Management and storage of parameters / INI files. More...

#include <OpenMS/DATASTRUCTURES/Param.h>

Classes
struct	ParamEntry
	Parameter entry used to store the actual information inside of a Param entry. More...

class	ParamIterator
	Forward const iterator for the Param class. More...

struct	ParamNode
	Node inside a Param object which is used to build the internal tree. More...

Public Member Functions
	Param ()
	Default constructor. More...

	Param (const Param &)=default
	Copy constructor. More...

	Param (Param &&)=default
	Move constructor. More...

	~Param ()
	Destructor. More...

Param &	operator= (const Param &)=default
	Assignment operator. More...

Param &	operator= (Param &&) &=default
	Move assignment operator. More...

bool	operator== (const Param &rhs) const
	Equality operator. More...

ParamIterator	begin () const
	Begin iterator for the internal tree. More...

ParamIterator	end () const
	End iterator for the internal tree. More...

Accessors for single parameters
void	setValue (const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
	Sets a value. More...

const DataValue &	getValue (const String &key) const
	Returns a value of a parameter. More...

const ParamEntry &	getEntry (const String &key) const
	Returns the whole parameter entry. More...

bool	exists (const String &key) const
	Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only) More...

ParamIterator	findFirst (const String &leaf) const
	Find leaf node by name (if it exists). More...

ParamIterator	findNext (const String &leaf, const ParamIterator &start_leaf) const
	Find next leaf node by name (if it exists), not considering the `start_leaf`. More...

Tags handling
void	addTag (const String &key, const String &tag)
	Adds the tag `tag` to the entry `key`. More...

void	addTags (const String &key, const StringList &tags)
	Adds the tags in the list `tags` to the entry `key`. More...

bool	hasTag (const String &key, const String &tag) const
	Returns if the parameter `key` has a tag. More...

StringList	getTags (const String &key) const
	Returns the tags of entry `key`. More...

void	clearTags (const String &key)
	Removes all tags from the entry `key`. More...

Descriptions handling
const String &	getDescription (const String &key) const
	Returns the description of a parameter. More...

void	setSectionDescription (const String &key, const String &description)
	Sets a description for an existing section. More...

const String &	getSectionDescription (const String &key) const
	Returns the description corresponding to the section with name `key`. More...

void	addSection (const String &key, const String &description)
	Adds a parameter section under the path `key` with the given `description`. More...

Manipulation of the whole parameter set
Size	size () const
	Returns the number of entries (leafs). More...

bool	empty () const
	Returns if there are no entries. More...

void	clear ()
	Deletes all entries. More...

void	insert (const String &prefix, const Param &param)

void	remove (const String &key)
	Remove the entry `key` or a section `key` (when suffix is ':') More...

void	removeAll (const String &prefix)
	Remove all entries that start with `prefix`. More...

Param	copy (const String &prefix, bool remove_prefix=false) const
	Returns a new Param object containing all entries that start with `prefix`. More...

Param	copySubset (const Param &subset) const
	Returns a new Param object containing all entries in the given subset. More...

bool	update (const Param &p_outdated, const bool add_unknown=false)
	Rescue parameter values from `p_outdated` to current param. More...

bool	update (const Param &p_outdated, const bool add_unknown, Logger::LogStream &stream)
	Rescue parameter values from `p_outdated` to current param. More...

bool	update (const Param &p_outdated, bool verbose, bool add_unknown, bool fail_on_invalid_values, bool fail_on_unknown_parameters, Logger::LogStream &stream)
	Rescue parameter values from `p_outdated` to current param. More...

void	merge (const Param &toMerge)
	Adds missing parameters from the given param `toMerge` to this param. Existing parameters will not be modified. More...

Default value handling
void	setDefaults (const Param &defaults, const String &prefix="", bool showMessage=false)
	Insert all values of `defaults` and adds the prefix `prefix`, if the values are not already set. More...

void	checkDefaults (const String &name, const Param &defaults, const String &prefix="") const
	Checks the current parameter entries against given `defaults`. More...

