each line (see also set_indent_first_line). */
  cli_formatter& set_indent(size_t value);

  /** Formats string using the current settings. */
  std::string format(std::string_view value) const;

private:
  //! Specifies whether or not to indent the first line of output.
  bool m_indent_first;
  //! Number of spaces to indent the 2+ lines in each paragraph.
  size_t m_ljust;
  //! The maximum number of columns (in characters).
  size_t m_columns;
  //! The number of spaces to indent each line (see also m_indent_first_line)
  size_t m_indentation;
};

/** Escapes a string to make it safe to use in copy/pasted commands */
std::string
shell_escape(std::string_view s);

/**
 * Escapes a string for use in logging; this is equivalent to shell_escape
 * except that strings are always quoted for readability.
 */
std::string
log_escape(std::string_view s);

/** Escapes a full shell command using shell_escape */
std::string
shell_escape_command(const string_vec& v);

/** Adds thousand separators to a number */
std::string
format_thousand_sep(size_t count);

/** Rounds a number using K, M, etc. units. */
std::string
format_rough_number(size_t value, size_t out_digits = 3);

/** Formats a fraction, returning "NA" if denominator is 0 */
std::string
format_fraction(uint64_t num, uint64_t denom, size_t precision = 2);

/** Formats a percentage, returning "NA" if denominator is 0 */
std::string
format_percentage(uint64_t num, uint64_t denom, size_t precision = 1);

