react-msaview 6.5.0 → 7.0.0

package/dist/components/tree/scaleBar.js

@@ -0,0 +1,24 @@
+/**
+ * A round branch-length step and its width in pixels: the largest 1/2/5 x 10^n
+ * substitutions-per-site that fits in `maxPx`, aiming at about half of it.
+ * Returns undefined in cladogram mode, where the x-positions carry no length.
+ */
+export function scaleBarLength(pxPerUnit, maxPx) {
+    if (pxPerUnit <= 0 || maxPx < 20) {
+        return undefined;
+    }
+    const target = maxPx / 2 / pxPerUnit;
+    const magnitude = 10 ** Math.floor(Math.log10(target));
+    const mantissa = target / magnitude;
+    const step = (mantissa >= 5 ? 5 : mantissa >= 2 ? 2 : 1) * magnitude;
+    const px = step * pxPerUnit;
+    return px > maxPx
+        ? undefined
+        : {
+            step,
+            px,
+            // a length of 0.02 reads as 0.02, not 0.020000000000000004
+            label: `${Number(step.toPrecision(2))}`,
+        };
+}
+//# sourceMappingURL=scaleBar.js.map

package/dist/components/tree/scaleBar.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"scaleBar.js","sourceRoot":"","sources":["../../../src/components/tree/scaleBar.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,MAAM,UAAU,cAAc,CAAC,SAAiB,EAAE,KAAa;IAC7D,IAAI,SAAS,IAAI,CAAC,IAAI,KAAK,GAAG,EAAE,EAAE,CAAC;QACjC,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,MAAM,GAAG,KAAK,GAAG,CAAC,GAAG,SAAS,CAAA;IACpC,MAAM,SAAS,GAAG,EAAE,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAA;IACtD,MAAM,QAAQ,GAAG,MAAM,GAAG,SAAS,CAAA;IACnC,MAAM,IAAI,GAAG,CAAC,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,SAAS,CAAA;IACpE,MAAM,EAAE,GAAG,IAAI,GAAG,SAAS,CAAA;IAC3B,OAAO,EAAE,GAAG,KAAK;QACf,CAAC,CAAC,SAAS;QACX,CAAC,CAAC;YACE,IAAI;YACJ,EAAE;YACF,2DAA2D;YAC3D,KAAK,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,EAAE;SACxC,CAAA;AACP,CAAC"}

package/dist/constants.d.ts

@@ -4,7 +4,7 @@ export declare const defaultHeight = 550;
 export declare const defaultScrollX = 0;
 export declare const defaultScrollY = 0;
 export declare const defaultCurrentAlignment = 0;
-export declare const defaultShowDomains = false;
+export declare const defaultShowDomains = true;
 export declare const defaultShowDomainLegend = true;
 export declare const defaultHideGaps = true;
 export declare const defaultAllowedGappyness = 100;
@@ -30,3 +30,5 @@ export declare const defaultTreeWidth = 300;
 export declare const defaultShowBranchLen = true;
 export declare const defaultDrawTree = true;
 export declare const defaultDrawNodeBubbles = true;
+export declare const maxNeighborJoiningRows = 500;
+export declare const maxInlineSnapshotBytes = 50000;

package/dist/constants.js

@@ -5,7 +5,11 @@ export const defaultHeight = 550;
 export const defaultScrollX = 0;
 export const defaultScrollY = 0;
 export const defaultCurrentAlignment = 0;
-export const defaultShowDomains = false;
+// Annotations are loaded on purpose -- a gff filehandle, a file picked in the
+// dialog -- so they are drawn unless the reader has said otherwise. Since only
+// the "no" is stored, a shared link with the overlay hidden reopens hidden, and
+// one that never mentions it opens showing whatever annotations it carries.
+export const defaultShowDomains = true;
 export const defaultShowDomainLegend = true;
 export const defaultHideGaps = true;
 export const defaultAllowedGappyness = 100;
@@ -54,4 +58,17 @@ export const defaultTreeWidth = 300;
 export const defaultShowBranchLen = true;
 export const defaultDrawTree = true;
 export const defaultDrawNodeBubbles = true;
+// Neighbor joining refuses above this many rows. The distance matrix is O(n^2*L)
+// and the join loop O(n^3), both on the main thread with no progress and no
+// cancel: 400 rows measured 1.5s, 800 rows 10s, and 1600 would be about seventy.
+// See agent-docs/ideas/neighbor-joining-scaling.md for why the RapidNJ fix is a
+// real algorithm change rather than a port, and why capping is the honest answer
+// -- NJ on thousands of sequences is the wrong tool however fast it runs.
+export const maxNeighborJoiningRows = 500;
+// The largest inline document the snapshot carries. Past this a pasted or
+// locally-opened file stays in the live model and leaves the snapshot, since a
+// session or a shared URL holding megabytes of sequence is not a link anyone
+// can send. `unshareableData` reads the same number, so what the viewer warns
+// about and what the snapshot drops cannot drift apart.
+export const maxInlineSnapshotBytes = 50_000;
 //# sourceMappingURL=constants.js.map

