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OpenMS
2.6.0
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173 public std::binary_function<typename Cmp::first_argument_type *, typename Cmp::second_argument_type *, typename Cmp::result_type>
182 template <
typename T1,
typename T2>
183 typename Cmp::result_type
186 return cmp_(*left, *right);
224 std::binary_function<typename Cmp::second_argument_type, typename Cmp::first_argument_type, typename Cmp::result_type>
233 template <
typename T1,
typename T2>
234 typename Cmp::result_type
237 return cmp_(right, left);
274 template <
typename Cmp1,
typename Cmp2>
276 std::binary_function<typename Cmp1::first_argument_type, typename Cmp1::second_argument_type, bool>
281 template <
typename T1,
typename T2>
285 if (
cmp1_(left, right))
291 if (
cmp1_(right, left))
297 return cmp2_(left, right);
315 template <
typename Cmp1,
typename Cmp2>
324 template <
typename PairType>
326 std::binary_function<PairType, PairType, bool>
328 bool operator()(
const PairType & left,
const PairType & right)
const
330 return left.first < right.first;
338 template <
typename PairType>
340 std::binary_function<PairType, PairType, bool>
342 bool operator()(
const PairType & left,
const PairType & right)
const
344 return left.second < right.second;
352 template <
typename PairType>
354 std::binary_function<PairType, PairType, bool>
356 bool operator()(
const PairType & left,
const PairType & right)
const
358 return left.first > right.first;
366 template <
typename PairType>
368 std::binary_function<PairType, PairType, bool>
370 bool operator()(
const PairType & left,
const PairType & right)
const
372 return left.second > right.second;
380 template <
typename PairType>
382 std::binary_function<PairType, PairType, bool>
384 bool operator()(
const PairType & left,
const PairType & right)
const
386 return left.first == right.first;
394 template <
typename PairType>
396 std::binary_function<PairType, PairType, bool>
398 bool operator()(
const PairType & left,
const PairType & right)
const
400 return left.second == right.second;
412 template <
typename CompareType>
414 public std::binary_function<CompareType, CompareType, bool>
424 CompareType diff = fabs(i - j);
PointerComparator(PointerComparator const &pCmp)
Definition: ComparatorUtils.h:175
static bool rename(const String &from, const String &to, bool overwrite_existing=true, bool verbose=true)
Rename a file.
EqualInTolerance(CompareType &c)
Definition: ComparatorUtils.h:418
Base class for TOPP applications.
Definition: TOPPBase.h:144
const Cmp1 & cmp1_
Definition: ComparatorUtils.h:303
Class for comparison of std::pair using first ONLY e.g. for use with std::sort.
Definition: ComparatorUtils.h:325
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
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.
Representation of a modification.
Definition: ResidueModification.h:76
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
const String & getOneLetterCode() const
returns the name as one letter code (String of size 1)
std::streampos findIndexListOffset(String filename, int buffersize=1023)
Tries to extract the indexList offset from an indexedmzML.
ReverseComparator< Cmp > reverseComparator(Cmp const &cmp)
Make-function to create a ReverseComparator from another comparator without the need to specify the t...
Definition: ComparatorUtils.h:260
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
bool operator()(T1 left, T2 right) const
Definition: ComparatorUtils.h:283
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Wrapper that takes a comparator for `something' and makes a comparator for pointers to `something' ou...
Definition: ComparatorUtils.h:172
Definition: ResidueModification.h:99
Class for comparison of std::pair using first ONLY e.g. for use with std::sort.
Definition: ComparatorUtils.h:353
Class for comparison of std::pair using second ONLY e.g. for use with std::sort.
Definition: ComparatorUtils.h:339
Class for comparison of std::pair using second ONLY e.g. for use with std::sort.
Definition: ComparatorUtils.h:367
ReverseComparator(Cmp const &cmp=Cmp())
Definition: ComparatorUtils.h:230
static ResidueDB * getInstance()
this member function serves as a replacement of the constructor
void getAllCometNames(std::vector< String > &all_names) const
returns all the enzyme names available for Comet
bool operator()(const PairType &left, const PairType &right) const
Definition: ComparatorUtils.h:384
ReverseComparator(ReverseComparator const &cmp)
Definition: ComparatorUtils.h:227
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
#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
Definition: ResidueModification.h:100
You can set more CMake variables adding< code > linking and adding include directories</td ></tr >< tr >< td valign="top"> c CMAKE_PREFIX_PATH</td >< td > Additional search path for the contrib libraries[MacOSX only] If you want to use libraries installed via Homebrew or MacPorts you might need to provide the corresponding paths< code > DCMAKE_PREFIX_PATH
Definition: common-cmake-parameters.doxygen:19
Struct for comparison of std::pair using second ONLY e.g. for use with std::sort.
