react-msaview 9.1.0 → 9.2.0

package/dist/blosum62.d.ts

@@ -0,0 +1,3 @@
+export declare const NUM_SYMBOLS: number;
+export declare const BLOSUM62: Int8Array<ArrayBuffer>;
+export declare const symbolOfCode: Int8Array<ArrayBuffer>;

package/dist/blosum62.js

@@ -0,0 +1,43 @@
+// BLOSUM62 (Henikoff & Henikoff 1992), shared by the neighbor-joining tree and
+// the blosum62_dynamic color scheme
+// prettier-ignore
+const BLOSUM62_KEYS = 'ARNDCQEGHILKMFPSTWYVBZX*';
+// prettier-ignore
+const BLOSUM62_DATA = [
+    [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4],
+    [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4],
+    [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4],
+    [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4],
+    [0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4],
+    [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4],
+    [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4],
+    [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4],
+    [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4],
+    [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4],
+    [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4],
+    [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4],
+    [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4],
+    [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4],
+    [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4],
+    [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4],
+    [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4],
+    [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4],
+    [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4],
+    [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4],
+    [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4],
+    [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4],
+    [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4],
+    [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1],
+];
+export const NUM_SYMBOLS = BLOSUM62_KEYS.length;
+export const BLOSUM62 = Int8Array.from(BLOSUM62_DATA.flat());
+// charCode -> row/column in BLOSUM62, -1 for anything the matrix does not name.
+// On a 120x800 alignment a Map keyed by upper-cased character took 2.6s to
+// build a tree, against 0.34s for this table.
+export const symbolOfCode = new Int8Array(128).fill(-1);
+for (let i = 0; i < NUM_SYMBOLS; i++) {
+    const key = BLOSUM62_KEYS[i];
+    symbolOfCode[key.charCodeAt(0)] = i;
+    symbolOfCode[key.toLowerCase().charCodeAt(0)] = i;
+}
+//# sourceMappingURL=blosum62.js.map

package/dist/blosum62.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"blosum62.js","sourceRoot":"","sources":["../src/blosum62.ts"],"names":[],"mappings":"AAAA,+EAA+E;AAC/E,oCAAoC;AAEpC,kBAAkB;AAClB,MAAM,aAAa,GAAG,0BAA0B,CAAA;AAChD,kBAAkB;AAClB,MAAM,aAAa,GAAG;IACpB,CAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC;IACzE,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAAC,CAAC,CAAC,EAA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package/dist/colorSchemes.js

@@ -75,6 +75,7 @@ const colorSchemes = {
         T: 'red',
     },
     percent_identity_dynamic: {},
+    blosum62_dynamic: {},
     // https://github.com/biotite-dev/biotite/blob/8c460972f8ab904312f130dfb80f3efc8c9bd7c5/src/biotite/sequence/graphics/color_schemes/flower.json
     flower: {
         A: '#b18a51',

package/dist/colorSchemes.js.map

@@ -1 +1 @@
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+{"version":3,"file":"colorSchemes.js","sourceRoot":"","sources":["../src/colorSchemes.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,sBAAsB,CAAA;AAC/D,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,OAAO,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAErC,8EAA8E;AAC9E,eAAe;AACf,MAAM,GAAG,GAAG;IACV,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC;IACb,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC;IACZ,CAAC,EAAE,MAAM,CAAC,GAAG,CAAC;IACd,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC;IACX,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC;CACZ,CAAA;AAED,gEAAgE;AAChE,MAAM,YAAY,GAA2C;IAC3D,IAAI,EAAE,EAAE;IACR,UAAU,EAAE,GAAG;IACf,OAAO,EAAE;QACP,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;KACX;IACD,IAAI,EAAE;QACJ,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;KACV;IACD,QAAQ,EAAE;QACR,CAAC,EAAE,YAAY;QACf,CAAC,EAAE,YAAY;QACf,CAAC,EAAE,OAAO;QACV,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,WAAW;QACd,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,UAAU;QACb,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,QAAQ;QACX,CAAC,EAAE,MAAM;QACT,CAAC,EAAE,KAAK;QACR,CAAC,EAAE,KAAK;KACT;IAED,wBAAwB,EAAE,EAAE;IAC5B,gBAAgB,EAAE,EAAE;IACpB,+IAA+I;IAC/I,MAAM,EAAE;QACN,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IACD,WAAW,EAAE;QACX,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,yJAAyJ;IACzJ,gBAAgB,EAAE;QAChB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,4BAA4B;IAC5B,wBAAwB,EAAE,EAAE;IAE5B,YAAY,EAAE;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IACD,WAAW,EAAE,GAAG;IAChB,cAAc,EAAE;QACd,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,sBAAsB,EAAE;QACtB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,iBAAiB,EAAE;QACjB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,kBAAkB,EAAE;QAClB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;KACb;IAED,gBAAgB,EAAE;QAChB,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAAC,EAAE,SAAS;QACZ,CAA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package/dist/components/Loading.d.ts

