ajobo.c

Datatypes: AjPObo AjPObotag AjPOboxref none

Datatype: AjPObo

Obo Term

Sections: constructors OBO term destructors Casts obo term modifiers

Section: constructors

Constructors

Functions: ajOboNew ajOboNewObo

Function ajOboNew

Term constructor

Synopsis

Prototype
AjPObo ajOboNew (
      void
);

TypeNameRead/WriteDescription
AjPObo RETURNNew object

Returns
AjPObo:New object

Description

Term constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboNewObo

Term copy constructor

Synopsis

Prototype
AjPObo ajOboNewObo (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputObo term
AjPObo RETURNNew object

Input
obo:(Input)Obo term
Returns
AjPObo:New object

Description

Term copy constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Section: OBO term destructors

Destruction destroys all internal data structures and frees the memory allocated for the obo term object.

Functions: ajOboDel

Function ajOboDel

Term destructor

Synopsis

Prototype
void ajOboDel (
      AjPObo* Pobo
);

TypeNameRead/WriteDescription
AjPObo*PoboDeleteObo term object to delete
void RETURN

Output
Pobo:(Delete)Obo term object to delete
Returns
void:No return value

Description

Term destructor

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Casts

Return values from an obo term object

Functions: ajOboGetDb ajOboGetDef ajOboGetEntry ajOboGetId ajOboGetNamespace ajOboGetParents ajOboGetQryC ajOboGetQryS ajOboGetReplaced ajOboGetTree ajOboIsObsolete

Function ajOboGetDb

Return the database name

Synopsis

Prototype
const AjPStr ajOboGetDb (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
const AjPStr RETURNDatabase name

Input
obo:(Input)OBO term
Returns
const AjPStr:Database name

Description

Return the database name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetDef

Return the definition string and the number of dbxrefs

Synopsis

Prototype
AjBool ajOboGetDef (
      const AjPObo obo,
      AjPStr* Pdefstr,
      ajuint* nrefs
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
AjPStr*PdefstrOutputReturned definition string
ajuint*nrefsOutputNumber of dbxrefs after the definition
AjBool RETURNTrue on success.

Input
obo:(Input)OBO term
Output
Pdefstr:(Output)Returned definition string
nrefs:(Output)Number of dbxrefs after the definition
Returns
AjBool:True on success.

Description

Return the definition string and the number of dbxrefs

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetEntry

Return the full text

Synopsis

Prototype
const AjPStr ajOboGetEntry (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
const AjPStr RETURNReturned full text

Input
obo:(Input)OBO term
Returns
const AjPStr:Returned full text

Description

Return the full text

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetId

Return the identifier

Synopsis

Prototype
const AjPStr ajOboGetId (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
const AjPStr RETURNReturned id

Input
obo:(Input)OBO term
Returns
const AjPStr:Returned id

Description

Return the identifier

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetNamespace

Return the namespace name

Synopsis

Prototype
const AjPStr ajOboGetNamespace (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
const AjPStr RETURNReturned namespace

Input
obo:(Input)OBO term
Returns
const AjPStr:Returned namespace

Description

Return the namespace name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetParents

Return a list of all parent terms derived from is_a tags in the current obo term

Synopsis

Prototype
ajuint ajOboGetParents (
      const AjPObo obo,
      AjPList uplist
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
AjPListuplistModifyList of parent terms
ajuint RETURNNumber of new terms added to list

Input
obo:(Input)OBO term
Input & Output
uplist:(Modify)List of parent terms
Returns
ajuint:Number of new terms added to list

Description

Return a list of all parent terms derived from is_a tags in the current obo term

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetQryC

Returns the query string of an obo term. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype
const char* ajOboGetQryC (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputObo term object.
const char* RETURNQuery as a character string.

Input
obo:(Input)Obo term object.
Returns
const char*:Query as a character string.

Description

Returns the query string of an obo term. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetQryS

Returns the query string of an obo term. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Synopsis

Prototype
const AjPStr ajOboGetQryS (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputObo term object.
const AjPStr RETURNQuery as a string.

Input
obo:(Input)Obo term object.
Returns
const AjPStr:Query as a string.