Definition: ComparatorUtils.h:395
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:193
Cmp::result_type operator()(T1 left, T2 right) const
Definition: ComparatorUtils.h:184
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
std::map< UInt, std::pair< Size, Size > > getCentroidInfo(const String &filename)
Gets info on centroidedness of spectra based on their metadata.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
CompareType & tolerance
Definition: ComparatorUtils.h:416
char getOrigin() const
Returns the origin (i.e. modified amino acid)
Representation of a residue.
Definition: Residue.h:62
const Cmp & cmp_
Definition: ComparatorUtils.h:241
You can set more CMake variables adding< code > linking and adding include directories</td ></tr >< tr >< td valign="top"> c CMAKE_PREFIX_PATH</td >< td > Additional search path for the contrib libraries[MacOSX only] If you want to use libraries installed via Homebrew or MacPorts you might need to provide the corresponding paths< code > this flag can be used to disable those parts of the documentation and the tests that need an X Server(Default:On)</td ></tr >< tr >< td valign
PointerComparator(Cmp const &cmp=Cmp())
Definition: ComparatorUtils.h:178
Definition: ResidueModification.h:98
You can set more CMake variables adding< code > DVARIABLE
Definition: common-cmake-parameters.doxygen:1
Definition: ResidueModification.h:101
double getDiffMonoMass() const
returns the diff monoisotopic mass, or 0.0 if not set
Class for comparison of std::pair using first ONLY e.g. for use with std::sort.
Definition: ComparatorUtils.h:381
const Cmp2 & cmp2_
Definition: ComparatorUtils.h:304
Struct for binary predicate to consider equality with a certain tolerance.
Definition: ComparatorUtils.h:413
bool operator()(const PairType &left, const PairType &right) const
Definition: ComparatorUtils.h:398
QString toQString() const
Conversion to Qt QString.
bool operator()(CompareType i, CompareType j)
Definition: ComparatorUtils.h:422
bool find(TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:884
Cmp::result_type operator()(T1 left, T2 right) const
Definition: ComparatorUtils.h:235
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
bool operator()(const PairType &left, const PairType &right) const
Definition: ComparatorUtils.h:370
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
const std::string ISOTOPE_ERROR
LexicographicComparator(Cmp1 const &cmp1=Cmp1(), Cmp2 const &cmp2=Cmp2())
Definition: ComparatorUtils.h:278
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
Class representing a temporary directory.
Definition: File.h:63
static const String & getTemporaryFile(const String &alternative_file="")
Obtain a temporary filename, ensuring automatic deletion upon exit.
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:240
bool operator()(const PairType &left, const PairType &right) const
Definition: ComparatorUtils.h:356
static String findDatabase(const String &db_name)
void load(const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name, const SpectrumMetaDataLookup &lookup)
Loads peptide sequences with modifications out of a PepXML file.
bool operator()(const PairType &left, const PairType &right) const
Definition: ComparatorUtils.h:342
static bool readable(const String &file)
Return true if the file exists and is readable.
ExitCodes
Exit codes.
Definition: TOPPBase.h:149
static String stripExtension(const String &filename)
If filename contains an extension, it will be removed (including the '.'). Special extensions,...
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
bool operator()(const PairType &left, const PairType &right) const
Definition: ComparatorUtils.h:328
const String & getName() const
returns the name of the residue
Used to load and store PepXML files.
Definition: PepXMLFile.h:63
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
const Residue * getResidue(const String &name) const
returns a pointer to the residue with name, 3 letter code or 1 letter code name
PointerComparator< Cmp > pointerComparator(Cmp const &cmp)
Make-function to create a PointerComparator from another comparator without the need to specify the t...
Definition: ComparatorUtils.h:209
LexicographicComparator< Cmp1, Cmp2 > lexicographicComparator(Cmp1 const &cmp1, Cmp2 const &cmp2)
Make-function to create a LexicographicComparator from two other comparators without the need to spec...
Definition: ComparatorUtils.h:316
File is empty.
Definition: Exception.h:594
A class to analyze indexedmzML files and extract the offsets of individual tags.
Definition: IndexedMzMLDecoder.h:58
Wrapper that reverses (exchanges) the two arguments of a comparator. Normally you should use the make...
Definition: ComparatorUtils.h:223
TermSpecificity getTermSpecificity() const
returns terminal specificity
A wrapper class that combines two comparators lexicographically. Normally you should use the make-fun...
Definition: ComparatorUtils.h:275
static void writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
Writes all parameters to meta values.
Used to load and store idXML files.
Definition: IdXMLFile.h:63
String & toLower()
Converts the string to lowercase.
const Cmp & cmp_
Definition: ComparatorUtils.h:190