package/dist/constants.js.map

@@ -1 +1 @@
-{"version":3,"file":"constants.js","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA,sBAAsB;AACtB,MAAM,CAAC,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAClC,MAAM,CAAC,MAAM,eAAe,GAAG,EAAE,CAAA;AACjC,MAAM,CAAC,MAAM,aAAa,GAAG,GAAG,CAAA;AAChC,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,uBAAuB,GAAG,CAAC,CAAA;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAA;AACvC,MAAM,CAAC,MAAM,uBAAuB,GAAG,IAAI,CAAA;AAC3C,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,uBAAuB,GAAG,GAAG,CAAA;AAC1C,MAAM,CAAC,MAAM,qBAAqB,GAAG,KAAK,CAAA;AAC1C,gEAAgE;AAChE,MAAM,CAAC,MAAM,mBAAmB,GAAG,CAAC,CAAA;AAEpC,8EAA8E;AAC9E,+EAA+E;AAC/E,6EAA6E;AAC7E,sEAAsE;AACtE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,GAAG,CAAC;IACzC,MAAM;IACN,KAAK;IACL,gBAAgB;IAChB,iBAAiB;IACjB,KAAK;IACL,QAAQ;CACT,CAAC,CAAA;AAEF,6DAA6D;AAC7D,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;AACnD,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI,CAAA;AACzC,MAAM,CAAC,MAAM,iBAAiB,GAAG,KAAK,CAAA;AAEtC,8EAA8E;AAC9E,+EAA+E;AAC/E,iDAAiD;AACjD,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC,CAAA;AACnC,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC,CAAA;AAElC,4EAA4E;AAC5E,uDAAuD;AACvD,MAAM,CAAC,MAAM,sBAAsB,GAAG,EAAE,CAAA;AAExC,+EAA+E;AAC/E,iFAAiF;AACjF,0BAA0B;AAC1B,MAAM,CAAC,MAAM,WAAW,GAAG,GAAG,CAAA;AAC9B,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,CAAA;AAC7B,MAAM,CAAC,MAAM,WAAW,GAAG,EAAE,CAAA;AAE7B,qBAAqB;AACrB,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAA;AAClC,MAAM,CAAC,MAAM,sBAAsB,GAAG,UAAU,CAAA;AAChD,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA;AAE1C,sBAAsB;AACtB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAA;AACrC,MAAM,CAAC,MAAM,uBAAuB,GAAG,KAAK,CAAA;AAC5C,MAAM,CAAC,MAAM,oBAAoB,GAAG,GAAG,CAAA;AACvC,MAAM,CAAC,MAAM,gBAAgB,GAAG,GAAG,CAAA;AACnC,MAAM,CAAC,MAAM,oBAAoB,GAAG,IAAI,CAAA;AACxC,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA"}
+{"version":3,"file":"constants.js","sourceRoot":"","sources":["../src/constants.ts"],"names":[],"mappings":"AAAA,sBAAsB;AACtB,MAAM,CAAC,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAClC,MAAM,CAAC,MAAM,eAAe,GAAG,EAAE,CAAA;AACjC,MAAM,CAAC,MAAM,aAAa,GAAG,GAAG,CAAA;AAChC,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,CAAA;AAC/B,MAAM,CAAC,MAAM,uBAAuB,GAAG,CAAC,CAAA;AACxC,8EAA8E;AAC9E,+EAA+E;AAC/E,gFAAgF;AAChF,4EAA4E;AAC5E,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAA;AACtC,MAAM,CAAC,MAAM,uBAAuB,GAAG,IAAI,CAAA;AAC3C,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,uBAAuB,GAAG,GAAG,CAAA;AAC1C,MAAM,CAAC,MAAM,qBAAqB,GAAG,KAAK,CAAA;AAC1C,gEAAgE;AAChE,MAAM,CAAC,MAAM,mBAAmB,GAAG,CAAC,CAAA;AAEpC,8EAA8E;AAC9E,+EAA+E;AAC/E,6EAA6E;AAC7E,sEAAsE;AACtE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,GAAG,CAAC;IACzC,MAAM;IACN,KAAK;IACL,gBAAgB;IAChB,iBAAiB;IACjB,KAAK;IACL,QAAQ;CACT,CAAC,CAAA;AAEF,6DAA6D;AAC7D,MAAM,CAAC,MAAM,aAAa,GAAG,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;AACnD,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI,CAAA;AACzC,MAAM,CAAC,MAAM,iBAAiB,GAAG,KAAK,CAAA;AAEtC,8EAA8E;AAC9E,+EAA+E;AAC/E,iDAAiD;AACjD,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC,CAAA;AACnC,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC,CAAA;AAElC,4EAA4E;AAC5E,uDAAuD;AACvD,MAAM,CAAC,MAAM,sBAAsB,GAAG,EAAE,CAAA;AAExC,+EAA+E;AAC/E,iFAAiF;AACjF,0BAA0B;AAC1B,MAAM,CAAC,MAAM,WAAW,GAAG,GAAG,CAAA;AAC9B,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,CAAA;AAC7B,MAAM,CAAC,MAAM,WAAW,GAAG,EAAE,CAAA;AAE7B,qBAAqB;AACrB,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAA;AAClC,MAAM,CAAC,MAAM,sBAAsB,GAAG,UAAU,CAAA;AAChD,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA;AAE1C,sBAAsB;AACtB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAA;AACrC,MAAM,CAAC,MAAM,uBAAuB,GAAG,KAAK,CAAA;AAC5C,MAAM,CAAC,MAAM,oBAAoB,GAAG,GAAG,CAAA;AACvC,MAAM,CAAC,MAAM,gBAAgB,GAAG,GAAG,CAAA;AACnC,MAAM,CAAC,MAAM,oBAAoB,GAAG,IAAI,CAAA;AACxC,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAA;AACnC,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAA;AAE1C,iFAAiF;AACjF,4EAA4E;AAC5E,iFAAiF;AACjF,gFAAgF;AAChF,iFAAiF;AACjF,0EAA0E;AAC1E,MAAM,CAAC,MAAM,sBAAsB,GAAG,GAAG,CAAA;AAEzC,0EAA0E;AAC1E,+EAA+E;AAC/E,6EAA6E;AAC7E,8EAA8E;AAC9E,wDAAwD;AACxD,MAAM,CAAC,MAAM,sBAAsB,GAAG,MAAM,CAAA"}

