mitoleaf cheatsheet

jennifer

import "@deckyard/mitoleaf/" as mitoleaf;

Errors and input rules: mitoleaf. tools/check-docs.sh checks every signature, field and value on this page against the code.

`mitoleaf`

Function	Returns	Does
`mitoleaf.parse(doc)`	`Tree`	parses a phm XML document; motifs are stored unvalidated
`mitoleaf.haplogroups(t)`	`list of string`	every haplogroup, in document order
`mitoleaf.has(t, hg)`	`bool`	whether `hg` is in the tree (exact, case-sensitive)
`mitoleaf.node(t, hg)`	`Node`	one haplogroup's node
`mitoleaf.children(t, hg)`	`list of string`	direct children, in document order
`mitoleaf.motif(t, hg)`	`list of string`	the tokens `hg` adds to its parent, verbatim
`mitoleaf.path(t, hg)`	`list of string`	root to `hg`, both included
`mitoleaf.haplotype(t, hg)`	`lineage.MtHaplotype`	motifs accumulated from the root, back mutations applied
`mitoleaf.distance(t, hg, h)`	`int`	`lineage.mtDistance` from `hg`'s haplotype to `h`
`mitoleaf.assign(t, h)`	`Match`	nearest haplogroup to `h`; ties go to the first in document order
`mitoleaf.parseMotifItem(token)`	`MotifItem`	interprets one motif token

Constant	Type	Value	Means
`mitoleaf.WHOLE_GENOME`	`string`	`"1-16569"`	the one range of every phylogeny haplotype

Field	Holds
`id as string`	haplogroup name, e.g. `"L0a1b2a"`
`parent as string`	parent haplogroup, `""` at the root
`motif as list of string`	tokens this node adds to its parent, verbatim
`children as list of string`	child haplogroups, in document order

Field	Holds
`root as string`	root haplogroup, `"mt-MRCA"` in the published tree
`nodes as map of string to Node`	haplogroup name to node, in document order

Field	Holds
`reversion as bool`	true for a back mutation (`A263`, `-5899.1`)
`position as int`	rCRS position the token names
`insertion as int`	n for the n-th base inserted after `position`, else 0
`designation as string`	normalised rCRS form of a gain; for a back mutation the token, trimmed and upper-cased

Field	Holds
`haplogroup as string`	haplogroup name
`distance as int`	`lineage.mtDistance` from the observed haplotype