Two passes so an automatic slot never duplicates a color the user pinned by hand: pass one reserves every explicit color, pass two hands each remaining track the next palette entry that isn't reserved. Past the end of the palette it wraps rather than falling back to a hash — a hashed color collides ~20% of the time at four tracks, and distinguishability is the whole point.

Positional, so colors reshuffle when tracks are added, hidden, or reordered. That is intended: this is a within-view distinguishability aid, not a stable identity. Anything worth keeping gets pinned.

// type signature
(tracks: readonly PalettableTrack[]) => Map<string, string>

Source code

attributeColorBy

The colorBy string that paints a named feature attribute.

// type signature
(attribute: string) => SyntenyColorBy

Source code

blendOverWhite

Composite a CSS color over white by a, returning an opaque rgb(...). The synteny canvas draws every ribbon at the view's global alpha over the white page (shadeFill in syntenyTypes.slang / resolveInstanceFill in the Canvas2D renderer), so a full-saturation legend swatch reads wrong — a red match ribbon shows as salmon, a blue deletion as pale blue. Blending the legend chip the same way keeps the key matched to what's actually on screen.

// type signature
(color: string, a: number) => string

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coerceColorBy

Coerce a persisted colorBy string (stored as plain types.string for snapshot-compat) to a valid SyntenyColorBy. Unknown values fall back to 'default'; the retired 'identityDiverging' mode maps to 'identity' so old saved sessions keep rendering instead of hitting an unhandled switch case.

// type signature
(value: string | undefined) => SyntenyColorBy

Source code

colorByAttributeName

The attribute a colorBy names, or undefined for a named preset. attribute: with nothing after it never reaches here — coerceColorBy rejects it.

// type signature
(colorBy: SyntenyColorBy) => string | undefined

Source code

colorByMenuItems

The palette-button menu shared by the dotplot and linear-synteny headers: the view-wide mode radios, a per-track section once more than one track is overlaid, and the legend toggle.

// type signature
(target: ColorByMenuTarget) => MenuItem[]

Source code

colorByMenuTargetFor

Project a view carrying TrackColorsMixin onto the menu builder's input. Both palette menus were building this by hand, walking the model's tracks a third time (after colorableTracks and the legend) and repeating the same five setter lambdas.

// type signature
(model: TrackColorsModel, { pointBased, showReference, }: { pointBased: boolean; showReference: boolean; }) => ColorByMenuTarget

Source code

ColorBySelector

The palette button both comparative headers render. The menu it opens was already shared (colorByMenuItems over the structural TrackColorsModel), and what was left in each plugin was the same button around it — which had already drifted: only the synteny one said what mode it was currently in.

The two flags are the whole of the difference, and each is a fact about the view rather than a preference, so the caller states it:

pointBased picks the point-based wording for the modes whose help text describes a ribbon (a dotplot's Default is black, synteny's is red).
showReference is whether there is a shared reference to anchor on: 'reference' coloring only carries meaning across a stack of two or more levels, and degenerates to query/target below that — a two-genome dotplot never has one.

// type signature
({ model, pointBased, showReference, }: { model: TrackColorsModel; pointBased: boolean; showReference: boolean; }) => Element

Source code

colorByShortLabel

Short human-readable title for the floating legend header. An attribute:<name> mode has no title but the column's own name, which is the point of it — the reader named that column.

// type signature
(colorBy: SyntenyColorBy) => string

Source code

ComparativeTrackModel

The slice of a track model a comparative view reads off its track list.

Annotated at every site that walks a synteny view's levels[].tracks or a dotplot's tracks, because those arrays type out as any: the level model is deliberately IAnyModelType to break a real type cycle, and any propagates through the array and switches off checking on everything read from it. That is not theoretical — it let getConf(t.configuration, ...) compile where getConf wants the MODEL, and it threw at runtime reading configuration.configuration.adapter. Naming the shape is what makes the compiler check those calls again.

Source code

LEGEND_CHIP_ALPHA_FLOOR

The alpha a legend chip is blended at however faint the ribbons are.

Matching the chip to the composited ribbon is right down to a point and then inverts: the linear-synteny default alpha is 0.2, and at that value every chip washes to within a few percent of white, so a key meant to say "blue is this track, orange is that one" identifies nothing. Below the floor the chip gives up exactness for the one job it has. The ribbons themselves still draw at the real alpha.

// type signature
0.45

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legendChipColor

blendOverWhite for a legend chip, floored at LEGEND_CHIP_ALPHA_FLOOR.

// type signature
(color: string, alpha: number) => string

Source code

nameColorCss

One name's chromosome-painting color, resolved against an assembly's refName list and handed back as CSS — what a Canvas2D overlay needs, where the renderers want packed ABGR.

The single-name form of the LUT above, because a second reader has turned up that is not painting features: the off-screen mate marks stand for alignments to a contig the facing row is not showing, and a mark colored like the ribbons to that contig is what says a ribbon did not vanish, it moved. Two palettes would put a mark and its ribbons in different colors, which is exactly the drift this module exists to prevent — see the header.

// type signature
(refName: string, nameOrder: readonly string[] | undefined) => string

Source code

trackLegendChips

The legend rows that name the overlaid tracks. Two cases produce them, and both views build them the same way so the on-screen and exported legends can't diverge:

every track on 'track': one chip per track, its palette color and name.
tracks on different modes: one row per track naming its mode, with a swatch only where the track has a single color to show (a track on an identity ramp has none).

Any other uniform mode has a fixed legend of its own and returns nothing.

// type signature
(tracks: readonly { name: string; colorBy: SyntenyColorBy; trackColor: string; }[], uniformColorBy: SyntenyColorBy | undefined) => ColorChip[]

Source code

Keywords

jbrowse jbrowse2 synteny dotplot