react-msaview 3.1.12 → 3.2.0

package/dist/parseNewick.js.map

@@ -1 +1 @@
-{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../src/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IACpB,8DAA8D;IAC9D,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QACvB,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,gBAAgB;gBACxB,IAAI,CAAC,SAAS,GAAG,CAAC,OAAO,CAAC,CAAA;gBAC1B,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACzC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACvB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
+{"version":3,"file":"parseNewick.js","sourceRoot":"","sources":["../src/parseNewick.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0DG;AACH,MAAM,CAAC,OAAO,UAAU,KAAK,CAAC,CAAS;IACrC,MAAM,SAAS,GAAG,EAAE,CAAA;IACpB,8DAA8D;IAC9D,IAAI,IAAI,GAAG,EAAyB,CAAA;IACpC,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAA;IAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QACvB,MAAM,OAAO,GAAG,EAAE,CAAA;QAClB,QAAQ,KAAK,EAAE,CAAC;YACd,KAAK,GAAG,EAAE,gBAAgB;gBACxB,IAAI,CAAC,SAAS,GAAG,CAAC,OAAO,CAAC,CAAA;gBAC1B,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,iBAAiB;gBACzB,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACzC,IAAI,GAAG,OAAO,CAAA;gBACd,MAAK;YACP,KAAK,GAAG,EAAE,qBAAqB;gBAC7B,IAAI,GAAG,SAAS,CAAC,GAAG,EAAG,CAAA;gBACvB,MAAK;YACP,KAAK,GAAG,EAAE,uBAAuB;gBAC/B,MAAK;YACP,OAAO,CAAC,CAAC,CAAC;gBACR,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACvB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACxC,IAAI,CAAC,IAAI,GAAG,KAAK,CAAA;gBACnB,CAAC;qBAAM,IAAI,CAAC,KAAK,GAAG,EAAE,CAAC;oBACrB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;gBACxC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}

package/dist/parsers/ClustalMSA.d.ts

@@ -1,4 +1,4 @@
-import { NodeWithIds } from '../util';
+import type { NodeWithIds } from '../util';
 export default class ClustalMSA {
     private MSA;
     constructor(text: string);

package/dist/parsers/FastaMSA.d.ts

@@ -1,4 +1,4 @@
-import { NodeWithIds } from '../util';
+import type { NodeWithIds } from '../util';
 export default class FastaMSA {
     private MSA;
     constructor(text: string);

package/dist/parsers/StockholmMSA.d.ts

@@ -1,4 +1,4 @@
-import { NodeWithIds } from '../util';
+import { type NodeWithIds } from '../util';
 interface StockholmEntry {
     gf: {
         DE?: string[];

