Skip to main content

DiagonalizeProgressMixin

Auto-generated @jbrowse/mobx-state-tree API for the current JBrowse release — see pluggable elements for concepts. Built into JBrowse core. View source.

The auto-diagonalize lifecycle state shared by the comparative views (LinearSyntenyView, DotplotView): the in-flight wait, its live RPC status and stop token, and the flag that gates settled so a screenshot or browser test can't capture a pre-reorder hairball.

withDiagonalizeProgress drives the wait and the status/token pair; the gate is raised and lowered by the view's own init autorun, which is the only thing that knows a reorder was asked for. Composed rather than duplicated so both views report progress, cancel, and gate identically.

Volatiles

MemberDescription
awaitingAutoDiagonalize
awaitingAutoDiagonalize: false		True while the init autorun is waiting on the diagonalize RPC. Gates the canvas off — otherwise the user watches an undiagonalized hairball flash before the reorder kicks in.
pendingAutoDiagonalize
pendingAutoDiagonalize: false		A reorder this init asked for that has not succeeded yet. Raised before any render can paint, and lowered only once the pass RESOLVES — a skipped or thrown reorder leaves it up, so the view's settled gate never reports done on an undiagonalized view and the capture fails loudly (times out) instead of committing a hairball.

One flag rather than a requested/complete pair: the two only ever moved together, and every state a pair can drift into either wedges the gate shut or opens it on the wrong pass.
diagonalizeStatus
diagonalizeStatus: createStatusChannel()		Live status from the auto-diagonalize RPC (download %, parse, algorithm phase) shown on the reordering spinner; blank outside that wait.

A StatusChannel rather than a status field plus a setter: there is one operation to narrate here, and the channel is that pair with the message/fraction split already done, so the spinner reads { message, fraction } instead of calling statusMessageText / statusFraction at every render site.
diagonalizeStopToken
diagonalizeStopToken: undefined as StopToken | undefined		Stop token for the in-flight auto-diagonalize, so the spinner's Cancel can abort it; undefined when none is running.

Actions

MemberDescription
setAwaitingAutoDiagonalize
(arg: boolean) => void
beginAutoDiagonalize
(requested: boolean) => void		Declare the gate at the top of one init apply pass: a reorder is pending iff THIS init asked for one. Assigning rather than raising is what hands the gate over cleanly — a superseded init that asked for a reorder and then skipped it would otherwise leave the flag up with nothing coming, wedging settled forever.
finishAutoDiagonalize
() => void		The init-time reorder resolved, so the view on screen is the diagonalized one — open the gate.
setDiagonalizeStopToken
(arg?: StopToken | undefined) => void
cancelAutoDiagonalize
() => void		Abort an in-flight auto-diagonalize; withDiagonalizeProgress's finally clears the wait flag, revealing the (undiagonalized) view.

Lowers the gate too. The abort reaches the caller as a throw, which skips its finishAutoDiagonalize() — right for a reorder that failed on its own (settled stays false and a capture times out loudly rather than committing a hairball), wrong for one the user stopped: cancelling IS the user settling for this view, and a gate nothing will lower again leaves settled false forever.