react-msaview 2.1.5 → 3.0.1

package/dist/model.js.map

@@ -1 +1 @@
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package/dist/parseNewick.js.map

@@ -1 +1 @@
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+{"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,MAAA,SAAS,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,0CAAE,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"}

package/dist/parsers/ClustalMSA.d.ts

@@ -3,7 +3,7 @@ export default class ClustalMSA {
     private MSA;
     constructor(text: string);
     getMSA(): import("clustal-js/dist/types").Results;
-    getRow(name: string): string[] | undefined;
+    getRow(name: string): string;
     getWidth(): number;
     getRowData(): undefined;
     getHeader(): import("clustal-js/dist/types").Header;

package/dist/parsers/ClustalMSA.js

@@ -8,7 +8,7 @@ export default class ClustalMSA {
     }
     getRow(name) {
         var _a;
-        return (_a = this.MSA.alns.find(aln => aln.id === name)) === null || _a === void 0 ? void 0 : _a.seq.split('');
+        return ((_a = this.MSA.alns.find(aln => aln.id === name)) === null || _a === void 0 ? void 0 : _a.seq) || '';
     }
     getWidth() {
         return this.MSA.alns[0].seq.length;

package/dist/parsers/ClustalMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/parsers/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAU;IAG7B,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;;QACjB,OAAO,MAAA,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;IAClE,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAA;IACpC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,SAAS,EAAE,EAAE;aACd,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;;QACR,OAAO,CAAA,MAAA,IAAI,CAAC,YAAY,0CAAE,IAAI,EAAE;YAC9B,CAAC,CAAC;gBACE;oBACE,EAAE,EAAE,cAAc;oBAClB,IAAI,EAAE,oBAAoB;oBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;oBACvB,iBAAiB,EAAE;wBACjB,GAAG,EAAE,OAAO;wBACZ,GAAG,EAAE,MAAM;wBACX,GAAG,EAAE,UAAU;wBACf,GAAG,EAAE,OAAO;qBACb;iBACF;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,CAAC;CACF"}
+{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/parsers/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAU;IAG7B,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;;QACjB,OAAO,CAAA,MAAA,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,0CAAE,GAAG,KAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAA;IACpC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,SAAS,EAAE,EAAE;aACd,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;;QACR,OAAO,CAAA,MAAA,IAAI,CAAC,YAAY,0CAAE,IAAI,EAAE;YAC9B,CAAC,CAAC;gBACE;oBACE,EAAE,EAAE,cAAc;oBAClB,IAAI,EAAE,oBAAoB;oBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;oBACvB,iBAAiB,EAAE;wBACjB,GAAG,EAAE,OAAO;wBACZ,GAAG,EAAE,MAAM;wBACX,GAAG,EAAE,UAAU;wBACf,GAAG,EAAE,OAAO;qBACb;iBACF;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,CAAC;CACF"}

package/dist/parsers/FastaMSA.d.ts

@@ -7,7 +7,7 @@ export default class FastaMSA {
     };
     getRowData(): undefined;
     getNames(): string[];
-    getRow(name: string): string[];
+    getRow(name: string): string;
     getWidth(): number;
     getStructures(): {};
     get alignmentNames(): never[];

package/dist/parsers/FastaMSA.js

@@ -27,8 +27,8 @@ export default class FastaMSA {
         return Object.keys(this.MSA.seqdata);
     }
     getRow(name) {
-        var _a, _b;
-        return (_b = (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata[name]) === null || _b === void 0 ? void 0 : _b.split('');
+        var _a;
+        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata[name]) || '';
     }
     getWidth() {
         var _a;

