Graphty

Appearance

@graphty/graph-io / @graphty/graph-io/obo / OboExportOptions

Interface: OboExportOptions ​

Defined in: formats/obo/exporter.ts:73

The format-specific options of the OBO exporter.

Extends ​

Properties ​

onMixedDirection? ​

optional onMixedDirection?: "directed" | "error" | "undirected"

Defined in: types.ts:395

What a format with one direction per file does with a graph that has both directed and undirected edges: "error" throws (E_DIRECTED), "directed" writes every edge as directed (an undirected edge once, as one directed edge), "undirected" writes the whole graph undirected. A format that keeps each edge's own direction (GraphML, GEXF, CSV, Pajek, XGMML, Cytoscape sessions, and the JGF and graphology JSON dialects) ignores it and writes both kinds; to make such a graph all one direction, read it with the import option onMixedDirection.

Default Value ​

ts
"error"

Inherited from ​

CommonExportOptions.onMixedDirection

ontology? ​

optional ontology?: string

Defined in: formats/obo/exporter.ts:87

The ontology id written in the header, such as go or uberon. It may hold letters, digits and _ . - /; any other character makes checkExport() and the save throw E_UNSUPPORTED. The default is the id an OBO import read, else the graph name with every other character replaced by _, else no ontology line.

Default Value ​

ts
as read, else the graph name

relation? ​

optional relation?: string

Defined in: formats/obo/exporter.ts:79

The relation written for an edge that has none of its own (no relation value): an OBO id such as is_a or part_of. Reasoners and ROBOT read is_a as subclassing.

Default Value ​

ts
"is_a"

sanitizeIds? ​

optional sanitizeIds?: "error" | "mangle"

Defined in: types.ts:385

What to do with node ids the format cannot hold. "error": the export throws (E_INVALID_ID) and no node is renamed. "mangle": such ids are rewritten and the originals are written to the file too, so an import with restoreMangledIds (on by default) reads the original ids back. Pajek is the exception: it always numbers nodes 1 to N and keeps the old ids as labels.

Default Value ​

ts
"error"

Inherited from ​

CommonExportOptions.sanitizeIds