package/dist/parsers/StockholmMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/parsers/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,cAAc,CAAA;AACpC,OAAO,WAAW,MAAM,gBAAgB,CAAA;AAExC,OAAO,EAAe,eAAe,EAAE,MAAM,SAAS,CAAA;AAiBtD,MAAM,CAAC,OAAO,OAAO,YAAY;IACvB,IAAI,CAAkB;IACtB,GAAG,CAAgB;IAE3B,YAAY,IAAY,EAAE,gBAAwB;QAChD,MAAM,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACpC,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,CAAA;IAClC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,EAAE,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACtC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE;YAC3B,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE;SACxB,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC;YACrC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC;SACnC,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,YAAY,KAAI,CAAC;IAEjB,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAA;QACpB,MAAM,IAAI,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC;aAC1C,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAU,CAAC;aACnD,MAAM,CAAC,CAAC,IAAI,EAAqC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;aAC9D,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;YAClC,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACtB,MAAM,QAAQ,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAC1B,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YACxB,OAAO,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAA;QAC7C,CAAC,CAAC,CAAA;QAEJ,MAAM,GAAG,GAAG,EAAoD,CAAA;QAChE,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;YACzB,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,EAAE,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBACb,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;YACd,CAAC;YACD,GAAG,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAClC,OAAO,IAAI;YACT,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;YACpC,CAAC,CAAC;gBACE,EAAE,EAAE,MAAM;gBACV,IAAI,EAAE,MAAM;gBACZ,MAAM,EAAE,IAAI;gBACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACtC,EAAE,EAAE,IAAI;oBACR,SAAS,EAAE,EAAE;oBACb,IAAI;iBACL,CAAC,CAAC;aACJ,CAAA;IACP,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,QAAQ,CAAA;IAC9B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAA;IAC7B,CAAC;IAED,IAAI,MAAM;QACR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,iBAAiB,EAAE;oBACjB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,WAAW;iBACjB;aACF;SACF,CAAA;IACH,CAAC;CACF"}
+{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/parsers/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,cAAc,CAAA;AACpC,OAAO,WAAW,MAAM,gBAAgB,CAAA;AAExC,OAAO,EAAoB,eAAe,EAAE,MAAM,SAAS,CAAA;AAiB3D,MAAM,CAAC,OAAO,OAAO,YAAY;IACvB,IAAI,CAAkB;IACtB,GAAG,CAAgB;IAE3B,YAAY,IAAY,EAAE,gBAAwB;QAChD,MAAM,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACpC,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,CAAA;IAClC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,EAAE,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACtC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE;YAC3B,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE;SACxB,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC;YACrC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC;SACnC,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,YAAY,KAAI,CAAC;IAEjB,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAA;QACpB,MAAM,IAAI,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC;aAC1C,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAU,CAAC;aACnD,MAAM,CAAC,CAAC,IAAI,EAAqC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;aAC9D,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;YAClC,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACtB,MAAM,QAAQ,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YAC1B,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YACxB,OAAO,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAA;QAC7C,CAAC,CAAC,CAAA;QAEJ,MAAM,GAAG,GAAG,EAAoD,CAAA;QAChE,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;YACzB,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,EAAE,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBACb,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;YACd,CAAC;YACD,GAAG,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAClC,OAAO,IAAI;YACT,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;YACpC,CAAC,CAAC;gBACE,EAAE,EAAE,MAAM;gBACV,IAAI,EAAE,MAAM;gBACZ,MAAM,EAAE,IAAI;gBACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACtC,EAAE,EAAE,IAAI;oBACR,SAAS,EAAE,EAAE;oBACb,IAAI;iBACL,CAAC,CAAC;aACJ,CAAA;IACP,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,QAAQ,CAAA;IAC9B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAA;IAC7B,CAAC;IAED,IAAI,MAAM;QACR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,iBAAiB,EAAE;oBACjB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,WAAW;iBACjB;aACF;SACF,CAAA;IACH,CAAC;CACF"}

package/dist/renderToSvg.d.ts

@@ -1,5 +1,5 @@
-import { Theme } from '@mui/material';
-import { MsaViewModel } from './model';
+import type { Theme } from '@mui/material';
+import type { MsaViewModel } from './model';
 export declare function renderToSvg(model: MsaViewModel, opts: {
     theme: Theme;
     includeMinimap?: boolean;

package/dist/renderToSvg.js

@@ -8,7 +8,7 @@ import { colorContrast } from './util';
 import MinimapSVG from './components/minimap/MinimapSVG';
 import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock';
 export async function renderToSvg(model, opts) {
-    await when(() => !!model.initialized);
+    await when(() => !!model.dataInitialized);
     const { width, height, scrollX, scrollY } = model;
     const { exportType, theme, includeMinimap } = opts;
     if (exportType === 'entire') {
@@ -22,7 +22,7 @@ export async function renderToSvg(model, opts) {
             includeMinimap,
         });
     }
-    else if (exportType === 'viewport') {
+    if (exportType === 'viewport') {
         return render({
             width,
             height,
@@ -33,9 +33,7 @@ export async function renderToSvg(model, opts) {
             includeMinimap,
         });
     }
-    else {
-        throw new Error('unknown export type');
-    }
+    throw new Error('unknown export type');
 }
 async function render({ width, height, offsetX, offsetY, theme, model, includeMinimap, }) {
     const { Context } = await import('svgcanvas');

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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package/dist/reparseTree.d.ts