package/dist/parsers/FastaMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/parsers/FastaMSA.ts"],"names":[],"mappings":"AAEA,SAAS,eAAe,CAAC,IAAY;IACnC,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACpD,MAAM,CAAC,EAAE,EAAE,GAAG,WAAW,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC/C,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QAClD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,cAAc,EAAE,QAAQ,EAAE,CAAA;IACtD,CAAC,CAAC,CAAA;AACN,CAAC;AACD,MAAM,CAAC,OAAO,OAAO,QAAQ;IAE3B,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG;YACT,OAAO,EAAE,MAAM,CAAC,WAAW,CACzB,eAAe,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CACxD;SACF,CAAA;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,MAAM,CAAC,IAAY;;QACjB,OAAO,MAAA,MAAA,IAAI,CAAC,GAAG,0CAAE,OAAO,CAAC,IAAI,CAAC,0CAAE,KAAK,CAAC,EAAE,CAAC,CAAA;IAC3C,CAAC;IAED,QAAQ;;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,MAAA,IAAI,CAAC,GAAG,0CAAE,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,SAAS,EAAE,EAAE;gBACb,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
+{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/parsers/FastaMSA.ts"],"names":[],"mappings":"AAEA,SAAS,eAAe,CAAC,IAAY;IACnC,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACpD,MAAM,CAAC,EAAE,EAAE,GAAG,WAAW,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC/C,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QAClD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,cAAc,EAAE,QAAQ,EAAE,CAAA;IACtD,CAAC,CAAC,CAAA;AACN,CAAC;AACD,MAAM,CAAC,OAAO,OAAO,QAAQ;IAE3B,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG;YACT,OAAO,EAAE,MAAM,CAAC,WAAW,CACzB,eAAe,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CACxD;SACF,CAAA;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,MAAM,CAAC,IAAY;;QACjB,OAAO,CAAA,MAAA,IAAI,CAAC,GAAG,0CAAE,OAAO,CAAC,IAAI,CAAC,KAAI,EAAE,CAAA;IACtC,CAAC;IAED,QAAQ;;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,MAAA,IAAI,CAAC,GAAG,0CAAE,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,SAAS,EAAE,EAAE;gBACb,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/parsers/StockholmMSA.d.ts

@@ -19,7 +19,7 @@ export default class StockholmMSA {
     private MSA;
     constructor(text: string, currentAlignment: number);
     getMSA(): StockholmEntry;
-    getRow(name: string): string[];
+    getRow(name: string): string;
     getWidth(): number;
     get alignmentNames(): string[];
     getHeader(): {

package/dist/parsers/StockholmMSA.js

@@ -11,8 +11,8 @@ export default class StockholmMSA {
         return this.MSA;
     }
     getRow(name) {
-        var _a, _b;
-        return (_b = (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata[name]) === null || _b === void 0 ? void 0 : _b.split('');
+        var _a;
+        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.seqdata[name]) || '';
     }
     getWidth() {
         var _a;

package/dist/parsers/StockholmMSA.js.map

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

@@ -40,5 +40,6 @@ export declare function skipBlanks(blanks: number[], arg: string | string[]): st
 export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;
 export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
 export declare function collapse(d: HierarchyNode<NodeWithIds>): void;
+export declare function filterHiddenLeafNodes(d: HierarchyNode<NodeWithIds> | null, hiddenId?: string): void;
 export declare function clamp(min: number, num: number, max: number): number;
 export {};

package/dist/util.js

@@ -58,16 +58,17 @@ export function skipBlanks(blanks, arg) {
     }
     return s;
 }
+// basically same as setRadius from https://observablehq.com/@d3/tree-of-life
 export function setBrLength(d, y0, k) {
-    var _a;
-    // @ts-expect-error
-    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
-    (_a = d.children) === null || _a === void 0 ? void 0 : _a.forEach(d => {
-        setBrLength(d, y0, k);
-    });
+    if (d.children) {
+        d.children.forEach(d => {
+            setBrLength(d, y0, k);
+        });
+    }
 }
+// basically same as maxLength from https://observablehq.com/@d3/tree-of-life
 export function maxLength(d) {
-    return ((d.data.length || 1) + (d.children ? max(d.children, maxLength) || 0 : 0));
+    return ((d.data.length || 0) + (d.children ? max(d.children, maxLength) || 0 : 0));
 }
 // Collapse the node and all it's children, from
 // https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd
@@ -81,6 +82,13 @@ export function collapse(d) {
         d.children = null;
     }
 }
+// Collapse the node and all it's children, from
+// https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd
+export function filterHiddenLeafNodes(d, hiddenId) {
+    if (d === null || d === void 0 ? void 0 : d.children) {
+        d.children = d.children.filter(f => f.id !== hiddenId);
+    }
+}
 export function clamp(min, num, max) {
     return Math.min(Math.max(num, min), max);
 }