package/dist/fetchUtils.d.ts

@@ -2,7 +2,6 @@ import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 import type { RpcStatus } from '@jbrowse/core/util';
 export interface FetchStatus {
     msg: string;
-    url?: string;
     onCancel?: () => void;
 }
 type Filehandle = Parameters<typeof fetchAndMaybeUnzipText>[0];
@@ -14,12 +13,13 @@ type ProgressFetcher = (loc: Filehandle, opts: {
  * Fetch text from a filehandle while reporting download/unzip progress through
  * setStatus, and wiring a Cancel handler that aborts the underlying request.
  * The status is always cleared once the fetch settles. The fetcher is injectable
- * for testing.
+ * for testing, and so is the AbortController: a caller that can supersede its
+ * own request -- the model's loaders, when the filehandle changes under them --
+ * holds one and aborts the download it no longer wants.
  */
-export declare function fetchTextWithProgress(loc: Filehandle, setStatus: (status?: FetchStatus) => void, fetcher?: ProgressFetcher): Promise<string>;
-export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
-export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
-export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
-export declare function timeout(time: number, signal?: AbortSignal): Promise<void>;
+export declare function fetchTextWithProgress(loc: Filehandle, setStatus: (status?: FetchStatus) => void, { fetcher, controller, }?: {
+    fetcher?: ProgressFetcher;
+    controller?: AbortController;
+}): Promise<string>;
 export declare function isAbortError(e: unknown): boolean;
 export {};

package/dist/fetchUtils.js

@@ -17,10 +17,11 @@ function statusMessageText(status) {
  * Fetch text from a filehandle while reporting download/unzip progress through
  * setStatus, and wiring a Cancel handler that aborts the underlying request.
  * The status is always cleared once the fetch settles. The fetcher is injectable
- * for testing.
+ * for testing, and so is the AbortController: a caller that can supersede its
+ * own request -- the model's loaders, when the filehandle changes under them --
+ * holds one and aborts the download it no longer wants.
  */
-export async function fetchTextWithProgress(loc, setStatus, fetcher = fetchAndMaybeUnzipText) {
-    const controller = new AbortController();
+export async function fetchTextWithProgress(loc, setStatus, { fetcher = fetchAndMaybeUnzipText, controller = new AbortController(), } = {}) {
     try {
         return await fetcher(loc, {
             signal: controller.signal,
@@ -41,35 +42,6 @@ export async function fetchTextWithProgress(loc, setStatus, fetcher = fetchAndMa
         setStatus(undefined);
     }
 }
-export async function myfetch(url, args) {
-    const response = await fetch(url, args);
-    if (!response.ok) {
-        throw new Error(`HTTP ${response.status} fetching ${url} ${await response.text()}`);
-    }
-    return response;
-}
-export async function textfetch(url, args) {
-    const response = await myfetch(url, args);
-    return response.text();
-}
-export async function jsonfetch(url, args) {
-    const response = await myfetch(url, args);
-    return response.json();
-}
-export function timeout(time, signal) {
-    return new Promise((resolve, reject) => {
-        if (signal?.aborted) {
-            reject(new DOMException('Aborted', 'AbortError'));
-        }
-        else {
-            const id = setTimeout(resolve, time);
-            signal?.addEventListener('abort', () => {
-                clearTimeout(id);
-                reject(new DOMException('Aborted', 'AbortError'));
-            });
-        }
-    });
-}
 export function isAbortError(e) {
     return e instanceof DOMException && e.name === 'AbortError';
 }

