ajobodata

Data type AjPOboin

Holds the obo term specification and information needed to read the obo term and possible further terms.

Alias name(s)

Name
AjSOboin
AjOOboin

Attributes

Name	Type	Description
Input	AjPTextin	General text input object
OboData	void*	Format data for reuse, e.g. multiple term input (unused in current code)

Data type AjPOboAccess

Holds information needed to read an obo term from a database. Access methods are defined for each known database type.

Obo terms are read from the database using the defined database access function, which is usually a static function within ajobodb.c

This should be a static data object but is needed for the definition of AjPOboin.

Alias name(s)

Name
AjSOboAccess
AjOOboAccess

Constructor(s)

Name	Description
ajOboMethod	returns a copy of a known access method definition.

Other related data structure(s)

Name	Description
AjPOboin	Obo input

Attributes

Name	Type	Description
Name	const char*	Access method name used in emboss.default
Access	AjBool function	Access function
AccessFree	AjBool function	Access cleanup function
Qlink	const char*	Supported query link operators
Desc	const char*	Description
Alias	AjBool	Alias for another name
Entry	AjBool	Supports retrieval of single entries
Query	AjBool	Supports retrieval of selected entries
All	AjBool	Supports retrieval of all entries
Chunked	AjBool	Supports retrieval of entries in chunks
Padding	AjBool	Padding to alignment boundary

Data type AjPOboData

Attributes

Name	Type	Description
Termtable	AjPTable	Table of terms by id
Termnametable	AjPTable	Table of terms by name
Typedeftable	AjPTable	Table of typedefs
Instancetable	AjPTable	Table of instances
Annotable	AjPTable	Table of annotation stanzas
Formulatable	AjPTable	Table of formula stanzas
Misctable	AjPTable	Table of other stanzas

Data type AjPObotag

Alias name(s)

Name
AjSObotag
AjOObotag

Attributes

Name	Type	Description
Name	AjPStr	Tag name
Value	AjPStr	Tag value
Modifier	AjPStr	Tag modifier
Comment	AjPStr	Tag comment
Linenumber	ajuint	OBO file line number
Padding	ajuint	Padding to align structure

Data type AjPOboxref

Alias name(s)

Name
AjSOboxref
AjOOboxref

Attributes

Name	Type	Description
Name	AjPStr	Dbxref name
Desc	AjPStr	Description (optional)

Data type AjPOboalias

Alias name(s)

Name
AjSOboalias
AjOOboalias

Attributes

Name	Type	Description
Alias	AjPStr	Alias name of term
Id	AjPStr	Id of term

Data type AjPObo

Holds the term itself, plus associated information.

Alias name(s)

Name
AjOObo
AjSObo

Attributes

Name	Type	Description
Id	AjPStr	Id of term
Trueid	AjPStr	True id of an alt_id
Fullid	AjPStr	Id of term with prefix
Name	AjPStr	Name of term
Namespace	AjPStr	Namespace of term
Def	AjPStr	Definition of term
Dbxrefs	AjPList	List of AjPOboxref names descriptions and modifiers
Comment	AjPStr	Comment tag in term stanza
Replaced	AjPStr	Replacement term for an obsolete term
Taglist	AjPList	List of other AjPObotag tag name-value pairs
Obsolete	AjBool	True if term is obsolete
Builtin	AjBool	True if term is an OBO Built-in term
Db	AjPStr	Database name from input
Setdb	AjPStr	Database name from command line
Full	AjPStr	Full name
Qry	AjPStr	Query for re-reading
Formatstr	AjPStr	Input format name
Filename	AjPStr	Original filename
TextPtr	AjPStr	Full text
Fpos	ajlong	File position (fseek) for Query
Format	AjEnum	Input format enum
Padding	ajuint	Padding to alignment boundary

Data type AjPOboall

Inherits an AjPObo but allows more obo terms to be read from the same input by also inheriting the AjPOboin input object.

Alias name(s)

Name
AjSOboall
AjOOboall

Attributes

Name	Type	Description
Obo	AjPObo	Current term
Oboin	AjPOboin	Obo input for reading next
Totterms	ajulong	Count of terms so far
Count	ajuint	Count of terms so far
Multi	AjBool	True if multiple values are expected
Returned	AjBool	if true: Obo object has been returned to a new owner and is not to be deleted by the destructor
Padding	char[4]	Padding to alignment boundary