Restriction handling
void	setValidStrings (const String &key, const std::vector< String > &strings)
	Sets the valid strings for the parameter `key`. More...

void	setMinInt (const String &key, Int min)
	Sets the minimum value for the integer or integer list parameter `key`. More...

void	setMaxInt (const String &key, Int max)
	Sets the maximum value for the integer or integer list parameter `key`. More...

void	setMinFloat (const String &key, double min)
	Sets the minimum value for the floating point or floating point list parameter `key`. More...

void	setMaxFloat (const String &key, double max)
	Sets the maximum value for the floating point or floating point list parameter `key`. More...

Command line parsing
Param::ParamNode	root_
	Invisible root node that stores all the data. More...

void	parseCommandLine (const int argc, const char **argv, const String &prefix="")
	Parses command line arguments. More...

void	parseCommandLine (const int argc, const char **argv, const Map< String, String > &options_with_one_argument, const Map< String, String > &options_without_argument, const Map< String, String > &options_with_multiple_argument, const String &misc="misc", const String &unknown="unknown")
	Parses command line arguments to specified key locations. More...

ParamEntry &	getEntry_ (const String &key) const
	Returns a mutable reference to a parameter entry. More...

	Param (const Param::ParamNode &node)
	Constructor from a node which is used as root node. More...

Detailed Description

Management and storage of parameters / INI files.

This class provides a means to associate string names to int/double/string/StringList values. It allows for parameter hierarchies and to save/load the data as XML. Hierarchy levels are separated from each other by colons.
Example: 'common:file_options:default_file_open_path = /share/'

Each parameter and section has a description. Newline characters in the description are possible.

Each parameter can be annotated with an arbitrary number of tags. Tags must not contain comma characters!
E.g. the advanced tag indicates if this parameter is shown to all users or in advanced mode only.

See also: DefaultParamHandler

Constructor & Destructor Documentation

◆ Param() [1/4]

Param ( )

Default constructor.

◆ Param() [2/4]

Param ( const Param & )

default

Copy constructor.

◆ Param() [3/4]

Param ( Param && )

default

Move constructor.

◆ ~Param()

~Param ( )

Destructor.

◆ Param() [4/4]

Param ( const Param::ParamNode & node )

protected

Constructor from a node which is used as root node.

Member Function Documentation

◆ addSection()

void addSection	(	const String &	key,
		const String &	description
	)

Adds a parameter section under the path key with the given description.

If the section already exists, the description is only overwritten if not empty.

◆ addTag()

void addTag	(	const String &	key,
		const String &	tag
	)

Adds the tag tag to the entry key.

E.g. "advanced", "required", "input file", "output file"

Exceptions

Exception::ElementNotFound	is thrown if the parameter does not exists.
Exception::InvalidValue	is thrown if the tag contain a comma character.

◆ addTags()

void addTags	(	const String &	key,
		const StringList &	tags
	)

Adds the tags in the list tags to the entry key.

Exceptions

Exception::ElementNotFound	is thrown if the parameter does not exists.
Exception::InvalidValue	is thrown if a tag contain a comma character.

◆ begin()

ParamIterator begin ( ) const

Begin iterator for the internal tree.

Referenced by TOPPViewBase::loadPreferences(), main(), and DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::readEnzymesFromFile_().

◆ checkDefaults()

void checkDefaults	(	const String &	name,
		const Param &	defaults,
		const String &	prefix = `""`
	)		const

Checks the current parameter entries against given defaults.

Several checks are performed:

If a parameter is present for which no default value is specified, a warning is issued to os.
If the type of a parameter and its default do not match, an exception is thrown.
If a string parameter contains an invalid string, an exception is thrown.
If parameter entry is a string list, an exception is thrown, if one or more list members are invalid strings
If a numeric parameter is out of the valid range, an exception is thrown.
If entry is a numeric list an exception is thrown, if one or more list members are out of the valid range

Parameters

name	The name that is used in error messages.
defaults	The default values.
prefix	The prefix where to check for the defaults.

Warnings etc. will be send to OPENMS_LOG_WARN.

Exceptions

Exception::InvalidParameter is thrown if errors occur during the check

◆ clear()

void clear ( )

Deletes all entries.

Referenced by INIFileEditorWindow::openFile().