package/dist/fetchUtils.js.map

@@ -1 +1 @@
-{"version":3,"file":"fetchUtils.js","sourceRoot":"","sources":["../src/fetchUtils.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AAI3D;;;;;;;;;;GAUG;AACH,SAAS,iBAAiB,CAAC,MAA6B;IACtD,OAAO,OAAO,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,OAAO,CAAA;AAC9D,CAAC;AAeD;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,qBAAqB,CACzC,GAAe,EACf,SAAyC,EACzC,OAAO,GAAoB,sBAAsB;IAEjD,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAAA;IACxC,IAAI,CAAC;QACH,OAAO,MAAM,OAAO,CAAC,GAAG,EAAE;YACxB,MAAM,EAAE,UAAU,CAAC,MAAM;YACzB,cAAc,EAAE,MAAM,CAAC,EAAE;gBACvB,MAAM,GAAG,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAA;gBACrC,SAAS,CACP,GAAG;oBACD,CAAC,CAAC;wBACE,GAAG;wBACH,QAAQ,EAAE,GAAG,EAAE;4BACb,UAAU,CAAC,KAAK,EAAE,CAAA;wBACpB,CAAC;qBACF;oBACH,CAAC,CAAC,SAAS,CACd,CAAA;YACH,CAAC;SACF,CAAC,CAAA;IACJ,CAAC;YAAS,CAAC;QACT,SAAS,CAAC,SAAS,CAAC,CAAA;IACtB,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAkB;IAC3D,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAEvC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;QACjB,MAAM,IAAI,KAAK,CACb,QAAQ,QAAQ,CAAC,MAAM,aAAa,GAAG,IAAI,MAAM,QAAQ,CAAC,IAAI,EAAE,EAAE,CACnE,CAAA;IACH,CAAC;IAED,OAAO,QAAQ,CAAA;AACjB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,GAAW,EAAE,IAAkB;IAC7D,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACzC,OAAO,QAAQ,CAAC,IAAI,EAAE,CAAA;AACxB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAI,GAAW,EAAE,IAAkB;IAChE,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACzC,OAAO,QAAQ,CAAC,IAAI,EAAO,CAAA;AAC7B,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,IAAY,EAAE,MAAoB;IACxD,OAAO,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;QAC3C,IAAI,MAAM,EAAE,OAAO,EAAE,CAAC;YACpB,MAAM,CAAC,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC,CAAA;QACnD,CAAC;aAAM,CAAC;YACN,MAAM,EAAE,GAAG,UAAU,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACpC,MAAM,EAAE,gBAAgB,CAAC,OAAO,EAAE,GAAG,EAAE;gBACrC,YAAY,CAAC,EAAE,CAAC,CAAA;gBAChB,MAAM,CAAC,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAC,CAAA;YACnD,CAAC,CAAC,CAAA;QACJ,CAAC;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,CAAU;IACrC,OAAO,CAAC,YAAY,YAAY,IAAI,CAAC,CAAC,IAAI,KAAK,YAAY,CAAA;AAC7D,CAAC"}
+{"version":3,"file":"fetchUtils.js","sourceRoot":"","sources":["../src/fetchUtils.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AAI3D;;;;;;;;;;GAUG;AACH,SAAS,iBAAiB,CAAC,MAA6B;IACtD,OAAO,OAAO,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,OAAO,CAAA;AAC9D,CAAC;AAcD;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,qBAAqB,CACzC,GAAe,EACf,SAAyC,EACzC,EACE,OAAO,GAAG,sBAAsB,EAChC,UAAU,GAAG,IAAI,eAAe,EAAE,GACnC,GAAgE,EAAE;IAEnE,IAAI,CAAC;QACH,OAAO,MAAM,OAAO,CAAC,GAAG,EAAE;YACxB,MAAM,EAAE,UAAU,CAAC,MAAM;YACzB,cAAc,EAAE,MAAM,CAAC,EAAE;gBACvB,MAAM,GAAG,GAAG,iBAAiB,CAAC,MAAM,CAAC,CAAA;gBACrC,SAAS,CACP,GAAG;oBACD,CAAC,CAAC;wBACE,GAAG;wBACH,QAAQ,EAAE,GAAG,EAAE;4BACb,UAAU,CAAC,KAAK,EAAE,CAAA;wBACpB,CAAC;qBACF;oBACH,CAAC,CAAC,SAAS,CACd,CAAA;YACH,CAAC;SACF,CAAC,CAAA;IACJ,CAAC;YAAS,CAAC;QACT,SAAS,CAAC,SAAS,CAAC,CAAA;IACtB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,CAAU;IACrC,OAAO,CAAC,YAAY,YAAY,IAAI,CAAC,CAAC,IAAI,KAAK,YAAY,CAAA;AAC7D,CAAC"}

