History

SgffHistory

Main history model managing the tree, nodes, and modifiers.

from sgffp import SgffHistory

BLOCK_IDS: (7, 11, 29, 30)

Tree Access (Block 7)

Member	Description
tree → SgffHistoryTree | None	History tree structure (settable)
get_tree_node(node_id) → SgffHistoryTreeNode | None	Get tree node by ID
walk_tree() → Iterator[SgffHistoryTreeNode]	Iterate all tree nodes depth-first

Node Access (Block 11)

Member	Description
nodes → Dict[int, SgffHistoryNode]	Sequence snapshots indexed by node_index
get_node(index) → SgffHistoryNode | None	Get snapshot by index
get_sequence_at(index) → str | None	Get sequence at a history node
add_node(node) → int	Add snapshot and sync
remove_node(index) → bool	Remove snapshot and sync
update_node(index, **kwargs) → bool	Update snapshot attributes

Modifiers (Block 29)

Member	Description
modifiers → List[Dict]	Modifier metadata

Tree Modification

Method	Description
record_operation(blocks, new_seq, operation, name="", **kwargs)	Snapshot current state and create new root
snapshot_current_state(blocks) → SgffHistoryNode	Create block 11 entry from main blocks
update_for_new_sequence(new_seq)	Update root node's seqLen without recording
next_id() → int	Next available tree node ID
clear()	Remove all history (blocks 7, 11, 29, 30)

Dunder Methods

Method	Description
len(history)	Number of block 11 nodes
iter(history)	Iterate over SgffHistoryNode values

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SgffHistoryTree

Tree structure parsed from block 7.

from sgffp import SgffHistoryTree

Member	Description
root → SgffHistoryTreeNode | None	Root node (current state)
nodes → Dict[int, SgffHistoryTreeNode]	All nodes indexed by ID
get(node_id) → SgffHistoryTreeNode | None	Lookup by ID
walk(from_node=None) → Iterator	Pre-order traversal (parent first)
walk_reverse(from_node=None) → Iterator	Post-order traversal (children first, chronological)
ancestors(node_id) → List[SgffHistoryTreeNode]	Chain from node to root
to_dict() → Dict	Serialize to dict
from_dict(data) → SgffHistoryTree	Create from parsed dict
len(tree)	Total node count
iter(tree)	Pre-order walk

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SgffHistoryTreeNode

Single node in the history tree (block 7).

from sgffp import SgffHistoryTreeNode

Fields

Field	Type	Description
id	int	Unique node ID
name	str	Sequence filename
type	str	"DNA", "RNA", or "Protein"
seq_len	int	Sequence length
strandedness	str	"single" or "double"
circular	bool	Circular topology
operation	str	Operation that created this state
upstream_modification	str	e.g., "Unmodified"
downstream_modification	str	e.g., "Unmodified"
resurrectable	bool	User can restore this state

Nested Data

Field	Type	Description
oligos	List[SgffHistoryOligo]	Primers used in operation
parameters	Dict[str, str]	Key-value parameters
input_summaries	List[SgffInputSummary]	Range/enzyme selections
primers	Dict | None	Primer binding data
history_colors	Dict | None	Strand coloring
features	List[Dict]	Feature snapshots

Tree Structure

Field	Type	Description
children	List[SgffHistoryTreeNode]	Child nodes
parent	SgffHistoryTreeNode | None	Parent node
extras	Dict	Unmodeled attributes

Properties

Property	Description
input_summary	First SgffInputSummary (or None)

Methods: from_dict(data, parent=None), to_dict().

---

SgffHistoryNode

Sequence snapshot stored in block 11.

from sgffp import SgffHistoryNode

Fields

Field	Type	Default	Description
index	int		Node index (links to tree node ID)
sequence	str	""	Sequence at this history point
sequence_type	int	0	0=DNA, 1=compressed, 21=protein, 32=RNA
length	int	0	Sequence length
content	SgffHistoryNodeContent | None	None	Nested content (features, etc.)
format_version	int	30	Compressed DNA format version
strandedness_flag	int	1	1=double-stranded
property_flags	int	1	Compressed DNA property flags
header_seq_length	int | None	None	Header sequence length
tree_node	SgffHistoryTreeNode | None	None	Linked tree node

Model Accessors

Shortcuts to content models (delegate to content):

Property	Type
features	SgffFeatureList
primers	SgffPrimerList
notes	SgffNotes
properties	SgffProperties
traces	SgffTraceList

Methods: from_dict(data), to_dict().

