react-msaview 4.6.0 → 4.8.0

package/dist/seqPosToGlobalCol.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seqPosToGlobalCol.test.js","sourceRoot":"","sources":["../src/seqPosToGlobalCol.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,iBAAiB,EAAE,MAAM,qBAAqB,CAAA;AAEvD,QAAQ,CAAC,mBAAmB,EAAE,GAAG,EAAE;IACjC,IAAI,CAAC,0DAA0D,EAAE,GAAG,EAAE;QACpE,MAAM,GAAG,GAAG,UAAU,CAAA;QACtB,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACrD,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACrD,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACrD,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,WAAW;IACnE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uDAAuD,EAAE,GAAG,EAAE;QACjE,MAAM,GAAG,GAAG,aAAa,CAAA;QACzB,kEAAkE;QAClE,iEAAiE;QAEjE,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA,CAAC,IAAI;QAC3D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA,CAAC,WAAW;IACpE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC3D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,GAAG,GAAG,SAAS,CAAA;QACrB,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACrD,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,WAAW;IACnE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,wCAAwC,EAAE,GAAG,EAAE;QAClD,MAAM,GAAG,GAAG,SAAS,CAAA;QACrB,6CAA6C;QAC7C,wCAAwC;QAExC,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,WAAW;IACnE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,sBAAsB,EAAE,GAAG,EAAE;QAChC,MAAM,GAAG,GAAG,OAAO,CAAA;QACnB,mCAAmC;QACnC,mCAAmC;QAEnC,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;IAC5D,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;QACjC,MAAM,GAAG,GAAG,OAAO,CAAA;QACnB,mCAAmC;QACnC,yBAAyB;QAEzB,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,IAAI;QAC1D,MAAM,CAAC,iBAAiB,CAAC,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,WAAW;IACnE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}

package/dist/util.d.ts

@@ -1,10 +1,9 @@
-import type { Node, NodeWithIds } from './types';
+import type { NodeWithIds } from './types';
 import type { Theme } from '@mui/material';
 import type { HierarchyNode } from 'd3-hierarchy';
 export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
     [k: string]: T;
 };
-export declare function generateNodeIds(tree: Node, parent?: string, depth?: number): NodeWithIds;
 export declare function colorContrast(colorScheme: Record<string, string>, theme: Theme): {
     [k: string]: string;
 };

package/dist/util.js

@@ -5,15 +5,6 @@ extend([namesPlugin]);
 export function transform(obj, cb) {
     return Object.fromEntries(Object.entries(obj).map(cb));
 }
-export function generateNodeIds(tree, parent = 'node', depth = 0) {
-    const id = `${parent}-${depth}`;
-    return {
-        ...tree,
-        id,
-        name: tree.name || id,
-        children: tree.children?.map((b, i) => generateNodeIds(b, `${id}-${i}`, depth + 1)) || [],
-    };
-}
 export function colorContrast(colorScheme, theme) {
     return transform(colorScheme, ([letter, color]) => [
         letter,