◆ clearTags()

void clearTags ( const String & key )

Removes all tags from the entry key.

Exceptions

Exception::ElementNotFound is thrown if the parameter does not exists.

◆ copy()

Param copy	(	const String &	prefix,
		bool	remove_prefix = `false`
	)		const

Returns a new Param object containing all entries that start with prefix.

Parameters

prefix	should contain a ':' at the end if you want to extract a subtree. Otherwise not only nodes, but as well values with that prefix are copied.
remove_prefix	indicates if the prefix is removed before adding entries to the new Param

Referenced by FeatureDistance::DistanceParams_::DistanceParams_(), TOPPViewBase::getSpectrumParameters(), TOPPViewBase::loadPreferences(), TOPPXFDR::main_(), TOPPOpenPepXLLF::main_(), TOPPOpenPepXL::main_(), TOPPOpenSwathBase::performCalibration(), TOPPASBase::savePreferences(), TOPPViewBase::savePreferences(), and ProductModel< 2 >::updateMembers_().

◆ copySubset()

Param copySubset ( const Param & subset ) const

Returns a new Param object containing all entries in the given subset.

Parameters

subset The subset of Param nodes that should be copied out of the object here. Includes values etc. Does not check any compatibility. Just matches the names.

Note: Only matches entries and nodes at the root=top level and copies over whole subtrees if matched. This function is mainly used for copying subsection parameters that were not registered as as an actual subsection e.g. for backwards compatibility of param names.

◆ empty()

bool empty ( ) const

Returns if there are no entries.

Referenced by DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::readEnzymesFromFile_().

◆ end()

ParamIterator end ( ) const

End iterator for the internal tree.

Referenced by TOPPViewBase::loadPreferences(), main(), and DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::readEnzymesFromFile_().

◆ exists()

bool exists ( const String & key ) const

Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only)

Parameters

key	The fully qualified name of the parameter to check.

Returns: True if the parameter exists, false otherwise.

Referenced by TOPPASBase::loadPreferences(), TOPPViewBase::loadPreferences(), and main().

◆ findFirst()

ParamIterator findFirst ( const String & leaf ) const

Find leaf node by name (if it exists).

Parameters

leaf	The name of the parameter to find excluding the path parameter, e.g., given the parameter TextExporter:1:proteins_only the leaf would be named proteins_only.

Returns: Returns end() if leaf does not exist.

◆ findNext()

ParamIterator findNext	(	const String &	leaf,
		const ParamIterator &	start_leaf
	)		const

Find next leaf node by name (if it exists), not considering the start_leaf.

Parameters

leaf	The name of the parameter to find excluding the path parameter, e.g., given the parameter TextExporter:1:proteins_only the leaf would be named proteins_only.
start_leaf	The already found leaf, that should not be considered during this search.

Returns: Returns end() if leaf does not exist.

◆ getDescription()

const String& getDescription ( const String & key ) const

Returns the description of a parameter.

Exceptions

Exception::ElementNotFound is thrown if the parameter does not exists.

◆ getEntry()

const ParamEntry& getEntry ( const String & key ) const

Returns the whole parameter entry.

Exceptions

Exception::ElementNotFound is thrown if the parameter does not exists.

◆ getEntry_()

ParamEntry& getEntry_ ( const String & key ) const

protected

Returns a mutable reference to a parameter entry.

Exceptions

Exception::ElementNotFound is thrown for unset parameters

◆ getSectionDescription()

const String& getSectionDescription ( const String & key ) const

Returns the description corresponding to the section with name key.

If the section does not exist an empty string is returned.

◆ getTags()

StringList getTags ( const String & key ) const

Returns the tags of entry key.

Exceptions

Exception::ElementNotFound is thrown if the parameter does not exists.

◆ getValue()

const DataValue& getValue ( const String & key ) const

Returns a value of a parameter.

Exceptions

Exception::ElementNotFound is thrown if the parameter does not exists.

