utility::tag Namespace Reference

Classes
class	Tag
class	XMLSchemaComplexTypeGeneratorImpl
class	XMLSchemaType
	class XMLSchemaType represents the name of a defined type that can be used to describe either an XMLElement or an XMLAttribute. It may refer to either a complex type or to a primative type or to a simple type. More...
class	XMLSchemaTopLevelElement
	The XMLSchemaTopLevelElement class signifies a class that could be written out as an XML element, with possible sub-elemets, in an XML schema. When generating a schema, the developer will hand an instance of a class derived from an XMLSchemaTopLevelElement to an XMLSchemaDefinition object. More...
class	XMLSchemaAttribute
	class XMLSchemaAttribute represents what we refer to in Rosetta as an option for a tag. An attribute would reside inside of a tag, such as "scorefxn" in this tag (this XML Element): <MinMover name="min" scorefxn="talaris2014"> More...
class	XMLSchemaRestriction
	class XMLSchemaRestriction describes a refinement on the behavior of existing types. For example, one could define a restriction representing a list of residue indexes separating commas: "15,44,102" and then describe an attribute of a complex type as having to conform to that restriction. An xml-schema validator would be able to say that an input file with "fifteen,fortyfour,onehundredandtwo" did not meet the schema. More...
class	XMLSchemaParticle
	This abstract class is meant to represent either an XMLSChemaElement or an XMLSchemaModelGroup so that the interchangable set of these objects in a ModelGroup can be represented. I may be misusing the term "particle" in the way that it is meant within XML Schema – so the mapping of this term to the term used in XML Schema is probably imperfect. More...
class	XMLSchemaModelGroup
	The ModelGroup covers four XML Schema model groups: xs:sequence, xs:choice, xs:all, and xs:group. A ModelGroup may contain any number of XMLSchemaParticles, interchanging between XMLElements and XMLModelGroups, BUT there are some fairly heavy restrictions on the xs:all model group, marginally enforced by this class and by XMLSchemaComplexType. This class is not exactly a top-level element, in that only xs:group is allowed to appear at the top level, but it is definitely worthwhile for this class to implement the write_definition funciton. More...
class	XMLSchemaComplexType
	class XMLSchemaComplexType represents the definition of the type for an element – that is, the structure of a set of elements with the same name. If an XMLSchemaElement is analogous to a utility::tag::Tag, an XMLSchemaComplexType is analogous to the wiki page describing the valid format for an instance of that Tag. More...
class	XMLSchemaElement
	An XMLSchema element, e.g. the FixbbMover "tag" <FixbbMover name="fixbb" task_operations="ex1,ex2"> or the And element which contains a sub-element: <And><Chain id="A"></And>. An element can be defined with an unnamed complex type in-line, or it can say that its type is that of a complex type defined elsewhere. (In XML naming a tag is a single block beginning with "<" and ending with ">", so both "<And>" and "</And>" are tags. The block between the opening and closing tags is called an element. The utility::tag::Tag class represents a complete Element, and not simply the opening or closing tag of an element. This is certainly confusing. More...
class	XMLSchemaDefinition
	The XMLSchemaDefinition class's purpose is to collect all of the elements that go into an XML Schema, to filter out the elements that are repeated (e.g. a restriction such as the "int_cslist" given in the description for XMLSchemaRestriction above may be reported twice to the XMLSchemaDefinition by several attributes that rely upon it), to detect non-identical duplicates that have the same name, and to write out the elements that it has been handed into a single string. The XMLSchemaDefinition is intended to be passed between static functions / non-class-member functions as a container for the XML Schema representations that these functions define. Such functions will always take an XMLSchemaDefinition reference as one of their input parameters. It is perfectly legitimate / recommended for one XML-schema-defining function that relies on a complexType or restriction that it does not itself define to pass its input XMLSchemaDefinition to the function that does define that complexType or restriction. More...
class	XMLSchemaSimpleSubelementList
	The XMLSchemaSimpleSubelementList class defines an interface that can be used by those wishing to define a complexType that contains sub-elements. The structure of the XML Schema for the sub-elements will determined by how this list is given to the XMLSchemaComplexTypeGenerator. "simple" subelements are those which themselves contain no subelements (but may contain attributes). Also allowed are subelements that refer to previously-defined complexTypes or those that refer to previously defined xs:groups. More...
class	XMLSchemaComplexTypeGenerator
	The XMLComplexTypeSchemaGenerator is used to define the schema for a complex type as they typically occurr in Rosetta. More...
class	XMLSchemaRepeatableCTNode
class	XMLValidatorImpl
class	XMLErrorHandler
class	XMLValidator
class	XMLValidationOutput