package/dist/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAM9B,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;AAED,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,QAAQ,EACN,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC1B,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,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,OAAO,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACrD,CAAC;IACD,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,KAAK,MAAM,QAAQ,IAAI,MAAM,EAAE,CAAC;QAC9B,IAAI,QAAQ,GAAG,OAAO,EAAE,CAAC;YACvB,MAAM,CAAC,IAAI,CACT,OAAO,GAAG,KAAK,QAAQ;gBACrB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,QAAQ,CAAC;gBAC9B,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAC1C,CAAA;QACH,CAAC;QACD,OAAO,GAAG,QAAQ,GAAG,CAAC,CAAA;IACxB,CAAC;IACD,IAAI,OAAO,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;QACzB,MAAM,CAAC,IAAI,CACT,OAAO,GAAG,KAAK,QAAQ;YACrB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC;YACpB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAChC,CAAA;IACH,CAAC;IACD,OAAO,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACxB,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,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC;AAED,8CAA8C;AAC9C,oCAAoC;AACpC,MAAM,UAAU,OAAO,CAAC,CAAU;IAChC,OAAO,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAA;AAC/B,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAM9B,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;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,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,OAAO,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACrD,CAAC;IACD,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,KAAK,MAAM,QAAQ,IAAI,MAAM,EAAE,CAAC;QAC9B,IAAI,QAAQ,GAAG,OAAO,EAAE,CAAC;YACvB,MAAM,CAAC,IAAI,CACT,OAAO,GAAG,KAAK,QAAQ;gBACrB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,QAAQ,CAAC;gBAC9B,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAC1C,CAAA;QACH,CAAC;QACD,OAAO,GAAG,QAAQ,GAAG,CAAC,CAAA;IACxB,CAAC;IACD,IAAI,OAAO,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;QACzB,MAAM,CAAC,IAAI,CACT,OAAO,GAAG,KAAK,QAAQ;YACrB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC;YACpB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAChC,CAAA;IACH,CAAC;IACD,OAAO,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACxB,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,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC;AAED,8CAA8C;AAC9C,oCAAoC;AACpC,MAAM,UAAU,OAAO,CAAC,CAAU;IAChC,OAAO,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAA;AAC/B,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.5.0";
+export declare const version = "4.7.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '4.5.0';
+export const version = '4.7.0';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "4.6.0",
+  "version": "4.8.0",
   "license": "MIT",
   "repository": {
     "type": "git",
@@ -20,17 +20,17 @@
   },
   "scripts": {
     "clean": "rimraf dist",
-    "watch": "yarn build:esm --watch",
+    "watch": "pnpm build:esm --watch",
     "format": "prettier --write .",
-    "prebuild": "yarn clean",
+    "prebuild": "pnpm clean",
     "preversion": "node output-version.js > src/version.ts && git add -A src && git commit -m '[skip ci] Bump version.ts'",
     "build:esm": "tsc",
     "build:bundle": "webpack",
-    "build": "yarn build:esm && yarn build:bundle",
-    "prepack": "yarn build",
+    "build": "pnpm build:esm && pnpm build:bundle",
+    "prepack": "pnpm build",
     "postversion": "git push --follow-tags",
     "statedocs": "rm -rf apidocs && mkdir apidocs && node --experimental-strip-types docgen/generateStateModelDocs.ts",
-    "poststatedocs": "yarn format",
+    "poststatedocs": "pnpm format",
     "test": "vitest"
   },
   "peerDependencies": {
@@ -46,16 +46,14 @@
   "dependencies": {
     "@mui/icons-material": "^7.0.1",
     "@mui/material": "^7.0.1",
-    "clustal-js": "^2.0.0",
+    "@react-msaview/parsers": "workspace:*",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",
     "d3-array": "^3.2.3",
     "d3-hierarchy": "^3.1.2",
-    "emf-js": "^2.0.0",
     "file-saver": "^2.0.5",
     "flatbush": "^4.4.0",
     "pako": "^2.1.0",
-    "stockholm-js": "^1.0.10",
     "svgcanvas": "^2.5.0"
   }
 }

package/src/components/header/HeaderInfoArea.tsx

@@ -19,11 +19,8 @@ const HeaderInfoArea = observer(function ({ model }: { model: MsaViewModel }) {
   return mouseOverRowName && mouseCol !== undefined ? (
     <Typography className={classes.margin}>
       {mouseOverRowName}:
-      {model.mouseOverCoordToGapRemovedRowCoordOneBased(
-        mouseOverRowName,
-        mouseCol,
-      )}{' '}
-      ({model.mouseOverCoordToRowLetter(mouseOverRowName, mouseCol)})
+      {model.visibleColToSeqPosOneBased(mouseOverRowName, mouseCol)} (
+      {model.visibleColToRowLetter(mouseOverRowName, mouseCol)})
     </Typography>
   ) : null
 })

package/src/components/import/ImportForm.tsx

@@ -13,6 +13,7 @@ import type { FileLocation } from '@jbrowse/core/util/types'
 const ImportForm = observer(function ({ model }: { model: MsaViewModel }) {
   const [msaFile, setMsaFile] = useState<FileLocation>()
   const [treeFile, setTreeFile] = useState<FileLocation>()
+  const [gffFile, setGffFile] = useState<FileLocation>()
   const { error } = model
 
