OpenMS  2.6.0
OMSSACSVFile.h
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34 
35 #pragma once
36 
39 
40 #include <vector>
41 
42 
43 namespace OpenMS
44 {
45  class String;
54  class OPENMS_DLLAPI OMSSACSVFile
55  {
56 public:
57 
59  OMSSACSVFile();
61  virtual ~OMSSACSVFile();
62 
73  void load(const String & filename, ProteinIdentification & protein_identification, std::vector<PeptideIdentification> & id_data) const;
74  };
75 } // namespace OpenMS
76 
MSDataTransformingConsumer.h
DefaultParamHandler.h
OpenMS::ProteinIdentification::SearchParameters::digestion_enzyme
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
OpenMS::ProgressLogger::setProgress
void setProgress(SignedSize value) const
Sets the current progress.
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
OpenMS::OMSSACSVFile
File adapter for OMSSACSV files.
Definition: OMSSACSVFile.h:54
FileHandler.h
TextFile.h
OpenMS::SpectrumMetaDataLookup::addMissingSpectrumReferences
static bool addMissingSpectrumReferences(std::vector< PeptideIdentification > &peptides, const String &filename, bool stop_on_error=false, bool override_spectra_data=false, bool override_spectra_references=false, std::vector< ProteinIdentification > proteins=std::vector< ProteinIdentification >())
Add missing "spectrum_reference"s to peptide identifications based on raw data.
OpenMS::PeakFileOptions::setMetadataOnly
void setMetadataOnly(bool only)
sets whether or not to load only meta data
OpenMS::ResidueModification::getNeutralLossDiffFormulas
const std::vector< EmpiricalFormula > & getNeutralLossDiffFormulas() const
returns the neutral loss diff formula (if available)
ListUtilsIO.h
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::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::ProteaseDB::getAllOMSSANames
void getAllOMSSANames(std::vector< String > &all_names) const
returns all the enzyme names available for OMSSA
OpenMS::ResidueModification::ANYWHERE
Definition: ResidueModification.h:97
OpenMS::DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >::getInstance
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::ModificationDefinitionsSet
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
OpenMS::ProteinIdentification::PeakMassType
PeakMassType
Peak mass type.
Definition: ProteinIdentification.h:247
OpenMS::AASequence::end
Iterator end()
Definition: AASequence.h:585
OpenMS::Map::has
bool has(const Key &key) const
Test whether the map contains the given key.
Definition: Map.h:108
OpenMS::ResidueModification::getDiffAverageMass
double getDiffAverageMass() const
returns the difference average mass, or 0.0 if not set
OpenMS::ProteinIdentification::setSearchEngineVersion
void setSearchEngineVersion(const String &search_engine_version)
Sets the search engine version.
OpenMS::ProteinIdentification::SearchParameters::missed_cleavages
UInt missed_cleavages
The number of allowed missed cleavages.
Definition: ProteinIdentification.h:268
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:59
MzMLFile.h
OpenMS::OMSSAXMLFile
Used to load OMSSAXML files.
Definition: OMSSAXMLFile.h:60
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
OpenMS::Constants::c
const double c
OpenMS::ResidueModification::N_TERM
Definition: ResidueModification.h:99
OpenMS::ProteinIdentification::MONOISOTOPIC
Definition: ProteinIdentification.h:249
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
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::operator<
bool operator<(const QTCluster &q1, const QTCluster &q2)
SpectrumMetaDataLookup.h
SpectrumSettings.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
ListUtils.h
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance_ppm
bool fragment_mass_tolerance_ppm
Mass tolerance unit of fragment ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:270
OpenMS::File::find
static String find(const String &filename, StringList directories=StringList())
Looks up the location of the file filename.
OpenMS::ListUtils::concatenate
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
OpenMS::AASequence::Iterator
Iterator class for AASequence.
Definition: AASequence.h:256
OpenMS::AASequence::setModification
void setModification(Size index, const String &modification)
OpenMS::ModificationsDB::getInstance
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
OpenMS::ProteinIdentification::getIdentifier
const String & getIdentifier() const
Returns the identifier.
OpenMS::ProteinIdentification::SearchParameters::charges
String charges
The allowed charges for the search.
Definition: ProteinIdentification.h:264
OpenMS::DigestionEnzymeDB::getEnzyme
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:98
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProteinIdentification::AVERAGE
Definition: ProteinIdentification.h:250
OpenMS::ProteinIdentification::SearchParameters::variable_modifications
std::vector< String > variable_modifications
Allowed variable modifications.
Definition: ProteinIdentification.h:267
OpenMS::ProteinIdentification::SearchParameters::mass_type
PeakMassType mass_type
Mass type of the peaks.
