ajtax.c

Datatypes: AjPTax AjPTaxcit AjPTaxcode AjPTaxname none

Datatype: AjPTax

Taxonomy data

Sections: constructors Taxonomy data destructors Casts taxonomy data modifiers

Section: constructors

Constructors

Functions: ajTaxNew ajTaxNewTax

Function ajTaxNew

Tax data constructor

Synopsis

Prototype
AjPTax ajTaxNew (
      void
);

TypeNameRead/WriteDescription
AjPTax RETURNNew object

Returns
AjPTax:New object

Description

Tax data constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxNewTax

Taxon copy constructor

Synopsis

Prototype
AjPTax ajTaxNewTax (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
AjPTax RETURNNew object

Input
tax:(Input)Taxon
Returns
AjPTax:New object

Description

Taxon copy constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Taxonomy data destructors

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

Functions: ajTaxDel

Function ajTaxDel

Taxonomy data destructor

Synopsis

Prototype
void ajTaxDel (
      AjPTax* Ptax
);

TypeNameRead/WriteDescription
AjPTax*PtaxDeleteTaxonomy data object to delete
void RETURN

Output
Ptax:(Delete)Taxonomy data object to delete
Returns
void:No return value

Description

Taxonomy data destructor

See Also

See other functions in this section

Availability

In release 6.4.0

Section: Casts

Return values from a taxonomy data object

Functions: ajTaxGetDb ajTaxGetId ajTaxGetName ajTaxGetParent ajTaxGetQryC ajTaxGetQryS ajTaxGetRank ajTaxGetTree ajTaxIsHidden ajTaxIsSpecies

Function ajTaxGetDb

Return the database name

Synopsis

Prototype
const AjPStr ajTaxGetDb (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
const AjPStr RETURNDatabase name

Input
tax:(Input)Taxon
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 ajTaxGetId

Return the identifier

Synopsis

Prototype
const AjPStr ajTaxGetId (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
const AjPStr RETURNReturned id

Input
tax:(Input)Taxon
Returns
const AjPStr:Returned id

Description

Return the identifier

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxGetName

Return the name

Synopsis

Prototype
const AjPStr ajTaxGetName (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
const AjPStr RETURNReturned name

Input
tax:(Input)Taxon
Returns
const AjPStr:Returned name

Description

Return the name

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxGetParent

Return the parent id of a taxon

Synopsis

Prototype
ajuint ajTaxGetParent (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
ajuint RETURNParent id

Input
tax:(Input)Taxon
Returns
ajuint:Parent id

Description

Return the parent id of a taxon

See Also

See other functions in this section

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype
const char* ajTaxGetQryC (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxonomy data object.
const char* RETURNQuery as a character string.

Input
tax:(Input)Taxonomy data object.
Returns
const char*:Query as a character string.

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function 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.

Synopsis

Prototype
const AjPStr ajTaxGetQryS (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxonomy data object.
const AjPStr RETURNQuery as a string.

Input
tax:(Input)Taxonomy data object.
Returns
const AjPStr:Query as a string.

Description

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxGetRank

Return the taxonomic rank

Synopsis

Prototype
const AjPStr ajTaxGetRank (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
const AjPStr RETURNReturned rank

Input
tax:(Input)Taxon
Returns
const AjPStr:Returned rank

Description

Return the taxonomic rank

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxGetTree

Return a list with all this taxon's descendants appended

Synopsis

Prototype
ajuint ajTaxGetTree (
      const AjPTax tax,
      AjPList taxlist
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
AjPListtaxlistModifyList of taxons
ajuint RETURNNumber of taxons returned

Input
tax:(Input)Taxon
Input & Output
taxlist:(Modify)List of taxons
Returns
ajuint:Number of taxons returned

Description

Return a list with all this taxon's descendants appended

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxIsHidden

Tests whether a taxon had tghe GenBank "hidden" flag set.

Synopsis

Prototype
AjBool ajTaxIsHidden (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
AjBool RETURNTrue if node is hidden in GenBank taxonomy record

Input
tax:(Input)Taxon
Returns
AjBool:True if node is hidden in GenBank taxonomy record

Description

Tests whether a taxon had tghe GenBank "hidden" flag set.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxIsSpecies

Tests whether a taxon is at the rank of 'species'

Synopsis

Prototype
AjBool ajTaxIsSpecies (
      const AjPTax tax
);

TypeNameRead/WriteDescription
const AjPTaxtaxInputTaxon
AjBool RETURNTrue if taxon is a species

Input
tax:(Input)Taxon
Returns
AjBool:True if taxon is a species

Description

Tests whether a taxon is at the rank of 'species'