@@ -1,6 +1,7 @@
 import React from 'react';
 import type { MsaViewModel } from '../model.ts';
-declare const Loading: ({ model }: {
+import type { ToolbarSlots } from './header/Header.tsx';
+declare const Loading: ({ model, ...slots }: {
     model: MsaViewModel;
-}) => React.JSX.Element;
+} & ToolbarSlots) => React.JSX.Element;
 export default Loading;

package/dist/components/Loading.js

@@ -13,12 +13,12 @@ const Reset = observer(function ({ model, error, }) {
                 model.reset();
             } }, "Return to import form")) : null));
 });
-const Loading = observer(function ({ model }) {
+const Loading = observer(function ({ model, ...slots }) {
     const { isLoading, dataInitialized, data, error, resetCount, msaFilehandle, treeFilehandle, importForm, } = model;
     const hasData = !!(data.msa || data.tree);
     // a failed load keeps its filehandle, so the error outranks the spinner
     const loading = !error && !!(msaFilehandle || treeFilehandle || isLoading);
-    return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(StatusMessage, { model: model, variant: "page" })) : (React.createElement(MSAView, { model: model }))) : hasData ? (React.createElement(Reset, { model: model, error: error })) : (React.createElement(React.Fragment, null,
+    return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(StatusMessage, { model: model, variant: "page" })) : (React.createElement(MSAView, { model: model, ...slots }))) : hasData ? (React.createElement(Reset, { model: model, error: error })) : (React.createElement(React.Fragment, null,
         loading ? React.createElement(StatusMessage, { model: model, variant: "page" }) : null,
         importForm ? (React.createElement("div", { style: { display: loading ? 'none' : undefined } },
             React.createElement(ImportForm, { model: model }))) : error ? (React.createElement(ErrorMessage, { error: error })) : null)))));

package/dist/components/Loading.js.map

@@ -1 +1 @@
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package/dist/components/MSAView.d.ts

@@ -1,6 +1,7 @@
 import React from 'react';
 import type { MsaViewModel } from '../model.ts';
-declare const MSAView: ({ model }: {
+import type { ToolbarSlots } from './header/Header.tsx';
+declare const MSAView: ({ model, ...slots }: {
     model: MsaViewModel;
-}) => React.JSX.Element;
+} & ToolbarSlots) => React.JSX.Element;
 export default MSAView;

package/dist/components/MSAView.js

@@ -9,6 +9,7 @@ import MSAPanel from './msa/MSAPanel.js';
 import { clickColor, hoverColor, selectionFill } from './overlayColors.js';
 import RowPanelHeaders from './rowpanels/RowPanelHeaders.js';
 import RowPanels from './rowpanels/RowPanels.js';
+import SettingsPanel from './settings/SettingsPanel.js';
 import TreeOverview from './tree/TreeOverview.js';
 import TreePanel from './tree/TreePanel.js';
 import TreeRuler from './tree/TreeRuler.js';
@@ -80,12 +81,14 @@ const View = observer(function ({ model }) {
         React.createElement(TrackArea, { model: model }),
         React.createElement(MainArea, { model: model })));
 });
-const MSAView = observer(function ({ model }) {
-    const { height, hideHeader, viewInitialized, DialogComponent, DialogProps } = model;
+const MSAView = observer(function ({ model, ...slots }) {
+    const { height, headerHeight, hideHeader, settingsOpen, viewInitialized, DialogComponent, DialogProps, } = model;
     return (React.createElement("div", null, viewInitialized ? (React.createElement(React.Fragment, null,
         React.createElement("div", { style: { height, overflow: 'clip' } },
-            hideHeader ? null : React.createElement(Header, { model: model }),
-            React.createElement(View, { model: model })),
+            hideHeader ? null : React.createElement(Header, { model: model, ...slots }),
+            React.createElement("div", { style: { display: 'flex' } },
+                React.createElement(View, { model: model }),
+                settingsOpen ? (React.createElement(SettingsPanel, { model: model, height: height - headerHeight })) : null)),
         React.createElement(HorizontalResizeHandle, { model: model }),
         DialogComponent ? (React.createElement(Suspense, { fallback: null },
             React.createElement(DialogComponent, { ...DialogProps }))) : null)) : null));

