/usr/lib/emboss/include/ajtax.h is in emboss-lib 6.3.1-6ubuntu3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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extern "C"
{
#endif
#ifndef ajtax_h
#define ajtax_h
#include "ajax.h"
/* @data AjPTax ***************************************************************
**
** NCBI taxonomy node
**
** @alias AjSTax
** @alias AjOTax
**
** @attr Taxid [ajuint] Taxon node id
** @attr Parent [ajuint] Parent taxid
** @attr Divid [unsigned char] Division id
** @attr Gencode [unsigned char] Genetic code id
** @attr Mitocode [unsigned char] Mitochondrial genetic code id
** @attr Padchar [unsigned char] Padding to alignment boundary
** @attr 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
** @attr Rank [AjPStr] Rank in taxomony hierarchy
** @attr Emblcode [AjPStr] EMBL locus name prefix (not unique)
** @attr Comment [AjPStr] Comment
** @attr Namelist [AjPList] Names list
** @attr Citations [AjPList] Citation id list
**
******************************************************************************/
typedef struct AjSTax
{
ajuint Taxid;
ajuint Parent;
unsigned char Divid;
unsigned char Gencode;
unsigned char Mitocode;
unsigned char Padchar;
ajuint Flags;
AjPStr Rank;
AjPStr Emblcode;
AjPStr Comment;
AjPList Namelist;
AjPList Citations;
} AjOTax;
#define AjPTax AjOTax*
/* @data AjPTaxName *********************************************************
**
** NCBI taxonomy node name, listed within AjPTax
**
** @alias AjSTaxName
** @alias AjOTaxName
**
** @attr Name [AjPStr] Name of taxon node
** @attr UniqueName [AjPStr] Unique name of taxon node
** @attr NameClass [AjPStr] Synonym, common name, etc.
**
******************************************************************************/
typedef struct AjSTaxName
{
AjPStr Name;
AjPStr UniqueName;
AjPStr NameClass;
} AjOTaxName;
#define AjPTaxName AjOTaxName*
/* @data AjPTaxDiv *********************************************************
**
** NCBI taxonomy division
**
** @alias AjSTaxDiv
** @alias AjOTaxDiv
**
** @attr GbCode [AjPStr] GenBank division code (three characters)
** @attr GbName [AjPStr] GenBank division name
** @attr Comments [AjPStr] Comments
** @attr Divid [ajuint] Taxonomy division id
** @attr Padding [ajuint] Padding to alignment boundary
**
******************************************************************************/
typedef struct AjSTaxDiv
{
AjPStr GbCode;
AjPStr GbName;
AjPStr Comments;
ajuint Divid;
ajuint Padding;
} AjOTaxDiv;
#define AjPTaxDiv AjOTaxDiv*
/* @data AjPTaxCode *********************************************************
**
** NCBI taxonomy genetic code
**
** @alias AjSTaxCode
** @alias AjOTaxCode
**
** @attr Abbrev [AjPStr] Genetic code name abbreviation
** @attr Name [AjPStr] Genetic code full name
** @attr Trans [AjPStr] Amino acids for each codon
** @attr Starts [AjPStr] Start codons
** @attr Gencode [ajuint] NCBI genetic code id
** @attr Padding [ajuint] Padding to alignment boundary
**
******************************************************************************/
typedef struct AjSTaxCode
{
AjPStr Abbrev;
AjPStr Name;
AjPStr Trans;
AjPStr Starts;
ajuint Gencode;
ajuint Padding;
} AjOTaxCode;
#define AjPTaxCode AjOTaxCode*
/* @data AjPTaxDel *********************************************************
**
** NCBI taxonomy deleted node
**
** @alias AjSTaxDel
** @alias AjOTaxDel
**
** @attr Taxid [ajuint] Taxon node id
**
******************************************************************************/
typedef struct AjSTaxDel
{
ajuint Taxid;
} AjOTaxDel;
#define AjPTaxDel AjOTaxDel*
/* @data AjPTaxMerge *********************************************************
**
** NCBI taxonomy mergednode
**
** @alias AjSTaxMerge
** @alias AjOTaxMerge
**
** @attr Taxid [ajuint] Oldaxon node id
** @attr Mergeid [ajuint] Merged taxon node id
**
******************************************************************************/
typedef struct AjSTaxMerge
{
ajuint Taxid;
ajuint Mergeid;
} AjOTaxMerge;
#define AjPTaxMerge AjOTaxMerge*
/* @data AjPTaxCit *********************************************************
**
** NCBI taxonomy citation, listed within AjPTax
**
** @alias AjSTaxCit
** @alias AjOTaxCit
**
** @attr Citid [ajuint] Taxonomy citation id
** @attr Pubmed [ajuint] PubMed id (0 if not found)
** @attr Medline [ajuint] Medline id (0 if not found)
** @attr Refcount [ajuint] Reference count
** @attr Key [AjPStr] Citation key
** @attr Url [AjPStr] Url associated with citation
** @attr Text [AjPStr] Text, usually article name and authors
**
******************************************************************************/
typedef struct AjSTaxCit
{
ajuint Citid;
ajuint Pubmed;
ajuint Medline;
ajuint Refcount;
AjPStr Key;
AjPStr Url;
AjPStr Text;
} AjOTaxCit;
#define AjPTaxCit AjOTaxCit*
/*
** Prototype definitions
*/
AjPTax ajTaxNew(void);
AjPTaxCit ajTaxCitNew(void);
AjPTaxCode ajTaxCodeNew(void);
AjPTaxDel ajTaxDelNew(void);
AjPTaxDiv ajTaxDivNew(void);
AjPTaxMerge ajTaxMergeNew(void);
AjPTaxName ajTaxNameNew(void);
void ajTaxDel(AjPTax *Ptax);
AjBool ajTaxParse(AjPFile taxfile);
AjBool ajTaxLoad(const AjPDir taxdir);
/*
** End of prototype definitions
*/
#endif
#ifdef __cplusplus
}
#endif
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