Referenced by TOPPViewBase::addData(), TOPPViewBase::addDataFile(), TOPPViewBase::addRecentFile_(), FeatureDistance::DistanceParams_::DistanceParams_(), TOPPViewBase::fileChanged_(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::getSpectrumParameters(), TOPPASBase::loadPreferences(), TOPPViewBase::loadPreferences(), main(), TwoDOptimization::optimize(), TwoDOptimization::optimizeRegionsScanwise_(), TOPPOpenSwathBase::performCalibration(), TOPPViewBase::preferencesDialog(), TOPPASBase::savePreferences(), TOPPViewBase::savePreferences(), TOPPViewBase::showSpectrumGenerationDialog(), TOPPViewBase::showTOPPDialog_(), TOPPASBase::TOPPASBase(), TOPPViewBase::TOPPViewBase(), TOPPASBase::updateCurrentPath(), TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateLayerBar(), BaseModel< 2 >::updateMembers_(), SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_(), SignalToNoiseEstimatorMedian< ContainerT >::updateMembers_(), and TOPPViewBase::updateRecentMenu_().

◆ hasTag()

bool hasTag	(	const String &	key,
		const String &	tag
	)		const

Returns if the parameter key has a tag.

Example: The tag 'advanced' is used in the GUI to determine which parameters are always displayed and which parameters are displayed only in 'advanced mode'.

Exceptions

Exception::ElementNotFound is thrown if the parameter does not exists.

◆ insert()

void insert	(	const String &	prefix,
		const Param &	param
	)

Insert all values of param and adds the prefix prefix. You should append ':' to prefix manually when you want it to be a section.

Referenced by TOPPViewBase::initializeDefaultParameters_().

◆ merge()

void merge ( const Param & toMerge )

Adds missing parameters from the given param toMerge to this param. Existing parameters will not be modified.

Parameters

toMerge The Param object from which parameters should be added to this param.

◆ operator=() [1/2]

Param& operator= ( const Param & )

default

Assignment operator.

◆ operator=() [2/2]

Param& operator= ( Param && ) &

default

Move assignment operator.

◆ operator==()

bool operator== ( const Param & rhs ) const

Equality operator.

◆ parseCommandLine() [1/2]

void parseCommandLine	(	const int	argc,
		const char **	argv,
		const Map< String, String > &	options_with_one_argument,
		const Map< String, String > &	options_without_argument,
		const Map< String, String > &	options_with_multiple_argument,
		const String &	misc = `"misc"`,
		const String &	unknown = `"unknown"`
	)

Parses command line arguments to specified key locations.

Parses command line arguments to specified key locations and stores the result internally.

Parameters

argc	argc variable from command line
argv	argv variable from command line
options_with_one_argument	a map of options that are followed by one argument (with key where they are stored)
options_without_argument	a map of options that are not followed by an argument (with key where they are stored). Options specified on the command line are set to the string 'true'.
options_with_multiple_argument	a map of options that are followed by several arguments (with key where they are stored)
misc	key where a StringList of all non-option arguments are stored
unknown	key where a StringList of all unknown options are stored

◆ parseCommandLine() [2/2]

void parseCommandLine	(	const int	argc,
		const char **	argv,
		const String &	prefix = `""`
	)

Parses command line arguments.

This method discriminates three types of arguments:
(1) options (starting with '-') that have a text argument
(2) options (starting with '-') that have no text argument
(3) text arguments (not starting with '-')

Command line arguments '-a avalue -b -c bvalue misc1 misc2' would be stored like this:
"prefix:-a" -> "avalue"
"prefix:-b" -> ""
"prefix:-c" -> "bvalue"
"prefix:misc" -> list("misc1","misc2")

Parameters

argc	argc variable from command line
argv	argv variable from command line
prefix	prefix for all options

Referenced by main().

◆ remove()

void remove ( const String & key )

Remove the entry key or a section key (when suffix is ':')

Remove deletes either an entry or a section (when key ends with ':'), by matching the exact name. No partial matches are accepted.

If an empty internal node remains, the tree is pruned until every node has either a successor node or a leaf, i.e. no naked nodes remain.

◆ removeAll()

void removeAll ( const String & prefix )

Remove all entries that start with prefix.

Partial are valid as well. All entries and sections which match the prefix are deleted.

If an empty internal node remains, the tree is pruned until every node has either a successor node or a leaf, i.e. no naked nodes remain.

