Extras Reference

Every model uses an extras dict to preserve unmodeled XML attributes through roundtrip. This page documents the known extras keys, their types, and meanings.

All extras values are strings unless noted otherwise.

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SgffFeature

Accessed via feature.extras.

Key	Type	Description
recentID	str	Internal SnapGene ID for the feature
translationMW	str	Molecular weight of translated protein (Da)
hitsStopCodon	str	"1" if translation hits a stop codon
consecutiveTranslationNumbering	str	"1" to use consecutive numbering

readingFrame was formerly in extras; it is now the typed field reading_frame.

SgffSegment

Accessed via segment.extras.

Key	Type	Description
name	str	Optional segment name

type and translated were formerly in extras; they are now typed fields.

SgffPrimer

Accessed via primer.extras.

Key	Type	Description
recentID	str	Internal SnapGene ID
color	str	Hex color (e.g., "#FF0000")
description	str	User-provided description
dateAdded	str	Creation date

SgffBindingSite

Accessed via binding_site.extras.

Key	Type	Description
Component	dict	Nested structure with hybridization details (hybridizedRange, bases)

SgffHistoryTreeNode

Accessed via node.extras.

Key	Type	Description
hideHistory	str	"1" to hide node from history tree view
customMapLabel	str	Custom label for map view
useCustomMapLabel	str	"1" to enable custom map label
upstreamStickiness	str	Upstream sticky end sequence (e.g., "AATT")
downstreamStickiness	str	Downstream sticky end sequence (e.g., "TTAA")
RegeneratedSite	dict	Enzyme info ({"name": "BamHI"})

SgffInputSummary

Accessed via summary.extras.

Key	Type	Description
strainName	str	Bacterial strain (e.g., "DH5alpha")
methylationChanges	str	Methylation pattern (e.g., "dam+")
dam2	str	"1" for Dam methylation flag

SgffAlignment

Accessed via alignment.extras.

Key	Type	Description
ID	str	Unique identifier
sortOrder	str	Display ordering index
trimmedRange	str	Quality trimming range (e.g., "5-100")
isTrace	str	"0" or "1"

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Wrapper-level Extras

List models store wrapper-level extras in _wrapper_extras (not part of the public API but preserved for lossless roundtrip).

SgffPrimerList

Key	Type	Description
HybridizationParams	dict	Hybridization parameters (minContinuous, etc.)
nextValidID	str	Next available primer ID counter

SgffFeatureList

Key	Type	Description
nextValidID	str	Next available feature ID counter
recycledIDs	str	Comma-separated list of deleted feature IDs

SgffAlignmentList

Key	Type	Description
trimStringency	str	Alignment quality threshold (e.g., "0.05")