package/dist/hierarchy.d.ts

@@ -13,6 +13,8 @@ export interface HierarchyNode<T = NodeWithIds> extends CoreHierarchyNode<T> {
     parent: HierarchyNode<T> | null;
     x?: number;
     y?: number;
+    xMin?: number;
+    xMax?: number;
     len?: number;
     depthToLeaf?: number;
     _children?: HierarchyNode<T>[] | null;
@@ -27,6 +29,5 @@ export declare function collapsedSubtreeMaxLength<T extends {
     length?: number;
 }>(node: HierarchyNode<T>): number;
 export declare function calcDepthToLeaf<T>(node: HierarchyNode<T>): number;
-export declare function findMaxBranchLen(node: HierarchyNode): number;
 export declare function maxLength(d: HierarchyNode): number;
 export declare function setBrLength(d: HierarchyNode, y0: number, k: number): void;

package/dist/hierarchy.js

@@ -20,16 +20,27 @@ export function clusterLayout(root, sizeX, sizeY) {
         leafNodes[i].x = (i + 0.5) * step;
     }
     // x of an internal node is the mean of its children's x, so process in
-    // post-order (children before parents)
+    // post-order (children before parents). The subtree span comes from the same
+    // pass, for the block culls in the tree renderer.
     const nodes = descendants(root);
     for (let i = nodes.length - 1; i >= 0; i--) {
         const node = nodes[i];
         if (node.children) {
             let sum = 0;
+            let min = Infinity;
+            let max = -Infinity;
             for (const child of node.children) {
                 sum += child.x;
+                min = Math.min(min, child.xMin);
+                max = Math.max(max, child.xMax);
             }
             node.x = sum / node.children.length;
+            node.xMin = min;
+            node.xMax = max;
+        }
+        else {
+            node.xMin = node.x;
+            node.xMax = node.x;
         }
     }
     const rootHeight = root.height;
@@ -111,14 +122,9 @@ export function calcDepthToLeaf(node) {
     }
     return node.depthToLeaf;
 }
-export function findMaxBranchLen(node) {
-    let maxLen = 0;
-    for (const n of descendants(node)) {
-        maxLen = Math.max(maxLen, n.len || 0);
-    }
-    return maxLen;
-}
-// Max root-to-leaf sum of branch lengths within the subtree at d
+// Max root-to-leaf sum of branch lengths within the subtree at d. Negative
+// lengths are floored at zero, the same as setBrLength does when it lays the
+// tree out, so the extent this reports is the one that gets drawn
 export function maxLength(d) {
     const nodes = descendants(d);
     const pathLen = new Map();
@@ -130,7 +136,7 @@ export function maxLength(d) {
                 childMax = Math.max(childMax, pathLen.get(child));
             }
         }
-        pathLen.set(n, (n.data.length || 0) + childMax);
+        pathLen.set(n, Math.max(n.data.length || 0, 0) + childMax);
     }
     return pathLen.get(d);
 }