Definition: ProteinIdentification.h:265
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::ResidueModification::getOrigin
char getOrigin() const
Returns the origin (i.e. modified amino acid)
ProteaseDB.h
OpenMS::ProteinIdentification::setPrimaryMSRunPath
void setPrimaryMSRunPath(const StringList &s, bool raw=false)
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
ProgressLogger.h
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::ResidueModification::C_TERM
Definition: ResidueModification.h:98
int
OpenMS::ProteinIdentification::SearchParameters::db
String db
The used database.
Definition: ProteinIdentification.h:261
OpenMS::AASequence::setNTerminalModification
void setNTerminalModification(const String &modification)
OpenMS::ProteinIdentification::getHits
const std::vector< ProteinHit > & getHits() const
Returns the protein hits.
QProcess
ModificationDefinitionsSet.h
ProteinIdentification.h
OpenMS::ResidueModification::getDiffMonoMass
double getDiffMonoMass() const
returns the diff monoisotopic mass, or 0.0 if not set
OpenMS::AASequence::setCTerminalModification
void setCTerminalModification(const String &modification)
OpenMS::MSDataTransformingConsumer
Transforming consumer of MS data.
Definition: MSDataTransformingConsumer.h:58
OMSSAXMLFile.h
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
MascotGenericFile.h
OpenMS::MascotGenericFile
Read/write Mascot generic files (MGF).
Definition: MascotGenericFile.h:61
OpenMS::ProteinIdentification::setSearchParameters
void setSearchParameters(const SearchParameters &search_parameters)
Sets the search parameters.
OpenMS::ProteinIdentification::SearchParameters::fragment_mass_tolerance
double fragment_mass_tolerance
Mass tolerance of fragment ions (Dalton or ppm)
Definition: ProteinIdentification.h:269
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::ProteinIdentification::SearchParameters::fixed_modifications
std::vector< String > fixed_modifications
Used fixed modifications.
Definition: ProteinIdentification.h:266
ModificationsDB.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::ProteinIdentification::setSearchEngine
void setSearchEngine(const String &search_engine)
Sets the search engine type.
MSExperiment.h
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance
double precursor_mass_tolerance
Mass tolerance of precursor ions (Dalton or ppm)
Definition: ProteinIdentification.h:271
OpenMS::OMSSAXMLFile::setModificationDefinitionsSet
void setModificationDefinitionsSet(const ModificationDefinitionsSet &rhs)
sets the valid modifications
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::absolutePath
static String absolutePath(const String &file)
Replaces the relative path in the argument with the absolute path.
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
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::File::findDatabase
static String findDatabase(const String &db_name)
OpenMS::MzMLFile::transform
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false)
Transforms a map while loading using the supplied MSDataConsumer.
OpenMS::File::readable
static bool readable(const String &file)
Return true if the file exists and is readable.
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::OpenMS_Log_info
Logger::LogStream OpenMS_Log_info
Global static instance of a LogStream to capture messages classified as information....
OpenMS::ModificationsDB::getAllSearchModifications
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
OpenMS::ProteinIdentification::SearchParameters::precursor_mass_tolerance_ppm
bool precursor_mass_tolerance_ppm
Mass tolerance unit of precursor ions (true: ppm, false: Dalton)
Definition: ProteinIdentification.h:272
OpenMS::File::getTempDirectory
static String getTempDirectory()
The current OpenMS temporary data path (for temporary files)
OpenMS::AASequence::begin
Iterator begin()
Definition: AASequence.h:581
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
OpenMS::Exception::FileEmpty
File is empty.
Definition: Exception.h:594
PeptideIdentification.h
OpenMS::ProteinIdentification::setHits
void setHits(const std::vector< ProteinHit > &hits)
Sets the protein hits.
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::String::suffix
String suffix(SizeType length) const
returns the suffix of length length
OpenMS::OMSSAXMLFile::load
void load(const String &filename, ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &id_data, bool load_proteins=true, bool load_empty_hits=true)
loads data from a OMSSAXML file
OpenMS::TextFile::ConstIterator
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
OpenMS::MzMLFile::setOptions
void setOptions(const PeakFileOptions &)
set options for loading/storing
OpenMS::ResidueModification::getTermSpecificity
TermSpecificity getTermSpecificity() const
returns terminal specificity
OpenMS::ProteinIdentification::SearchParameters::taxonomy
String taxonomy
The taxonomy restriction.
Definition: ProteinIdentification.h:263
OpenMS::ModificationsDB::getModification
const ResidueModification * getModification(Size index) const
Returns the modification with the given index. note: out-of-bounds check is only performed in debug m...
File.h
OpenMS::Internal::ClassTest::infile
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
OpenMS::DefaultParamHandler::writeParametersToMetaValues
static void writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
Writes all parameters to meta values.
TOPPBase.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63