package/dist/components/MSAView.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSAView.js","sourceRoot":"","sources":["../../src/components/MSAView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,sBAAsB,EACtB,oBAAoB,GACrB,MAAM,oBAAqB,CAAA;AAC5B,OAAO,KAAK,MAAM,YAAa,CAAA;AAC/B,OAAO,iBAAiB,MAAM,wBAAyB,CAAA;AACvD,OAAO,MAAM,MAAM,oBAAqB,CAAA;AACxC,OAAO,OAAO,MAAM,sBAAuB,CAAA;AAC3C,OAAO,QAAQ,MAAM,mBAAoB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAC1E,OAAO,eAAe,MAAM,gCAAiC,CAAA;AAC7D,OAAO,SAAS,MAAM,0BAA2B,CAAA;AACjD,OAAO,aAAa,MAAM,6BAA8B,CAAA;AACxD,OAAO,YAAY,MAAM,wBAAyB,CAAA;AAClD,OAAO,SAAS,MAAM,qBAAsB,CAAA;AAC5C,OAAO,SAAS,MAAM,qBAAsB,CAAA;AAK5C,wEAAwE;AACxE,4EAA4E;AAC5E,gFAAgF;AAChF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,uBAAuB,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IAC9E,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE;YAC1B,gBAAgB,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YACzD,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CACvB;QACN,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,6BAAK,KAAK,EAAE,EAAE,KAAK,EAAE,iBAAiB,EAAE,UAAU,EAAE,CAAC,EAAE,GAAI;QAC1D,uBAAuB,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CACvD,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,KAAK,GAGN;IACC,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,QAAQ,EACR,OAAO,EACP,sBAAsB,EACtB,cAAc,EACd,iBAAiB,EACjB,oBAAoB,EACpB,cAAc,EACd,iBAAiB,GAClB,GAAG,KAAK,CAAA;IAET,0EAA0E;IAC1E,8BAA8B;IAC9B,MAAM,KAAK,GAAG;QACZ;YACE,KAAK,EAAE,iBAAiB,EAAE,QAAQ;YAClC,GAAG,EAAE,iBAAiB,EAAE,MAAM;YAC9B,KAAK,EAAE,aAAa;SACrB;QACD,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,UAAU,EAAE;QACrD,EAAE,KAAK,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,KAAK,EAAE,UAAU,EAAE;KAChE,CAAA;IAED,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,sBAAsB,GAAG,cAAc,GAAG,iBAAiB;YACjE,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,cAAc;YACrB,MAAM,EAAE,oBAAoB;YAC5B,QAAQ,EAAE,QAAQ;YAClB,aAAa,EAAE,MAAM;SACtB,IAEA,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,EAAE,CACnC,KAAK,KAAK,SAAS,IAAI,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAChD,6BACE,GAAG,EAAE,KAAK,EACV,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,KAAK,GAAG,QAAQ,GAAG,OAAO;YAChC,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,CAAC,GAAG,GAAG,KAAK,GAAG,CAAC,CAAC,GAAG,QAAQ;YACnC,MAAM,EAAE,oBAAoB;YAC5B,eAAe,EAAE,KAAK;YACtB,MAAM,EAAE,GAAG;SACZ,GACD,CACH,CACF,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,IAAI,cAAc,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAChC,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACrC,cAAc,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAC3B,oBAAC,KAAK,IAAC,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CAC3D,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACpE,MAAM,EAAE,qBAAqB,EAAE,GAAG,KAAK,CAAA;IAEvC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,qBAAqB,CAAC,CAAC,CAAC,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CAC/D,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAChE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CACtB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EACjC,KAAK,EACL,GAAG,KAAK,EAC+B;IACvC,MAAM,EACJ,MAAM,EACN,YAAY,EACZ,UAAU,EACV,YAAY,EACZ,eAAe,EACf,eAAe,EACf,WAAW,GACZ,GAAG,KAAK,CAAA;IAET,OAAO,CACL,iCACG,eAAe,CAAC,CAAC,CAAC,CACjB;QACE,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE;YACrC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,oBAAC,MAAM,IAAC,KAAK,EAAE,KAAK,KAAM,KAAK,GAAI;YACxD,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;gBAC7B,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI;gBACrB,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAG,YAAY,GAAI,CAC/D,CAAC,CAAC,CAAC,IAAI,CACJ,CACF;QACN,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QAEvC,eAAe,CAAC,CAAC,CAAC,CACjB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,eAAe,OAAK,WAAW,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/MSAViewer.d.ts