Typedefs
typedef ::utility::pointer::shared_ptr< Tag >	TagPtr
typedef ::utility::pointer::shared_ptr< Tag >	TagOP
typedef ::utility::pointer::shared_ptr< Tag const >	TagCOP
typedef ::utility::pointer::weak_ptr< Tag >	TagAP
typedef ::utility::pointer::weak_ptr< Tag const >	TagCAP
typedef utility::pointer::shared_ptr< XMLSchemaType >	XMLSchemaTypeOP
typedef utility::pointer::shared_ptr< XMLSchemaType const >	XMLSchemaTypeCOP
typedef utility::pointer::shared_ptr< XMLSchemaAttribute >	XMLSchemaAttributeOP
typedef utility::pointer::shared_ptr< XMLSchemaAttribute const >	XMLSchemaAttributeCOP
typedef std::list< utility::tag::XMLSchemaAttribute >	AttributeList
typedef utility::pointer::shared_ptr< XMLSchemaElement >	XMLSchemaElementOP
typedef utility::pointer::shared_ptr< XMLSchemaElement const >	XMLSchemaElementCOP
typedef utility::pointer::shared_ptr< XMLSchemaRestriction >	XMLSchemaRestrictionOP
typedef utility::pointer::shared_ptr< XMLSchemaRestriction const >	XMLSchemaRestrictionCOP
typedef utility::pointer::shared_ptr< XMLSchemaParticle >	XMLSchemaParticleOP
typedef utility::pointer::shared_ptr< XMLSchemaParticle const >	XMLSchemaParticleCOP
typedef utility::pointer::shared_ptr< XMLSchemaModelGroup >	XMLSchemaModelGroupOP
typedef utility::pointer::shared_ptr< XMLSchemaModelGroup const >	XMLSchemaModelGroupCOP
typedef utility::pointer::shared_ptr< XMLSchemaComplexType >	XMLSchemaComplexTypeOP
typedef utility::pointer::shared_ptr< XMLSchemaComplexType const >	XMLSchemaComplexTypeCOP
typedef utility::pointer::shared_ptr< XMLSchemaElementType >	XMLSchemaElementTypeOP
typedef utility::pointer::shared_ptr< XMLSchemaElementType const >	XMLSchemaElementTypeCOP
typedef utility::pointer::shared_ptr< XMLSchemaDefinition >	XMLSchemaDefinitionOP
typedef utility::pointer::shared_ptr< XMLSchemaDefinition const >	XMLSchemaDefinitionCOP
typedef utility::pointer::shared_ptr< XMLSchemaSimpleSubelementList >	XMLSchemaSimpleSubelementListOP
typedef utility::pointer::shared_ptr< XMLSchemaSimpleSubelementList const >	XMLSchemaSimpleSubelementListCOP
typedef utility::pointer::shared_ptr< XMLSchemaComplexTypeGenerator >	XMLSchemaComplexTypeGeneratorOP
typedef utility::pointer::shared_ptr< XMLSchemaComplexTypeGenerator const >	XMLSchemaComplexTypeGeneratorCOP
typedef utility::pointer::shared_ptr< XMLSchemaRepeatableCTNode >	XMLSchemaRepeatableCTNodeOP
typedef utility::pointer::shared_ptr< XMLSchemaRepeatableCTNode const >	XMLSchemaRepeatableCTNodeCOP
typedef utility::pointer::weak_ptr< XMLSchemaRepeatableCTNode >	XMLSchemaRepeatableCTNodeAP
typedef utility::pointer::weak_ptr< XMLSchemaRepeatableCTNode const >	XMLSchemaRepeatableCTNodeCAP
typedef utility::pointer::shared_ptr< XMLValidator >	XMLSchemaValidatorOP
typedef utility::pointer::shared_ptr< XMLValidator const >	XMLSchemaValidatorCOP

Enumerations
enum class	AutoBool { False = 0 , True , Auto }
enum	XMLSchemaDataType {   xs_string , xs_decimal , xs_integer , xs_boolean ,   xs_date , xs_time , xs_common , xs_custom }
	The simple types provided by the XMLSchema language itself. These are not always the types that you want to use. More...
enum	XMLSchemaMinOccursMaxOccurs { xsminmax_unbounded = -2 , xsminmax_unspecified = -1 }
enum	XMLSchemaRestrictionType {   xsr_enumeration , xsr_fractionDigits , xsr_length , xsr_maxExclusive ,   xsr_maxInclusive , xsr_maxLength , xsr_minExclusive , xsr_minInclusive ,   xsr_minLength , xsr_pattern , xsr_totalDigits , xsr_whitespace }
enum	XMLSchemaModelGroupType { xsmgt_sequence , xsmgt_all , xsmgt_choice , xsmgt_group }
enum	XMLSchemaElementCategory { xs_element_is_type_reference , xs_element_is_abstract , xs_element_is_complex_type_w_definition , xs_element_is_element_reference }
enum	CTGenSubelementBehavior {   se_none , se_repeatable , se_choice_req , se_choice_opt ,   se_single_req , se_single_opt , se_single_req_ordered , se_ordered_sets }
enum	XMLSchemaCommonType {   xsct_none , xsct_int_cslist , xsct_string_cslist , xsct_int_wsslist ,   xsct_nnegative_int_cslist , xsct_nnegative_int_wsslist , xsct_real , xsct_real_cslist ,   xsct_real_cslist_w_ws , xsct_real_wsslist , xsct_bool_cslist , xsct_bool_wsslist ,   xsct_positive_integer_cslist , xsct_positive_integer_wsslist , xsct_non_negative_integer , xsct_positive_integer ,   xsct_rosetta_bool , xsct_rosetta_autobool , xsct_residue_number , xsct_residue_number_cslist ,   xsct_refpose_enabled_residue_number , xsct_refpose_enabled_residue_number_cslist , xsct_char , xsct_minimizer_type ,   xsct_size_cs_pair , xsct_chain_cslist , xsct_dssp_string , xsct_canonical_res_char ,   xsct_packer_palette , xsct_task_operation , xsct_task_operation_comma_separated_list , xsct_pose_cached_task_operation }
	An enum listing lots of commonly-used simple types so they don't have to be added manually in lots of places. If you create an XMLSchemaType using this enum, then the corresponding restriction will be added to the XMLSchemaDefintion automatically. More...

