OpenMS  3.0.0
MassDecomposer.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Anton Pervukhin <Anton.Pervukhin@CeBiTec.Uni-Bielefeld.DE> $
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34 //
35 
36 #pragma once
37 
38 #include <vector>
39 
40 namespace OpenMS
41 {
42 
43  namespace ims
44  {
65  template <typename ValueType,
66  typename DecompositionValueType>
68  {
69 public:
73  typedef ValueType value_type;
74 
78  typedef DecompositionValueType decomposition_value_type;
79 
83  typedef std::vector<decomposition_value_type> decomposition_type;
84 
88  typedef std::vector<decomposition_type> decompositions_type;
89 
93  virtual ~MassDecomposer(){}
94 
101  virtual bool exist(value_type mass) = 0;
102 
110 
119 
127 
128  };
129 
130  } // namespace ims
131 } // namespace OpenMS
132 
LogStream.h
OpenMS::Residue::SizeOfResidueType
Definition: Residue.h:170
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
Size
OpenMS::ims::MassDecomposer::decomposition_value_type
DecompositionValueType decomposition_value_type
Definition: MassDecomposer.h:78
OpenMS::ims::MassDecomposer::getNumberOfDecompositions
virtual decomposition_value_type getNumberOfDecompositions(value_type mass)=0
OpenMS::String
A more convenient string class.
Definition: String.h:58
Int
OpenMS::Exception::ConversionError
Invalid conversion exception.
Definition: Exception.h:354
OpenMS::AASequence::getMonoWeight
double getMonoWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
OpenMS::ims::MassDecomposer::value_type
ValueType value_type
Definition: MassDecomposer.h:73
OpenMS::ims::MassDecomposer::getDecomposition
virtual decomposition_type getDecomposition(value_type mass)=0
OpenMS::AASequence::toString
String toString() const
returns the peptide as string with modifications embedded in brackets
OpenMS::ims::MassDecomposer::decomposition_type
std::vector< decomposition_value_type > decomposition_type
Definition: MassDecomposer.h:83
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OPENMS_LOG_WARN
#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
OpenMS::ims::MassDecomposer::getAllDecompositions
virtual decompositions_type getAllDecompositions(value_type mass)=0
OpenMS::ims::MassDecomposer::~MassDecomposer
virtual ~MassDecomposer()
Definition: MassDecomposer.h:93
ListUtils.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Residue
Representation of an amino acid residue.
Definition: Residue.h:62
OpenMS::SVOutStream
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:56
OpenMS::ims::MassDecomposer::exist
virtual bool exist(value_type mass)=0
OpenMS::ims::MassDecomposer
An interface to handle decomposing of integer values/masses over a set of integer weights (alphabet).
Definition: MassDecomposer.h:67
OpenMS::String::unquote
String & unquote(char q='"', QuotingMethod method = ESCAPE)
Reverses changes made by the quote method.
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:151
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::ims::MassDecomposer::decompositions_type
std::vector< decomposition_type > decompositions_type
Definition: MassDecomposer.h:88
SVOutStream.h
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::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
AASequence.h
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::Residue::getResidueTypeName
static String getResidueTypeName(const ResidueType res_type)
returns the ion name given as a residue type
OpenMS::StringUtils::prefix
static String prefix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:147
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::AASequence::getAverageWeight
double getAverageWeight(Residue::ResidueType type=Residue::Full, Int charge=0) const
returns the average weight of the peptide
OpenMS::String::toInt
Int toInt() const
Conversion to int.
File.h
TOPPBase.h