@@ -1,2 +1,2 @@
-import { NodeWithIds } from './util';
+import type { NodeWithIds } from './util';
 export declare function reparseTree(tree: NodeWithIds): NodeWithIds;

package/dist/util.d.ts

@@ -1,5 +1,5 @@
-import { HierarchyNode } from 'd3-hierarchy';
-import { Theme } from '@mui/material';
+import type { HierarchyNode } from 'd3-hierarchy';
+import type { Theme } from '@mui/material';
 export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
     [k: string]: T;
 };

package/dist/util.js

@@ -54,8 +54,6 @@ export function collapse(d) {
         // @ts-expect-error
         d._children = d.children;
         // @ts-expect-error
-        d._children.forEach(collapse);
-        // @ts-expect-error
         d.children = null;
     }
 }

package/dist/util.js.map

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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAE9B,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAE9C,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,MAAM,UAAU,SAAS,CACvB,GAAsB,EACtB,EAAsC;IAEtC,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAwBD,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,EAAE,GAAG,GAAG,MAAM,IAAI,KAAK,EAAE,CAAA;IAE/B,OAAO;QACL,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,SAAS,EACP,IAAI,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC3B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,IAAI,EAAE;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,WAAmC,EACnC,KAAY;IAEZ,OAAO,SAAS,CAAC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QACjD,MAAM;QACN,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;KACrD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,MAAgB,EAAE,GAAsB;IACjE,IAAI,CAAC,GAAG,EAAE,CAAA;IACV,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACpC,IAAI,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AAED,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,CAA6B;IACpD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,mBAAmB;QACnB,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,QAAQ,CAAA;QACxB,mBAAmB;QACnB,CAAC,CAAC,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,GAAW,EAAE,GAAW,EAAE,GAAW;IACzD,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.1.12";
+export declare const version = "3.2.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.12';
+export const version = '3.2.0';
 //# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -1 +1 @@
-{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAA"}
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,OAAO,CAAA"}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.12",
+  "version": "3.2.0",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",
@@ -15,6 +15,7 @@
   },
   "scripts": {
     "clean": "rimraf dist",
+    "format": "prettier --write .",
     "prebuild": "npm run clean",
     "prepublishOnly": "node output-version.js > src/version.ts && git add -A src && git commit -m '[skip ci] Bump version.ts'",
     "build:esm": "tsc",
@@ -23,7 +24,8 @@
     "prepack": "npm run build",
     "postversion": "git push --follow-tags",
     "prestatedocs": "yarn tsc --build docgen/tsconfig.json",
-    "statedocs": "rm -rf apidocs && mkdir apidocs && node docgen/dist/generateStateModelDocs.js"
+    "statedocs": "rm -rf apidocs && mkdir apidocs && node docgen/dist/generateStateModelDocs.js",
+    "poststatedocs": "npm run format"
   },
   "peerDependencies": {
     "@jbrowse/core": ">=2.0.0",
@@ -42,6 +44,7 @@
     "d3-array": "^3.2.3",
     "d3-hierarchy": "^3.1.2",
     "file-saver": "^2.0.5",
+    "pako": "^2.1.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^4.0.13",
     "stockholm-js": "^1.0.10",

package/src/colorSchemes.ts

@@ -5,6 +5,7 @@ import { transform } from './util'
 extend([namesPlugin])
 
 const colorSchemes = {
+  none: {},
   clustal: {
     G: 'orange',
     P: 'orange',
@@ -351,11 +352,11 @@ export default transform(colorSchemes, ([key, val]) => [
 // should be WLVIMAFCHPY, colprot.xml says e.g. %#ACFHILMVWYPp" which has Y
 export function getClustalXColor(
   stats: Record<string, number>,
+  total: number,
   model: { columns: Record<string, string> },
   row: string,
   col: number,
 ) {
-  const total = Object.values(stats).reduce((a, b) => a + b, 0)
   const l = model.columns[row][col]
   const {
     W = 0,
@@ -498,11 +499,11 @@ export function getClustalXColor(
 // should be WLVIMAFCHPY, colprot.xml says e.g. %#ACFHILMVWYPp" which has Y
 export function getPercentIdentityColor(
   stats: Record<string, number>,
+  total: number,
   model: { columns: Record<string, string> },
   row: string,
   col: number,
 ) {
-  const total = Object.values(stats).reduce((a, b) => a + b, 0)
   const l = model.columns[row][col]
   const entries = Object.entries(stats)
   let ent = 0

package/src/components/Checkbox2.tsx

@@ -2,7 +2,7 @@ import React from 'react'
 import {
   Checkbox,
   FormControlLabel,
-  FormControlLabelProps,
+  type FormControlLabelProps,
 } from '@mui/material'
 
 function FormControlLabel2(rest: FormControlLabelProps) {

package/src/components/Loading.tsx

@@ -7,9 +7,15 @@ import { ErrorMessage } from '@jbrowse/core/ui'
 // locals
 import ImportForm from './import/ImportForm'
 import MSAView from './MSAView'
-import { MsaViewModel } from '../model'
+import type { MsaViewModel } from '../model'
 