package/dist/hierarchy.js.map

@@ -1 +1 @@
-{"version":3,"file":"hierarchy.js","sourceRoot":"","sources":["../src/hierarchy.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,WAAW,EACX,IAAI,EACJ,iBAAiB,EACjB,WAAW,EACX,SAAS,IAAI,aAAa,EAC1B,MAAM,EACN,KAAK,EACL,IAAI,EACJ,GAAG,GACJ,MAAM,cAAc,CAAA;AAyBrB,gFAAgF;AAChF,iFAAiF;AACjF,+EAA+E;AAC/E,uEAAuE;AACvE,OAAO,EACL,WAAW,EACX,IAAI,EACJ,iBAAiB,EACjB,WAAW,EACX,MAAM,EACN,KAAK,EACL,IAAI,EACJ,GAAG,GACJ,CAAA;AAGD,gFAAgF;AAChF,iFAAiF;AACjF,6EAA6E;AAC7E,wEAAwE;AACxE,yBAAyB;AACzB,MAAM,UAAU,SAAS,CACvB,IAAO,EACP,gBAA2C;IAE3C,OAAO,aAAa,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;AAC9C,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,IAAsB,EACtB,KAAa,EACb,KAAa;IAEb,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;IAC9B,MAAM,CAAC,GAAG,SAAS,CAAC,MAAM,CAAA;IAC1B,MAAM,IAAI,GAAG,KAAK,GAAG,CAAC,CAAA;IAEtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,SAAS,CAAC,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,CAAA;IACpC,CAAC;IAED,uEAAuE;IACvE,uCAAuC;IACvC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACtB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,IAAI,GAAG,GAAG,CAAC,CAAA;YACX,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,GAAG,IAAI,KAAK,CAAC,CAAE,CAAA;YACjB,CAAC;YACD,IAAI,CAAC,CAAC,GAAG,GAAG,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAA;QACrC,CAAC;IACH,CAAC;IAED,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAA;IAC9B,MAAM,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAA;IACxC,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACpC,IAAI,CAAC,CAAC,GAAG,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,UAAU,CAAC,GAAG,KAAK,CAAA;QAChE,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;YAC/C,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAI,IAAsB;IAChD,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAClB,oEAAoE;QACpE,uEAAuE;QACvE,0EAA0E;QAC1E,uEAAuE;QACvE,sDAAsD;QACtD,eAAe,CAAC,IAAI,CAAC,CAAA;QACrB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,QAAQ,CAAA;QAC9B,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAA;IACtB,CAAC;AACH,CAAC;AAED,iFAAiF;AACjF,+EAA+E;AAC/E,8CAA8C;AAC9C,MAAM,UAAU,yBAAyB,CACvC,IAAsB;IAEtB,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,QAAQ,CAAA;IAC7C,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,KAAK,EAAE,CAAC;QACV,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;YAChC,IAAI,EAAE,KAAK;YACX,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC;SACzC,CAAC,CAAC,CAAA;QACH,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACxB,MAAM,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;YACrC,MAAM,IAAI,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,SAAS,CAAA;YACtC,IAAI,IAAI,EAAE,MAAM,EAAE,CAAC;gBACjB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;oBACzB,KAAK,CAAC,IAAI,CAAC;wBACT,IAAI,EAAE,KAAK;wBACX,GAAG,EAAE,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC;qBAC/C,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAC1B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,+EAA+E;AAC/E,gFAAgF;AAChF,gFAAgF;AAChF,wEAAwE;AACxE,MAAM,UAAU,eAAe,CAAI,IAAsB;IACvD,+EAA+E;IAC/E,+EAA+E;IAC/E,+EAA+E;IAC/E,gEAAgE;IAChE,IAAI,IAAI,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;QACnC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;QAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACnB,IAAI,CAAC,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;gBAChC,IAAI,QAAQ,GAAG,CAAC,CAAA;gBAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;wBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,KAAK,CAAC,WAAY,CAAC,CAAA;oBACvD,CAAC;gBACH,CAAC;gBACD,CAAC,CAAC,WAAW,GAAG,QAAQ,CAAA;YAC1B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAC,WAAY,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAmB;IAClD,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,CAAC,IAAI,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC;QAClC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAA;IACvC,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,iEAAiE;AACjE,MAAM,UAAU,SAAS,CAAC,CAAgB;IACxC,MAAM,KAAK,GAAG,WAAW,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAChD,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,QAAQ,GAAG,CAAC,CAAA;QAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAE,CAAC,CAAA;YACpD,CAAC;QACH,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;IACjD,CAAC;IACD,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,CAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,CAAgB,EAAE,EAAU,EAAE,CAAS;IACjE,MAAM,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;IAC/B,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtC,MAAM,IAAI,GAAG,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;QACrD,IAAI,CAAC,GAAG,GAAG,IAAI,GAAG,CAAC,CAAA;QACnB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}
+{"version":3,"file":"hierarchy.js","sourceRoot":"","sources":["../src/hierarchy.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,WAAW,EACX,IAAI,EACJ,iBAAiB,EACjB,WAAW,EACX,SAAS,IAAI,aAAa,EAC1B,MAAM,EACN,KAAK,EACL,IAAI,EACJ,GAAG,GACJ,MAAM,cAAc,CAAA;AA8BrB,gFAAgF;AAChF,iFAAiF;AACjF,+EAA+E;AAC/E,uEAAuE;AACvE,OAAO,EACL,WAAW,EACX,IAAI,EACJ,iBAAiB,EACjB,WAAW,EACX,MAAM,EACN,KAAK,EACL,IAAI,EACJ,GAAG,GACJ,CAAA;AAGD,gFAAgF;AAChF,iFAAiF;AACjF,6EAA6E;AAC7E,wEAAwE;AACxE,yBAAyB;AACzB,MAAM,UAAU,SAAS,CACvB,IAAO,EACP,gBAA2C;IAE3C,OAAO,aAAa,CAAC,IAAI,EAAE,gBAAgB,CAAC,CAAA;AAC9C,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,IAAsB,EACtB,KAAa,EACb,KAAa;IAEb,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;IAC9B,MAAM,CAAC,GAAG,SAAS,CAAC,MAAM,CAAA;IAC1B,MAAM,IAAI,GAAG,KAAK,GAAG,CAAC,CAAA;IAEtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3B,SAAS,CAAC,CAAC,CAAE,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,CAAA;IACpC,CAAC;IAED,uEAAuE;IACvE,6EAA6E;IAC7E,kDAAkD;IAClD,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACtB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,IAAI,GAAG,GAAG,CAAC,CAAA;YACX,IAAI,GAAG,GAAG,QAAQ,CAAA;YAClB,IAAI,GAAG,GAAG,CAAC,QAAQ,CAAA;YACnB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,GAAG,IAAI,KAAK,CAAC,CAAE,CAAA;gBACf,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,KAAK,CAAC,IAAK,CAAC,CAAA;gBAChC,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,KAAK,CAAC,IAAK,CAAC,CAAA;YAClC,CAAC;YACD,IAAI,CAAC,CAAC,GAAG,GAAG,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAA;YACnC,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;YACf,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,CAAC,CAAA;YAClB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IAED,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAA;IAC9B,MAAM,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,CAAA;IACxC,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACpC,IAAI,CAAC,CAAC,GAAG,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,UAAU,CAAC,GAAG,KAAK,CAAA;QAChE,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;YAC/C,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,QAAQ,CAAI,IAAsB;IAChD,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;QAClB,oEAAoE;QACpE,uEAAuE;QACvE,0EAA0E;QAC1E,uEAAuE;QACvE,sDAAsD;QACtD,eAAe,CAAC,IAAI,CAAC,CAAA;QACrB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,QAAQ,CAAA;QAC9B,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAA;IACtB,CAAC;AACH,CAAC;AAED,iFAAiF;AACjF,+EAA+E;AAC/E,8CAA8C;AAC9C,MAAM,UAAU,yBAAyB,CACvC,IAAsB;IAEtB,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,QAAQ,CAAA;IAC7C,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,KAAK,EAAE,CAAC;QACV,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;YAChC,IAAI,EAAE,KAAK;YACX,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC;SACzC,CAAC,CAAC,CAAA;QACH,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACxB,MAAM,EAAE,IAAI,EAAE,CAAC,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;YACrC,MAAM,IAAI,GAAG,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,SAAS,CAAA;YACtC,IAAI,IAAI,EAAE,MAAM,EAAE,CAAC;gBACjB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;oBACzB,KAAK,CAAC,IAAI,CAAC;wBACT,IAAI,EAAE,KAAK;wBACX,GAAG,EAAE,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC;qBAC/C,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;YAC1B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,+EAA+E;AAC/E,gFAAgF;AAChF,gFAAgF;AAChF,wEAAwE;AACxE,MAAM,UAAU,eAAe,CAAI,IAAsB;IACvD,+EAA+E;IAC/E,+EAA+E;IAC/E,+EAA+E;IAC/E,gEAAgE;IAChE,IAAI,IAAI,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;QACnC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;QAC/B,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACnB,IAAI,CAAC,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;gBAChC,IAAI,QAAQ,GAAG,CAAC,CAAA;gBAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;wBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,KAAK,CAAC,WAAY,CAAC,CAAA;oBACvD,CAAC;gBACH,CAAC;gBACD,CAAC,CAAC,WAAW,GAAG,QAAQ,CAAA;YAC1B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAC,WAAY,CAAA;AAC1B,CAAC;AAED,2EAA2E;AAC3E,6EAA6E;AAC7E,kEAAkE;AAClE,MAAM,UAAU,SAAS,CAAC,CAAgB;IACxC,MAAM,KAAK,GAAG,WAAW,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAChD,KAAK,IAAI,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,QAAQ,GAAG,CAAC,CAAA;QAChB,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;YACf,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBAC/B,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAE,CAAC,CAAA;YACpD,CAAC;QACH,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,CAAE,CAAA;AACxB,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,CAAgB,EAAE,EAAU,EAAE,CAAS;IACjE,MAAM,KAAK,GAAG,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;IAC/B,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,GAAG,EAAG,CAAA;QACtC,MAAM,IAAI,GAAG,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAA;QACrD,IAAI,CAAC,GAAG,GAAG,IAAI,GAAG,CAAC,CAAA;QACnB,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC,CAAA;YACvC,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/index.d.ts