Functions
template<>
std::string	Tag::getOption< std::string > (std::string const &key, char const *default_as_string_literal) const
	Special-casing the string literal version for string options. In this case, there shouldn't be an error thrown. A string literal should be allowed to set the default value for a string. More...
template<>
platform::Size	Tag::getOption< platform::Size > (std::string const &key, int const default_int) const
	Special-casing to ensure that 0 gets interpreted as Size(0) rather than nullptr. More...
std::ostream &	operator<< (std::ostream &out, Tag const &tag)
std::ostream &	operator<< (std::ostream &out, TagCOP const &tag_ptr)
void	add_schema_restrictions_for_strings (XMLSchemaDefinition &xsd, std::string type_name, vector1< std::string > const &restrictions)
	Add a SchemaRestriction for a set of strings. Useful for enums. The type name is then used as the type when adding an attribute. More...
template<class Creator >
void	define_xml_schema_group (typename std::map< std::string, utility::pointer::shared_ptr< Creator > > const &creator_map, std::string const &widget_group_name, std::function< std::string(std::string const &) > const &complex_type_name_for_widget_func, XMLSchemaDefinition &xsd)
char	string_contains_gt_lt_or_ampersand (std::string const &s)
	Check if given string contain any of '<>&' and if so return found character. If no character is found return 0. More...
std::string	chr_chains_nonrepeated ()
std::string	name_for_common_type (XMLSchemaCommonType common_type)
std::ostream &	operator<< (std::ostream &os, XMLSchemaCommonType common_type)
void	indent_w_spaces (int indentation, std::ostream &os)
void	write_min_occurs_max_occurs_if_necessary (int min_occurs, int max_occurs, std::ostream &os)
std::string	real_regex_pattern ()
std::string	rosetta_bool_string ()
	the set of all strings recognized as booleans according to Rosetta (in utility/string_util.cc) More...
std::string	rosetta_autobool_string ()
std::string	chain_cslist_string ()
std::string	residue_number_string ()
std::string	residue_number_cslist_string ()
std::string	refpose_enabled_residue_number_string ()
std::string	refpose_enabled_residue_number_cslist_string ()
std::string	canonical_res_char_string ()
std::string	task_operation_name_pattern ()
void	activate_common_simple_type (utility::tag::XMLSchemaDefinition &xsd, XMLSchemaCommonType common_type)
AttributeList &	operator+ (AttributeList &attributes, XMLSchemaAttribute const &attribute_to_append)
std::string	restriction_type_name (XMLSchemaRestrictionType type)
std::ostream &	operator<< (std::ostream &os, XMLSchemaRestrictionType type)
std::string	xs_model_group_name (XMLSchemaModelGroupType xsmgt)
std::ostream &	operator<< (std::ostream &os, XMLSchemaModelGroupType type)
XMLSchemaRestriction	integer_range_restriction (std::string const &name, int lower_inclusive, int upper_inclusive)
	Convenience function for defining an inclusive range restriction. More...
XMLSchemaAttribute	optional_name_attribute (std::string const &description="")
	This function creates an attribute named "name" of type xs_string that is optional; naming is not always required – it is not even mostly required. This is probably the function you need; very few classes actually need to have a name – the name is often only used by the function reading in the name, but there are reasonable times when a Mover, e.g. could go nameless – for instance, in the fixbb_jd3 application, a PackRotamersMover can be given as a subtag of the <Job> tag. In this case, the PackRotamersMover doesn't need to be given a name. More...
XMLSchemaAttribute	required_name_attribute (std::string const &description="")
	This function creates an attribute named "name" of type xs_string that is required; naming is not always required – it is not even mostly required. This function is probably not what you need. Use with care. See comments for the "optional_name_attribute" function above. More...
void	append_name_and_attributes_to_complex_type (AttributeList const &attributes, XMLSchemaComplexType &type_definition)
	append an attribute of "name" with type "xs:string" along with the other attributes in the input attribute list to the input complex type. More...
void	append_required_name_and_attributes_to_complex_type (AttributeList const &attributes, XMLSchemaComplexType &type_definition)
	append a required attribute of "name" with type "xs:string" along with the other attributes in the input attribute list to the input complex type. More...
bool	attribute_w_name_in_attribute_list (std::string const &attname, AttributeList const &attlist)
	check whether an attribute with name attname already exists in AttributeList attlist to avoid collisions More...
std::string	element_type_name (xmlElementType element_type)
int	length_of_message (const char *message, va_list args)
char *	make_message (int length, const char *message, va_list args)
void	handle_structured_xml_error (void *ctxt, xmlErrorPtr error)
void	handle_xml_error (void *ctxt, char const *message,...)
void	handle_xml_warning (void *ctxt, char const *message,...)
void	print_node_stack (utility::vector1< xmlNode * > const &node_stack, std::ostringstream &oss)
std::string	concat_stringlist (std::list< std::string > const &strings)
int	recurse_through_tree (xmlSchemaValidCtxtPtr ctxt, xmlNodePtr node, XMLErrorHandler handler)
XMLValidationOutput	validate_xml_against_xsd (std::string const &xml_string, std::string const &xsd_string)
XMLValidationOutput	test_if_schema_is_valid (std::string const &xsd_string)

