ajtaxdata

Data type AjPTax

Holds the tax itself, plus associated information.

Alias name(s)

Name
AjSTax
AjOTax

Attributes

Name	Type	Description
Id	AjPStr	Taxonomy id
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
Rank	AjPStr	Rank in taxomony hierarchy
Emblcode	AjPStr	EMBL locus name prefix (not unique)
Comment	AjPStr	Comment
Name	AjPStr	Standard name
Namelist	AjPList	Names list
Citations	AjPList	Citations list
Lines	AjPStr*	Lines of input data
Fpos	ajlong	File position
Format	AjEnum	Input format enum
Count	ajuint	Number of lines read
Taxid	ajuint	Taxon node id
Parent	ajuint	Parent taxid
Flags	ajuint	Flags: if node inherits division from parent if node inherits genetic code from parent if node inherits mito gencode from parent if name is suppressed in GB entry lineage if this subtree has no sequence data yet
Divid	unsigned char	Division id
Gencode	unsigned char	Genetic code id
Mitocode	unsigned char	Mitochondrial genetic code id
Padchar	unsigned char	Padding to alignment boundary

Data type AjPTaxin

Holds the input specification and information needed to read the tax and possible further entries

Alias name(s)

Name
AjSTaxin
AjOTaxin

Attributes

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

Data type AjPTaxall

Inherits an AjPTax but allows more taxons to be read from the same input by also inheriting the AjPTaxin input object.

Alias name(s)

Name
AjSTaxall
AjOTaxall

Attributes

Name	Type	Description
Tax	AjPTax	Current taxon
Taxin	AjPTaxin	Taxon 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: Taxon object has been returned to a new owner and is not to be deleted by the destructor
Padding	char[4]	Padding to alignment boundary

Data type AjPTaxname

Alias name(s)

Name
AjSTaxname
AjOTaxname

Attributes

Name	Type	Description
Name	AjPStr	Name of taxon node
UniqueName	AjPStr	Unique name of taxon node
NameClass	AjPStr	Synonym, common name, etc.

Data type AjPTaxdiv

Alias name(s)

Name
AjSTaxdiv
AjOTaxdiv

Attributes

Name	Type	Description
GbCode	AjPStr	GenBank division code (three characters)
GbName	AjPStr	GenBank division name
Comments	AjPStr	Comments
Divid	ajuint	Taxonomy division id
Padding	ajuint	Padding to alignment boundary

Data type AjPTaxcode

Alias name(s)

Name
AjSTaxcode
AjOTaxcode

Attributes

Name	Type	Description
Abbrev	AjPStr	Genetic code name abbreviation
Name	AjPStr	Genetic code full name
Trans	AjPStr	Amino acids for each codon
Starts	AjPStr	Start codons
Gencode	ajuint	NCBI genetic code id
Padding	ajuint	Padding to alignment boundary

Data type AjPTaxdel

Alias name(s)

Name
AjSTaxdel
AjOTaxdel

Attributes

Name	Type	Description
Taxid	ajuint	Taxon node id

Data type AjPTaxmerge

Alias name(s)

Name
AjSTaxmerge
AjOTaxmerge

Attributes

Name	Type	Description
Taxid	ajuint	Oldaxon node id
Mergeid	ajuint	Merged taxon node id

Data type AjPTaxcit

Alias name(s)

Name
AjSTaxcit
AjOTaxcit

Attributes

Name	Type	Description
Citid	ajuint	Taxonomy citation id
Pubmed	ajuint	PubMed id (0 if not found)
Medline	ajuint	Medline id (0 if not found)
Refcount	ajuint	Reference count
Key	AjPStr	Citation key
Url	AjPStr	Url associated with citation
Text	AjPStr	Text, usually article name and authors

Data type AjPTaxAccess

Holds information needed to read a tax entry from a database. Access methods are defined for each known database type.

Tax entries are read from the database using the defined database access function, which is usually a static function within ajtaxdb.c

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

Alias name(s)

Name
AjSTaxAccess
AjOTaxAccess

Attributes

Name	Type	Description
Name	const char*	Access method name used in emboss.default
Access	(AjBool*)	Access function
AccessFree	(AjBool*)	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