-function Reset({ model, error }: { model: MsaViewModel; error: unknown }) {
+const Reset = observer(function ({
+  model,
+  error,
+}: {
+  model: MsaViewModel
+  error: unknown
+}) {
   return (
     <div>
       <ErrorMessage error={error} />
@@ -18,17 +24,17 @@ function Reset({ model, error }: { model: MsaViewModel; error: unknown }) {
       </Button>
     </div>
   )
-}
+})
 
 const Loading = observer(function ({ model }: { model: MsaViewModel }) {
-  const { isLoading, initialized } = model
+  const { isLoading, dataInitialized } = model
 
   return (
     <div>
       <ErrorBoundary
         fallbackRender={props => <Reset model={model} error={props.error} />}
       >
-        {initialized ? (
+        {dataInitialized ? (
           isLoading ? (
             <Typography variant="h4">Loading...</Typography>
           ) : (

package/src/components/MSAView.tsx

@@ -3,55 +3,64 @@ import { observer } from 'mobx-react'
 
 // locals
 import { HorizontalResizeHandle, VerticalResizeHandle } from './ResizeHandles'
-import { MsaViewModel } from '../model'
+import type { MsaViewModel } from '../model'
 import TreeRuler from './tree/TreeRuler'
 import Header from './header/Header'
 import MSAPanel from './msa/MSAPanel'
 import TreePanel from './tree/TreePanel'
 import Minimap from './minimap/Minimap'
+import VerticalScrollbar from './VerticalScrollbar'
 
-function TopArea({ model }: { model: MsaViewModel }) {
+const TopArea = observer(function ({ model }: { model: MsaViewModel }) {
+  const { showHorizontalScrollbar } = model
   return (
     <div style={{ display: 'flex' }}>
       <TreeRuler model={model} />
-      <Minimap model={model} />
+      {showHorizontalScrollbar ? <Minimap model={model} /> : null}
     </div>
   )
-}
-function MainArea({ model }: { model: MsaViewModel }) {
+})
+
+const MainArea = observer(function ({ model }: { model: MsaViewModel }) {
+  const { showVerticalScrollbar } = model
+
   return (
     <div style={{ display: 'flex' }}>
       <TreePanel model={model} />
       <VerticalResizeHandle model={model} />
       <MSAPanel model={model} />
+      {showVerticalScrollbar ? <VerticalScrollbar model={model} /> : null}
     </div>
   )
-}
+})
 
 const View = observer(function ({ model }: { model: MsaViewModel }) {
   return (
     <div style={{ position: 'relative' }}>
       <TopArea model={model} />
-
       <MainArea model={model} />
     </div>
   )
 })
 
 const MSAView = observer(function ({ model }: { model: MsaViewModel }) {
-  const { height, DialogComponent, DialogProps } = model
+  const { height, viewInitialized, DialogComponent, DialogProps } = model
   return (
     <div>
-      <div style={{ height, overflow: 'hidden' }}>
-        <Header model={model} />
-        <View model={model} />
-      </div>
-      <HorizontalResizeHandle model={model} />
-
-      {DialogComponent ? (
-        <Suspense fallback={null}>
-          <DialogComponent {...DialogProps} />
-        </Suspense>
+      {viewInitialized ? (
+        <>
+          <div style={{ height, overflow: 'hidden' }}>
+            <Header model={model} />
+            <View model={model} />
+          </div>
+          <HorizontalResizeHandle model={model} />
+
+          {DialogComponent ? (
+            <Suspense fallback={null}>
+              <DialogComponent {...DialogProps} />
+            </Suspense>
+          ) : null}
+        </>
       ) : null}
     </div>
   )

package/src/components/ResizeHandles.tsx

@@ -2,7 +2,7 @@ import React, { useEffect, useRef, useState } from 'react'
 import { observer } from 'mobx-react'
 