@@ -1,6 +1,7 @@
 export { renderToSvg } from './renderToSvg.tsx';
 export type { ExportSvgOptions } from './renderToSvg.tsx';
 export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv.ts';
+export { maxNeighborJoiningRows } from './constants.ts';
 export { default as MSAView } from './components/Loading.tsx';
 export { default as MSAViewer } from './components/MSAViewer.tsx';
 export { type MsaViewModel, default as MSAModelF } from './model.ts';
@@ -8,4 +9,4 @@ export type { MSAFormat, MSAParserType } from 'msa-parsers';
 export type { HierarchyNode } from './hierarchy.ts';
 export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
-export type { Accession, Annotation, BasicTrack, BasicTrackModel, ColumnTrackSpec, DomainBand, Highlight, Node, NodeWithIds, NodeWithIdsAndLength, ResolvedHighlight, TextTrackModel, TidyDomainAnnotation, } from './types.ts';
+export type { Accession, Annotation, Arc, ArcSpec, ArcTrackModel, BasicTrack, BasicTrackModel, ColumnTrackSpec, DomainBand, Highlight, Node, MappedStructure, NodeWithIds, NodeWithIdsAndLength, ResidueMapping, ResidueMappingProblem, ResidueSegment, ResolvedHighlight, RowResidue, StructureResidue, TextTrackModel, TidyDomainAnnotation, UnshareableData, } from './types.ts';