package/dist/util.js.map

@@ -1 +1 @@
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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,CAAA,MAAA,IAAI,CAAC,SAAS,0CAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC3B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,KAAI,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,QAAQ,CAAC,GAAY;IACnC,OAAO,GAAG,aAAH,GAAG,uBAAH,GAAG,CACN,KAAK,CAAC,IAAI,EACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,EACjB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EACrC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,CAAC,GAClE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEf,OAAO;YACL,MAAM;YACN,MAAM;YACN,IAAI;YACJ,KAAK,EAAE,CAAC,KAAK;YACb,GAAG,EAAE,CAAC,GAAG;YACT,KAAK,EAAE,CAAC,KAAK;YACb,MAAM;YACN,KAAK;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI;iBACD,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;iBACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;gBACnB,GAAG,CAAC,IAAI,EAAE;gBACV,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;aACpD,CAAC,CACL;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,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,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,SAAS,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QAC7B,mBAAmB;QACnB,CAAC,CAAC,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,UAAU,qBAAqB,CACnC,CAAoC,EACpC,QAAiB;IAEjB,IAAI,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,QAAQ,EAAE,CAAC;QAChB,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,QAAQ,CAAC,CAAA;IACxD,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"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.1.5";
+export declare const version = "3.0.1";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '2.1.5';
+export const version = '3.0.1';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "2.1.5",
+  "version": "3.0.1",
   "license": "MIT",
   "main": "dist/index.js",
   "files": [
@@ -45,14 +45,16 @@
     "@types/d3": "^7.4.0",
     "@types/react": "^18.2.33",
     "@types/react-dom": "^18.2.1",
-    "eslint-plugin-unicorn": "^49.0.0",
-    "rollup": "^3.0.2",
-    "rollup-plugin-polyfill-node": "^0.12.0",
+    "eslint-plugin-unicorn": "^50.0.1",
+    "rollup": "^4.9.1",
+    "rollup-plugin-polyfill-node": "^0.13.0",
     "slugify": "^1.6.6",
     "tslib": "^2.1.0",
     "typescript": "^5.0.4"
   },
   "dependencies": {
+    "@typescript-eslint/eslint-plugin": "^6.7.2",
+    "@typescript-eslint/parser": "^6.7.2",
     "clustal-js": "^1.0.3",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",

package/src/DialogQueue.ts

@@ -0,0 +1,47 @@
+import { DialogComponentType } from '@jbrowse/core/util'
+import { types } from 'mobx-state-tree'
+
+/**
+ * #stateModel DialogQueueSessionMixin
+ */
+export function DialogQueueSessionMixin() {
+  return types
+    .model('DialogQueueSessionMixin', {})
+    .volatile(() => ({
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      queueOfDialogs: [] as [DialogComponentType, any][],
+    }))
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get DialogComponent() {
+        return self.queueOfDialogs[0]?.[0]
+      },
+      /**
+       * #getter
+       */
+      get DialogProps() {
+        return self.queueOfDialogs[0]?.[1]
+      },
+    }))
+    .actions(self => ({
+      /**
+       * #action
+       */
+      removeActiveDialog() {
+        self.queueOfDialogs = self.queueOfDialogs.slice(1)
+      },
+      /**
+       * #action
+       */
+      queueDialog(
+        cb: (doneCallback: () => void) => [DialogComponentType, unknown],
+      ) {
+        const [component, props] = cb(() => {
+          this.removeActiveDialog()
+        })
+        self.queueOfDialogs = [...self.queueOfDialogs, [component, props]]
+      },
+    }))
+}