Typedef Documentation

AttributeList

typedef std::list< utility::tag::XMLSchemaAttribute > utility::tag::AttributeList

TagAP

typedef ::utility::pointer::weak_ptr< Tag > utility::tag::TagAP

TagCAP

typedef ::utility::pointer::weak_ptr< Tag const > utility::tag::TagCAP

TagCOP

typedef ::utility::pointer::shared_ptr< Tag const > utility::tag::TagCOP

TagOP

typedef ::utility::pointer::shared_ptr< Tag > utility::tag::TagOP

TagPtr

typedef ::utility::pointer::shared_ptr< Tag > utility::tag::TagPtr

XMLSchemaAttributeCOP

typedef utility::pointer::shared_ptr< XMLSchemaAttribute const > utility::tag::XMLSchemaAttributeCOP

XMLSchemaAttributeOP

typedef utility::pointer::shared_ptr< XMLSchemaAttribute > utility::tag::XMLSchemaAttributeOP

XMLSchemaComplexTypeCOP

typedef utility::pointer::shared_ptr< XMLSchemaComplexType const > utility::tag::XMLSchemaComplexTypeCOP

XMLSchemaComplexTypeGeneratorCOP

typedef utility::pointer::shared_ptr< XMLSchemaComplexTypeGenerator const > utility::tag::XMLSchemaComplexTypeGeneratorCOP

XMLSchemaComplexTypeGeneratorOP

typedef utility::pointer::shared_ptr< XMLSchemaComplexTypeGenerator > utility::tag::XMLSchemaComplexTypeGeneratorOP

XMLSchemaComplexTypeOP

typedef utility::pointer::shared_ptr< XMLSchemaComplexType > utility::tag::XMLSchemaComplexTypeOP

XMLSchemaDefinitionCOP

typedef utility::pointer::shared_ptr< XMLSchemaDefinition const > utility::tag::XMLSchemaDefinitionCOP

XMLSchemaDefinitionOP

typedef utility::pointer::shared_ptr< XMLSchemaDefinition > utility::tag::XMLSchemaDefinitionOP

XMLSchemaElementCOP

typedef utility::pointer::shared_ptr< XMLSchemaElement const > utility::tag::XMLSchemaElementCOP

XMLSchemaElementOP

typedef utility::pointer::shared_ptr< XMLSchemaElement > utility::tag::XMLSchemaElementOP

XMLSchemaElementTypeCOP

typedef utility::pointer::shared_ptr< XMLSchemaElementType const > utility::tag::XMLSchemaElementTypeCOP

XMLSchemaElementTypeOP

typedef utility::pointer::shared_ptr< XMLSchemaElementType > utility::tag::XMLSchemaElementTypeOP

XMLSchemaModelGroupCOP

typedef utility::pointer::shared_ptr< XMLSchemaModelGroup const > utility::tag::XMLSchemaModelGroupCOP

XMLSchemaModelGroupOP

typedef utility::pointer::shared_ptr< XMLSchemaModelGroup > utility::tag::XMLSchemaModelGroupOP

XMLSchemaParticleCOP

typedef utility::pointer::shared_ptr< XMLSchemaParticle const > utility::tag::XMLSchemaParticleCOP

XMLSchemaParticleOP

typedef utility::pointer::shared_ptr< XMLSchemaParticle > utility::tag::XMLSchemaParticleOP

XMLSchemaRepeatableCTNodeAP

typedef utility::pointer::weak_ptr< XMLSchemaRepeatableCTNode > utility::tag::XMLSchemaRepeatableCTNodeAP

XMLSchemaRepeatableCTNodeCAP

typedef utility::pointer::weak_ptr< XMLSchemaRepeatableCTNode const > utility::tag::XMLSchemaRepeatableCTNodeCAP

XMLSchemaRepeatableCTNodeCOP

typedef utility::pointer::shared_ptr< XMLSchemaRepeatableCTNode const > utility::tag::XMLSchemaRepeatableCTNodeCOP

XMLSchemaRepeatableCTNodeOP

typedef utility::pointer::shared_ptr< XMLSchemaRepeatableCTNode > utility::tag::XMLSchemaRepeatableCTNodeOP

XMLSchemaRestrictionCOP

typedef utility::pointer::shared_ptr< XMLSchemaRestriction const > utility::tag::XMLSchemaRestrictionCOP

XMLSchemaRestrictionOP

typedef utility::pointer::shared_ptr< XMLSchemaRestriction > utility::tag::XMLSchemaRestrictionOP

XMLSchemaSimpleSubelementListCOP

typedef utility::pointer::shared_ptr< XMLSchemaSimpleSubelementList const > utility::tag::XMLSchemaSimpleSubelementListCOP

XMLSchemaSimpleSubelementListOP

typedef utility::pointer::shared_ptr< XMLSchemaSimpleSubelementList > utility::tag::XMLSchemaSimpleSubelementListOP

XMLSchemaTypeCOP

typedef utility::pointer::shared_ptr< XMLSchemaType const > utility::tag::XMLSchemaTypeCOP

XMLSchemaTypeOP

typedef utility::pointer::shared_ptr< XMLSchemaType > utility::tag::XMLSchemaTypeOP

XMLSchemaValidatorCOP

typedef utility::pointer::shared_ptr< XMLValidator const > utility::tag::XMLSchemaValidatorCOP

XMLSchemaValidatorOP

typedef utility::pointer::shared_ptr< XMLValidator > utility::tag::XMLSchemaValidatorOP

Enumeration Type Documentation

AutoBool

enum utility::tag::AutoBool

strong

Enumerator
False
True
Auto

CTGenSubelementBehavior

enum utility::tag::CTGenSubelementBehavior

Enumerator
se_none
se_repeatable
se_choice_req
se_choice_opt
se_single_req
se_single_opt
se_single_req_ordered
se_ordered_sets

XMLSchemaCommonType

enum utility::tag::XMLSchemaCommonType

An enum listing lots of commonly-used simple types so they don't have to be added manually in lots of places. If you create an XMLSchemaType using this enum, then the corresponding restriction will be added to the XMLSchemaDefintion automatically.

