/usr/lib/emboss/include/ajfeatdata.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
/*
**
** ajfeatdata.h - AJAX Sequence Feature include file
** Version 1.0 - March 2001
**
*/
#ifndef ajfeatdata_h
#define ajfeatdata_h
/******************************************************************************
** Table Classes *************************************************************
******************************************************************************/
/* @data AjPFeattabIn *********************************************************
**
** Ajax class for feature table input
**
** @alias AjSFeattabIn
** @alias AjOFeattabIn
**
** @new ajFeattabInNew Constructor
** @new ajFeattabInNewSS Constructor with format, name and type
** @new ajFeattabInNewSSF Constructor with format, name, type and input file
** @delete ajFeattabInDel Destructor
**
** @attr Ufo [AjPStr] Original UFO
** @attr Formatstr [AjPStr] Input format name
** @attr Filename [AjPStr] Original filename
** @attr Seqid [AjPStr] Sequence entryname
** @attr Type [AjPStr] Type N or P
** @attr Handle [AjPFilebuff] Input buffered file
** @attr Seqname [AjPStr] name of AjPSeq assoc. with feature table
** @attr Format [ajint] Input format index
** @attr Local [AjBool] Opened as a local file if ajTrue
** @@
******************************************************************************/
typedef struct AjSFeattabIn {
AjPStr Ufo;
AjPStr Formatstr;
AjPStr Filename;
AjPStr Seqid;
AjPStr Type;
AjPFilebuff Handle;
AjPStr Seqname;
ajint Format;
AjBool Local;
} AjOFeattabIn;
#define AjPFeattabIn AjOFeattabIn*
/* @data AjPFeattabOut ********************************************************
**
** Ajax class for feature table output
**
** @alias AjSFeattabOut
** @alias AjOFeattabOut
**
** @new ajFeattabOutNew Constructor
** @new ajFeattabOutNewSSF Constructor with format, name, type and
** output file
** @delete ajFeattabOutDel Destructor
**
** @attr Ufo [AjPStr] Original output UFO
** @attr Formatstr [AjPStr] Output format name
** @attr Filename [AjPStr] Output filename
** @attr Directory [AjPStr] Output directory
** @attr Seqid [AjPStr] Output entryname
** @attr Type [AjPStr] Type N or P
** @attr Handle [AjPFile] Output file
** @attr Seqname [AjPStr] AjPSeq assoc. with feature table
** @attr Basename [AjPStr] Basename for output file
** @attr Format [ajint] Output format index
** @attr Local [AjBool] Opened as a local file if ajTrue
** @attr Count [ajuint] Number of feature tables written
** @attr Padding [char[4]] Padding to alignment boundary
** @attr Cleanup [(void*)] Function to write remaining lines on closing
** @@
******************************************************************************/
typedef struct AjSFeattabOut
{
AjPStr Ufo;
AjPStr Formatstr;
AjPStr Filename;
AjPStr Directory;
AjPStr Seqid;
AjPStr Type;
AjPFile Handle;
AjPStr Seqname;
AjPStr Basename;
ajint Format;
AjBool Local;
ajuint Count;
char Padding[4];
void (*Cleanup) (AjPFile filethys);
} AjOFeattabOut;
#define AjPFeattabOut AjOFeattabOut*
/* @data AjPFeattable *********************************************************
**
** Ajax data type for collecting AjPFeatures in a 'feature table'.
** The features themselves may be accessed via iteration methods.
**
** @alias AjSFeattable
** @alias AjOFeattable
**
** @new ajFeattableNew Constructor
** @delete ajFeattableDel Default destructor
** @modify ajFeattableAdd Adds an AjPFeature to a set
** @new ajFeatRead Reads in a feature set in a specified format
**
** @attr Seqid [AjPStr] Sequence name
** @attr Type [AjPStr] Sequence type: P or N
** @attr Features [AjPList] List of AjPFeatures...
** @attr DefFormat [ajuint] Original input or 'source' format of feature table
** @attr Start [ajuint] First position used (like sequence begin)
** @attr End [ajuint] Last position used (like sequence end)
** @attr Len [ajuint] Maximum length
** @attr Offset [ajuint] Offset when trimmed
** @attr Groups [ajuint] Number of current group being added
** @@
******************************************************************************/
typedef struct AjSFeattable
{
AjPStr Seqid;
AjPStr Type;
AjPList Features;
ajuint DefFormat;
ajuint Start;
ajuint End;
ajuint Len;
ajuint Offset;
ajuint Groups;
} AjOFeattable;
#define AjPFeattable AjOFeattable*
/******************************************************************************
** Feature Classes ***********************************************************
******************************************************************************/
/* @data AjPFeature ***********************************************************
**
** Ajax Biological Feature object superclass.
**
** Holds generic data describing a single genome feature.
**
** A feature is a description of a
** sequence location which was determined by some 'source' analysis
** (which may be of 'wet lab' experimental or 'in silico'
** computational nature), has a 'primary' descriptor ('Type'),
** may have some 'score' asserting the level of analysis confidence in
** its identity (e.g. log likelihood relative to a null hypothesis or
** other similar entity), has a 'Location' in the genome, and may have
** any arbitrary number of descriptor Tags and TagValues associated with it.
**
**
** @alias AjSFeature
** @alias AjOFeature
**
** @new ajFeatNew Constructor - must specify the associated
** (non-null) AjPFeattable
** @new ajFeatNewII Simple constructor with only start and end
** positions
** @new ajFeatNewIIRev Simple constructor with only start and end
** positions, sets feature to be
** on the reverse strand
** @new ajFeatNewProt Protein-specific constructor -
** must specify the associated
** (non-null) AjPFeattable
** @delete ajFeatDel Default destructor
** @new ajFeatCopy Copy constructor
**
** @attr Source [AjPStr] Source program name (or EMBL)
** @attr Type [AjPStr] Feature type (feature key) from internal list
** for protein or nucleotide
** @attr Protein [AjBool] true for a protein feature
** @attr Start [ajuint] Start position
** @attr End [ajuint] End position
** @attr Start2 [ajuint] Second start position - EMBL (a.b)
** @attr End2 [ajuint] Second end position - EMBL ..(a.b)
** @attr Frame [ajint] Frame 1..3, -1..-3 or 0
** @attr Tags [AjPList] Tag-value list (qualifier list)
** @attr Flags [ajuint] Flag bit mask for EMBL location
** @attr Group [ajuint] Group for join/order/one-of
** @attr Remote [AjPStr] Remote ID - EMBL Remote:a.b
** @attr Label [AjPStr] Label name for location - EMBL legacy
** @attr Exon [ajuint] Exon number
** @attr Score [float] Score or 0.0 if none
** @attr Strand [char] Strand +/- or NULL
** @attr Padding [char[7]] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct AjSFeature {
AjPStr Source;
AjPStr Type;
AjBool Protein;
ajuint Start;
ajuint End;
ajuint Start2;
ajuint End2;
ajint Frame;
AjPList Tags;
ajuint Flags;
ajuint Group;
AjPStr Remote;
AjPStr Label;
ajuint Exon;
float Score;
char Strand;
char Padding[7];
} AjOFeature;
#define AjPFeature AjOFeature*
#endif /* ajfeatdata_h */
#ifdef __cplusplus
}
#endif
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