package/src/components/BoxTrackBlock.tsx

@@ -26,6 +26,7 @@ const BoxTrackBlock = observer(function ({
     blanks,
     rowHeight,
     highResScaleFactor,
+    fontSize,
     scrollX,
   } = model
   const { height, features, associatedRowName } = track.model
@@ -75,7 +76,7 @@ const BoxTrackBlock = observer(function ({
     ctx.clearRect(0, 0, blockSize, height)
     ctx.translate(-offsetX, 0)
     ctx.textAlign = 'center'
-    ctx.font = ctx.font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`)
+    ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`)
 
     const xStart = Math.max(0, Math.floor(offsetX / colWidth))
     ctx.fillStyle = 'goldenrod'
@@ -91,6 +92,7 @@ const BoxTrackBlock = observer(function ({
     })
   }, [
     associatedRowName,
+    fontSize,
     blockSize,
     colWidth,
     layout.rectangles,

package/src/components/Header.tsx

@@ -1,5 +1,5 @@
 import React, { Suspense, lazy, useState } from 'react'
-import { IconButton, Typography } from '@mui/material'
+import { IconButton } from '@mui/material'
 import { observer } from 'mobx-react'
 
 // locals
@@ -11,26 +11,18 @@ import Settings from '@mui/icons-material/Settings'
 import Help from '@mui/icons-material/Help'
 import Assignment from '@mui/icons-material/Assignment'
 import List from '@mui/icons-material/List'
+
+// locals
 import ZoomControls from './ZoomControls'
 import MultiAlignmentSelector from './MultiAlignmentSelector'
+import HeaderInfoArea from './HeaderInfoArea'
 
-const SettingsDialog = lazy(() => import('./dialogs/SettingsDlg'))
-const AboutDialog = lazy(() => import('./dialogs/AboutDlg'))
-const MetadataDialog = lazy(() => import('./dialogs/MetadataDlg'))
-const TracklistDialog = lazy(() => import('./dialogs/TracklistDlg'))
+const SettingsDialog = lazy(() => import('./dialogs/SettingsDialog'))
+const AboutDialog = lazy(() => import('./dialogs/AboutDialog'))
+const MetadataDialog = lazy(() => import('./dialogs/MetadataDialog'))
+const TracklistDialog = lazy(() => import('./dialogs/TracklistDialog'))
 
-const InfoArea = observer(({ model }: { model: MsaViewModel }) => {
-  const { mouseOverRowName, mouseCol } = model
-  return (
-    <div>
-      <Typography display="inline">Row name: {mouseOverRowName}</Typography>
-      <span style={{ marginLeft: 10 }} />
-      <Typography display="inline">Position: {mouseCol}</Typography>
-    </div>
-  )
-})
-
-const Header = observer(({ model }: { model: MsaViewModel }) => {
+const Header = observer(function ({ model }: { model: MsaViewModel }) {
   const [settingsDialogViz, setSettingsDialogViz] = useState(false)
   const [aboutDialogViz, setAboutDialogViz] = useState(false)
   const [detailsDialogViz, setMetadataDialogViz] = useState(false)
@@ -42,11 +34,12 @@ const Header = observer(({ model }: { model: MsaViewModel }) => {
         onClick={async () => {
           try {
             model.setData({ tree: '', msa: '' })
-            await model.setTreeFilehandle(undefined)
-            await model.setMSAFilehandle(undefined)
+            model.clearSelectedStructures()
             model.setScrollY(0)
             model.setScrollX(0)
             model.setCurrentAlignment(0)
+            await model.setTreeFilehandle(undefined)
+            await model.setMSAFilehandle(undefined)
           } catch (e) {
             console.error(e)
             model.setError(e)
@@ -90,7 +83,7 @@ const Header = observer(({ model }: { model: MsaViewModel }) => {
       </Suspense>
       <MultiAlignmentSelector model={model} />
       <ZoomControls model={model} />
-      <InfoArea model={model} />
+      <HeaderInfoArea model={model} />
       <Spacer />
       <IconButton onClick={() => setAboutDialogViz(true)}>
         <Help />