   return (
@@ -48,6 +49,10 @@ const ImportForm = observer(function ({ model }: { model: MsaViewModel }) {
             <Typography>Tree file or URL</Typography>
             <FileSelector location={treeFile} setLocation={setTreeFile} />
           </div>
+          <div>
+            <Typography>InterProScan GFF file or URL (optional)</Typography>
+            <FileSelector location={gffFile} setLocation={setGffFile} />
+          </div>
         </div>
         <div>
           <Button
@@ -55,7 +60,7 @@ const ImportForm = observer(function ({ model }: { model: MsaViewModel }) {
               // eslint-disable-next-line @typescript-eslint/no-floating-promises
               ;(async () => {
                 try {
-                  await load(model, msaFile, treeFile)
+                  await load(model, msaFile, treeFile, gffFile)
                 } catch (e) {
                   console.error(e)
                   model.setError(e)

package/src/components/import/util.ts

@@ -5,6 +5,7 @@ export async function load(
   model: MsaViewModel,
   msaFile?: FileLocation,
   treeFile?: FileLocation,
+  gffFile?: FileLocation,
 ) {
   model.setError(undefined)
   if (msaFile) {
@@ -13,4 +14,7 @@ export async function load(
   if (treeFile) {
     model.setTreeFilehandle(treeFile)
   }
+  if (gffFile) {
+    model.setGFFFilehandle(gffFile)
+  }
 }

package/src/components/msa/renderBoxFeatureCanvasBlock.ts

@@ -69,8 +69,13 @@ function drawTiles({
     if (entry) {
       for (let j = 0, l2 = entry.length; j < l2; j++) {
         const { start, end, accession } = entry[j]!
-        const m1 = model.seqCoordToRowSpecificGlobalCoord(name, start - 1)
-        const m2 = model.seqCoordToRowSpecificGlobalCoord(name, end)
+        // Convert sequence positions to visible column positions
+        // seqPos is 1-based from InterPro, so subtract 1 for 0-based
+        const m1 = model.seqPosToVisibleCol(name, start - 1)
+        const m2 = model.seqPosToVisibleCol(name, end)
+        if (m1 === undefined || m2 === undefined) {
+          continue // Skip if either position is hidden
+        }
         const x = m1 * colWidth
         ctx.fillStyle = fillPalette[accession]!
         ctx.strokeStyle = strokePalette[accession]!

package/src/components/msa/renderMSABlock.ts

@@ -224,7 +224,11 @@ function drawText({
             : bgColor
               ? contrast
               : color || 'black'
-          ctx.fillText(displayLetter, j * colWidth + offsetXAligned + halfColWidth, y)
+          ctx.fillText(
+            displayLetter,
+            j * colWidth + offsetXAligned + halfColWidth,
+            y,
+          )
         }
       }
     }

package/src/components/tree/renderTreeCanvas.ts

@@ -52,10 +52,11 @@ export function renderTree({
     }
     const sy = source.x!
     const ty = target.x!
-    // @ts-expect-error
-    const tx = showBranchLen ? target.len : target.y
-    // @ts-expect-error
-    const sx = showBranchLen ? source.len : source.y
+    const tx = showBranchLen ? (target as { len?: number }).len : target.y
+    const sx = showBranchLen ? (source as { len?: number }).len : source.y
+    if (tx === undefined || sx === undefined) {
+      continue
+    }
 
     const y1 = Math.min(sy, ty)
     const y2 = Math.max(sy, ty)
@@ -94,9 +95,11 @@ export function renderNodeBubbles({
   } = model
   const by = blockSizeYOverride || blockSize
   for (const node of hierarchy.descendants()) {
-    const val = showBranchLen ? 'len' : 'y'
-    // @ts-expect-error
-    const { [val]: x, data } = node
+    const x = showBranchLen ? (node as { len?: number }).len : node.y
+    if (x === undefined) {
+      continue
+    }
+    const { data } = node
     const y = node.x!
     const { id, name } = data
     if (
@@ -167,9 +170,8 @@ export function renderTreeLabels({
   for (const node of leaves) {
     const {
       data: { name, id },
-      // @ts-expect-error
-      len,
     } = node
+    const len = (node as { len?: number }).len
     const y = node.x!
     const x = node.y!
 

