OpenMS  3.0.0
File.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Andreas Bertsch, Chris Bielow, Marc Sturm $
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34 
35 #pragma once
36 
38 #include <OpenMS/config.h>
39 #include <cstdlib>
40 #include <mutex>
41 
42 
43 namespace OpenMS
44 {
45  class Param;
46  class TOPPBase;
47 
53  class OPENMS_DLLAPI File
54  {
55 public:
56 
57  friend class TOPPBase;
58 
64  class OPENMS_DLLAPI TempDir
65  {
66  public:
67 
70  TempDir(bool keep_dir = false);
71 
73  ~TempDir();
74 
76  TempDir(const TempDir&) = delete;
77  TempDir& operator=(const TempDir&) = delete;
78  TempDir(TempDir&&) = delete;
79  TempDir& operator=(TempDir&&) = delete;
80 
82  const String& getPath() const;
83 
84  private:
86  bool keep_dir_;
87  };
88 
93  static String getExecutablePath();
94 
96  static bool exists(const String& file);
97 
99  static bool empty(const String& file);
100 
102  static bool executable(const String& file);
103 
118  static bool rename(const String& from, const String& to, bool overwrite_existing = true, bool verbose = true);
119 
136  enum class CopyOptions {OVERWRITE,SKIP,CANCEL};
137  static bool copyDirRecursively(const QString &from_dir, const QString &to_dir, File::CopyOptions option = CopyOptions::OVERWRITE);
138 
144  static bool remove(const String& file);
145 
147  static bool removeDirRecursively(const String& dir_name);
148 
150  static bool removeDir(const QString& dir_name);
151 
153  static String absolutePath(const String& file);
154 
158  static String basename(const String& file);
159 
164  static String path(const String& file);
165 
167  static bool readable(const String& file);
168 
170  static bool writable(const String& file);
171 
173  static bool isDirectory(const String& path);
174 
185  static String find(const String& filename, StringList directories = StringList());
186 
193  static bool fileList(const String& dir, const String& file_pattern, StringList& output, bool full_path = false);
194 
211  static String findDoc(const String& filename);
212 
219  static String getUniqueName(bool include_hostname = true);
220 
222  static String getOpenMSDataPath();
223 
225  static String getOpenMSHomePath();
226 
232  static String getTempDirectory();
233 
239  static String getUserDirectory();
240 
246  static Param getSystemParameters();
247 
251  static String findDatabase(const String& db_name);
252 
263  static StringList getPathLocations(const String& path = std::getenv("PATH"));
264 
278  static bool findExecutable(OpenMS::String& exe_filename);
279 
286  static String findSiblingTOPPExecutable(const String& toolName);
287 
304  static String getTemporaryFile(const String& alternative_file = "");
305 
326  static bool validateMatchingFileNames(const StringList& sl1, const StringList& sl2, bool basename = true, bool ignore_extension = true, bool strict = false);
327 private:
328 
330  static Param getSystemParameterDefaults_();
331 
333  static bool isOpenMSDataPath_(const String& path);
334 
335 #ifdef OPENMS_WINDOWSPLATFORM
336 
346  static StringList executableExtensions_(const String& ext = std::getenv("PATHEXT"));
347 #endif
348 
353  {
354  public:
355  TemporaryFiles_(const TemporaryFiles_&) = delete; // copy is forbidden
356  TemporaryFiles_& operator=(const TemporaryFiles_&) = delete;
357  TemporaryFiles_();
359  String newFile();
360 
361  ~TemporaryFiles_();
362  private:
364  std::mutex mtx_;
365  };
366 
367 
370  };
371 }
372 
OpenMS::File::TempDir::keep_dir_
bool keep_dir_
Definition: File.h:86
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::PeptideProteinResolution
Resolves shared peptides based on protein scores.
Definition: PeptideProteinResolution.h:79
OpenMS::File
Basic file handling operations.
Definition: File.h:53
OpenMS::File::TemporaryFiles_
Internal helper class, which holds temporary filenames and deletes these files at program exit.
Definition: File.h:352
Size
OpenMS::ProteinIdentification::getIndistinguishableProteins
const std::vector< ProteinGroup > & getIndistinguishableProteins() const
Returns the indistinguishable proteins.
Param
@TODO loop over all runs
Definition: BayesianProteinInferenceAlgorithm.h:98
OpenMS::IdXMLFile::store
void store(const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
OpenMS::PeptideHit::getSequence
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
OpenMS::ProteinIdentification::setInferenceEngine
void setInferenceEngine(const String &search_engine)
Sets the inference engine type.
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not fo...
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ProteinIdentification::ProteinGroup::accessions
std::vector< String > accessions
Accessions of (indistinguishable) proteins that belong to the same group.