Enumerator
xsct_none
xsct_int_cslist
xsct_string_cslist
xsct_int_wsslist
xsct_nnegative_int_cslist
xsct_nnegative_int_wsslist
xsct_real
xsct_real_cslist
xsct_real_cslist_w_ws
xsct_real_wsslist
xsct_bool_cslist
xsct_bool_wsslist
xsct_positive_integer_cslist
xsct_positive_integer_wsslist
xsct_non_negative_integer
xsct_positive_integer
xsct_rosetta_bool
xsct_rosetta_autobool
xsct_residue_number
xsct_residue_number_cslist
xsct_refpose_enabled_residue_number
xsct_refpose_enabled_residue_number_cslist
xsct_char
xsct_minimizer_type
xsct_size_cs_pair
xsct_chain_cslist
xsct_dssp_string
xsct_canonical_res_char
xsct_packer_palette
xsct_task_operation
xsct_task_operation_comma_separated_list
xsct_pose_cached_task_operation

XMLSchemaDataType

enum utility::tag::XMLSchemaDataType

The simple types provided by the XMLSchema language itself. These are not always the types that you want to use.

In particular, xs_decimal does not support scientific notation, so you probably want to use xsct_real (defined in the XMLSchemaCommonType enumeration in XMLSchemaGeneration.hh) to represent real-valued numbers.

Also, the boolean-value reading function in tag::getOption< bool > accepts more values for "true" and "false" than the xs_boolean so you want to use xsct_rosetta_bool in your schemas instead.

Enumerator
xs_string
xs_decimal
xs_integer
xs_boolean
xs_date
xs_time
xs_common
xs_custom

XMLSchemaElementCategory

enum utility::tag::XMLSchemaElementCategory

Enumerator
xs_element_is_type_reference
xs_element_is_abstract
xs_element_is_complex_type_w_definition
xs_element_is_element_reference

XMLSchemaMinOccursMaxOccurs

enum utility::tag::XMLSchemaMinOccursMaxOccurs

Enumerator
xsminmax_unbounded
xsminmax_unspecified

XMLSchemaModelGroupType

enum utility::tag::XMLSchemaModelGroupType

Enumerator
xsmgt_sequence
xsmgt_all
xsmgt_choice
xsmgt_group

XMLSchemaRestrictionType

enum utility::tag::XMLSchemaRestrictionType

Enumerator
xsr_enumeration
xsr_fractionDigits
xsr_length
xsr_maxExclusive
xsr_maxInclusive
xsr_maxLength
xsr_minExclusive
xsr_minInclusive
xsr_minLength
xsr_pattern
xsr_totalDigits
xsr_whitespace

Function Documentation

activate_common_simple_type()

void utility::tag::activate_common_simple_type	(	utility::tag::XMLSchemaDefinition &	xsd,
		XMLSchemaCommonType	common_type
	)

References utility::tag::XMLSchemaRestriction::add_restriction(), utility::tag::XMLSchemaDefinition::add_top_level_element(), utility::tag::XMLSchemaRestriction::base_type(), canonical_res_char_string(), chain_cslist_string(), utility::tag::XMLSchemaRestriction::name(), name_for_common_type(), basic::options::OptionKeys::james::real, real_regex_pattern(), refpose_enabled_residue_number_cslist_string(), refpose_enabled_residue_number_string(), residue_number_cslist_string(), residue_number_string(), rosetta_autobool_string(), rosetta_bool_string(), task_operation_name_pattern(), xs_integer, xs_string, xsct_bool_cslist, xsct_bool_wsslist, xsct_canonical_res_char, xsct_chain_cslist, xsct_char, xsct_dssp_string, xsct_int_cslist, xsct_int_wsslist, xsct_minimizer_type, xsct_nnegative_int_cslist, xsct_nnegative_int_wsslist, xsct_non_negative_integer, xsct_packer_palette, xsct_pose_cached_task_operation, xsct_positive_integer, xsct_positive_integer_cslist, xsct_positive_integer_wsslist, xsct_real, xsct_real_cslist, xsct_real_cslist_w_ws, xsct_real_wsslist, xsct_refpose_enabled_residue_number, xsct_refpose_enabled_residue_number_cslist, xsct_residue_number, xsct_residue_number_cslist, xsct_rosetta_autobool, xsct_rosetta_bool, xsct_size_cs_pair, xsct_string_cslist, xsct_task_operation, xsct_task_operation_comma_separated_list, xsr_enumeration, xsr_maxLength, xsr_minInclusive, and xsr_pattern.

