| OpenMS 2.5.0

Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
OpenMS::Internal Namespace Reference

Namespace used to hide implementation details from users. More...

## Namespaces

| ClassTest
| Namespace for class tests.
| SqliteHelper

## Classes

class | AcqusHandler
| Read-only acqus File handler for XMass Analysis. More...
class | AreaIterator
| Forward iterator for an area of peaks in an experiment. More...
class | CachedMzMLHandler
| An class that uses on-disk caching to read and write spectra and chromatograms. More...
class | DIntervalBase
| A base class for D-dimensional interval. More...
class | FidHandler
| Read-only fid File handler for XMass Analysis. More...
struct | FileMapping
| Maps input/output files to filenames for the external program. More...
class | IDBoostGraph
| Creates and maintains a boost graph based on the OpenMS ID datastructures. More...
class | IndexedMzMLHandler
| A low-level class to read an indexedmzML file. More...
class | IntensityIteratorWrapper
| An iterator wrapper to access peak intensities instead of the peak itself. More...
class | ListEditorDelegate
| Internal delegate class. More...
class | ListTable
struct | Looper
struct | Looper< grid_size, grid_size, EvalResult, Tuple, TupleTypes... >
struct | Looper< param_index, grid_size, EvalResult, Tuple, FirstTupleType, TupleTypes... >
struct | MappingParam
| Filename mappings for all input/output files. More...
class | MascotXMLHandler
| Handler that is used for parsing MascotXML data. More...
class | MessagePasserFactory
class | MzDataHandler
class | MzDataValidator
| Semantically validates MzXML files. More...
class | MzIdentMLDOMHandler
| XML DOM handler for MzIdentMLFile. More...
class | MzIdentMLHandler
| XML STREAM handler for MzIdentMLFile. More...
class | MzIdentMLValidator
| Semantically validates MzXML files. More...
class | MzMLHandler
| Handler for mzML file format. More...
class | MzMLHandlerHelper
| Helper for mzML file format. More...
class | MzMLSqliteHandler
| Sqlite handler for storing spectra and chromatograms in sqMass format. More...
class | MzMLSqliteSwathHandler
| Sqlite handler for SWATH data sets. More...
class | MzMLValidator
| Semantically validates MzXML files. More...
class | MzQuantMLHandler
| XML handler for MzQuantMLFile. More...
class | MzQuantMLValidator
| Semantically validates MzQuantML files. More...
class | MzXMLHandler
class | OpenMSLineEdit
| Custom QLineEdit which emits a signal when losing focus (such that we can commit its data) More...
struct | OpenMSOSInfo
class | ParamEditorDelegate
| Internal delegate class for QTreeWidget. More...
class | ParamTree
| QTreeWidget that emits a signal whenever a new row is selected. More...
class | ParamXMLHandler
| XML Handler for Param files. More...
class | PTMXMLHandler
| Handler that is used for parsing PTMXML data. More...
class | RNPxlFragmentAnnotationHelper
| Convenience functions to construct appealing fragment annotation strings and store them as PeptideHit::PeakAnnotation. More...
class | SemanticValidator
| Semantically validates XML files using CVMappings and a ControlledVocabulary. More...
class | Spectrum1DPrefDialog
| Preferences dialog for Spectrum1DWidget. More...
class | Spectrum2DPrefDialog
| Preferences dialog for Spectrum2DWidget. More...
class | Spectrum3DPrefDialog
| Preferences dialog for Spectrum3DWidget. More...
class | StringManager
struct | ToolDescription
class | ToolDescriptionHandler
| XML handler for ToolDescriptionFile. More...
struct | ToolDescriptionInternal
| ToolDescription Class. More...
struct | ToolExternalDetails
class | TOPPViewPrefDialog
| Preferences dialog for TOPPView. More...
class | TraMLHandler
| XML handler for TraMLFile. More...
class | TraMLValidator
| Semantically validates MzXML files. More...
class | UnimodXMLHandler
| Handler that is used for parsing XTandemXML data. More...
class | XMLFile
| Base class for loading/storing XML files that have a handler derived from XMLHandler. More...
class | XMLHandler
| Base class for XML handlers. More...
class | XQuestResultXMLHandler
| XMLHandler for the result files of XQuest. More...