Referenced by TOPPViewBase::savePreferences().

◆ setDefaults()

void setDefaults	(	const Param &	defaults,
		const String &	prefix = `""`,
		bool	showMessage = `false`
	)

Insert all values of defaults and adds the prefix prefix, if the values are not already set.

Parameters

defaults	The default values.
prefix	The prefix to add to all defaults.
showMessage	If `true` each default that is actually set is printed to stdout as well.

See also: checkDefaults

◆ setMaxFloat()

void setMaxFloat	(	const String &	key,
		double	max
	)

Sets the maximum value for the floating point or floating point list parameter key.

It is only checked in checkDefaults().

Exceptions

Exception::ElementNotFound is thrown if key is not found or if the parameter type is wrong

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::SignalToNoiseEstimatorMeanIterative(), and SignalToNoiseEstimatorMedian< ContainerT >::SignalToNoiseEstimatorMedian().

◆ setMaxInt()

void setMaxInt	(	const String &	key,
		Int	max
	)

Sets the maximum value for the integer or integer list parameter key.

It is only checked in checkDefaults().

Exceptions

Exception::ElementNotFound is thrown if key is not found or if the parameter type is wrong

Referenced by TOPPViewBase::initializeDefaultParameters_(), SignalToNoiseEstimatorMeanIterative< Container >::SignalToNoiseEstimatorMeanIterative(), and SignalToNoiseEstimatorMedian< ContainerT >::SignalToNoiseEstimatorMedian().

◆ setMinFloat()

void setMinFloat	(	const String &	key,
		double	min
	)

Sets the minimum value for the floating point or floating point list parameter key.

It is only checked in checkDefaults().

Exceptions

Exception::ElementNotFound is thrown if key is not found or if the parameter type is wrong

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::SignalToNoiseEstimatorMeanIterative(), and SignalToNoiseEstimatorMedian< ContainerT >::SignalToNoiseEstimatorMedian().

◆ setMinInt()

void setMinInt	(	const String &	key,
		Int	min
	)

Sets the minimum value for the integer or integer list parameter key.

It is only checked in checkDefaults().

Exceptions

Exception::ElementNotFound is thrown if key is not found or if the parameter type is wrong

Referenced by TOPPViewBase::initializeDefaultParameters_(), SignalToNoiseEstimatorMeanIterative< Container >::SignalToNoiseEstimatorMeanIterative(), and SignalToNoiseEstimatorMedian< ContainerT >::SignalToNoiseEstimatorMedian().

◆ setSectionDescription()

void setSectionDescription	(	const String &	key,
		const String &	description
	)

Sets a description for an existing section.

Descriptions for values cannot be set with this method. They have to be set when inserting the value itself.

Exceptions

Exception::ElementNotFound is thrown if the section does not exists.

Referenced by TOPPViewBase::initializeDefaultParameters_().

◆ setValidStrings()

void setValidStrings	(	const String &	key,
		const std::vector< String > &	strings
	)

Sets the valid strings for the parameter key.

It is only checked in checkDefaults().

Exceptions

Exception::InvalidParameter	is thrown, if one of the strings contains a comma character
Exception::ElementNotFound	exception is thrown, if the parameter is no string parameter

Referenced by TOPPViewBase::initializeDefaultParameters_(), SignalToNoiseEstimatorMedian< ContainerT >::SignalToNoiseEstimatorMedian(), and TOPPASBase::TOPPASBase().

◆ setValue()

void setValue	(	const String &	key,
		const DataValue &	value,
		const String &	description = `""`,
		const StringList &	tags = `StringList()`
	)

Sets a value.