@@ -139,7 +139,7 @@ export interface MSAViewerProps {
  * of those props changes and keeps its model across every other change,
  * including a new annotation file. A `ref` holds the current model.
  */
-declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.RefAttributes<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.RefAttributes<import("@jbrowse/mobx-state-tree").ModelInstanceTypeProps<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
@@ -150,6 +150,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -157,15 +158,17 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    domainFill: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").ILiteralType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    embeddedMode: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [undefined]>;
     height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -543,6 +546,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
+    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -552,6 +556,11 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    settingsOpen: boolean;
+    zoomHeld: {
+        col: number;
+        row: number;
+    };
     hideHeader: boolean;
     importForm: boolean;
     status: {
@@ -559,6 +568,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
+    zoomSnapshot: import("../zoomSnapshot.ts").ZoomSnapshot | undefined;
     loadingMSA: boolean;
     loadingTree: boolean;
     volatileWidth: number | undefined;
@@ -589,6 +599,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setLoadingMSA(arg: boolean): void;
     setLoadingTree(arg: boolean): void;
     setWidth(arg: number): void;
+    setSettingsOpen(arg: boolean): void;
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
@@ -605,6 +616,8 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     applyHighlight(owner: string, highlights: Highlight[]): void;
     clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
+    setDomainFill(arg: boolean): void;
+    setCellFill(mode: 'residue' | 'domain' | 'none'): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
     setMouseClickPos(col?: number, row?: number): void;
@@ -632,8 +645,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
-    readonly allAnnotations: import("msa-parsers").Annotation[];
-    readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
@@ -661,6 +672,8 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     rowDataOf(name: string): Record<string, string> | undefined;
     readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
+    readonly actuallyShowDomains: boolean;
     readonly numColumns: number;
     readonly inputTree: import("../types.ts").NodeWithIds;
     readonly tree: import("../types.ts").NodeWithIds;
@@ -724,6 +737,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
         color: string | undefined;
     }[];
     readonly colClustalX: Record<string, string>[];
+    readonly colSimilarity: Record<string, string>[];
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
@@ -759,6 +773,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     readonly adapterTrackModels: import("../types.ts").BasicTrack[];
     readonly basePairTrackModels: import("../types.ts").BasicTrack[];
     readonly computedTrackModels: import("../types.ts").BasicTrack[];
+    readonly referenceTrackModels: import("../types.ts").BasicTrack[];
     readonly tracks: import("../types.ts").BasicTrack[];
     readonly turnedOnTracks: import("../types.ts").BasicTrack[];
     readonly showHorizontalScrollbar: boolean;
@@ -792,7 +807,10 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
     readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly defaultOffAccessions: Set<string>;
+    featureOff(accession: string): boolean;
     readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly cellFill: 'residue' | 'domain' | 'none';
     readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
@@ -805,6 +823,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     readonly msaCanvasWidth: number;
     readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
+    readonly wheelZooming: boolean;
     readonly isLoading: boolean;
     readonly dataWarnings: string[];
     readonly warnings: string[];
@@ -824,6 +843,8 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     zoomIn(): void;
     zoomOut(): void;
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: import("../constants.ts").ScrollZoomAxis): void;
+    wheelZoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    endWheelZoom(): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
     setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
@@ -836,6 +857,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setRowPanels(panels: RowPanelSpec[]): void;
     setResidueMappings(mappings: ResidueMapping[]): void;