See Also

See other functions in this section

Availability

In release 6.4.0

Section: taxonomy data modifiers

Taxonomy data modifiers

Functions: ajTaxClear

Function ajTaxClear

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

Synopsis

Prototype
void ajTaxClear (
      AjPTax tax
);

TypeNameRead/WriteDescription
AjPTaxtaxModifyTaxonomy data object
void RETURN

Input & Output
tax:(Modify)Taxonomy data object
Returns
void:No return value

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Datatype: AjPTaxcit

Taxonomy citation data

Sections: constructors destructors

Section: constructors

Constructors

Functions: ajTaxcitNew

Function ajTaxcitNew

Taxonomy citation constructor

Synopsis

Prototype
AjPTaxcit ajTaxcitNew (
      void
);

TypeNameRead/WriteDescription
AjPTaxcit RETURNNew object

Returns
AjPTaxcit:New object

Description

Taxonomy citation constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for the taxon citation object.

Functions: ajTaxcitDel

Function ajTaxcitDel

Taxonomy citation destructor

Synopsis

Prototype
void ajTaxcitDel (
      AjPTaxcit* Pcit
);

TypeNameRead/WriteDescription
AjPTaxcit*PcitDeleteTaxon citation object
void RETURN

Output
Pcit:(Delete)Taxon citation object
Returns
void:No return value

Description

Taxonomy citation destructor

See Also

See other functions in this section

Availability

In release 6.4.0

Datatype: AjPTaxcode

Taxonomy genetic code data

Sections: constructors

Section: constructors

Constructors

Functions: ajTaxcodeNew

Function ajTaxcodeNew

Taxonomy genetic code constructor

Synopsis

Prototype
AjPTaxcode ajTaxcodeNew (
      void
);

TypeNameRead/WriteDescription
AjPTaxcode RETURNNew object

Returns
AjPTaxcode:New object

Description

Taxonomy genetic code constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxdelNew

Taxonomy deleted id constructor

Synopsis

Prototype
AjPTaxdel ajTaxdelNew (
      void
);

TypeNameRead/WriteDescription
AjPTaxdel RETURNNew object

Returns
AjPTaxdel:New object

Description

Taxonomy deleted id constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxdivNew

Taxonomy division constructor

Synopsis

Prototype
AjPTaxdiv ajTaxdivNew (
      void
);

TypeNameRead/WriteDescription
AjPTaxdiv RETURNNew object

Returns
AjPTaxdiv:New object

Description

Taxonomy division constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxmergeNew

Taxonomy merged id constructor

Synopsis

Prototype
AjPTaxmerge ajTaxmergeNew (
      void
);

TypeNameRead/WriteDescription
AjPTaxmerge RETURNNew object

Returns
AjPTaxmerge:New object

Description

Taxonomy merged id constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxnameNew

Taxonomy names constructor

Synopsis

Prototype
AjPTaxname ajTaxnameNew (
      void
);

TypeNameRead/WriteDescription
AjPTaxname RETURNNew object

Returns
AjPTaxname:New object

Description

Taxonomy names constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajTaxnameNewName

Taxonomy names copy constructor

Synopsis

Prototype
AjPTaxname ajTaxnameNewName (
      const AjPTaxname name
);

TypeNameRead/WriteDescription
const AjPTaxnamenameInputName
AjPTaxname RETURNNew object

Input
name:(Input)Name
Returns
AjPTaxname:New object

Description

Taxonomy names copy constructor

See Also

See other functions in this section

Availability

In release 6.4.0

Datatype: AjPTaxname

Taxonomy name data

Sections: destructors

Section: destructors

Destruction destroys all internal data structures and frees the memory allocated for the taxon name object.

Functions: ajTaxnameDel

Function ajTaxnameDel

Taxonomy names destructor

Synopsis

Prototype
void ajTaxnameDel (
      AjPTaxname* Pname
);

TypeNameRead/WriteDescription
AjPTaxname*PnameDeleteTaxon name object
void RETURN

Output
Pname:(Delete)Taxon name object
Returns
void:No return value

Description

Taxonomy names destructor

See Also

See other functions in this section

Availability

In release 6.4.0

Datatype: none

Miscellaneous functions

Sections: exit

Section: exit

Functions called on exit from the program by ajExit to do any necessary cleanup and to report internal statistics to the debug file

Functions: ajTaxExit

Function ajTaxExit

Cleans up taxonomy processing internal memory

Synopsis

Prototype
void ajTaxExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up taxonomy processing internal memory

See Also

See other functions in this section

Availability

In release 6.4.0