Parameters

key	String key. Can contain ':' which separates section names
value	The actual value
description	Verbose description of the parameter
tags	list of tags associated to this parameter

Referenced by TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::annotateWithID(), BaseModel< 2 >::BaseModel(), NucleicAcidSearchEngine::calculateAndFilterFDR_(), TOPPViewBase::getSpectrumParameters(), TOPPViewBase::initializeDefaultParameters_(), TOPPViewBase::loadFiles(), TOPPASBase::loadPreferences(), TOPPViewBase::loadPreferences(), NucleicAcidSearchEngine::main_(), SpectraMerger::mergeSpectra_(), TOPPOpenSwathBase::performCalibration(), PeakPickerIterative::pick(), TOPPViewBase::preferencesDialog(), NucleicAcidSearchEngine::preprocessSpectra_(), TOPPASBase::savePreferences(), TOPPViewBase::savePreferences(), BaseModel< 2 >::setCutOff(), TOPPViewBase::showSpectrumAlignmentDialog(), TOPPViewBase::showSpectrumGenerationDialog(), SignalToNoiseEstimatorMeanIterative< Container >::SignalToNoiseEstimatorMeanIterative(), SignalToNoiseEstimatorMedian< ContainerT >::SignalToNoiseEstimatorMedian(), SignalToNoiseOpenMS< ContainerT >::SignalToNoiseOpenMS(), TOPPASBase::TOPPASBase(), and TOPPViewBase::updateRecentMenu_().

◆ size()

Size size ( ) const

Returns the number of entries (leafs).

Referenced by TOPPViewBase::loadPreferences().

◆ update() [1/3]

bool update	(	const Param &	p_outdated,
		bool	verbose,
		bool	add_unknown,
		bool	fail_on_invalid_values,
		bool	fail_on_unknown_parameters,
		Logger::LogStream &	stream
	)

Rescue parameter values from p_outdated to current param.

All parameters present in both param objects will be transferred into this object, given that:

the name is equal
the type is equal
the value from p_outdated meets the new restrictions

Not transferred are values from parameter "version" (to preserve the new version) or "type" (to preserve layout).

Parameters

p_outdated	Old/outdated param object, whose values (as long as they are still valid) are used to update this object
verbose	Print information about expected value updates
add_unknown	Add unknown parameters from @p_outdated to this param object.
fail_on_invalid_values	Return false if outdated parameters hold invalid values
fail_on_unknown_parameters	Return false if outdated parameters contain unknown parameters (takes precedence over `add_unknown`)
stream	The stream where all the logging output is send to.

Returns: true on success, false on failure

◆ update() [2/3]

bool update	(	const Param &	p_outdated,
		const bool	add_unknown,
		Logger::LogStream &	stream
	)

Rescue parameter values from p_outdated to current param.

Calls ::update(p_outdated, true, add_unknown, false, false, stream) and returns its value.

◆ update() [3/3]

bool update	(	const Param &	p_outdated,
		const bool	add_unknown = `false`
	)

Rescue parameter values from p_outdated to current param.

Calls ::update(p_outdated, true, add_unknown, false, false, OPENMS_LOG_WARN) and returns its value.

Referenced by TOPPXFDR::main_(), TOPPOpenPepXLLF::main_(), and TOPPOpenPepXL::main_().

Member Data Documentation

◆ root_

Param::ParamNode root_

mutableprotected

Invisible root node that stores all the data.

Classes

Public Member Functions

Command line parsing

Detailed Description

Constructor & Destructor Documentation

◆ Param() [1/4]

◆ Param() [2/4]

◆ Param() [3/4]

◆ ~Param()

◆ Param() [4/4]

Member Function Documentation

◆ addSection()

◆ addTag()

◆ addTags()

◆ begin()

◆ checkDefaults()

◆ clear()

◆ clearTags()

◆ copy()

◆ copySubset()

◆ empty()

◆ end()

◆ exists()

◆ findFirst()

◆ findNext()

◆ getDescription()

◆ getEntry()

◆ getEntry_()

◆ getSectionDescription()

◆ getTags()

◆ getValue()

◆ hasTag()

◆ insert()

◆ merge()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ parseCommandLine() [1/2]

◆ parseCommandLine() [2/2]

◆ remove()

◆ removeAll()

◆ setDefaults()

◆ setMaxFloat()

◆ setMaxInt()

◆ setMinFloat()

◆ setMinInt()

◆ setSectionDescription()

◆ setValidStrings()

◆ setValue()

◆ size()

◆ update() [1/3]

◆ update() [2/3]

◆ update() [3/3]

Member Data Documentation

◆ root_