} // namespace adapterremoval

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com *
5	* *
6	* This program 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	* 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, see <http://www.gnu.org/licenses/>. *
18	\*************************************************************************/
19	#pragma once
20
21	#include <cstddef> // for size_t
22	#include <cstdint> // for uint64_t
23	#include <ostream> // for ostream
24	#include <sstream> // for ostringstream
25	#include <string> // for string
26	#include <string_view> // for string_view
27	#include <vector> // for vector
28
29	namespace adapterremoval {
30
31	using string_vec = std::vector<std::string>;
32
33	const size_t DEFAULT_MAX_COLUMNS = 78;
34	const size_t DEFAULT_INDENTATION = 4;
35
36	/** Computes the Levenshtein distance between two strings. */
37	size_t
38	levenshtein(std::string_view s, std::string_view t);
39
40	/**
41	* Returns a timestamp in the specified format, see
42	* https://en.cppreference.com/w/cpp/io/manip/put_time
43	*/
44	std::string
45	timestamp(const char* format, bool milliseconds = false);
46
47	/**
48	* Convert a string to an unsigned integer.
49	*
50	* Throws std::invalid_argument if the string does not contain a proper number,
51	* if it contains more than just a number, or if the number overflows a
52	* unsigned integer.
53	*/
54	unsigned
55	str_to_unsigned(const std::string& s);
56
57	/** Lowercases letters in the range a-z */
58	constexpr char
59	to_lower(char c)	48✔
60	{
61	return (c >= 'A' && c <= 'Z') ? static_cast<char>(c + 32) : c;	48✔
62	}
63
64	/** Lowercases letters in the range a-z */
65	std::string
66	to_lower(std::string str);
67
68	/** Uppercase letters in the range a-z */
69	constexpr char
70	to_upper(char c)	12✔
71	{
72	return (c >= 'a' && c <= 'z') ? static_cast<char>(c - 32) : c;	12✔
73	}
74
75	/** Uppercase letters in the range a-z */
76	std::string
77	to_upper(std::string str);
78
79	/** Returns true if str1 ends with str2 (case sensitive) */
80	bool
81	starts_with(std::string_view str1, std::string_view str2);
82
83	/** Returns true if str1 ends with str2 (case sensitive) */
84	bool
85	ends_with(std::string_view str1, std::string_view str2);
86
87	string_vec
88	split_text(std::string_view text, char separator);
89
90	/** Split text by newlines */
91	inline string_vec
92	split_lines(std::string_view text)	173✔
93	{
94	return split_text(text, '\n');	173✔
95	}
96
97	/** Split text by newlines and add fixed indentation following newlines. */
98	std::string
99	indent_lines(std::string_view lines, size_t indentation = DEFAULT_INDENTATION);
100
101	/**
102	* Formats text into fixed-width columns.
103	*
104	* @param value Text representing a single paragraph to be formatted.
105	* @param max_width Maximum width of output lines in characters.
106	* @param ljust Indent lines after the first line by this amount of characters.
107	*
108	* Note that all whitespace in the input string is consumed; output words are
109	* separated by a single space, and the terminal line does not end with a
110	* newline.
111	*/
112	string_vec
113	wrap_text(const std::string& value,
114	size_t max_width = DEFAULT_MAX_COLUMNS,
115	size_t ljust = 0);
116
117	template<typename T>
118	std::string
119	join_text(const std::vector<T>& values,	113✔
120	std::string_view sep,
121	std::string_view final_sep)
122	{
123	std::ostringstream stream;	113✔
124	for (auto it = values.begin(); it != values.end(); ++it) {	962✔
125	if (it != values.begin()) {	495✔
126	if (it + 1 == values.end()) {	216✔
127	stream << final_sep;	165✔
128	} else {
129	stream << sep;	165✔
130	}
131	}
132
133	stream << *it;	315✔
134	}
135
136	return stream.str();	226✔
137	}	113✔
138		7✔
139	template<typename T>
140	std::string
141	join_text(const std::vector<T>& values, std::string_view sep)	101✔
142	{	7✔
143	return join_text(values, sep, sep);	189✔
144	}	45✔
145		32✔
146	/**	15✔
147	* Wrapper around 'indent_lines' and 'wrap_text'.
148	*	15✔
149	* Defaults to 78 character columns, with 4 character indentation, and no ljust,
150	* corresponding to function defaults. Unlike simply combining 'indent_lines'
151	* and 'wrap_text', the 'format' function preserves newlines, allowing
152	* paragraphs to be printed easily.	15✔
153	*/
154	class cli_formatter
155	{	14✔
156	public:	7✔
157	/** Creates formatter using default parameters (see above). */	×
158	cli_formatter();
159
160	/** Include (or not) indentation on the first line of output. */
161	cli_formatter& set_indent_first_line(bool value);	×
162	/** Maximum number of columns in each line in output. */	×
163	cli_formatter& set_column_width(size_t value);	×
164	/** Number of spaces to indent line 2+ in each paragraph. */	×
165	cli_formatter& set_ljust(size_t value);	×
166	/** Fixed indentation for each line (see also set_indent_first_line). */
167	cli_formatter& set_indent(size_t value);	×
168
169	/** Formats string using the current settings. */
170	std::string format(std::string_view value) const;
171		×
172	private:
173	//! Specifies whether or not to indent the first line of output.
174	bool m_indent_first;	×
175	//! Number of spaces to indent the 2+ lines in each paragraph.
176	size_t m_ljust;
177	//! The maximum number of columns (in characters).
178	size_t m_columns;
179	//! The number of spaces to indent each line (see also m_indent_first_line)	4✔
180	size_t m_indentation;
181	};	4✔
182
183	/** Escapes a string to make it safe to use in copy/pasted commands */
184	std::string
185	shell_escape(std::string_view s);
186
187	/**
188	* Escapes a string for use in logging; this is equivalent to shell_escape
189	* except that strings are always quoted for readability.
190	*/
191	std::string
192	log_escape(std::string_view s);
193
194	/** Escapes a full shell command using shell_escape */
195	std::string
196	shell_escape_command(const string_vec& v);
197
198	/** Adds thousand separators to a number */
199	std::string
200	format_thousand_sep(size_t count);
201
202	/** Rounds a number using K, M, etc. units. */
203	std::string
204	format_rough_number(size_t value, size_t out_digits = 3);
205
206	/** Formats a fraction, returning "NA" if denominator is 0 */
207	std::string
208	format_fraction(uint64_t num, uint64_t denom, size_t precision = 2);
209
210	/** Formats a percentage, returning "NA" if denominator is 0 */
211	std::string
212	format_percentage(uint64_t num, uint64_t denom, size_t precision = 1);
213
214	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #39

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