package/src/declare.d.ts

@@ -1,2 +1 @@
-declare module 'stockholm-js'
 declare module 'svgcanvas'

package/src/model.ts

@@ -9,14 +9,25 @@ import {
 } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst'
+import {
+  A3mMSA,
+  ClustalMSA,
+  EmfMSA,
+  FastaMSA,
+  StockholmMSA,
+  generateNodeIds,
+  gffToInterProResults,
+  parseEmfTree,
+  parseGFF,
+  parseNewick,
+  stockholmSniff,
+} from '@react-msaview/parsers'
 import { colord } from 'colord'
 import { ascending } from 'd3-array'
 import { cluster, hierarchy } from 'd3-hierarchy'
-import { parseEmfTree } from 'emf-js'
 import { saveAs } from 'file-saver'
 import { autorun, transaction } from 'mobx'
 import { addDisposer, cast, types } from 'mobx-state-tree'
-import Stockholm from 'stockholm-js'
 
 import { blocksX, blocksY } from './calculateBlocks'
 import colorSchemes from './colorSchemes'
@@ -55,26 +66,14 @@ import { MSAModelF } from './model/msaModel'
 import { TreeModelF } from './model/treeModel'
 import { calculateNeighborJoiningTree } from './neighborJoining'
 import { parseAsn1 } from './parseAsn1'
-import parseNewick from './parseNewick'
-import A3mMSA from './parsers/A3mMSA'
-import ClustalMSA from './parsers/ClustalMSA'
-import EmfMSA from './parsers/EmfMSA'
-import FastaMSA from './parsers/FastaMSA'
-import StockholmMSA from './parsers/StockholmMSA'
 import { reparseTree } from './reparseTree'
 import {
-  mouseOverCoordToGapRemovedRowCoord,
-  mouseOverCoordToGlobalCoord,
+  globalColToVisibleCol,
+  visibleColToGlobalCol,
+  visibleColToSeqPosForRow,
 } from './rowCoordinateCalculations'
-import { seqCoordToRowSpecificGlobalCoord } from './seqCoordToRowSpecificGlobalCoord'
-import {
-  collapse,
-  generateNodeIds,
-  len,
-  maxLength,
-  setBrLength,
-  skipBlanks,
-} from './util'
+import { seqPosToGlobalCol } from './seqPosToGlobalCol'
+import { collapse, len, maxLength, setBrLength, skipBlanks } from './util'
 
 import type { InterProScanResults } from './launchInterProScan'
 import type {
@@ -193,6 +192,12 @@ function stateModelFactory() {
          */
         treeMetadataFilehandle: types.maybe(FileLocation),
 
+        /**
+         * #property
+         * filehandle object for InterProScan GFF file
+         */
+        gffFilehandle: types.maybe(FileLocation),
+
         /**
          * #property
          *
@@ -569,6 +574,13 @@ function stateModelFactory() {
         self.treeFilehandle = treeFilehandle
       },
 
+      /**
+       * #action
+       */
+      setGFFFilehandle(gffFilehandle?: FileLocationType) {
+        self.gffFilehandle = gffFilehandle
+      },
+
       /**
        * #action
        */
@@ -690,7 +702,7 @@ function stateModelFactory() {
       get MSA() {
         const text = self.data.msa
         if (text) {
-          if (Stockholm.sniff(text)) {
+          if (stockholmSniff(text)) {
             return new StockholmMSA(text, self.currentAlignment)
           } else if (A3mMSA.sniff(text)) {
             return new A3mMSA(text)
@@ -1485,7 +1497,7 @@ function stateModelFactory() {
             .map(t => ({
               model: {
                 ...t,
-                data: hideGapsEffective ? skipBlanks(blanks, t.data!) : t.data,
+                data: hideGapsEffective ? skipBlanks(blanks, t.data!) : t.data!,
                 height: rowHeight,
               } as TextTrackModel,
               ReactComponent: TextTrack,
@@ -1531,22 +1543,30 @@ function stateModelFactory() {
 
       /**
        * #method
-       * return a row-specific letter, or undefined if gap
+       * Return a row-specific letter at a visible column, or undefined if gap.
+       *
+       * @param rowName - The name of the row
+       * @param visibleCol - The visible column index (what the user sees on screen)
+       * @returns The letter at that position, or undefined if it's a gap
        */
-      mouseOverCoordToRowLetter(rowName: string, pos: number) {
+      visibleColToRowLetter(rowName: string, visibleCol: number) {
         const { rowMap, blanks } = self
-        return rowMap.get(rowName)?.[mouseOverCoordToGlobalCoord(blanks, pos)]
+        return rowMap.get(rowName)?.[visibleColToGlobalCol(blanks, visibleCol)]
       },
 
