| OpenMS 2.5.0

File.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Andreas Bertsch, Chris Bielow, Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/StringListUtils.h>
38 #include <OpenMS/config.h>
39 #include <cstdlib>
40
41
42 namespace OpenMS
43 {
44 class Param;
45 class TOPPBase;
46
52 class OPENMS_DLLAPI File
53 {
54 public:
55
56 friend class TOPPBase;
57
62 static String getExecutablePath();
63
65 static bool exists(const String& file);
66
68 static bool empty(const String& file);
69
84 static bool rename(const String& from, const String& to, bool overwrite_existing = true, bool verbose = true);
85
102 enum class CopyOptions {OVERWRITE,SKIP,CANCEL};
103 static bool copyDirRecursively(const QString &from_dir, const QString &to_dir, File::CopyOptions option = CopyOptions::OVERWRITE);
104
110 static bool remove(const String& file);
111
113 static bool removeDirRecursively(const String& dir_name);
114
116 static bool removeDir(const QString& dir_name);
117
119 static String absolutePath(const String& file);
120
122 static String basename(const String& file);
123
125 static String path(const String& file);
126
134 static String removeExtension(const String& file);
135
137 static bool readable(const String& file);
138
140 static bool writable(const String& file);
141
143 static bool isDirectory(const String& path);
144
155 static String find(const String& filename, StringList directories = StringList());
156
163 static bool fileList(const String& dir, const String& file_pattern, StringList& output, bool full_path = false);
164
181 static String findDoc(const String& filename);
182
189 static String getUniqueName(bool include_hostname = true);
190
192 static String getOpenMSDataPath();
193
195 static String getOpenMSHomePath();
196
198 static String getTempDirectory();
199
205 static String getUserDirectory();
206
212 static Param getSystemParameters();
213
217 static String findDatabase(const String& db_name);
218
229 static StringList getPathLocations(const String& path = std::getenv("PATH"));
230
244 static bool findExecutable(OpenMS::String& exe_filename);
245
252 static String findSiblingTOPPExecutable(const String& toolName);
253
270 static const String& getTemporaryFile(const String& alternative_file = "");
271
272 private:
273
275 static Param getSystemParameterDefaults_();
276
278 static bool isOpenMSDataPath_(const String& path);
279
280 #ifdef OPENMS_WINDOWSPLATFORM
281
291 static StringList executableExtensions_(const String& ext = std::getenv("PATHEXT"));
292 #endif
293
297 class TemporaryFiles_
298 {
299 public:
300 TemporaryFiles_();
302 const String& newFile();
303
304 ~TemporaryFiles_();
305 private:
306 TemporaryFiles_(const TemporaryFiles_&) = delete; // copy is forbidden
307 TemporaryFiles_& operator=(const TemporaryFiles_&) = delete;
308 StringList filenames_;
309 };
310
311
313 static TemporaryFiles_ temporary_files_;
314
315 };
316
317 }
318
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::File::CopyOptions
CopyOptions
Copy directory recursively.
Definition: File.h:102
OpenMS::File
Basic file handling operations.
Definition: File.h:52
OpenMS::Internal::ClassTest::verbose
int verbose
Verbosity level ( "-v" is 1 and "-V" is 2 )
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
OpenMS::File::TemporaryFiles_
Internal helper class, which holds temporary filenames and deletes these files at program exit...
Definition: File.h:297
StringListUtils.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
seqan::find
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::File::TemporaryFiles_::filenames_
StringList filenames_
Definition: File.h:308
OpenMS::File::temporary_files_
static TemporaryFiles_ temporary_files_
private list of temporary filenames, which are deleted upon program exit
Definition: File.h:313