Description

Returns the query string of an obo term. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetReplaced

Return the recommended replacement for an obsolete term

Synopsis

Prototype
const AjPStr ajOboGetReplaced (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
const AjPStr RETURNReturned id

Input
obo:(Input)OBO term
Returns
const AjPStr:Returned id

Description

Return the recommended replacement for an obsolete term

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboGetTree

Return a list with all this term's descendants appended

Synopsis

Prototype
ajuint ajOboGetTree (
      const AjPObo obo,
      AjPList obolist
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
AjPListobolistModifyList of obo terms
ajuint RETURNNumber of terms returned

Input
obo:(Input)OBO term
Input & Output
obolist:(Modify)List of obo terms
Returns
ajuint:Number of terms returned

Description

Return a list with all this term's descendants appended

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboIsObsolete

Test whether an obo term is obsolete

Synopsis

Prototype
AjBool ajOboIsObsolete (
      const AjPObo obo
);

TypeNameRead/WriteDescription
const AjPObooboInputOBO term
AjBool RETURNTrue if term is obsolete

Input
obo:(Input)OBO term
Returns
AjBool:True if term is obsolete

Description

Test whether an obo term is obsolete

See Also

See other functions in this section

Availability

In release 6.4.0

Section: obo term modifiers

Obo term modifiers

Functions: ajOboClear

Function ajOboClear

Resets all data for an obo term object so that it can be reused.

Synopsis

Prototype
void ajOboClear (
      AjPObo obo
);

TypeNameRead/WriteDescription
AjPObooboModifyObo term
void RETURN

Input & Output
obo:(Modify)Obo term
Returns
void:No return value

Description

Resets all data for an obo term object so that it can be reused.

See Also

See other functions in this section

Availability

In release 6.4.0

Datatype: AjPObotag

Obo tags

Sections: constructors obo tag destructors

Section: constructors

Constructors

Functions: ajObotagNewData ajObotagNewTag

Function ajObotagNewData

Tag constructor

Synopsis

Prototype
AjPObotag ajObotagNewData (
      const AjPStr name,
      const AjPStr value,
      const AjPStr modifier,
      const AjPStr comment,
      ajuint linenum
);

TypeNameRead/WriteDescription
const AjPStrnameInputName
const AjPStrvalueInputValue
const AjPStrmodifierInputModifier
const AjPStrcommentInputComment
ajuintlinenumInputOBO file line number
AjPObotag RETURNNew object

Input
name:(Input)Name
value:(Input)Value
modifier:(Input)Modifier
comment:(Input)Comment
linenum:(Input)OBO file line number
Returns
AjPObotag:New object

Description

Tag constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajObotagNewTag

Tag copy constructor

Synopsis

Prototype
AjPObotag ajObotagNewTag (
      const AjPObotag tag
);

TypeNameRead/WriteDescription
const AjPObotagtagInputObo tag
AjPObotag RETURNNew object

Input
tag:(Input)Obo tag
Returns
AjPObotag:New object

Description

Tag copy constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Section: obo tag destructors

Destruction destroys all internal data structures and frees the memory allocated for the obo tag object.

Functions: ajObotagDel

Function ajObotagDel

Tag destructor

Synopsis

Prototype
void ajObotagDel (
      AjPObotag* Ptag
);

TypeNameRead/WriteDescription
AjPObotag*PtagDeleteTag object to delete
void RETURN

Output
Ptag:(Delete)Tag object to delete
Returns
void:No return value

Description

Tag destructor

See Also

See other functions in this section

Availability

In release 6.4.0

Datatype: AjPOboxref

Obo dbxrefs

Sections: constructors obo dbxref destructors

Section: constructors

Constructors

Functions: ajOboxrefNewData ajOboxrefNewXref

Function ajOboxrefNewData

Dbxref constructor

Synopsis

Prototype
AjPOboxref ajOboxrefNewData (
      const AjPStr name,
      const AjPStr desc
);

TypeNameRead/WriteDescription
const AjPStrnameInputName
const AjPStrdescInputDescription
AjPOboxref RETURNNew object

Input
name:(Input)Name
desc:(Input)Description
Returns
AjPOboxref:New object

Description

Dbxref constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajOboxrefNewXref

Dbxref copy constructor

Synopsis

Prototype
AjPOboxref ajOboxrefNewXref (
      const AjPOboxref xref
);

TypeNameRead/WriteDescription
const AjPOboxrefxrefInputDbxref
AjPOboxref RETURNNew object

Input
xref:(Input)Dbxref
Returns
AjPOboxref:New object

Description

Dbxref copy constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Section: obo dbxref destructors

Destruction destroys all internal data structures and frees the memory allocated for the obo dbxref object.

Functions: ajOboxrefDel

Function ajOboxrefDel

Dbxref destructor

Synopsis

Prototype
void ajOboxrefDel (
      AjPOboxref* Pxref
);

TypeNameRead/WriteDescription
AjPOboxref*PxrefDeleteDbxref object to delete
void RETURN

Output
Pxref:(Delete)Dbxref object to delete
Returns
void:No return value

Description

Dbxref destructor

See Also

See other functions in this section

Availability

In release 6.4.0

Datatype: none

Miscellaneous functions

Sections: Miscellaneous

Section: Miscellaneous

Functions to initialise and clean up internals

Functions: ajOboExit

Function ajOboExit

Cleans up obo term internal memory

Synopsis

Prototype
void ajOboExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up obo term internal memory

See Also

See other functions in this section

Availability

In release 6.4.0