Referenced by utility::tag::XMLSchemaAttribute::prepare_for_output(), utility::tag::XMLSchemaRestriction::prepare_for_output(), and utility::tag::XMLSchemaElement::prepare_for_output().

add_schema_restrictions_for_strings()

void utility::tag::add_schema_restrictions_for_strings	(	XMLSchemaDefinition &	xsd,
		std::string	type_name,
		vector1< std::string > const &	restrictions
	)

Add a SchemaRestriction for a set of strings. Useful for enums. The type name is then used as the type when adding an attribute.

Example: attlist+ XMLScemaAttribute(tag_name, type_name, description);

References utility::tag::XMLSchemaRestriction::add_restriction(), utility::tag::XMLSchemaDefinition::add_top_level_element(), utility::tag::XMLSchemaRestriction::base_type(), utility::tag::XMLSchemaRestriction::name(), res, xs_string, and xsr_enumeration.

append_name_and_attributes_to_complex_type()

void utility::tag::append_name_and_attributes_to_complex_type	(	AttributeList const &	attributes,
		XMLSchemaComplexType &	type_definition
	)

append an attribute of "name" with type "xs:string" along with the other attributes in the input attribute list to the input complex type.

Most XML tags have a "name" attribute; this function does not require that the name be provided.

References utility::tag::XMLSchemaComplexType::add_attribute(), utility::tag::XMLSchemaComplexType::add_attributes(), and optional_name_attribute().

append_required_name_and_attributes_to_complex_type()

void utility::tag::append_required_name_and_attributes_to_complex_type	(	AttributeList const &	attributes,
		XMLSchemaComplexType &	type_definition
	)

append a required attribute of "name" with type "xs:string" along with the other attributes in the input attribute list to the input complex type.

Most XML tags in Rosetta have a "name" attribute; this function appends an attribute "name" and states that the attribute is required

References utility::tag::XMLSchemaComplexType::add_attribute(), utility::tag::XMLSchemaComplexType::add_attributes(), and required_name_attribute().

attribute_w_name_in_attribute_list()

bool utility::tag::attribute_w_name_in_attribute_list	(	std::string const &	attname,
		AttributeList const &	attlist
	)

check whether an attribute with name attname already exists in AttributeList attlist to avoid collisions

Referenced by basic::resource_manager::resource_loader_xsd_type_definition_w_attributes(), basic::resource_manager::resource_loader_xsd_type_definition_w_attributes_and_repeatable_subelements(), basic::resource_manager::locator::xsd_type_definition_w_attributes(), and basic::resource_manager::locator::xsd_type_definition_w_attributes_and_repeatable_subelements().

canonical_res_char_string()

std::string utility::tag::canonical_res_char_string

(

)

Referenced by activate_common_simple_type().

chain_cslist_string()

std::string utility::tag::chain_cslist_string

(

)

References chr_chains_nonrepeated().

Referenced by activate_common_simple_type().

chr_chains_nonrepeated()

std::string utility::tag::chr_chains_nonrepeated

(

)

Referenced by chain_cslist_string().

concat_stringlist()

std::string utility::tag::concat_stringlist

(

std::list< std::string > const &

strings

)

References test.T008_Serialization::oss.

Referenced by utility::tag::XMLValidationOutput::error_messages(), and utility::tag::XMLValidationOutput::warning_messages().

define_xml_schema_group()

template<class Creator >

void utility::tag::define_xml_schema_group	(	typename std::map< std::string, utility::pointer::shared_ptr< Creator > > const &	creator_map,
		std::string const &	widget_group_name,
		std::function< std::string(std::string const &) > const &	complex_type_name_for_widget_func,
		XMLSchemaDefinition &	xsd
	)

Creator must define a single function: provide_xml_schema()

Exceptions

In

the event that the Creator does not define a complex type with the name coming from the complex_type_name_for_widget_func, this function will throw a utility::excn::Excn_Msg_Excption. Classes calling this function should wrap it in a try/catch block and append extra information informing the user (presumably the programmer) which function should be called when defining the schema for the offending class.

References utility::tag::XMLSchemaDefinition::add_top_level_element(), utility::tag::XMLSchemaModelGroup::append_particle(), CREATE_EXCEPTION, test.T009_Exceptions::e, utility::tag::XMLSchemaModelGroup::group_name(), utility::tag::XMLSchemaDefinition::has_top_level_element(), and xsmgt_choice.

element_type_name()

std::string utility::tag::element_type_name

(

xmlElementType

element_type

)

Referenced by utility::xsd_util::get_rosetta_module_options_from_xsd(), and print_node_stack().

handle_structured_xml_error()

void utility::tag::handle_structured_xml_error	(	void *	ctxt,
		xmlErrorPtr	error
	)

References closure_error::error, and test.T008_Serialization::oss.

Referenced by utility::tag::XMLValidatorImpl::set_schema(), test_if_schema_is_valid(), utility::tag::XMLValidatorImpl::validate_xml_against_schema(), and validate_xml_against_xsd().

handle_xml_error()

void utility::tag::handle_xml_error	(	void *	ctxt,
		char const *	message,
			...
	)

References find_lowest_scoring_relaxed_struct::args, utility::tag::XMLErrorHandler::handle_xml_error(), oop_conformations::length, length_of_message(), make_message(), and pyrosetta.utility.array::message.

handle_xml_warning()

void utility::tag::handle_xml_warning	(	void *	ctxt,
		char const *	message,
			...
	)

References find_lowest_scoring_relaxed_struct::args, utility::tag::XMLErrorHandler::handle_xml_warning(), oop_conformations::length, length_of_message(), make_message(), and pyrosetta.utility.array::message.

indent_w_spaces()

void utility::tag::indent_w_spaces	(	int	indentation,
		std::ostream &	os
	)

References create_a3b_hbs::ii.