 // locals
-import { MsaViewModel } from '../model'
+import type { MsaViewModel } from '../model'
 
 export const VerticalResizeHandle = observer(function ({
   model,
@@ -62,7 +62,7 @@ export const VerticalResizeHandle = observer(function ({
           cursor: 'ew-resize',
           height: '100%',
           width: resizeHandleWidth,
-          background: `rgba(200,200,200)`,
+          background: 'rgba(200,200,200)',
           position: 'relative',
         }}
       />
@@ -128,7 +128,7 @@ export const HorizontalResizeHandle = observer(function ({
           cursor: 'ns-resize',
           width: '100%',
           height: resizeHandleWidth,
-          background: `rgba(200,200,200)`,
+          background: 'rgba(200,200,200)',
           position: 'relative',
         }}
       />

package/src/components/TextTrack.tsx

@@ -2,7 +2,7 @@ import React, { useRef, useMemo, useEffect } from 'react'
 import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 // locals
-import { MsaViewModel, ITextTrack } from '../model'
+import type { MsaViewModel, ITextTrack } from '../model'
 import { colorContrast } from '../util'
 
 const AnnotationBlock = observer(function ({

package/src/components/Track.tsx

@@ -8,7 +8,7 @@ import { makeStyles } from 'tss-react/mui'
 import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown'
 
 // locals
-import { MsaViewModel } from '../model'
+import type { MsaViewModel } from '../model'
 
 // lazies
 const TrackInfoDialog = lazy(() => import('./dialogs/TrackInfoDialog'))

package/src/components/VerticalScrollbar.tsx

@@ -0,0 +1,85 @@
+import { observer } from 'mobx-react'
+import React, { useEffect, useRef, useState } from 'react'
+import type { MsaViewModel } from '../model'
+import { clamp } from '../util'
+
+const VerticalScrollbar = observer(({ model }: { model: MsaViewModel }) => {
+  const { msaAreaHeight, scrollY, totalHeight } = model
+  const [hovered, setHovered] = useState(false)
+  const scheduled = useRef(false)
+  const [mouseDown, setMouseDown] = useState<{
+    clientY: number
+    scrollY: number
+  }>()
+  const fill = 'rgba(66, 119, 127, 0.3)'
+  const unit = msaAreaHeight / totalHeight
+  const top = -scrollY
+  const bottom = top + msaAreaHeight
+  const t = top * unit
+  const b = bottom * unit
+  useEffect(() => {
+    function fn(event: MouseEvent) {
+      if (mouseDown !== undefined) {
+        if (!scheduled.current) {
+          scheduled.current = true
+          window.requestAnimationFrame(() => {
+            model.setScrollY(
+              clamp(
+                -totalHeight,
+                mouseDown.scrollY - (event.clientY - mouseDown.clientY) / unit,
+                0,
+              ),
+            )
+            scheduled.current = false
+          })
+        }
+      }
+    }
+    function fn2() {
+      setMouseDown(undefined)
+    }
+    if (mouseDown !== undefined) {
+      document.addEventListener('mousemove', fn)
+      document.addEventListener('mouseup', fn2)
+      return () => {
+        document.removeEventListener('mousemove', fn)
+        document.removeEventListener('mousemove', fn2)
+      }
+    }
+  }, [model, unit, totalHeight, mouseDown])
+  return (
+    <div
+      style={{
+        position: 'relative',
+        width: 20,
+        height: msaAreaHeight,
+        borderLeft: '1px solid #555',
+        borderTop: '1px solid #555',
+        boxSizing: 'border-box',
+      }}
+    >
+      <div
+        style={{
+          position: 'absolute',
+          top: Math.max(0, t),
+          left: 0,
+          background: hovered ? 'rgba(66,119,127,0.6)' : fill,
+          cursor: 'pointer',
+          boxSizing: 'border-box',
+          width: 20,
+          height: Math.max(b - t, 20),
+          zIndex: 100,
+        }}
+        onMouseOver={() => setHovered(true)}
+        onMouseOut={() => setHovered(false)}
+        onMouseDown={event => {
+          setMouseDown({
+            clientY: event.clientY,
+            scrollY: model.scrollY,
+          })
+        }}
+      />
+    </div>
+  )
+})
+export default VerticalScrollbar

