An instance of this class represents all the parameters specified in UniGene section of mascot.dat. More...

#include <ms_unigeneoptions.hpp>

Inheritance diagram for ms_unigeneoptions:

Collaboration diagram for ms_unigeneoptions:

Public Member Functions
	ms_unigeneoptions ()
	Default constructor.

	ms_unigeneoptions (const ms_unigeneoptions &src)
	Copying constructor.

virtual	~ms_unigeneoptions ()
	Destructor.

void	appendProperty (const char name, const char value, const char *delimiter, const bool bFirstPlace=false)
	Adds a new property with the given parameters.

void	appendText (const char *line, const bool bFirstPlace=false)
	Adds a new non-parsed property.

void	copyFrom (const ms_customproperty *src)
	Copies all properties and comments from another instance.

void	copyFrom (const ms_unigeneoptions *right)
	Can be used to create a copy of another object.

virtual void	defaultValues ()
	Initialises the instance with default values.

void	delNonEmpty ()
	Deletes all non-comment properties.

void	delProp (const char *name)
	Deletes all properties with the specified name.

void	delPropByNumber (const int index)
	Deletes a single property with the specified number only.

void	delPropStart (const char *nameBeginning)
	Deletes all properties whose names start with the given string.

int	findProperty (const char *name, const int startFrom=0) const
	Searches the list for a property with the given name.

int	findPropertyBeginning (const char *nameBeginning, const int startFrom=0) const
	Searches the list for a property with the partially matching name.

std::string	getDefaultDelimiter () const
	Return current default delimiter string used for parsing/storing properties.

std::string	getDelimiterByNumber (const int index) const
	Returns a specific delimiter used for the property.

int	getNumberOfProperties () const
	Returns a total number of property/comment entries.

std::string	getPreceedingComments () const
	Returns any comments preceeding the section.

std::string	getPropertyName (const int index) const
	Returns a property name for a given index.

std::string	getPropValStringByName (const char *name) const
	Retrieves property value by name.

std::string	getPropValStringByNumber (const int index) const
	Retrieves property raw text values by number.

bool	isSectionAvailable () const
	Indicates whether the section has been actually read from the file.

ms_unigeneoptions &	operator= (const ms_unigeneoptions &right)
	C++ style assignment operator.

void	setDefaultDelimiter (const char *delim)
	Allows to set a specific delimiter string to be used when no property-specific delimiter is supplied.

void	setPreceedingComments (const std::string &comments)
	Sets any comments preceeding the section.

void	setPropertyName (const int index, const char *name)
	Changes name of the property with the given index.

void	setPropValBoolByName (const char *name, const bool value, const bool bFirstPlace=false)
	Changes a boolean value of the first entry with the given name or creates a new property if it is not found.

void	setPropValCharByName (const char *name, const char value, const bool bFirstPlace=false)
	Changes a single character value of the first entry with the given name or creates a new property if it is not found.

void	setPropValFloatByName (const char *name, const double value, const bool bFirstPlace=false)
	Changes an floating point value of the first entry with the given name or creates a new property if it is not found.

void	setPropValInt64ByName (const char *name, const INT64 value, const bool bFirstPlace=false)
	Changes a long 64-bit integer value of the first entry with the given name or creates a new property if it is not found.

void	setPropValIntByName (const char *name, const int value, const bool bFirstPlace=false)
	Changes an integer value of the first entry with the given name or creates a new property if it is not found.

void	setPropValStringByName (const char name, const char value, const bool bFirstPlace=false)
	Changes a string value of the first entry with the given name or creates a new property if it is not found.

void	setPropValStringByNumber (const int index, const char *value)
	Changes an string value of an existing property with the given index.

void	setSectionAvailable (const bool value)
	Changes availability of the section, i.e. should it be saved in a file.

bool	uncommentProp (const int index, const char *delimeter=0)
	Uncomments a line in the configuration file.

Detailed Description

An instance of this class represents all the parameters specified in UniGene section of mascot.dat.

An instance of this class is created and populated in ms_datfile and is available by calling ms_datfile::getUniGeneOptions(). It can also be created separately and initialised with default values. You can create an instance of the class or copy from another instance in order to pass it then as an options-containing object.