     toggleTrack(id: string): void;
+    setTracksShown(ids: string[], shown: boolean): void;
     setStatus(status?: {
         msg: string;
         onCancel?: () => void;
@@ -919,6 +941,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
 } & {
     setHeaderHeight(arg: number): void;
     setHideHeader(arg: boolean): void;
+    setEmbeddedMode(arg: boolean): void;
     setImportForm(arg: boolean): void;
     treeOverviewClick(y: number): void;
     setTrackHeight(heightKey: string, height: number): void;
@@ -927,7 +950,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
-    fitVertically(): void;
+    fitVertically(maxRowHeight?: any): void;
     zoomToRegion(region: Region): void;
     revealRegion(region: Region): void;
     zoomToSelection(): void;
@@ -938,9 +961,9 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
         col: number;
         row?: number;
     }): void;
-    fitHorizontally(): void;
+    fitHorizontally(maxColWidth?: any): void;
     afterCreate(): void;
-} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+} & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "showTreeScaleBar" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
@@ -951,6 +974,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -958,15 +982,17 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "domainFill" | "drawMsaLetters" | "embeddedMode" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks" | "type"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    domainFill: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showDomainLegend: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     allowedGappyness: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     subFeatureRows: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     type: import("@jbrowse/mobx-state-tree").ILiteralType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    embeddedMode: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scrollZoom: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     scrollZoomAxis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"both" | "horizontal" | "vertical">, [undefined]>;
     height: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -1344,6 +1370,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setDrawNodeBubbles(arg: boolean): void;
     setDrawNodeLabels(arg: boolean): void;
     setShowTreeOverview(arg: boolean): void;
+    setShowTreeScaleBar(arg: boolean): void;
     setDrawLabels(arg: boolean): void;
 } & {
     setColorSchemeName(name: string): void;
@@ -1353,6 +1380,11 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
+    settingsOpen: boolean;
+    zoomHeld: {
+        col: number;
+        row: number;
+    };
     hideHeader: boolean;
     importForm: boolean;
     status: {
@@ -1360,6 +1392,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
         onCancel?: () => void;
     } | undefined;
     highResScaleFactor: number;
+    zoomSnapshot: import("../zoomSnapshot.ts").ZoomSnapshot | undefined;
     loadingMSA: boolean;
     loadingTree: boolean;
     volatileWidth: number | undefined;
@@ -1390,6 +1423,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setLoadingMSA(arg: boolean): void;
     setLoadingTree(arg: boolean): void;
     setWidth(arg: number): void;
+    setSettingsOpen(arg: boolean): void;
     setHighResScaleFactor(arg: number): void;
     setHeight(height: number): void;
     setError(error?: unknown): void;
@@ -1406,6 +1440,8 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     applyHighlight(owner: string, highlights: Highlight[]): void;
     clearHighlight(owner: string): void;
     setShowDomains(arg: boolean): void;
+    setDomainFill(arg: boolean): void;
+    setCellFill(mode: 'residue' | 'domain' | 'none'): void;
     setShowDomainLegend(arg: boolean): void;
     setSubFeatureRows(arg: boolean): void;
     setMouseClickPos(col?: number, row?: number): void;
@@ -1433,8 +1469,6 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
-    readonly allAnnotations: import("msa-parsers").Annotation[];
-    readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
     readonly width: number;
@@ -1462,6 +1496,8 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     rowDataOf(name: string): Record<string, string> | undefined;
     readonly rowFields: string[];
     readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly allAnnotations: import("msa-parsers").Annotation[];
+    readonly actuallyShowDomains: boolean;
     readonly numColumns: number;
     readonly inputTree: import("../types.ts").NodeWithIds;
     readonly tree: import("../types.ts").NodeWithIds;
@@ -1525,6 +1561,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
         color: string | undefined;
     }[];
     readonly colClustalX: Record<string, string>[];
+    readonly colSimilarity: Record<string, string>[];