Definition: ProteinIdentification.h:134
Int
IdXMLFile.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:58
OpenMS::DataValue::toString
String toString(bool full_precision=true) const
Conversion to String full_precision Controls number of fractional digits for all double types or list...
OpenMS::ProteinIdentification::findHit
std::vector< ProteinHit >::iterator findHit(const String &accession)
Finds a protein hit by accession (returns past-the-end iterator if not found)
OpenMS::AASequence::toUnmodifiedString
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
OpenMS::File::getUniqueName
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::File::temporary_files_
static TemporaryFiles_ temporary_files_
private list of temporary filenames, which are deleted upon program exit
Definition: File.h:369
OpenMS::DateTime::now
static DateTime now()
Returns the current date and time.
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::String::chop
String chop(Size n) const
Returns a substring where n characters were removed from the end of the string.
OpenMS::StringUtils::hasPrefix
static bool hasPrefix(const String &this_s, const String &string)
Definition: StringUtilsSimple.h:111
OpenMS::ProteinIdentification::getIdentifier
const String & getIdentifier() const
Returns the identifier.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::IDFilter::removeUnreferencedProteins
static void removeUnreferencedProteins(ConsensusMap &cmap, bool include_unassigned)
OpenMS::StringUtils::remove
static String & remove(String &this_s, char what)
Definition: StringUtilsSimple.h:595
OpenMS::MetaInfoInterface::setMetaValue
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
OpenMS::ProteinIdentification::setScoreType
void setScoreType(const String &type)
Sets the protein score type.
OpenMS::ProteinIdentification::getHits
const std::vector< ProteinHit > & getHits() const
Returns the protein hits.
QProcess
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
OpenMS::String::split
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
OpenMS::File::CopyOptions
CopyOptions
Copy directory recursively.
Definition: File.h:136
OpenMS::File::TemporaryFiles_::mtx_
std::mutex mtx_
Definition: File.h:364
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::String::hasSuffix
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
OpenMS::PeptideHit::extractProteinAccessionsSet
std::set< String > extractProteinAccessionsSet() const
extracts the set of non-empty protein accessions from peptide evidences
OpenMS::PeptideProteinResolution::resolveGraph
void resolveGraph(ProteinIdentification &protein, std::vector< PeptideIdentification > &peptides)
OpenMS::AASequence::empty
bool empty() const
check if sequence is empty
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ProteinIdentification::insertHit
void insertHit(const ProteinHit &input)
Appends a protein hit.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::PeptideProteinResolution::buildGraph
void buildGraph(ProteinIdentification &protein, const std::vector< PeptideIdentification > &peptides, bool skip_sort=false)
OpenMS::ProteinIdentification::setSearchEngine
void setSearchEngine(const String &search_engine)
Sets the search engine type.
OpenMS::Internal::ClassTest::verbose
int verbose
Verbosity level ( "-v" is 1 and "-V" is 2 )
OpenMS::File::TemporaryFiles_::filenames_
StringList filenames_
Definition: File.h:363
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::File::TempDir
Class representing a temporary directory.
Definition: File.h:64
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::String::substr
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
OpenMS::PeptideHit::getScore
double getScore() const
returns the PSM score
OpenMS::StringUtils::number
static String number(double d, UInt n)
Definition: StringUtils.h:196
OpenMS::ProteinIdentification::setHigherScoreBetter
void setHigherScoreBetter(bool higher_is_better)
Sets the orientation of the score (is higher better?)
OpenMS::ProteinIdentification::setDateTime
void setDateTime(const DateTime &date)
Sets the date of the protein identification run.
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::File::getTempDirectory
static String getTempDirectory()
OpenMS::String::remove
String & remove(char what)
Remove all occurrences of the character what.
OpenMS::ProteinIdentification::getScoreType
const String & getScoreType() const
Returns the protein score type.
IDFilter.h
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:186
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::ProteinIdentification::setIdentifier
void setIdentifier(const String &id)
Sets the identifier.
OpenMS::File::removeDirRecursively
static bool removeDirRecursively(const String &dir_name)
Removes the subdirectories of the specified directory (absolute path). Returns true if successful.
OpenMS::ProteinIdentification::ProteinGroup::probability
double probability
Probability of this group.
Definition: ProteinIdentification.h:131
File.h
PeptideProteinResolution.h
TOPPBase.h
OpenMS::File::TempDir::temp_dir_
String temp_dir_
Definition: File.h:85
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::String::toLower
String & toLower()
Converts the string to lowercase.
OpenMS::ProteinIdentification::ProteinGroup
Bundles multiple (e.g. indistinguishable) proteins in a group.
Definition: ProteinIdentification.h:117
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55
StringListUtils.h