OpenMS  3.0.0
CommonDefs.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
37 
38 namespace OpenMS
39 {
40 
46  #define CONNECTCAST(class,func,args) static_cast<void(class::*)args>(&class::func)
47 
48 
50  enum class WidgetHeader
51  {
54  };
55 
56 }
DefaultParamHandler.h
OpenMS::File::rename
static bool rename(const String &from, const String &to, bool overwrite_existing=true, bool verbose=true)
Rename a file.
Size
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
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::ResidueModification
Representation of a modification on an amino acid residue.
Definition: ResidueModification.h:78
OpenMS::DigestionEnzymeDB::getInstance
static InstanceType * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Residue::getOneLetterCode
const String & getOneLetterCode() const
returns the name as one letter code (String of size 1)
OpenMS::IndexedMzMLDecoder::findIndexListOffset
std::streampos findIndexListOffset(String filename, int buffersize=1023)
Tries to extract the indexList offset from an indexedmzML.
OpenMS::PepXMLFile::setPreferredFixedModifications
void setPreferredFixedModifications(const std::vector< const ResidueModification * > &mods)
sets the preferred fixed modifications
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
SearchEngineBase.h
IdXMLFile.h
OpenMS::Constants::c
const double c
Definition: Constants.h:209
OpenMS::ResidueModification::N_TERM
The modification can only be N-terminal on the peptide.
Definition: ResidueModification.h:101
OpenMS::ResidueDB::getInstance
static ResidueDB * getInstance()
singleton
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
ResidueDB.h
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::ResidueModification::PROTEIN_C_TERM
The modification can only be protein C-terminal (on a C-terminal peptide)
Definition: ResidueModification.h:102
DCMAKE_PREFIX_PATH
You can set more CMake variables adding< code > linking and adding include directories</td ></tr >< tr >< td valign="top"> c CMAKE_PREFIX_PATH</td >< td > Additional search path for the contrib libraries[MacOSX only] If you want to use libraries installed via Homebrew or MacPorts you might need to provide the corresponding paths< code > DCMAKE_PREFIX_PATH
Definition: common-cmake-parameters.doxygen:19
OpenMS::ListUtils::concatenate
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:209
OpenMS::ModificationsDB::getInstance
static ModificationsDB * getInstance()
Returns a pointer to the modifications DB (singleton)
OpenMS::WidgetHeader::VISIBLE_ONLY
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ResidueModification::getOrigin
char getOrigin() const
Returns the origin (i.e. modified amino acid)
ProteaseDB.h
OpenMS::Residue
Representation of an amino acid residue.
Definition: Residue.h:62
Server
You can set more CMake variables adding< code > linking and adding include directories</td ></tr >< tr >< td valign="top"> c CMAKE_PREFIX_PATH</td >< td > Additional search path for the contrib libraries[MacOSX only] If you want to use libraries installed via Homebrew or MacPorts you might need to provide the corresponding paths< code > this flag can be used to disable those parts of the documentation and the tests that need an X Server(Default:On)</td ></tr >< tr >< td valign
OpenMS::ResidueModification::C_TERM
The modification can only be C-terminal on the peptide.
Definition: ResidueModification.h:100
DVARIABLE
You can set more CMake variables adding< code > DVARIABLE
Definition: common-cmake-parameters.doxygen:1
OpenMS::ResidueModification::PROTEIN_N_TERM
The modification can only be protein N-terminal (on a N-terminal peptide)
Definition: ResidueModification.h:103
OpenMS::ResidueModification::getDiffMonoMass
double getDiffMonoMass() const
returns the diff monoisotopic mass, or 0.0 if not set
IndexedMzMLDecoder.h
OpenMS::WidgetHeader
WidgetHeader
Enum to decide which headers(=column) names should be get/set in a table/tree widget.
Definition: CommonDefs.h:50
PepXMLFile.h
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::SearchEngineBase
Base class for Search Engine Adapters.
Definition: SearchEngineBase.h:54
ModificationsDB.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::Constants::UserParam::ISOTOPE_ERROR
const std::string ISOTOPE_ERROR
Definition: Constants.h:327
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::File::TempDir
Class representing a temporary directory.
Definition: File.h:64
OpenMS::PlainMSDataWritingConsumer
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:240
OpenMS::PeptideIndexing
Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds ...
Definition: PeptideIndexing.h:113
OpenMS::File::getTemporaryFile
static String getTemporaryFile(const String &alternative_file="")
Obtain a temporary filename, ensuring automatic deletion upon exit.
OpenMS::TOPPBase::ExitCodes
ExitCodes
Exit codes.
Definition: TOPPBase.h:152
PeptideIndexing.h
OpenMS::FileHandler::stripExtension
static String stripExtension(const String &filename)
If filename contains an extension, it will be removed (including the '.'). Special extensions,...
OpenMS::ModificationsDB::getAllSearchModifications
void getAllSearchModifications(std::vector< String > &modifications) const
Collects all modifications that can be used for identification searches.
OpenMS::AA
Definition: AhoCorasickAmbiguous.h:124
OpenMS::Residue::getName
const String & getName() const
returns the name of the residue
OpenMS::PepXMLFile
Used to load and store PepXML files.
Definition: PepXMLFile.h:63
OpenMS::WidgetHeader::WITH_INVISIBLE
ResidueModification.h
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::ResidueDB::getResidue
const Residue * getResidue(const String &name) const
returns a pointer to the residue with name, 3 letter code or 1 letter code name
MSDataWritingConsumer.h
OpenMS::IndexedMzMLDecoder
A class to analyze indexedmzML files and extract the offsets of individual tags.
Definition: IndexedMzMLDecoder.h:58
OpenMS::ResidueModification::getTermSpecificity
TermSpecificity getTermSpecificity() const
returns terminal specificity
OpenMS::DefaultParamHandler::writeParametersToMetaValues
static void writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
Writes all parameters to meta values.
File.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::String::toLower
String & toLower()
Converts the string to lowercase.