ajfeatdata


Data type AjPFeattable

Ajax data type for collecting AjPFeatures in a 'feature table'. The features themselves may be accessed via iteration methods.

Alias name(s)

Name
AjSFeattable
AjOFeattable

Constructor(s)

NameDescription
ajFeattableNewConstructor

Destructor(s)

NameDescription
ajFeattableDelDefault destructor

Modifier(s)

NameDescription
ajFeattableAddAdds an AjPFeature to a set

Constructor(s)

NameDescription
ajFeatReadReads in a feature set in a specified format

Attributes

NameTypeDescription
SeqidAjPStrSequence name
TypeAjPStrSequence type: P or N
FeaturesAjPListList of AjPFeatures...
GroupsajuintMaximum group number
StartajuintFirst position used (like sequence begin)
EndajuintLast position used (like sequence end)
LenajuintMaximum length
OffsetajuintOffset when trimmed
RevAjBoolreversed if true
ReversedAjBooltrue: has been reverse-complemented
TrimmedAjBooltrue: has been trimmed
DbAjPStrDatabase name from input
SetdbAjPStrDatabase name from command line
FullAjPStrFull name
QryAjPStrUFO query for re-reading
FormatstrAjPStrInput format name
FilenameAjPStrOriginal filename
TextPtrAjPStrFull text
FposajlongFile position (fseek) for Query
FormatAjEnumInput format enum
CircularAjBooltrue: circular nucleotide molecule


Data type AjPFeattabin

Ajax class for feature table input

Alias name(s)

Name
AjSFeattabin
AjOFeattabin
AjPFeattabIn

Constructor(s)

NameDescription
ajFeattabinNewConstructor
ajFeattabinNewSSConstructor with format, name and type
ajFeattabinNewSSFConstructor with format, name, type and input file

Destructor(s)

NameDescription
ajFeattabinDelDestructor

Attributes

NameTypeDescription
InputAjPTextinText file input object
UfoAjPStrOriginal UFO
FormatstrAjPStrInput format name
FilenameAjPStrOriginal filename
SeqidAjPStrSequence entryname
TypeAjPStrType N or P
SeqnameAjPStrname of AjPSeq assoc. with feature table
LocalAjBoolOpened as a local file if ajTrue
RevAjBoolReverse/complement if true
StartajintStart position
EndajintEnd position
CircularAjBooltrue: circular nucleotide molecule
Paddingchar[4]Padding to alignment boundary


Data type AjPFeattaball

Ajax feature all (stream) object.

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

NameTypeDescription
FeattableAjPFeattableCurrent feature table
FeattabinAjPFeattabinFeature input for reading next
TotfeattablesajulongCount of feature tables so far
CountajuintCount of feature tables so far
MultiAjBoolTrue if multiple values are expected
ReturnedAjBoolif true: featuure table object has been returned to a new owner and is not to be deleted by the destructor
Paddingchar[4]Padding to alignment boundary


Data type AjPFeattabAccess

Ajax feature table access database reading object.

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

NameTypeDescription
Nameconst char*Access method name used in emboss.default
AccessAjBool functionAccess function
AccessFreeAjBool functionAccess cleanup function
Qlinkconst char*Supported query link operators
Descconst char*Description
AliasAjBoolAlias for another name
EntryAjBoolSupports retrieval of single entries
QueryAjBoolSupports retrieval of selected entries
AllAjBoolSupports retrieval of all entries
ChunkedAjBoolSupports retrieval of entries in chunks
PaddingAjBoolPadding to alignment boundary


Data type AjPFeattabOut

Ajax class for feature table output

Alias name(s)

Name
AjSFeattabOut
AjOFeattabOut

Constructor(s)

NameDescription
ajFeattabOutNewConstructor
ajFeattabOutNewSSFConstructor with format, name, type and output file

Destructor(s)

NameDescription
ajFeattabOutDelDestructor

Attributes

NameTypeDescription
UfoAjPStrOriginal output UFO
FormatstrAjPStrOutput format name
FilenameAjPStrOutput filename
DirectoryAjPStrOutput directory
SeqidAjPStrOutput entryname
TypeAjPStrType N or P
HandleAjPFileOutput file
SeqnameAjPStrAjPSeq assoc. with feature table
BasenameAjPStrBasename for output file
FormatajintOutput format index
LocalAjBoolOpened as a local file if ajTrue
CountajuintNumber of feature tables written
Paddingchar[4]Padding to alignment boundary
Cleanupvoid functionFunction to write remaining lines on closing


Data type 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 name(s)

Name
AjSFeature
AjOFeature

Constructor(s)

NameDescription
ajFeatNewConstructor - must specify the associated (non-null) AjPFeattable
ajFeatNewIISimple constructor with only start and end positions
ajFeatNewIIRevSimple constructor with only start and end positions, sets feature to be on the reverse strand
ajFeatNewProtProtein-specific constructor - must specify the associated (non-null) AjPFeattable

Destructor(s)

NameDescription
ajFeatDelDefault destructor

Constructor(s)

NameDescription
ajFeatCopyCopy constructor

Attributes

NameTypeDescription
SourceAjPStrSource program name (or EMBL)
TypeAjPStrFeature type (feature key) from internal list for protein or nucleotide
SubfeaturesAjPListSubfeatures
TagsAjPListTag-value list (qualifier list)
GffTagsAjPListGFF3 Tag-value list (qualifier list)
ProteinAjBooltrue for a protein feature
StartajuintStart position
EndajuintEnd position
Start2ajuintSecond start position - EMBL (a.b)
End2ajuintSecond end position - EMBL ..(a.b)
FrameajintFrame 1..3, -1..-3 or 0
FlagsajuintFlag bit mask for EMBL location
GroupajuintGroup for join/order/one-of
RemoteAjPStrRemote ID - EMBL Remote:a.b
LabelAjPStrLabel name for location - EMBL legacy
ExonajuintExon number
ScorefloatScore or 0.0 if none
StrandcharStrand +/- or NULL
Paddingchar[7]Padding to alignment boundary


Data type AjPFeatGfftags

Biological feature GFF3 special tags

Alias name(s)

Name
AjSFeatGfftags
AjOFeatGfftags

Attributes

NameTypeDescription
IdAjPStrIdentifier attribute. Features with the same id are one feature with multiple locations
NameAjPStrDisplay name attribute, can be shared
AliasAjPStrAlias attribute (list) e.g. locus name, can be shared
ParentAjPStrParent attribute (list) for part_of grouping
TargetAjPStrTarget attribute "target_id start end [strand]"
GapAjPStrGap attribute in exonerate CIGAR format
DerivesFromAjPStrDerives_from attribute for relations
NoteAjPStrNote attribute (list)
DbxrefAjPStrDbxref attribute (list) in format DBTAG:ID
OntologyTermAjPStrOntology_term attribute (list) in format DBTAG:ID
IsCircularAjPStrIs_circular attribute