       /**
        * #method
-       * return a row-specific sequence coordinate, skipping gaps, given a
-       * global coordinate
+       * Convert a visible column to a row-specific sequence position (0-based).
+       * Returns undefined if the position is a gap in the sequence.
+       *
+       * @param rowName - The name of the row
+       * @param visibleCol - The visible column index
+       * @returns The sequence position (0-based), or undefined if it's a gap
        */
-      mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number) {
-        return mouseOverCoordToGapRemovedRowCoord({
+      visibleColToSeqPos(rowName: string, visibleCol: number) {
+        return visibleColToSeqPosForRow({
           rowName,
-          position,
+          visibleCol,
           rowMap: self.rowMap,
           blanks: self.blanks,
         })
@@ -1554,32 +1574,67 @@ function stateModelFactory() {
 
       /**
        * #method
-       * return a row-specific sequence coordinate, skipping gaps, given a
-       * global coordinate
-       */
-      mouseOverCoordToGapRemovedRowCoordOneBased(
-        rowName: string,
-        position: number,
-      ) {
-        const val = this.mouseOverCoordToGapRemovedRowCoord(rowName, position)
+       * Convert a visible column to a row-specific sequence position (1-based).
+       * Returns undefined if the position is a gap in the sequence.
+       *
+       * @param rowName - The name of the row
+       * @param visibleCol - The visible column index
+       * @returns The sequence position (1-based), or undefined if it's a gap
+       */
+      visibleColToSeqPosOneBased(rowName: string, visibleCol: number) {
+        const val = this.visibleColToSeqPos(rowName, visibleCol)
         return val !== undefined ? val + 1 : undefined
       },
 
       /**
        * #method
-       * return a global coordinate given a row-specific sequence coordinate
-       * which does not not include gaps
+       * Convert a global column index to a visible column index.
+       * Returns undefined if the column is hidden (in blanks).
+       * This is the inverse of visibleColToGlobalCol.
+       *
+       * @param globalCol - The global column index in the full MSA
+       * @returns The visible column index, or undefined if the column is hidden
+       */
+      globalColToVisibleCol(globalCol: number) {
+        const { blanks, hideGapsEffective } = self
+        if (!hideGapsEffective) {
+          return globalCol
+        }
+        return globalColToVisibleCol(blanks, globalCol)
+      },
+
+      /**
+       * #method
+       * Convert a sequence position (ungapped) to a global column index.
+       *
+       * @param rowName - The name of the row
+       * @param seqPos - The sequence position (0-based, ungapped)
+       * @returns The global column index in the full MSA
        */
-      seqCoordToRowSpecificGlobalCoord(rowName: string, position: number) {
+      seqPosToGlobalCol(rowName: string, seqPos: number) {
         const { rowNames, rows } = self
         const index = rowNames.indexOf(rowName)
         return index !== -1 && rows[index]
-          ? seqCoordToRowSpecificGlobalCoord({
+          ? seqPosToGlobalCol({
               row: rows[index][1],
-              position,
+              seqPos,
             })
           : 0
       },
+
+      /**
+       * #method
+       * Convert a sequence position (ungapped) directly to a visible column index.
+       * This combines seqPosToGlobalCol and globalColToVisibleCol.
+       *
+       * @param rowName - The name of the row
+       * @param seqPos - The sequence position (0-based, ungapped)
+       * @returns The visible column index, or undefined if the column is hidden
+       */
+      seqPosToVisibleCol(rowName: string, seqPos: number) {
+        const globalCol = this.seqPosToGlobalCol(rowName, seqPos)
+        return this.globalColToVisibleCol(globalCol)
+      },
     }))
 
     .views(self => ({
@@ -1851,6 +1906,31 @@ function stateModelFactory() {
           }),
         )
 
+        // autorun opens gffFilehandle for InterProScan domains
+        addDisposer(
+          self,
+          autorun(async () => {
+            const { gffFilehandle } = self
+            if (gffFilehandle) {
+              try {
+                const gffText = await fetchAndMaybeUnzipText(
+                  openLocation(gffFilehandle),
+                )
+                const gffRecords = parseGFF(gffText)
+                const interProResults = gffToInterProResults(gffRecords)
+                self.setInterProAnnotations(interProResults)
+                self.setShowDomains(true)
+                if (gffFilehandle.locationType === 'BlobLocation') {
+                  self.setGFFFilehandle(undefined)
+                }
+              } catch (e) {
+                console.error(e)
+                self.setError(e)
+              }
+            }
+          }),
+        )
+
         // autorun opens msaFilehandle
         addDisposer(
           self,