For detailed information on any of the options please consult Mascot manual.

Currently, access to the values is only provided through the ms_customproperty class, from which this class is derived. It facilitates the following tasks:

Retrieving an unsupported property.
Retrieving a raw/text/XML property representation.
Checking for existence of a certain property rather than dealing with its default value.
Accessing commented lines in a section.

More functionality is described in the documentation for ms_customproperty.

Constructor & Destructor Documentation

◆ ms_unigeneoptions() [1/2]

ms_unigeneoptions ( )

Default constructor.

Note: Not normally called from outside Mascot Parser.

◆ ms_unigeneoptions() [2/2]

ms_unigeneoptions ( const ms_unigeneoptions & src )

Copying constructor.

Note: Not normally called from outside Mascot Parser.

Parameters

src	unigene options object

◆ ~ms_unigeneoptions()

~ms_unigeneoptions ( )

virtual

Destructor.

Note: Not normally called from outside Mascot Parser.

Member Function Documentation

◆ appendProperty()

void appendProperty	(	const char *	name,
		const char *	value,
		const char *	delimiter,
		const bool	bFirstPlace = `false`
	)

inherited

Adds a new property with the given parameters.

Parameters

name	a property name to use.
value	a property value to use.
delimiter	a specific delimiter or an empty string for a default one to be used.
bFirstPlace	forces a new property to be put on top of the list.

◆ appendText()

void appendText	(	const char *	l,
		const bool	bFirstPlace = `false`
	)

inherited

Adds a new non-parsed property.

All property elements will be retrieved from the first parameter. Before calling this method, a specific default delimiter can be set using setDefaultDelimiter().

Parameters

l	raw text representation of the property to be parsed.
bFirstPlace	forces a new property to be put on top of the list.

◆ copyFrom()

void copyFrom ( const ms_unigeneoptions * right )

Can be used to create a copy of another object.

Note: Not normally called from outside Mascot Parser.

Parameters

right is the source to be copied.

◆ defaultValues()

void defaultValues ( )

virtual

Initialises the instance with default values.

Note: Not normally called from outside Mascot Parser.

◆ delProp()

void delProp ( const char * str )

inherited

Deletes all properties with the specified name.

Parameters

str	Property name to find a match and then delete.

◆ delPropStart()

void delPropStart ( const char * str )

inherited

Deletes all properties whose names start with the given string.

Parameters

str	Beginning a first part of the property name to delete.

◆ findProperty()

int findProperty	(	const char *	name,
		const int	startFrom = `0`
	)		const

inherited

Searches the list for a property with the given name.

If no property found with the given name -1 will be returned. There may be several property entries in the list with the same name.

Parameters

name	a property name to be found.
startFrom	a minimal property index to start search from.

Returns: a property index or -1 if no property found.

◆ findPropertyBeginning()

int findPropertyBeginning	(	const char *	nameBeginning,
		const int	startFrom = `0`
	)		const

inherited

Searches the list for a property with the partially matching name.

If no property found with the given name part -1 will be returned. There may be several property entries in the list whose names start with the given string.

Parameters

nameBeginning	first part of a property name to be found.
startFrom	a minimal property index to start search from.

Returns: a property index or -1 if no property found.

◆ getDefaultDelimiter()

std::string getDefaultDelimiter ( ) const

inherited

Return current default delimiter string used for parsing/storing properties.

Returns: default delimiter

◆ getDelimiterByNumber()

std::string getDelimiterByNumber ( const int index ) const

inherited

Returns a specific delimiter used for the property.

Parameters

index Index for which to get a delimiter

Returns: corresponding delimiter

◆ getNumberOfProperties()

int getNumberOfProperties ( ) const

inherited

Returns a total number of property/comment entries.

Returns: Number of property/comment entries

◆ getPreceedingComments()

std::string getPreceedingComments ( ) const

inherited

Returns any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also: setPreceedingComments()

Returns: any comments preceeding the section

◆ getPropertyName()

std::string getPropertyName ( const int index ) const

inherited

Returns a property name for a given index.

Parameters

index property number from 0 to (getNumberOfProperties()-1).

Returns: Rroperty name of an empty string for comments.

◆ getPropValStringByName()

std::string getPropValStringByName ( const char * name ) const

inherited

Retrieves property value by name.