Referenced by utility::tag::XMLSchemaAttribute::write_definition(), utility::tag::XMLSchemaRestriction::write_definition(), utility::tag::XMLSchemaModelGroup::write_definition(), utility::tag::XMLSchemaComplexType::write_definition(), and utility::tag::XMLSchemaElement::write_definition().

integer_range_restriction()

XMLSchemaRestriction utility::tag::integer_range_restriction	(	std::string const &	name,
		int	lower,
		int	upper
	)

Convenience function for defining an inclusive range restriction.

References utility::tag::XMLSchemaRestriction::add_restriction(), utility::tag::XMLSchemaRestriction::base_type(), utility::lower(), utility::tag::XMLSchemaRestriction::name(), utility::to_string(), utility::upper(), xs_integer, xsr_maxInclusive, and xsr_minInclusive.

length_of_message()

int utility::tag::length_of_message	(	const char *	message,
		va_list	args
	)

References find_lowest_scoring_relaxed_struct::args, and pyrosetta.utility.array::message.

Referenced by handle_xml_error(), and handle_xml_warning().

make_message()

char* utility::tag::make_message	(	int	length,
		const char *	message,
		va_list	args
	)

References find_lowest_scoring_relaxed_struct::args, oop_conformations::length, and pyrosetta.utility.array::message.

Referenced by handle_xml_error(), and handle_xml_warning().

name_for_common_type()

std::string utility::tag::name_for_common_type

(

XMLSchemaCommonType

common_type

)

References CREATE_EXCEPTION, xsct_bool_cslist, xsct_bool_wsslist, xsct_canonical_res_char, xsct_chain_cslist, xsct_char, xsct_dssp_string, xsct_int_cslist, xsct_int_wsslist, xsct_minimizer_type, xsct_nnegative_int_cslist, xsct_nnegative_int_wsslist, xsct_non_negative_integer, xsct_none, xsct_packer_palette, xsct_pose_cached_task_operation, xsct_positive_integer, xsct_positive_integer_cslist, xsct_positive_integer_wsslist, xsct_real, xsct_real_cslist, xsct_real_cslist_w_ws, xsct_real_wsslist, xsct_refpose_enabled_residue_number, xsct_refpose_enabled_residue_number_cslist, xsct_residue_number, xsct_residue_number_cslist, xsct_rosetta_autobool, xsct_rosetta_bool, xsct_size_cs_pair, xsct_string_cslist, xsct_task_operation, and xsct_task_operation_comma_separated_list.

Referenced by activate_common_simple_type(), operator<<(), and utility::tag::XMLSchemaType::type_name().

operator+()

AttributeList& utility::tag::operator+	(	AttributeList &	attributes,
		XMLSchemaAttribute const &	attribute_to_append
	)

operator<<() [1/5]

std::ostream & utility::tag::operator<<	(	std::ostream &	os,
		XMLSchemaCommonType	common_type
	)

References name_for_common_type().

operator<<() [2/5]

std::ostream & utility::tag::operator<<	(	std::ostream &	os,
		XMLSchemaModelGroupType	type
	)

References xs_model_group_name().

operator<<() [3/5]

std::ostream & utility::tag::operator<<	(	std::ostream &	os,
		XMLSchemaRestrictionType	type
	)

References restriction_type_name().

operator<<() [4/5]

std::ostream & utility::tag::operator<<	(	std::ostream &	out,
		Tag const &	tag
	)

References erraser_single_res_analysis::out, and tag.

operator<<() [5/5]

std::ostream & utility::tag::operator<<	(	std::ostream &	out,
		TagCOP const &	tag_ptr
	)

References erraser_single_res_analysis::out.

optional_name_attribute()

XMLSchemaAttribute utility::tag::optional_name_attribute

(

std::string const &

desc

)

This function creates an attribute named "name" of type xs_string that is optional; naming is not always required – it is not even mostly required. This is probably the function you need; very few classes actually need to have a name – the name is often only used by the function reading in the name, but there are reasonable times when a Mover, e.g. could go nameless – for instance, in the fixbb_jd3 application, a PackRotamersMover can be given as a subtag of the <Job> tag. In this case, the PackRotamersMover doesn't need to be given a name.

References options_will::desc, and xs_string.

Referenced by utility::tag::XMLSchemaComplexTypeGenerator::add_optional_name_attribute(), append_name_and_attributes_to_complex_type(), basic::resource_manager::resource_loader_xsd_type_definition_w_attributes(), basic::resource_manager::resource_loader_xsd_type_definition_w_attributes_and_repeatable_subelements(), basic::resource_manager::locator::xsd_type_definition_w_attributes(), and basic::resource_manager::locator::xsd_type_definition_w_attributes_and_repeatable_subelements().

print_node_stack()

void utility::tag::print_node_stack	(	utility::vector1< xmlNode * > const &	node_stack,
		std::ostringstream &	oss
	)

References element_type_name(), create_a3b_hbs::ii, and test.T008_Serialization::oss.

real_regex_pattern()

std::string utility::tag::real_regex_pattern

(

)

Referenced by activate_common_simple_type().

recurse_through_tree()

int utility::tag::recurse_through_tree	(	xmlSchemaValidCtxtPtr	ctxt,
		xmlNodePtr	node,
		XMLErrorHandler	handler
	)

References closure_error::error, utility::tag::XMLErrorHandler::pop_node(), and utility::tag::XMLErrorHandler::push_node().

refpose_enabled_residue_number_cslist_string()

std::string utility::tag::refpose_enabled_residue_number_cslist_string

(

)

References refpose_enabled_residue_number_string().

