ajfeatdata

Data type AjPFeattable

Alias name(s)

Name
AjSFeattable
AjOFeattable

Constructor(s)

Name	Description
ajFeattableNew	Constructor

Destructor(s)

Name	Description
ajFeattableDel	Default destructor

Modifier(s)

Name	Description
ajFeattableAdd	Adds an AjPFeature to a set

Constructor(s)

Name	Description
ajFeatRead	Reads in a feature set in a specified format

Attributes

Name	Type	Description
Seqid	AjPStr	Sequence name
Type	AjPStr	Sequence type: P or N
Features	AjPList	List of AjPFeatures...
Groups	ajuint	Maximum group number
Start	ajuint	First position used (like sequence begin)
End	ajuint	Last position used (like sequence end)
Len	ajuint	Maximum length
Offset	ajuint	Offset when trimmed
Rev	AjBool	reversed if true
Reversed	AjBool	true: has been reverse-complemented
Trimmed	AjBool	true: has been trimmed
Db	AjPStr	Database name from input
Setdb	AjPStr	Database name from command line
Full	AjPStr	Full name
Qry	AjPStr	UFO query for re-reading
Formatstr	AjPStr	Input format name
Filename	AjPStr	Original filename
TextPtr	AjPStr	Full text
Fpos	ajlong	File position (fseek) for Query
Format	AjEnum	Input format enum
Circular	AjBool	true: circular nucleotide molecule

Data type AjPFeattabin

Alias name(s)

Name
AjSFeattabin
AjOFeattabin
AjPFeattabIn

Constructor(s)

Name	Description
ajFeattabinNew	Constructor
ajFeattabinNewSS	Constructor with format, name and type
ajFeattabinNewSSF	Constructor with format, name, type and input file

Destructor(s)

Name	Description
ajFeattabinDel	Destructor

Attributes

Name	Type	Description
Input	AjPTextin	Text file input object
Ufo	AjPStr	Original UFO
Formatstr	AjPStr	Input format name
Filename	AjPStr	Original filename
Seqid	AjPStr	Sequence entryname
Type	AjPStr	Type N or P
Seqname	AjPStr	name of AjPSeq assoc. with feature table
Local	AjBool	Opened as a local file if ajTrue
Rev	AjBool	Reverse/complement if true
Start	ajint	Start position
End	ajint	End position
Circular	AjBool	true: circular nucleotide molecule
Padding	char[4]	Padding to alignment boundary

Data type AjPFeattaball

Inherits an AjPFeattable but allows more data resources to be read from the same input by also inheriting the AjPFeattabin input object.

Alias name(s)

Name
AjSFeattaball
AjOFeattaball

Attributes

Name	Type	Description
Feattable	AjPFeattable	Current feature table
Feattabin	AjPFeattabin	Feature input for reading next
Totfeattables	ajulong	Count of feature tables so far
Count	ajuint	Count of feature tables so far
Multi	AjBool	True if multiple values are expected
Returned	AjBool	if true: featuure table 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 AjPFeattabAccess

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

Feature tables are read from the database using the defined database access function, which is usually a static function within ajtextdb.c or ajfeatdb.c

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

Alias name(s)

Name
AjSFeattabAccess
AjOFeattabAccess

Attributes

Name	Type	Description
Name	const char*	Access method name used in emboss.default
Access	AjBool function	Access function
AccessFree	AjBool function	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
Padding	AjBool	Padding to alignment boundary

Data type AjPFeattabOut

Alias name(s)

Name
AjSFeattabOut
AjOFeattabOut

Constructor(s)

Name	Description
ajFeattabOutNew	Constructor
ajFeattabOutNewSSF	Constructor with format, name, type and output file

Destructor(s)

Name	Description
ajFeattabOutDel	Destructor

Attributes

Name	Type	Description
Ufo	AjPStr	Original output UFO
Formatstr	AjPStr	Output format name
Filename	AjPStr	Output filename
Directory	AjPStr	Output directory
Seqid	AjPStr	Output entryname
Type	AjPStr	Type N or P
Handle	AjPFile	Output file
Seqname	AjPStr	AjPSeq assoc. with feature table
Basename	AjPStr	Basename for output file
Format	ajint	Output format index
Local	AjBool	Opened as a local file if ajTrue
Count	ajuint	Number of feature tables written
Padding	char[4]	Padding to alignment boundary
Cleanup	void function	Function to write remaining lines on closing

Data type AjPFeature

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 name(s)

Name
AjSFeature
AjOFeature

Constructor(s)

Name	Description
ajFeatNew	Constructor - must specify the associated (non-null) AjPFeattable
ajFeatNewII	Simple constructor with only start and end positions
ajFeatNewIIRev	Simple constructor with only start and end positions, sets feature to be on the reverse strand
ajFeatNewProt	Protein-specific constructor - must specify the associated (non-null) AjPFeattable

Destructor(s)

Name	Description
ajFeatDel	Default destructor

Constructor(s)

Name	Description
ajFeatCopy	Copy constructor

Attributes

Name	Type	Description
Source	AjPStr	Source program name (or EMBL)
Type	AjPStr	Feature type (feature key) from internal list for protein or nucleotide
Subfeatures	AjPList	Subfeatures
Tags	AjPList	Tag-value list (qualifier list)
GffTags	AjPList	GFF3 Tag-value list (qualifier list)
Protein	AjBool	true for a protein feature
Start	ajuint	Start position
End	ajuint	End position
Start2	ajuint	Second start position - EMBL (a.b)
End2	ajuint	Second end position - EMBL ..(a.b)
Frame	ajint	Frame 1..3, -1..-3 or 0
Flags	ajuint	Flag bit mask for EMBL location
Group	ajuint	Group for join/order/one-of
Remote	AjPStr	Remote ID - EMBL Remote:a.b
Label	AjPStr	Label name for location - EMBL legacy
Exon	ajuint	Exon number
Score	float	Score or 0.0 if none
Strand	char	Strand +/- or NULL
Padding	char[7]	Padding to alignment boundary

Data type AjPFeatGfftags

Alias name(s)

Name
AjSFeatGfftags
AjOFeatGfftags

Attributes

Name	Type	Description
Id	AjPStr	Identifier attribute. Features with the same id are one feature with multiple locations
Name	AjPStr	Display name attribute, can be shared
Alias	AjPStr	Alias attribute (list) e.g. locus name, can be shared
Parent	AjPStr	Parent attribute (list) for part_of grouping
Target	AjPStr	Target attribute "target_id start end [strand]"
Gap	AjPStr	Gap attribute in exonerate CIGAR format
DerivesFrom	AjPStr	Derives_from attribute for relations
Note	AjPStr	Note attribute (list)
Dbxref	AjPStr	Dbxref attribute (list) in format DBTAG:ID
OntologyTerm	AjPStr	Ontology_term attribute (list) in format DBTAG:ID
IsCircular	AjPStr	Is_circular attribute