ajtax.c

Datatypes:

AjPTax	Taxonomy data
AjPTaxcit	Taxonomy citation data
AjPTaxcode	Taxonomy genetic code data
AjPTaxname	Taxonomy name data
none	Miscellaneous functions

Datatype: AjPTax

Sections:

constructors	Constructors
Taxonomy data destructors	Destructors
Casts	Casts
taxonomy data modifiers	Modifiers

AjPTax: constructors

Functions:

ajTaxNew	Tax data constructor
ajTaxNewTax	Taxon copy constructor

Function ajTaxNew

Prototype

AjPTax ajTaxNew (
      void
);

Type	Name	Read/Write	Description
AjPTax		RETURN	New object

From EMBOSS 6.3.0

Function ajTaxNewTax

Prototype

AjPTax ajTaxNewTax (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
AjPTax		RETURN	New object

From EMBOSS 6.4.0

AjPTax: Taxonomy data destructors

Functions:

ajTaxDel

Taxonomy data destructor

Function ajTaxDel

Prototype

void ajTaxDel (
      AjPTax* Ptax
);

Type	Name	Read/Write	Description
AjPTax*	Ptax	Delete	Taxonomy data object to delete
void		RETURN

From EMBOSS 6.3.0

AjPTax: Casts

Functions:

ajTaxGetDb	Return the database name
ajTaxGetId	Return the identifier
ajTaxGetName	Return the name
ajTaxGetParent	Return the parent id of a taxon
ajTaxGetQryC	Returns the query string of a taxonomy data object. 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.
ajTaxGetQryS	Returns the query string of a taxonomy data object. 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.
ajTaxGetRank	Return the taxonomic rank
ajTaxGetTree	Return a list with all this taxon's descendants appended
ajTaxIsHidden	Tests whether a taxon had tghe GenBank "hidden" flag set.
ajTaxIsSpecies	Tests whether a taxon is at the rank of 'species'

Function ajTaxGetDb

Prototype

const AjPStr ajTaxGetDb (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
const AjPStr		RETURN	Database name

From EMBOSS 6.4.0

Function ajTaxGetId

Prototype

const AjPStr ajTaxGetId (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
const AjPStr		RETURN	Returned id

From EMBOSS 6.4.0

Function ajTaxGetName

Prototype

const AjPStr ajTaxGetName (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
const AjPStr		RETURN	Returned name

From EMBOSS 6.4.0

Function ajTaxGetParent

Prototype

ajuint ajTaxGetParent (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
ajuint		RETURN	Parent id

From EMBOSS 6.4.0

Function ajTaxGetQryC

Prototype

const char* ajTaxGetQryC (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxonomy data object.
const char*		RETURN	Query as a character string.

From EMBOSS 6.4.0

Function ajTaxGetQryS

Prototype

const AjPStr ajTaxGetQryS (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxonomy data object.
const AjPStr		RETURN	Query as a string.

From EMBOSS 6.4.0

Function ajTaxGetRank

Prototype

const AjPStr ajTaxGetRank (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
const AjPStr		RETURN	Returned rank

From EMBOSS 6.4.0

Function ajTaxGetTree

Prototype

ajuint ajTaxGetTree (
      const AjPTax tax,
      AjPList taxlist
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
AjPList	taxlist	Modify	List of taxons
ajuint		RETURN	Number of taxons returned

From EMBOSS 6.4.0

Function ajTaxIsHidden

Prototype

AjBool ajTaxIsHidden (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
AjBool		RETURN	True if node is hidden in GenBank taxonomy record

From EMBOSS 6.4.0

Function ajTaxIsSpecies

Prototype

AjBool ajTaxIsSpecies (
      const AjPTax tax
);

Type	Name	Read/Write	Description
const AjPTax	tax	Input	Taxon
AjBool		RETURN	True if taxon is a species

From EMBOSS 6.4.0

AjPTax: taxonomy data modifiers

Functions:

ajTaxClear

Resets all data for a taxonomy data object so that it can be reused.

Function ajTaxClear

Prototype

void ajTaxClear (
      AjPTax tax
);

Type	Name	Read/Write	Description
AjPTax	tax	Modify	Taxonomy data object
void		RETURN

From EMBOSS 6.4.0

Datatype: AjPTaxcit

Sections:

constructors	Constructors
destructors	Destructors

AjPTaxcit: constructors

Functions:

ajTaxcitNew

Taxonomy citation constructor

Function ajTaxcitNew

Prototype

AjPTaxcit ajTaxcitNew (
      void
);

Type	Name	Read/Write	Description
AjPTaxcit		RETURN	New object

From EMBOSS 6.4.0

AjPTaxcit: destructors

Functions:

ajTaxcitDel

Taxonomy citation destructor

Function ajTaxcitDel

Prototype

void ajTaxcitDel (
      AjPTaxcit* Pcit
);

Type	Name	Read/Write	Description
AjPTaxcit*	Pcit	Delete	Taxon citation object
void		RETURN

From EMBOSS 6.4.0

Datatype: AjPTaxcode

Sections:

constructors

Constructors

AjPTaxcode: constructors

Functions:

ajTaxcodeNew

Taxonomy genetic code constructor

Function ajTaxcodeNew

Prototype

AjPTaxcode ajTaxcodeNew (
      void
);

Type	Name	Read/Write	Description
AjPTaxcode		RETURN	New object

From EMBOSS 6.4.0

Function ajTaxdelNew

Prototype

AjPTaxdel ajTaxdelNew (
      void
);

Type	Name	Read/Write	Description
AjPTaxdel		RETURN	New object

From EMBOSS 6.4.0

Function ajTaxdivNew

Prototype

AjPTaxdiv ajTaxdivNew (
      void
);

Type	Name	Read/Write	Description
AjPTaxdiv		RETURN	New object

From EMBOSS 6.4.0

Function ajTaxmergeNew

Prototype

AjPTaxmerge ajTaxmergeNew (
      void
);

Type	Name	Read/Write	Description
AjPTaxmerge		RETURN	New object

From EMBOSS 6.4.0

Function ajTaxnameNew

Prototype

AjPTaxname ajTaxnameNew (
      void
);

Type	Name	Read/Write	Description
AjPTaxname		RETURN	New object

From EMBOSS 6.4.0

Function ajTaxnameNewName

Prototype

AjPTaxname ajTaxnameNewName (
      const AjPTaxname name
);

Type	Name	Read/Write	Description
const AjPTaxname	name	Input	Name
AjPTaxname		RETURN	New object

From EMBOSS 6.4.0

Datatype: AjPTaxname

Sections:

destructors

Destructors

AjPTaxname: destructors

Functions:

ajTaxnameDel

Taxonomy names destructor

Function ajTaxnameDel

Prototype

void ajTaxnameDel (
      AjPTaxname* Pname
);

Type	Name	Read/Write	Description
AjPTaxname*	Pname	Delete	Taxon name object
void		RETURN

From EMBOSS 6.4.0

Datatype: none

Sections:

exit	Miscellaneous

Section: exit

Functions:

ajTaxExit

Cleans up taxonomy processing internal memory

Function ajTaxExit

Prototype

void ajTaxExit (
      void
);

Type	Name	Read/Write	Description
void		RETURN

From EMBOSS 6.4.0