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OpenMS
2.6.0
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65 template <
typename ValueType,
66 typename DecompositionValueType>
Definition: Residue.h:170
Base class for TOPP applications.
Definition: TOPPBase.h:144
DecompositionValueType decomposition_value_type
Definition: MassDecomposer.h:78
virtual decomposition_value_type getNumberOfDecompositions(value_type mass)=0
A more convenient string class.
Definition: String.h:59
Invalid conversion exception.
Definition: Exception.h:362
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
ValueType value_type
Definition: MassDecomposer.h:73
virtual decomposition_type getDecomposition(value_type mass)=0
String toString() const
returns the peptide as string with modifications embedded in brackets
std::vector< decomposition_value_type > decomposition_type
Definition: MassDecomposer.h:83
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
#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
virtual decompositions_type getAllDecompositions(value_type mass)=0
virtual ~MassDecomposer()
Definition: MassDecomposer.h:93
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Representation of a residue.
Definition: Residue.h:62
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:54
virtual bool exist(value_type mass)=0
An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet).
Definition: MassDecomposer.h:67
String & unquote(char q='"', QuotingMethod method = ESCAPE)
Reverses changes made by the quote method.
ResidueType
Definition: Residue.h:151
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
std::vector< decomposition_type > decompositions_type
Definition: MassDecomposer.h:88
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
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 String getResidueTypeName(const ResidueType res_type)
returns the ion name given as a residue type
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
double getAverageWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
returns the average weight of the peptide
Int toInt() const
Conversion to int.