Don't use this method for comments as they all have empty name. Also note that there might be several entries corresponding to the same name . – only the first value will be returned. If in doubt use findProperty() and getPropValStringByNumber() instead.

Parameters

name	Name for which to get a property value

Returns: corresponding property value

◆ getPropValStringByNumber()

std::string getPropValStringByNumber ( const int index ) const

inherited

Retrieves property raw text values by number.

Parameters

index Index for which to get a property value

Returns: corresponding property value

◆ isSectionAvailable()

bool isSectionAvailable ( ) const

Indicates whether the section has been actually read from the file.

By default the UniGene section is unavailable until it has been set to a different state.

Returns: true if the section is available.

◆ setDefaultDelimiter()

void setDefaultDelimiter ( const char * delim )

inherited

Allows to set a specific delimiter string to be used when no property-specific delimiter is supplied.

Parameters

delim String to set the default delimiter

◆ setPreceedingComments()

void setPreceedingComments ( const std::string & comments )

inherited

Sets any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also: getPreceedingComments()

Parameters

comments any comments preceeding the section

◆ setPropertyName()

void setPropertyName	(	const int	index,
		const char *	name
	)

inherited

Changes name of the property with the given index.

Parameters

index	property number from 0 to (getNumberOfProperties()-1).
name	new name to be given to the property.

◆ setPropValBoolByName()

void setPropValBoolByName	(	const char *	name,
		const bool	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a boolean value of the first entry with the given name or creates a new property if it is not found.

A new value will be converted into 1 (for TRUE) or 0 (for FALSE) character.

Parameters

name	a name of the property to find or add.
value	a new boolean value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValCharByName()

void setPropValCharByName	(	const char *	name,
		const char	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a single character value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new single character value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValFloatByName()

void setPropValFloatByName	(	const char *	name,
		const double	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes an floating point value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new floating point value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValInt64ByName()

void setPropValInt64ByName	(	const char *	name,
		const INT64	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a long 64-bit integer value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new long 64-bit integer value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValIntByName()

void setPropValIntByName	(	const char *	name,
		const int	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes an integer value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new integer value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValStringByName()

void setPropValStringByName	(	const char *	name,
		const char *	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a string value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new string value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValStringByNumber()

void setPropValStringByNumber	(	const int	index,
		const char *	str
	)

inherited

Changes an string value of an existing property with the given index.

Parameters

index	an index of an existing property.
str	String value for the property.

◆ setSectionAvailable()

void setSectionAvailable ( const bool value )

Changes availability of the section, i.e. should it be saved in a file.

Parameters

value should be true to make the section available.

◆ uncommentProp()

bool uncommentProp	(	const int	index,
		const char *	delimeter = `0`
	)

inherited

Uncomments a line in the configuration file.

Removes a # and any white space. Finds the delimeter and extracts the property name and value.

Parameters

index	must be a value between 0 and getNumberOfProperties().
delimeter	will often be a space. If not supplied, the default delimeter will be used.

Returns: true if the delimiter was found, false otherwise

The documentation for this class was generated from the following files:

ms_unigeneoptions.hpp
ms_unigeneoptions.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_unigeneoptions() [1/2]

◆ ms_unigeneoptions() [2/2]

◆ ~ms_unigeneoptions()

Member Function Documentation

◆ appendProperty()

◆ appendText()

◆ copyFrom()

◆ defaultValues()

◆ delProp()

◆ delPropStart()

◆ findProperty()

◆ findPropertyBeginning()

◆ getDefaultDelimiter()

◆ getDelimiterByNumber()

◆ getNumberOfProperties()

◆ getPreceedingComments()

◆ getPropertyName()

◆ getPropValStringByName()

◆ getPropValStringByNumber()

◆ isSectionAvailable()

◆ setDefaultDelimiter()

◆ setPreceedingComments()

◆ setPropertyName()

◆ setPropValBoolByName()

◆ setPropValCharByName()

◆ setPropValFloatByName()

◆ setPropValInt64ByName()

◆ setPropValIntByName()

◆ setPropValStringByName()

◆ setPropValStringByNumber()

◆ setSectionAvailable()

◆ uncommentProp()