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OpenMS
2.5.0
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73 void store(
const String& filename);
83 void handlePTMs(
const String& modification_line,
const String& modifications_filename,
const bool monoisotopic);
90 const String& getSpectra()
const;
91 void setSpectra(
const String& spectra);
98 const String& getDb()
const;
99 void setDb(
const String& db);
102 const String& getEnzyme()
const;
103 void setEnzyme(
const String& enzyme);
106 Int getModificationsPerPeptide()
const;
107 void setModificationsPerPeptide(
Int modifications_per_peptide);
114 UInt getBlind()
const;
115 void setBlind(
UInt blind);
122 float getMaxPTMsize()
const;
123 void setMaxPTMsize(
float maxptmsize);
130 float getPrecursorMassTolerance()
const;
131 void setPrecursorMassTolerance(
float precursor_mass_tolerance);
138 float getPeakMassTolerance()
const;
139 void setPeakMassTolerance(
float peak_mass_tolerance);
142 UInt getMulticharge()
const;
143 void setMulticharge(
UInt multicharge);
146 const String& getInstrument()
const;
147 void setInstrument(
const String& instrument);
150 Int getTagCount()
const;
151 void setTagCount(
Int TagCount);
154 const std::map<String, std::vector<String> >& getModifications()
const;
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:236
Base class for TOPP applications.
Definition: TOPPBase.h:144
Int getModificationsPerPeptide() const
Number of PTMs permitted in a single peptide.
void setDb(const String &db)
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.
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
std::map< String, std::vector< String > > PTMname_residues_mass_type_
the modification names map to the affected residues, the mass change and the type
Definition: InspectInfile.h:182
A more convenient string class.
Definition: String.h:58
void handlePTMs(const String &modification_line, const String &modifications_filename, const bool monoisotopic)
File not found exception.
Definition: Exception.h:523
void getExperiment(PeakMap &exp, String &type, const String &in_filename)
Definition: InspectOutfile.h:141
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< Size > getWantedRecords(const String &result_filename, double p_value_threshold)
void setBlind(UInt blind)
bool getSearchEngineAndVersion(const String &cmd_output, ProteinIdentification &protein_identification)
float maxptmsize_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:169
void generateTrieDB(const String &source_database_filename, const String &database_filename, const String &index_filename, bool append=false, const String species="")
Definition: ProteinIdentification.h:213
Int modifications_per_peptide_
allowed number of modifications per peptide
Definition: InspectInfile.h:164
void setMaxPTMsize(float maxptmsize)
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:52
float getPrecursorMassTolerance() const
Specifies the parent mass tolerance, in Daltons.
#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
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
UInt blind_
Definition: InspectInfile.h:166
void load(const String &filename, std::map< String, std::pair< String, String > > &ptm_informations)
Loads the information of a PTMXML file.
void setPeakMassTolerance(float peak_mass_tolerance)
void store(const String &filename)
static bool writable(const String &file)
Return true if the file is writable.
Used to load and store PTMXML files.
Definition: PTMXMLFile.h:52
void setEnzyme(const String &enzyme)
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:98
static bool exists(const String &file)
Method used to test if a file exists.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Definition: ProteinIdentification.h:214
const String & getEnzyme() const
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
void setPrecursorMassTolerance(float precursor_mass_tolerance)
float getPeakMassTolerance() const
How far b and y peaks can be shifted from their expected masses.
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:228
Representation of an Inspect outfile.
Definition: InspectOutfile.h:57
void store(const String &filename, const MapType &map) const
Stores a map in a MzXML file.
String spectra_
Specifies a spectrum file to search.
Definition: InspectInfile.h:158
void setModificationsPerPeptide(Int modifications_per_peptide)
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
Int getTagCount() const
Number of tags to generate.
QString toQString() const
Conversion to Qt QString.
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
void setSearchParameters(const SearchParameters &search_parameters)
Sets the search parameters.
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:232
UInt multicharge_
Definition: InspectInfile.h:175
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void setTagCount(Int TagCount)
String enzyme_
Specifies the name of a enzyme. "Trypsin", "None", and "Chymotrypsin" are the available values.
Definition: InspectInfile.h:162
float peak_mass_tolerance_
How far b and y peaks can be shifted from their expected masses. Default is 0.5. Higher values produc...
Definition: InspectInfile.h:173
Int tag_count_
Number of tags to generate. <0 is not set.
Definition: InspectInfile.h:180
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void setSearchEngine(const String &search_engine)
Sets the search engine type.
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:234
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
Parse Error exception.
Definition: Exception.h:622
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...
static bool readable(const String &file)
Return true if the file exists and is readable.
static bool empty(const String &file)
Return true if the file does not exist or the file is empty.
float precursor_mass_tolerance_
Specifies the parent mass tolerance, in Daltons. A candidate's flanking mass can differ from the tag'...
Definition: InspectInfile.h:171
std::vector< Size > load(const String &result_filename, std::vector< PeptideIdentification > &peptide_identifications, ProteinIdentification &protein_identification, const double p_value_threshold, const String &database_filename="")
const char * getMessage() const noexcept
Returns the message.
void setSpectra(const String &spectra)
const String & getDb() const
Specifies the name of a database (.trie file) to search.
void concatenate(StringIterator first, StringIterator last, const String &glue="")
Concatenates all elements from first to last-1 and inserts glue between the elements.
Definition: String.h:466
String db_
Specifies the name of a database (.trie file) to search. The .trie file contains one or more protein ...
Definition: InspectInfile.h:160
String & ensureLastChar(char end)
Makes sure the string ends with the character end.
void setInstrument(const String &instrument)
float getMaxPTMsize() const
the maximum modification size (in Da) to consider in a blind search
String instrument_
0 - false, 1 - true, 2 - not set
Definition: InspectInfile.h:178
const std::map< String, std::vector< String > > & getModifications() const
return the modifications (the modification names map to the affected residues, the mass change and th...
void compressTrieDB(const String &database_filename, const String &index_filename, std::vector< Size > &wanted_records, const String &snd_database_filename, const String &snd_index_filename, bool append=false)
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
Inspect input file adapter.
Definition: InspectInfile.h:50
File not readable exception.
Definition: Exception.h:537
void setMulticharge(UInt multicharge)
Used to load and store idXML files.
Definition: IdXMLFile.h:63