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OpenMS
2.5.0
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static DateTime now()
Returns the current date and time.
#define SEP
Definition: DigestorMotif.cpp:49
static FileTypes::Type getTypeByFileName(const String &filename)
Determines the file type from a file name.
bool readNext(FASTAEntry &protein)
Reads the next FASTA entry from file.
void setHits(const std::vector< PeptideHit > &hits)
Sets the peptide hits.
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
void writeEnd()
Closes the file (flush). Called implicitly when FASTAFile object does out of scope.
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
void writeStart(const String &filename)
Prepares a FASTA file given by 'filename' for streamed writing using writeNext().
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
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
A container for features.
Definition: FeatureMap.h:95
Representation of a protein hit.
Definition: ProteinHit.h:57
void setIdentifier(const String &id)
sets the identifier
static String typeToName(Type type)
Returns the name/extension of the type.
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
Stores elements.
Definition: ElementDB.h:69
void insertHit(const PeptideHit &hit)
Appends a peptide hit.
Base class for TOPP applications.
Definition: TOPPBase.h:144
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:60
String description
Definition: FASTAFile.h:79
DateTime Class.
Definition: DateTime.h:54
void setAccession(const String &accession)
sets the accession of the protein
FASTA file (.fasta)
Definition: FileTypes.h:92
Unknown file extension.
Definition: FileTypes.h:60
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
SignedSize getNumberOf(const Element *element) const
returns the number of atoms for a certain element (can be negative)
Protease digestion_enzyme
The cleavage site information in details (from ProteaseDB)
Definition: ProteinIdentification.h:236
void readStart(const String &filename)
Prepares a FASTA file given by 'filename' for streamed reading using readNext().
void setSequence(const AASequence &sequence)
sets the peptide sequence
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
void setProteinAccession(const String &s)
set the protein accession the peptide matches to. If not available set to empty string.
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
String sequence
Definition: FASTAFile.h:80
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
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.
Type
Actual file types enum.
Definition: FileTypes.h:58
Used to load and store idXML files.
Definition: IdXMLFile.h:63
void getAllNames(std::vector< String > &all_names) const
returns all the enzyme names (does NOT include synonym names)
Definition: DigestionEnzymeDB.h:122
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
void writeNext(const FASTAEntry &protein)
Stores the data given by protein. Call writeStart() once before calling writeNext().
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
void setPeptideEvidences(const std::vector< PeptideEvidence > &peptide_evidences)
set information on peptides (potentially) identified by this PSM
A more convenient string class.
Definition: String.h:58
Representation of a peptide hit.
Definition: PeptideHit.h:54
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.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Simulates protein digestion.
Definition: DigestSimulation.h:55
static const ElementDB * getInstance()
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void get(UInt &month, UInt &day, UInt &year, UInt &hour, UInt &minute, UInt &second) const
Fills the arguments with the date and the time.
void setSequence(const String &sequence)
sets the protein sequence
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
const DigestionEnzymeType * getEnzyme(const String &name) const
Definition: DigestionEnzymeDB.h:98
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
static Type nameToType(const String &name)
Converts a file type name into a Type.
Representation of an element.
Definition: Element.h:53
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
String identifier
Definition: FASTAFile.h:78