ajfeatdata

Data type AjPFeattabIn

Alias name(s)

Name	Description
AjSFeattabIn
AjOFeattabIn

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
Ufo	Original UFO
Formatstr	Input format name
Filename	Original filename
Seqid	Sequence entryname
Type	Type N or P
Handle	Input buffered file
Seqname	name of AjPSeq assoc. with feature table
Format	Input format index
Local	Opened as a local file if ajTrue

Data type AjPFeattabOut

Alias name(s)

Name	Description
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	Original output UFO
Formatstr	Output format name
Filename	Output filename
Directory	Output directory
Seqid	Output entryname
Type	Type N or P
Handle	Output file
Seqname	AjPSeq assoc. with feature table
Basename	Basename for output file
Format	Output format index
Local	Opened as a local file if ajTrue

Data type AjPFeattable

Alias name(s)

Name	Description
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	Sequence name
Type	Sequence type: P or N
Features	List of AjPFeatures...
DefFormat	Original input or 'source' format of feature table
Start	First position used (like sequence begin)
End	Last position used (like sequence end)
Len	Maximum length
Offset	Offset when trimmed
Groups	Number of current group being added

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