OpenMS  3.0.0
DigestSimulation.h
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31 // $Maintainer: Chris Bielow$
32 // $Authors: Stephan Aiche, Chris Bielow$
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34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42 
55  class OPENMS_DLLAPI DigestSimulation :
56  public DefaultParamHandler
57  {
58 
59 public:
65 
67  DigestSimulation(const DigestSimulation& source);
68 
70  ~DigestSimulation() override;
72 
74  DigestSimulation& operator=(const DigestSimulation& source);
75 
76 
86  void digest(SimTypes::FeatureMapSim& feature_map);
87 
88 private:
90  void setDefaultParams_();
91 
92  };
93 
94 }
95 
DefaultParamHandler.h
OpenMS::EmpiricalFormula::getNumberOf
SignedSize getNumberOf(const Element *element) const
returns the number of atoms for a certain element (can be negative)
OpenMS::ProteinIdentification::SearchParameters::digestion_enzyme
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:273
OpenMS::ElementDB::getInstance
static ElementDB * getInstance()
OpenMS::ElementDB
Singleton that stores elements and isotopes.
Definition: ElementDB.h:69
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
FileHandler.h
SimTypes.h
Size
OpenMS::PeptideHit::setPeptideEvidences
void setPeptideEvidences(const std::vector< PeptideEvidence > &peptide_evidences)
set information on peptides (potentially) identified by this PSM
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::ProteinHit::setSequence
void setSequence(const String &sequence)
sets the protein sequence
OpenMS::ProteaseDigestion::setEnzyme
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
OpenMS::PeptideIdentification::insertHit
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
OpenMS::FASTAFile::FASTAEntry::identifier
String identifier
Definition: FASTAFile.h:73
OpenMS::DigestionEnzymeDB::getInstance
static InstanceType * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::Element
Representation of an element.
Definition: Element.h:57
OpenMS::PeptideIdentification::setIdentifier
void setIdentifier(const String &id)
sets the identifier which links this PI to its corresponding ProteinIdentification
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::FileHandler::getTypeByFileName
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
OpenMS::FASTAFile::FASTAEntry::sequence
String sequence
Definition: FASTAFile.h:75
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::PeptideEvidence::setProteinAccession
void setProteinAccession(const String &s)
set the protein accession the peptide matches to. If not available set to empty string.
OpenMS::FASTAFile::FASTAEntry::description
String description
Definition: FASTAFile.h:74
IdXMLFile.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:58
SEP
#define SEP
Definition: DigestorMotif.cpp:49
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
OpenMS::FileTypes::FASTA
FASTA file (.fasta)
Definition: FileTypes.h:91
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence) The first String corresponds to the identifie...
Definition: FASTAFile.h:71
OpenMS::EnzymaticDigestion::setMissedCleavages
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
OpenMS::PeptideIdentification::setHits
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::DateTime::now
static DateTime now()
Returns the current date and time.
Element.h
OpenMS::ProteinHit::setAccession
void setAccession(const String &accession)
sets the accession of the protein
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::DateTime::get
void get(UInt &month, UInt &day, UInt &year, UInt &hour, UInt &minute, UInt &second) const
Fills the arguments with the date and the time.
ProteaseDigestion.h
ProteaseDB.h
FASTAFile.h
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
ProteinIdentification.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::PeptideEvidence
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
OpenMS::precisionWrapper
const PrecisionWrapper< FloatingPointType > precisionWrapper(const FloatingPointType rhs)
Wrapper function that sets the appropriate precision for output temporarily. The original precision i...
Definition: PrecisionWrapper.h:95
OpenMS::IntensityAveragingMethod::MIN
OpenMS::ProteaseDigestion::digest
Size digest(const AASequence &protein, std::vector< AASequence > &output, Size min_length=1, Size max_length=0) const
: Performs the enzymatic digestion of a protein.
OpenMS::FASTAFile::writeNext
void writeNext(const FASTAEntry &protein)
Stores the data given by protein. Call writeStart() once before calling writeNext()....
OpenMS::FASTAFile::writeEnd
void writeEnd()
Closes the file (flush). Called implicitly when FASTAFile object goes out of scope.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::FASTAFile::writeStart
void writeStart(const String &filename)
Prepares a FASTA file given by 'filename' for streamed writing using writeNext().
OpenMS::PeptideHit::setSequence
void setSequence(const AASequence &sequence)
sets the peptide sequence
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::ProteaseDigestion
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:59
OpenMS::FASTAFile::readNext
bool readNext(FASTAEntry &protein)
Reads the next FASTA entry from file. If you want to read all entries in one go, use load().
OpenMS::FASTAFile::readStart
void readStart(const String &filename)
Prepares a FASTA file given by 'filename' for streamed reading using readNext().
OpenMS::FASTAFile::load
void load(const String &filename, std::vector< FASTAEntry > &data) const
loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than r...
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
ElementDB.h
OpenMS::FilterLayout::BOTH
combine COMPACT and ONE_BY_ONE
OpenMS::FileTypes::nameToType
static Type nameToType(const String &name)
OpenMS::IntensityAveragingMethod::MAX
OpenMS::DigestSimulation
Simulates protein digestion.
Definition: DigestSimulation.h:55
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::AASequence::fromString
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:58
TOPPBase.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55