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OpenMS
2.5.0
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Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:236
Stores elements.
Definition: ElementDB.h:69
Base class for TOPP applications.
Definition: TOPPBase.h:144
void setPeptideEvidences(const std::vector< PeptideEvidence > &peptide_evidences)
set information on peptides (potentially) identified by this PSM
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.
void setSequence(const String &sequence)
sets the protein sequence
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
String identifier
Definition: FASTAFile.h:78
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
Representation of an element.
Definition: Element.h:53
void setIdentifier(const String &id)
sets the identifier
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
String sequence
Definition: FASTAFile.h:80
A more convenient string class.
Definition: String.h:58
void setProteinAccession(const String &s)
set the protein accession the peptide matches to. If not available set to empty string.
void getAllNames(std::vector< String > &all_names) const
returns all the enzyme names (does NOT include synonym names)
Definition: DigestionEnzymeDB.h:122
String description
Definition: FASTAFile.h:79
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Representation of a protein hit.
Definition: ProteinHit.h:57
#define SEP
Definition: DigestorMotif.cpp:49
Unknown file extension.
Definition: FileTypes.h:60
FASTA file (.fasta)
Definition: FileTypes.h:92
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
static DateTime now()
Returns the current date and time.
void setAccession(const String &accession)
sets the accession of the protein
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:98
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void get(UInt &month, UInt &day, UInt &year, UInt &hour, UInt &minute, UInt &second) const
Fills the arguments with the date and the time.
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
Type
Actual file types enum.
Definition: FileTypes.h:58
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
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
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.
void writeNext(const FASTAEntry &protein)
Stores the data given by protein. Call writeStart() once before calling writeNext().
void writeEnd()
Closes the file (flush). Called implicitly when FASTAFile object does out of scope.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void writeStart(const String &filename)
Prepares a FASTA file given by 'filename' for streamed writing using writeNext().
void setSequence(const AASequence &sequence)
sets the peptide sequence
static const ElementDB * getInstance()
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
A container for features.
Definition: FeatureMap.h:95
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:60
bool readNext(FASTAEntry &protein)
Reads the next FASTA entry from file.
void readStart(const String &filename)
Prepares a FASTA file given by 'filename' for streamed reading using readNext().
static Type nameToType(const String &name)
Converts a file type name into a Type.
Simulates protein digestion.
Definition: DigestSimulation.h:55
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
DateTime Class.
Definition: DateTime.h:54
Used to load and store idXML files.
Definition: IdXMLFile.h:63
static String typeToName(Type type)
Returns the name/extension of the type.
Representation of a peptide hit.
Definition: PeptideHit.h:54