package/src/components/dialogs/AddTrackDialog.tsx

@@ -8,9 +8,9 @@ import {
   Typography,
 } from '@mui/material'
 import { Dialog, FileSelector } from '@jbrowse/core/ui'
-import { FileLocation } from '@jbrowse/core/util/types'
+import type { FileLocation } from '@jbrowse/core/util/types'
 import { observer } from 'mobx-react'
-import { MsaViewModel } from '../../model'
+import type { MsaViewModel } from '../../model'
 
 export default observer(function ({
   model,

package/src/components/dialogs/DomainDialog.tsx

@@ -3,10 +3,10 @@ import { Dialog } from '@jbrowse/core/ui'
 import { Tab, Tabs } from '@mui/material'
 
 // locals
-import InterProScanPanel from './InterProScanPanel'
-import UserProvidedResultPanel from './UserProvidedResultPanel'
+import InterProScanPanel from './InterProScanDialog'
+import UserProvidedResultPanel from './UserProvidedDomainsDialog'
 import TabPanel from './TabPanel'
-import { MsaViewModel } from '../../model'
+import type { MsaViewModel } from '../../model'
 
 export default function LaunchDomainViewDialog({
   handleClose,

package/src/components/dialogs/ExportSVGDialog.tsx

@@ -13,7 +13,7 @@ import {
   useTheme,
 } from '@mui/material'
 // locals
-import { MsaViewModel } from '../../model'
+import type { MsaViewModel } from '../../model'
 import Checkbox2 from '../Checkbox2'
 
 export default function ExportSVGDialog({

package/src/components/dialogs/FeatureDialog.tsx

@@ -4,7 +4,7 @@ import { Dialog } from '@jbrowse/core/ui'
 import { Button, DialogContent } from '@mui/material'
 
 // locals
-import { MsaViewModel } from '../../model'
+import type { MsaViewModel } from '../../model'
 import { getPalette } from '../../ggplotPalettes'
 
 const Toggles = observer(function ({ model }: { model: MsaViewModel }) {
@@ -44,7 +44,7 @@ const Table = observer(function ({ model }: { model: MsaViewModel }) {
       <table>
         <thead>
           <tr>
-            <td></td>
+            <td />
             <td>accession</td>
             <td>name</td>
             <td>description</td>
@@ -75,7 +75,7 @@ const Table = observer(function ({ model }: { model: MsaViewModel }) {
                     height: 20,
                     background: palette[idx] || 'black',
                   }}
-                ></div>
+                />
               </td>
             </tr>
           ))}

package/src/components/dialogs/{InterProScanPanel.tsx → InterProScanDialog.tsx}

@@ -3,9 +3,10 @@ import { observer } from 'mobx-react'
 import { Button, DialogActions, DialogContent, Typography } from '@mui/material'
 
 // locals
-import { MsaViewModel } from '../../model'
+import type { MsaViewModel } from '../../model'
 import { getSession } from '@jbrowse/core/util'
 import { launchInterProScan } from '../../launchInterProScan'
+import { Dialog } from '@jbrowse/core/ui'
 
 const InterProScanDialog = observer(function ({
   handleClose,
@@ -147,10 +148,16 @@ const InterProScanDialog = observer(function ({
   const [show, setShow] = useState(false)
 
   return (
-    <>
+    <Dialog
+      maxWidth="xl"
+      title="Query InterProScan API for domains"
+      onClose={() => handleClose()}
+      open
+    >
       <DialogContent>
         <Typography>
-          This will run InterProScan on all rows of the current MSA
+          This will run InterProScan via the InterProScan API on all rows of the
+          current MSA
         </Typography>
         <Button onClick={() => setShow(!show)}>
           {show ? 'Hide' : 'Show'} advanced options
@@ -254,7 +261,7 @@ const InterProScanDialog = observer(function ({
           Send sequences to InterProScan
         </Button>
       </DialogActions>
-    </>
+    </Dialog>
   )
 })
 

package/src/components/dialogs/MetadataDialog.tsx

@@ -8,7 +8,7 @@ import {
 } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
 
 // locals
-import { MsaViewModel } from '../../model'
+import type { MsaViewModel } from '../../model'
 import SequenceTextArea from '../SequenceTextArea'
 
 const MetadataDialog = observer(function ({