---

SgffHistoryNodeContent

Content snapshot with model accessors. Wraps a blocks dict.

from sgffp import SgffHistoryNodeContent

Member	Description
blocks → Dict[int, List]	Raw blocks dict
block_types → List[int]	Block types present
exists → bool	Any content present
features	SgffFeatureList
primers	SgffPrimerList
notes	SgffNotes
properties	SgffProperties
alignments	SgffAlignmentList
traces	SgffTraceList
has_features, has_primers, has_notes, has_properties, has_alignments, has_traces	Existence checks

---

SgffHistoryOligo

Primer/oligo used in a cloning operation.

from sgffp import SgffHistoryOligo

Field	Type	Default
name	str
sequence	str
phosphorylated	bool	False

Methods: from_dict(data), to_dict().

---

SgffInputSummary

Describes range/selection for an operation.

from sgffp import SgffInputSummary

Field	Type	Default	Description
manipulation	str		e.g., "select", "insert", "digest"
val1	int		Start position
val2	int		End position
enzymes	List[tuple]	[]	[(name, site_count), ...]
extras	Dict	{}	Unmodeled attributes

Property	Description
enzyme_names → List[str]	List of enzyme names

Methods: from_dict(data), to_dict().

---

HistoryOperation

String enum of known operation types.

from sgffp import HistoryOperation

Values by Category

Base:

Enum	Value
INVALID	"invalid"

Create:

Enum	Value
MAKE_DNA	"makeDna"
MAKE_RNA	"makeRna"
MAKE_PROTEIN	"makeProtein"

Cloning:

Enum	Value
AMPLIFY	"amplifyFragment"
INSERT	"insertFragment"
INSERT_MULTI	"insertFragments"
DIGEST	"digest"
LIGATE	"ligateFragments"
GATEWAY_LR	"gatewayLRCloning"
GATEWAY_BP	"gatewayBPCloning"
GIBSON	"gibsonAssembly"
GOLDEN_GATE	"goldenGateAssembly"
RESTRICTION_CLONE	"restrictionCloning"
TA_CLONE	"taCloning"
TOPO_CLONE	"topoCloning"
IN_FUSION	"inFusionCloning"

Edit:

Enum	Value
REPLACE	"replace"
FLIP	"flip"
NEW_FROM_SELECTION	"newFileFromSelection"
MUTAGENESIS	"primerDirectedMutagenesis"

Metadata:

Enum	Value
CHANGE_METHYLATION	"changeMethylation"
CHANGE_PHOSPHORYLATION	"changePhosphorylation"
CHANGE_STRANDEDNESS	"changeStrandedness"
CHANGE_TOPOLOGY	"changeTopology"

Unknown operation strings are handled gracefully via _missing_().

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SgffOps

Operations API for recording history. See the History & Operations guide for usage examples.

All methods return SgffObject for chaining. Access via sgff.ops.

Methods

Metadata: change_methylation(**kw), change_phosphorylation(**kw), change_strandedness(**kw), change_topology(**kw)

Create: make_dna(seq, *, topology=, strandedness=, **kw), make_rna(seq, *, topology=, **kw), make_protein(seq, **kw)

Edit: replace(seq, **kw), insert_fragment(seq, **kw), insert_fragments(seq, **kw), flip(seq, **kw), new_from_selection(seq, **kw), mutagenesis(seq, **kw)

Cloning: amplify(seq, **kw), digest(seq, **kw), ligate(seq, **kw), gateway_lr(seq, **kw), gateway_bp(seq, **kw), gibson(seq, **kw), golden_gate(seq, **kw), restriction_clone(seq, **kw), ta_clone(seq, **kw), topo_clone(seq, **kw), in_fusion(seq, **kw)

Generic: custom(operation, new_seq, **kw)

Bulk: build_from_spec(nodes, final_sequence) → SgffObject

Edit node: edit_node(node_id, **kwargs) → SgffObject