package/dist/index.js

@@ -1,14 +1,20 @@
 // PUBLIC API — consumed by external JBrowse 2 plugins. Changing or removing any
 // export here is a breaking change for downstream repos:
-//   - jbrowse-plugin-msaview   (wraps MSAModelF + MSAView into a JBrowse view)
-//   - jbrowse-plugin-protein3d (drives MSA<->structure hover/highlight sync)
+//   - jbrowse-plugin-msaview (wraps MSAModelF + MSAView into a JBrowse view)
+//   - jbrowse-plugin-tview   (the same, for a tree-first view)
 // Those plugins also reach into the MsaViewModel instance at runtime; the model
 // members they rely on (e.g. mouseCol/setMousePos, setHighlightedColumns,
 // seqPosToVisibleCol/visibleColToSeqPos) are flagged inline in model.ts.
+// jbrowse-plugin-protein3d no longer depends on this package at all: it reads
+// the msaview plugin's model through a structural type of its own.
 export { renderToSvg } from './renderToSvg.js';
 // renderToSvg outside a browser needs DOM bits jsdom omits; react-msaview-cli
 // and the README figure generator both drive it that way
 export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv.js';
+// the row count past which calculateNeighborJoiningTreeFromMSA refuses, so a
+// host can gate its own menu item on the same number instead of offering a
+// button that throws
+export { maxNeighborJoiningRows } from './constants.js';
 export { default as MSAView } from './components/Loading.js';
 export { default as MSAViewer } from './components/MSAViewer.js';
 export { default as MSAModelF } from './model.js';

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,gFAAgF;AAChF,yDAAyD;AACzD,+EAA+E;AAC/E,6EAA6E;AAC7E,gFAAgF;AAChF,0EAA0E;AAC1E,yEAAyE;AACzE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAmB,CAAA;AAE/C,8EAA8E;AAC9E,yDAAyD;AACzD,OAAO,EACL,gBAAgB,EAChB,wBAAwB,GACzB,MAAM,wBAAwB,CAAA;AAC/B,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AACjE,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,gFAAgF;AAChF,yDAAyD;AACzD,6EAA6E;AAC7E,+DAA+D;AAC/D,gFAAgF;AAChF,0EAA0E;AAC1E,yEAAyE;AACzE,8EAA8E;AAC9E,mEAAmE;AACnE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAmB,CAAA;AAE/C,8EAA8E;AAC9E,yDAAyD;AACzD,OAAO,EACL,gBAAgB,EAChB,wBAAwB,GACzB,MAAM,wBAAwB,CAAA;AAC/B,6EAA6E;AAC7E,2EAA2E;AAC3E,qBAAqB;AACrB,OAAO,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAA;AACvD,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AACjE,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/model/DataModel.js

@@ -1,4 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
+import { maxInlineSnapshotBytes } from '../constants.js';
 /**
  * #stateModel DataModel
  * the data stored for the model. this is sometimes temporary in the case that
@@ -55,10 +56,12 @@ export function DataModelF() {
         .postProcessSnapshot(snap => 
     // a large document is dropped from the snapshot rather than inlined
     // into a session or a shared URL, and every field here holds one, so
-    // the rule is the same for all of them
+    // the rule is the same for all of them. The parent model's
+    // `unshareableData` reports what this drops, since dropping it silently
+    // is how a copied link comes to open an empty viewer
     Object.fromEntries(Object.entries(snap).map(([key, text]) => [
         key,
-        text && text.length > 50_000 ? undefined : text,
+        text && text.length > maxInlineSnapshotBytes ? undefined : text,
     ])));
 }
 //# sourceMappingURL=DataModel.js.map

package/dist/model/DataModel.js.map

@@ -1 +1 @@
-{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD;;;;;;GAMG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACvC;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KAC/B,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;IAC1B,oEAAoE;IACpE,qEAAqE;IACrE,uCAAuC;IACvC,MAAM,CAAC,WAAW,CAChB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,CAAC;QACxC,GAAG;QACH,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;KAChD,CAAC,CACH,CACF,CAAA;AACL,CAAC"}
+{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAExD;;;;;;GAMG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACvC;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KAC/B,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;IAC1B,oEAAoE;IACpE,qEAAqE;IACrE,2DAA2D;IAC3D,wEAAwE;IACxE,qDAAqD;IACrD,MAAM,CAAC,WAAW,CAChB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,CAAC;QACxC,GAAG;QACH,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,sBAAsB,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;KAChE,CAAC,CACH,CACF,CAAA;AACL,CAAC"}