package/src/components/HeaderInfoArea.tsx

@@ -0,0 +1,21 @@
+import React from 'react'
+import { Typography } from '@mui/material'
+import { observer } from 'mobx-react'
+
+// locals
+import { MsaViewModel } from '../model'
+
+const HeaderInfoArea = observer(({ model }: { model: MsaViewModel }) => {
+  const { mouseOverRowName, mouseCol } = model
+  return (
+    <div>
+      {mouseOverRowName && mouseCol !== undefined ? (
+        <Typography>
+          {mouseOverRowName}:{model.relativePxToBp(mouseOverRowName, mouseCol)}
+        </Typography>
+      ) : null}
+    </div>
+  )
+})
+
+export default HeaderInfoArea

package/src/components/ImportForm/ImportFormExamples.tsx

@@ -0,0 +1,133 @@
+import React from 'react'
+import { Typography, Link } from '@mui/material'
+import { observer } from 'mobx-react'
+
+// locals
+import { MsaViewModel } from '../../model'
+import { smallTree, smallMSA, smallMSAOnly } from './data/seq2'
+import { load } from './util'
+
+const ListItem = ({
+  onClick,
+  model,
+  children,
+}: {
+  onClick: () => void
+  model: MsaViewModel
+  children: React.ReactNode
+}) => (
+  <li>
+    <Link
+      onClick={event => {
+        model.setError(undefined)
+        event.preventDefault()
+        onClick()
+      }}
+      href="#"
+    >
+      <Typography display="inline">{children}</Typography>
+    </Link>
+  </li>
+)
+
+const ImportFormExamples = observer(function ({
+  model,
+}: {
+  model: MsaViewModel
+}) {
+  return (
+    <ul>
+      <ListItem
+        model={model}
+        onClick={() =>
+          load(model, undefined, {
+            uri: 'https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh',
+            locationType: 'UriLocation',
+          })
+        }
+      >
+        230k COVID-19 samples (tree only)
+      </ListItem>
+      <ListItem
+        model={model}
+        onClick={() => {
+          model.setData({ msa: smallMSA, tree: smallTree })
+        }}
+      >
+        Small protein MSA+tree
+      </ListItem>
+      <ListItem
+        model={model}
+        onClick={() => {
+          model.setData({ msa: smallMSAOnly })
+        }}
+      >
+        Small MSA only
+      </ListItem>
+      <ListItem
+        model={model}
+        onClick={() =>
+          load(model, {
+            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/pfam-cov2.stock',
+            locationType: 'UriLocation',
+          })
+        }
+      >
+        PFAM SARS-CoV2 multi-stockholm
+      </ListItem>
+      <ListItem
+        model={model}
+        onClick={() =>
+          load(model, {
+            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock',
+            locationType: 'UriLocation',
+          })
+        }
+      >
+        Lysine stockholm file
+      </ListItem>
+      <ListItem
+        model={model}
+        onClick={() =>
+          load(model, {
+            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt',
+            locationType: 'UriLocation',
+          })
+        }
+      >
+        PF01601 stockholm file (SARS-CoV2 spike protein)
+      </ListItem>
+      <ListItem
+        model={model}
+        onClick={() =>
+          load(model, {
+            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa',
+            locationType: 'UriLocation',
+          })
+        }
+      >
+        Europe COVID full genomes (LR883044.1 and 199 other sequences)
+      </ListItem>
+      <ListItem
+        model={model}
+        onClick={() =>
+          load(
+            model,
+            {
+              uri: '/rhv_test-only.aligned_with_mafft_auto.fa',
+              locationType: 'UriLocation',
+            },
+            {
+              uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh',
+              locationType: 'UriLocation',
+            },
+          )
+        }
+      >
+        MAFFT+VeryFastTree(17.9k samples)
+      </ListItem>
+    </ul>
+  )
+})
+
+export default ImportFormExamples