     readonly conservation: number[];
     readonly alphabetMaxBits: number;
     readonly propertyConservation: number[];
@@ -1560,6 +1597,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     readonly adapterTrackModels: import("../types.ts").BasicTrack[];
     readonly basePairTrackModels: import("../types.ts").BasicTrack[];
     readonly computedTrackModels: import("../types.ts").BasicTrack[];
+    readonly referenceTrackModels: import("../types.ts").BasicTrack[];
     readonly tracks: import("../types.ts").BasicTrack[];
     readonly turnedOnTracks: import("../types.ts").BasicTrack[];
     readonly showHorizontalScrollbar: boolean;
@@ -1593,7 +1631,10 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
     readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly defaultOffAccessions: Set<string>;
+    featureOff(accession: string): boolean;
     readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly cellFill: 'residue' | 'domain' | 'none';
     readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
@@ -1606,6 +1647,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     readonly msaCanvasWidth: number;
     readonly maxScrollX: number;
     readonly blocks2d: (readonly [number, number])[];
+    readonly wheelZooming: boolean;
     readonly isLoading: boolean;
     readonly dataWarnings: string[];
     readonly warnings: string[];
@@ -1625,6 +1667,8 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     zoomIn(): void;
     zoomOut(): void;
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: import("../constants.ts").ScrollZoomAxis): void;
+    wheelZoomToPos(scaleFactor: number, offsetX: number, offsetY: number): void;
+    endWheelZoom(): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
     setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
@@ -1637,6 +1681,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     setRowPanels(panels: RowPanelSpec[]): void;
     setResidueMappings(mappings: ResidueMapping[]): void;
     toggleTrack(id: string): void;
+    setTracksShown(ids: string[], shown: boolean): void;
     setStatus(status?: {
         msg: string;
         onCancel?: () => void;
@@ -1720,6 +1765,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
 } & {
     setHeaderHeight(arg: number): void;
     setHideHeader(arg: boolean): void;
+    setEmbeddedMode(arg: boolean): void;
     setImportForm(arg: boolean): void;
     treeOverviewClick(y: number): void;
     setTrackHeight(heightKey: string, height: number): void;
@@ -1728,7 +1774,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     exportNewick(): void;
     setFilter(accession: string, shown: boolean): void;
     fit(): void;
-    fitVertically(): void;
+    fitVertically(maxRowHeight?: any): void;
     zoomToRegion(region: Region): void;
     revealRegion(region: Region): void;
     zoomToSelection(): void;
@@ -1739,7 +1785,7 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
         col: number;
         row?: number;
     }): void;
-    fitHorizontally(): void;
+    fitHorizontally(maxColWidth?: any): void;
     afterCreate(): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
     bgColor: boolean;
@@ -1757,16 +1803,19 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
+    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks: ColumnTrackSpec[];
     id: string;
     showDomains: boolean;
+    domainFill: boolean;
     showDomainLegend: boolean;
     hideGaps: boolean;
     allowedGappyness: number;
     subFeatureRows: boolean;
     type: "MsaView";
     drawMsaLetters: boolean;
+    embeddedMode: boolean;
     scrollZoom: boolean;
     scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;
@@ -1894,16 +1943,19 @@ declare const MSAViewer: React.ForwardRefExoticComponent<MSAViewerProps & React.
     drawNodeBubbles: boolean;
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
+    showTreeScaleBar: boolean;
     overviewHeight: number;
     columnTracks?: undefined;
     id: string;
     showDomains: boolean;
+    domainFill: boolean;
     showDomainLegend: boolean;
     hideGaps: boolean;
     allowedGappyness: number;
     subFeatureRows: boolean;
     type: "MsaView";
     drawMsaLetters: boolean;
+    embeddedMode: boolean;
     scrollZoom: boolean;
     scrollZoomAxis: "both" | "horizontal" | "vertical";
     height: number;

package/dist/components/MetadataTable.d.ts

@@ -1,5 +1,8 @@
 import React from 'react';
+export declare function isRecord(value: unknown): value is Record<string, unknown>;
 export declare function isEmpty(value: unknown): boolean;
-export default function MetadataTable({ record, }: {
+export default function MetadataTable({ record, labels, monospaceKeys, }: {
     record: Record<string, unknown>;
+    labels?: Record<string, string>;
+    monospaceKeys?: Set<string>;
 }): React.JSX.Element;