common-cmake-parameters.doxygen File Reference

Functions
scripts buildsystems vcpkg cmake</code > See ref	install_vcpkg_without (Default:Off;the presets set On)</td ></tr >< tr >< th valign
see ref	verifying_public_headers (Default:Off)</td ></tr >< tr >< th valign
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	d</code > (and< code >.d.zip</code >) input to CometAdapter
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > SimpleSearchEngine and	TransitionListEvidenceFilter (Default:On)</td ></tr >< tr >< th valign
does not apply for XCode or VS Should be either	Release (optimization enabled) or 'Debug'(debug info and precondition/postcondition checks enabled). @n The default is< code >Release</code >.</td ></tr >< tr >< th valign
the folder that contains the< code > dotnet</code > host and the< code > shared</code > sub	directory (e.g.< code >export DOTNET_ROOT=/usr/share/dotnet</code >) &mdash
so the runtime can be found The managed half of the	bridge (< code >ThermoWrapperManaged.dll</code >, its< code >runtimeconfig.json</code > and the Thermo CommonCore assemblies) is installed both next to the bridge library and into< code >share/OpenMS/openms_thermo_bridge/managed</code >

Variables
You can set more CMake variables adding< code >	DVARIABLE
You can set more CMake variables adding< code > CMake needs the vcpkg	toolchain
You can set more CMake variables adding< code > CMake needs the vcpkg or pass< code >	DCMAKE_TOOLCHAIN_FILE =&lt
vcpkg root &	gt
if none is	found
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	FeatureFinderIdentification
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	FeatureFinderLFQ
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	FeatureFinderMetaboIdent
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	FileConverter
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	IonMobilityBinning
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	MetaboliteSpectralMatcher
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	NucleicAcidSearchEngine
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	OpenSwathPeakMapExtractor
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	OpenSwathWorkflow
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	PeakPickerIM
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	ProSE
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	ProteomicsLFQ
if none is it is fetched and built automatically from source via CMake FetchContent Adds< code >	SageAdapter
with	vcpkg
with they also need the< code > lp coin</code > or< code > lp glpk</code > feature in< code > VCPKG_MANIFEST_FEATURES</code >< code >	AUTO</code >
with they also need the< code > lp coin</code > or< code > lp glpk</code > feature in< code > VCPKG_MANIFEST_FEATURES</code >< code > the former	default
with they also need the< code > lp coin</code > or< code > lp glpk</code > feature in< code > VCPKG_MANIFEST_FEATURES</code >< code > the former is an alias for< code > HIGHS</code ></td ></tr >< tr >< th valign="top">	WITH_THERMO_RAW
with they also need the< code > lp coin</code > or< code > lp glpk</code > feature in< code > VCPKG_MANIFEST_FEATURES</code >< code > the former is an alias for< code > HIGHS</code ></td ></tr >< tr >< th valign="top"> set the< code > DOTNET_ROOT</code > environment variable to that directory &	mdash
OpenMS looks in the< code > OPENMS_THERMO_MANAGED_DIR</code > environment variable	first
OpenMS looks in the< code > OPENMS_THERMO_MANAGED_DIR</code > environment variable then in the share	directory
OpenMS looks in the< code > OPENMS_THERMO_MANAGED_DIR</code > environment variable then in the share then next to the bridge library To build without a NuGet GitHub round trip for those	assemblies
OpenMS looks in the< code > OPENMS_THERMO_MANAGED_DIR</code > environment variable then in the share then next to the bridge library To build without a NuGet GitHub round trip for those pass the bridge s own< code >	DOPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR

Function Documentation

bridge()

so the runtime can be found The managed half of the bridge	(	< code >ThermoWrapperManaged.dll</code >	,
		its< code >runtimeconfig.json</code > and the Thermo CommonCore	assemblies
	)

d</code >()

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > d</code >

(

and< code >.d.zip</code >

)

directory()

the folder that contains the< code > dotnet</code > host and the< code > shared</code > sub directory

(

e.g.< code >export

DOTNET_ROOT = /usr/share/dotnet</code >

)

&

install_vcpkg_without()

scripts buildsystems vcpkg cmake</code > See ref install_vcpkg_without

(

Default:Off;the presets set

On

)

Release()

does not apply for XCode or VS Should be either Release

(

optimization

enabled

)

TransitionListEvidenceFilter()

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > SimpleSearchEngine and TransitionListEvidenceFilter

(

Default:On

)

verifying_public_headers()

see ref verifying_public_headers

(

Default:Off

)

Variable Documentation

assemblies

OpenMS looks in the<code> OPENMS_THERMO_MANAGED_DIR</code> environment variable then in the share then next to the bridge library To build without a NuGet GitHub round trip for those assemblies

AUTO</code >

with they also need the<code> lp coin</code> or<code> lp glpk</code> feature in<code> VCPKG_MANIFEST_FEATURES</code><code> AUTO</code >

DCMAKE_TOOLCHAIN_FILE

You can set more CMake variables adding<code> CMake needs the vcpkg or pass<code> DCMAKE_TOOLCHAIN_FILE =&lt

default

with they also need the<code> lp coin</code> or<code> lp glpk</code> feature in<code> VCPKG_MANIFEST_FEATURES</code><code> the former default

directory

OpenMS looks in the<code> OPENMS_THERMO_MANAGED_DIR</code> environment variable then in the share directory

DOPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR

OpenMS looks in the<code> OPENMS_THERMO_MANAGED_DIR</code> environment variable then in the share then next to the bridge library To build without a NuGet GitHub round trip for those pass the bridge s own<code> DOPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR

Initial value:

=/path/to/extracted-zip</code> (the zip is
    published with every openms-thermo-bridge release) or
    <code>-DOPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED=ON</code>

DVARIABLE

You can set more CMake variables adding<code> DVARIABLE

Initial value:

=VALUE</code> options when calling CMake.
<br>
The most important CMake variables are:
<br>
 
<table style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;">
  <tr>
    <th valign="top">OPENMS_USE_VCPKG=On/Off</th>
    <td>Take the third-party libraries from vcpkg (On) or from system packages and
    <code>CMAKE_PREFIX_PATH</code> (Off). With On

FeatureFinderIdentification

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > FeatureFinderIdentification

FeatureFinderLFQ

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > FeatureFinderLFQ

FeatureFinderMetaboIdent

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > FeatureFinderMetaboIdent

FileConverter

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > FileConverter

first

OpenMS looks in the<code> OPENMS_THERMO_MANAGED_DIR</code> environment variable first

Referenced by ExposedVector< VectorElement >::assign(), DIAQCMetrics::compute(), MRMTransitionGroupPicker::computeQuality_(), OpenMS::StringUtils::concatenate(), OpenMS::StringUtils::concatenate(), ConstRefVector< ContainerT >::erase(), MSExperiment::extractXICs(), SavitzkyGolayFilter::filter(), ScoredProcessingResult::getMostRecentScore(), SpectrumAlignment::getSpectrumAlignment(), CrossValidation::gridSearch1D(), Mobilogram::insert(), GaussFilterAlgorithm::integrate_(), ScoreType::isBetterScore(), SpectraMerger::mergeSpectra_(), FragmentIndex::Peptide::Span::operator std::pair< uint16_t, uint16_t >(), SpectraMerger::SpectraDistance_::operator()(), TransformationModel::DataPoint::operator<(), TransformationModel::DataPoint::operator==(), RandomShuffler::portable_random_shuffle(), NucleicAcidSearchEngine::preprocessSpectra_(), OpenMS::Internal::ClassTest::detail::printValue(), OpenMS::printXLRegionDetails(), OpenMS::printXLSiteDetails(), LinearResampling::raster(), and LinearResamplerAlign::raster_align().

found

if none is found

Referenced by KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >::_M_find(), KDTree< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >::_M_find_exact(), RangeManager< RangeBases >::assignUnsafe(), RangeManager< RangeBases >::clampToUnsafe(), FullSwathFileConsumer::consumeSpectrum(), RNAPrecursorCorrector::correct(), RangeManager< RangeBases >::extendUnsafe(), OpenMS::NuXLPresets::getPresets(), NeighborSeq::isNeighborPeptide(), IDFilter::HasMetaValue< HitType >::operator()(), IDFilter::HasMaxMetaValue< HitType >::operator()(), IDFilter::HasMinMetaValue< HitType >::operator()(), and RangeManager< RangeBases >::pushIntoUnsafe().

gt

vcpkg root& gt

IonMobilityBinning

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > IonMobilityBinning

mdash

with they also need the<code> lp coin</code> or<code> lp glpk</code> feature in<code> VCPKG_MANIFEST_FEATURES</code><code> the former is an alias for<code> HIGHS</code></td></tr><tr><th valign="top"> set the<code> DOTNET_ROOT</code> environment variable to that directory& mdash

MetaboliteSpectralMatcher

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > MetaboliteSpectralMatcher

NucleicAcidSearchEngine

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > NucleicAcidSearchEngine

OpenSwathPeakMapExtractor

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > OpenSwathPeakMapExtractor

OpenSwathWorkflow

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > OpenSwathWorkflow

PeakPickerIM

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > PeakPickerIM

ProSE

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > ProSE

ProteomicsLFQ

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > ProteomicsLFQ

SageAdapter

if none is it is fetched and built automatically from source via CMake FetchContent Adds< code > SageAdapter

toolchain

You can set more CMake variables adding<code> CMake needs the vcpkg toolchain

vcpkg

with vcpkg

WITH_THERMO_RAW

with they also need the<code> lp coin</code> or<code> lp glpk</code> feature in<code> VCPKG_MANIFEST_FEATURES</code><code> the former is an alias for<code> HIGHS</code></td></tr><tr><th valign="top"> WITH_THERMO_RAW

Initial value:

=On/Off</td>
    <td>Enable native reading of Thermo Fisher RAW files via the openms-thermo-bridge C++/.NET library
    (fetched automatically via CMake FetchContent from GitHub).
    Requires a .NET runtime to be present at run time so that the managed bridge DLLs can be loaded.
    Install the .NET 8 runtime from <a href="https://dotnet.microsoft.com/download">https:
    or install the <code>dotnet-runtime-8.0</code> package from your distribution's package manager.
    On Windows and macOS the required <code>nethost</code> library is bundled with the .NET SDK/runtime installer.
    On Linux you may need to install the additional <code>libnethost-dev</code> (Debian/Ubuntu) or
    <code>dotnet-runtime-8.0</code> package explicitly.
    At run time the bridge's <code>nethost</code>/<code>hostfxr</code> locates the installed runtime
    automatically when .NET sits in a standard location. If you installed .NET to a non-default
    directory (for example via the <code>dotnet-install.sh</code> script or an xcopy install of the
    runtime)