## Typedefs

typedef PeakMap | MapType
| XML handler for MzDataFile. More...
typedef MSSpectrum | SpectrumType
typedef MSChromatogram | ChromatogramType

## Enumerations

enum | OpenMS_OS { OS_UNKNOWN, OS_MACOS, OS_WINDOWS, OS_LINUX }
enum | OpenMS_Architecture { ARCH_UNKNOWN, ARCH_32BIT, ARCH_64BIT }

## Functions

bool | PermutScoreComparator (const CompNovoIdentificationBase::Permut &p1, const CompNovoIdentificationBase::Permut &p2)
template<UInt D>
std::ostream & | operator<< (std::ostream &os, const DIntervalBase< D > &rhs)
| Print the contents to a stream. More...
template<typename IteratorT >
IntensityIteratorWrapper< IteratorT > | intensityIteratorWrapper (const IteratorT &rhs)
| make-function so that we need no write out all those type names to get the wrapped iterator. More...
String | encodeTab (const String &to_encode)
| Encodes tabs '' in the string as &#x9; and returns the encoded string. More...
static OpenMSOSInfo | getOSInfo ()
OpenMS_Architecture | getBinaryArchitecture ()

## Variables

const char * | OpenMS_locale
std::string | OpenMS_OSNames [] = {"unknown", "MacOS", "Windows", "Linux"}
std::string | OpenMS_ArchNames [] = {"unknown", "32 bit", "64 bit"}

## Detailed Description

Namespace used to hide implementation details from users.

## Class Documentation

## ◆ OpenMS::Internal::Looper

struct OpenMS::Internal::Looper

### template<size_t param_index, size_t grid_size, typename EvalResult, typename Tuple, typename... TupleTypes>
struct OpenMS::Internal::Looper< param_index, grid_size, EvalResult, Tuple, TupleTypes >

## ◆ OpenMS::Internal::ToolExternalDetails

struct OpenMS::Internal::ToolExternalDetails

Class Members
String | category |
String | commandline |
Param | param |
String | path | filename to external tool
String | text_fail |
String | text_finish |
String | text_startup |
MappingParam | tr_table |
String | working_directory | folder where the command will be executed from

## Typedef Documentation

## ◆ ChromatogramType

typedef MSChromatogram ChromatogramType

## ◆ MapType

typedef PeakMap MapType

XML handler for MzDataFile.

XML handlers for MzXMLFile.

MapType has to be a MSExperiment or have the same interface. Do not use this class. It is only needed in MzDataFile.

Improvement:
  Add implementation and tests of 'supDataArray' to store IntegerDataArray and StringDataArray of MSSpectrum (Hiwi)

MapType has to be a MSExperiment or have the same interface. Do not use this class. It is only needed in MzXMLFile.

## ◆ SpectrumType

typedef MSSpectrum SpectrumType

## Enumeration Type Documentation

## ◆ OpenMS_Architecture

enum OpenMS_Architecture

Enumerator
ARCH_UNKNOWN |
ARCH_32BIT |
ARCH_64BIT |

## ◆ OpenMS_OS

enum OpenMS_OS

Enumerator
OS_UNKNOWN |
OS_MACOS |
OS_WINDOWS |
OS_LINUX |

## Function Documentation

## ◆ encodeTab()

String OpenMS::Internal::encodeTab | ( | const String & | to_encode | ) |

Encodes tabs '' in the string as &#x9; and returns the encoded string.

Parameters

  to_encode | The String to encode.

Returns
  The encoded string.

## ◆ getBinaryArchitecture()

OpenMS_Architecture OpenMS::Internal::getBinaryArchitecture | ( |  | ) |

References ARCH_32BIT, ARCH_64BIT, and ARCH_UNKNOWN.

## ◆ getOSInfo()

static OpenMSOSInfo OpenMS::Internal::getOSInfo | ( |  | ) |

static

References OpenMSOSInfo::arch, ARCH_32BIT, ARCH_64BIT, OpenMSOSInfo::os, OS_LINUX, OS_MACOS, OpenMSOSInfo::os_version, and OS_WINDOWS.

## ◆ intensityIteratorWrapper()

IntensityIteratorWrapper<IteratorT> OpenMS::Internal::intensityIteratorWrapper | ( | const IteratorT & | rhs | ) |

make-function so that we need no write out all those type names to get the wrapped iterator.

Referenced by MorphologicalFilter::filter().

## ◆ operator<<()

std::ostream& OpenMS::Internal::operator<< | ( | std::ostream & | os,
|  | const DIntervalBase< D > & | rhs
| ) |  |

Print the contents to a stream.

References DIntervalBase< D >::minPosition().

## ◆ PermutScoreComparator()

bool OpenMS::Internal::PermutScoreComparator | ( | const CompNovoIdentificationBase::Permut & | p1,
|  | const CompNovoIdentificationBase::Permut & | p2
| ) |  |

## Variable Documentation

## ◆ OpenMS_ArchNames

std::string OpenMS_ArchNames[] = {"unknown", "32 bit", "64 bit"}

Referenced by OpenMSOSInfo::getArchAsString().

## ◆ OpenMS_locale

const char* OpenMS_locale

Used to set the locale to "C", to avoid problems on machines with incompatible locale settings (this overwrites the locale setting of the environment!)

## ◆ OpenMS_OSNames

std::string OpenMS_OSNames[] = {"unknown", "MacOS", "Windows", "Linux"}

Referenced by OpenMSOSInfo::getOSAsString().