Referenced by activate_common_simple_type().

refpose_enabled_residue_number_string()

std::string utility::tag::refpose_enabled_residue_number_string

(

)

Referenced by activate_common_simple_type(), and refpose_enabled_residue_number_cslist_string().

required_name_attribute()

XMLSchemaAttribute utility::tag::required_name_attribute

(

std::string const &

desc

)

This function creates an attribute named "name" of type xs_string that is required; naming is not always required – it is not even mostly required. This function is probably not what you need. Use with care. See comments for the "optional_name_attribute" function above.

References options_will::desc, utility::tag::XMLSchemaAttribute::required_attribute(), and xs_string.

Referenced by utility::tag::XMLSchemaComplexTypeGenerator::add_required_name_attribute(), append_required_name_and_attributes_to_complex_type(), and basic::resource_manager::ResourceManager::schema_for_resource_definition_file().

residue_number_cslist_string()

std::string utility::tag::residue_number_cslist_string

(

)

Referenced by activate_common_simple_type().

residue_number_string()

std::string utility::tag::residue_number_string

(

)

Referenced by activate_common_simple_type().

restriction_type_name()

std::string utility::tag::restriction_type_name

(

XMLSchemaRestrictionType

type

)

References xsr_enumeration, xsr_fractionDigits, xsr_length, xsr_maxExclusive, xsr_maxInclusive, xsr_maxLength, xsr_minExclusive, xsr_minInclusive, xsr_minLength, xsr_pattern, xsr_totalDigits, and xsr_whitespace.

Referenced by operator<<().

rosetta_autobool_string()

std::string utility::tag::rosetta_autobool_string

(

)

References rosetta_bool_string().

Referenced by activate_common_simple_type().

rosetta_bool_string()

std::string utility::tag::rosetta_bool_string

(

)

the set of all strings recognized as booleans according to Rosetta (in utility/string_util.cc)

Referenced by activate_common_simple_type(), and rosetta_autobool_string().

string_contains_gt_lt_or_ampersand()

char utility::tag::string_contains_gt_lt_or_ampersand

(

std::string const &

str

)

Check if given string contain any of '<>&' and if so return found character. If no character is found return 0.

Check if given string contain any of '<>&' and if so return found character. If no character is found return 0.

References str().

Referenced by utility::tag::XMLSchemaSimpleSubelementList::add_simple_subelement(), utility::tag::XMLSchemaComplexTypeGeneratorImpl::description(), utility::tag::XMLSchemaAttribute::description(), utility::tag::XMLSchemaComplexType::description(), utility::tag::XMLSchemaSimpleSubelementList::element_summary_as_simple_subelement(), utility::tag::XMLSchemaRepeatableCTNode::set_element_w_attributes(), and utility::tag::XMLSchemaAttribute::XMLSchemaAttribute().

Tag::getOption< platform::Size >()

template<>

platform::Size utility::tag::Tag::getOption< platform::Size >	(	std::string const &	key,
		int const	default_int
	)		const

Special-casing to ensure that 0 gets interpreted as Size(0) rather than nullptr.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References subloop_histogram::key, and runtime_assert_string_msg.

Tag::getOption< std::string >()

template<>

std::string utility::tag::Tag::getOption< std::string >	(	std::string const &	key,
		char const *	default_as_string_literal
	)		const

Special-casing the string literal version for string options. In this case, there shouldn't be an error thrown. A string literal should be allowed to set the default value for a string.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References subloop_histogram::key, and runtime_assert_string_msg.

task_operation_name_pattern()

std::string utility::tag::task_operation_name_pattern

(

)

Referenced by activate_common_simple_type().

test_if_schema_is_valid()

XMLValidationOutput utility::tag::test_if_schema_is_valid

(

std::string const &

xsd_string

)

References utility::tag::XMLErrorHandler::errors(), handle_structured_xml_error(), bin_torsions::output, utility::tag::XMLErrorHandler::set_file_contents(), and utility::tag::XMLErrorHandler::warnings().

validate_xml_against_xsd()

XMLValidationOutput utility::tag::validate_xml_against_xsd	(	std::string const &	xml_string,
		std::string const &	xsd_string
	)

References utility::tag::XMLErrorHandler::errors(), free(), handle_structured_xml_error(), test.T008_Serialization::oss, bin_torsions::output, utility::tag::XMLErrorHandler::set_file_contents(), and utility::tag::XMLErrorHandler::warnings().

write_min_occurs_max_occurs_if_necessary()

void utility::tag::write_min_occurs_max_occurs_if_necessary	(	int	min_occurs,
		int	max_occurs,
		std::ostream &	os
	)

Use "-1" for unspecified, use -2 for "unbounded"

References xsminmax_unbounded, and xsminmax_unspecified.

Referenced by utility::tag::XMLSchemaModelGroup::write_definition(), and utility::tag::XMLSchemaElement::write_definition().

xs_model_group_name()

std::string utility::tag::xs_model_group_name

(

XMLSchemaModelGroupType

xsmgt

)

References xsmgt_all, xsmgt_choice, xsmgt_group, and xsmgt_sequence.

Referenced by operator<<().