ajobo.c

Datatypes:

AjPObo	Obo Term
AjPObotag	Obo tags
AjPOboxref	Obo dbxrefs
none	Miscellaneous functions

Datatype: AjPObo

Sections:

constructors	Constructors
OBO term destructors	Destructors
Casts	Casts
obo term modifiers	Modifiers

AjPObo: constructors

Functions:

ajOboNew	Term constructor
ajOboNewObo	Term copy constructor

Function ajOboNew

Prototype

AjPObo ajOboNew (
      void
);

Type	Name	Read/Write	Description
AjPObo		RETURN	New object

From EMBOSS 6.3.0

Function ajOboNewObo

Prototype

AjPObo ajOboNewObo (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	Obo term
AjPObo		RETURN	New object

From EMBOSS 6.4.0

AjPObo: OBO term destructors

Functions:

ajOboDel

Term destructor

Function ajOboDel

Prototype

void ajOboDel (
      AjPObo* Pobo
);

Type	Name	Read/Write	Description
AjPObo*	Pobo	Delete	Obo term object to delete
void		RETURN

From EMBOSS 6.4.0

AjPObo: Casts

Functions:

ajOboGetDb	Return the database name
ajOboGetDef	Return the definition string and the number of dbxrefs
ajOboGetEntry	Return the full text
ajOboGetId	Return the identifier
ajOboGetNamespace	Return the namespace name
ajOboGetParents	Return a list of all parent terms derived from is_a tags in the current obo term
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.
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.
ajOboGetReplaced	Return the recommended replacement for an obsolete term
ajOboGetTree	Return a list with all this term's descendants appended
ajOboIsObsolete	Test whether an obo term is obsolete

Function ajOboGetDb

Prototype

const AjPStr ajOboGetDb (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
const AjPStr		RETURN	Database name

From EMBOSS 6.4.0

Function ajOboGetDef

Prototype

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

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
AjPStr*	Pdefstr	Output	Returned definition string
ajuint*	nrefs	Output	Number of dbxrefs after the definition
AjBool		RETURN	True on success.

From EMBOSS 6.4.0

Function ajOboGetEntry

Prototype

const AjPStr ajOboGetEntry (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
const AjPStr		RETURN	Returned full text

From EMBOSS 6.4.0

Function ajOboGetId

Prototype

const AjPStr ajOboGetId (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
const AjPStr		RETURN	Returned id

From EMBOSS 6.4.0

Function ajOboGetNamespace

Prototype

const AjPStr ajOboGetNamespace (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
const AjPStr		RETURN	Returned namespace

From EMBOSS 6.4.0

Function ajOboGetParents

Prototype

ajuint ajOboGetParents (
      const AjPObo obo,
      AjPList uplist
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
AjPList	uplist	Modify	List of parent terms
ajuint		RETURN	Number of new terms added to list

From EMBOSS 6.4.0

Function ajOboGetQryC

Prototype

const char* ajOboGetQryC (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	Obo term object.
const char*		RETURN	Query as a character string.

From EMBOSS 6.4.0

Function ajOboGetQryS

Prototype

const AjPStr ajOboGetQryS (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	Obo term object.
const AjPStr		RETURN	Query as a string.

From EMBOSS 6.4.0

Function ajOboGetReplaced

Prototype

const AjPStr ajOboGetReplaced (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
const AjPStr		RETURN	Returned id

From EMBOSS 6.4.0

Function ajOboGetTree

Prototype

ajuint ajOboGetTree (
      const AjPObo obo,
      AjPList obolist
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
AjPList	obolist	Modify	List of obo terms
ajuint		RETURN	Number of terms returned

From EMBOSS 6.4.0

Function ajOboIsObsolete

Prototype

AjBool ajOboIsObsolete (
      const AjPObo obo
);

Type	Name	Read/Write	Description
const AjPObo	obo	Input	OBO term
AjBool		RETURN	True if term is obsolete

From EMBOSS 6.4.0

AjPObo: obo term modifiers

Functions:

ajOboClear

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

Function ajOboClear

Prototype

void ajOboClear (
      AjPObo obo
);

Type	Name	Read/Write	Description
AjPObo	obo	Modify	Obo term
void		RETURN

From EMBOSS 6.4.0

Datatype: AjPObotag

Sections:

constructors	Constructors
obo tag destructors	Destructors

AjPObotag: constructors

Functions:

ajObotagNewData	Tag constructor
ajObotagNewTag	Tag copy constructor

Function ajObotagNewData

Prototype

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

Type	Name	Read/Write	Description
const AjPStr	name	Input	Name
const AjPStr	value	Input	Value
const AjPStr	modifier	Input	Modifier
const AjPStr	comment	Input	Comment
ajuint	linenum	Input	OBO file line number
AjPObotag		RETURN	New object

From EMBOSS 6.4.0

Function ajObotagNewTag

Prototype

AjPObotag ajObotagNewTag (
      const AjPObotag tag
);

Type	Name	Read/Write	Description
const AjPObotag	tag	Input	Obo tag
AjPObotag		RETURN	New object

From EMBOSS 6.4.0

AjPObotag: obo tag destructors

Functions:

ajObotagDel

Tag destructor

Function ajObotagDel

Prototype

void ajObotagDel (
      AjPObotag* Ptag
);

Type	Name	Read/Write	Description
AjPObotag*	Ptag	Delete	Tag object to delete
void		RETURN

From EMBOSS 6.4.0

Datatype: AjPOboxref

Sections:

constructors	Constructors
obo dbxref destructors	Destructors

AjPOboxref: constructors

Functions:

ajOboxrefNewData	Dbxref constructor
ajOboxrefNewXref	Dbxref copy constructor

Function ajOboxrefNewData

Prototype

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

Type	Name	Read/Write	Description
const AjPStr	name	Input	Name
const AjPStr	desc	Input	Description
AjPOboxref		RETURN	New object

From EMBOSS 6.4.0

Function ajOboxrefNewXref

Prototype

AjPOboxref ajOboxrefNewXref (
      const AjPOboxref xref
);

Type	Name	Read/Write	Description
const AjPOboxref	xref	Input	Dbxref
AjPOboxref		RETURN	New object

From EMBOSS 6.4.0

AjPOboxref: obo dbxref destructors

Functions:

ajOboxrefDel

Dbxref destructor

Function ajOboxrefDel

Prototype

void ajOboxrefDel (
      AjPOboxref* Pxref
);

Type	Name	Read/Write	Description
AjPOboxref*	Pxref	Delete	Dbxref object to delete
void		RETURN

From EMBOSS 6.4.0

Datatype: none

Sections:

Miscellaneous

Miscellaneous

Section: Miscellaneous

Functions:

ajOboExit

Cleans up obo term internal memory

Function ajOboExit

Prototype

void ajOboExit (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 6.4.0