@rivm-loculus-tools/common-frontend 0.2.0 → 0.4.0

package/dist/utils/DependencyContainerUtil/DependencyContainerUtil.d.ts

@@ -0,0 +1,6 @@
+import { DependencyContainer } from 'tsyringe';
+import { ConfigBase } from '../../models/config.models';
+export declare class DependencyContainerUtil {
+    static createContainer(): DependencyContainer;
+    static resolveConfig<TConfig extends ConfigBase = ConfigBase>(dependencyContainer?: DependencyContainer): TConfig;
+}

package/dist/utils/DependencyContainerUtil/index.d.ts

@@ -0,0 +1 @@
+export * from './DependencyContainerUtil';

package/dist/utils/DependencyContainerUtil/index.js

@@ -0,0 +1,18 @@
+import { CONFIG_TOKEN as e, DEVICE_PIXEL_RATIO_SERVICE_TOKEN as t, KEYBOARD_SHORTCUT_SERVICE_TOKEN as n, WINDOW_SERVICE_TOKEN as r } from "../../constants/config.constants.js";
+import { container as i } from "tsyringe";
+import { WindowService as a } from "@gen-epix/ui-core/classes/services/WindowService";
+import { DevicePixelRatioService as o } from "@gen-epix/ui-core/classes/services/DevicePixelRatioService";
+import { KeyboardShortcutService as s } from "@gen-epix/ui-core/classes/services/KeyboardShortcutService";
+//#region src/utils/DependencyContainerUtil/DependencyContainerUtil.ts
+var c = class {
+	static createContainer() {
+		return i.registerInstance(r, a.getInstance()), i.registerInstance(t, o.getInstance()), i.registerInstance(n, s.getInstance()), i;
+	}
+	static resolveConfig(t = i) {
+		return t.resolve(e);
+	}
+};
+//#endregion
+export { c as DependencyContainerUtil };
+
+//# sourceMappingURL=index.js.map

package/dist/utils/DependencyContainerUtil/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":["DependencyContainerUtil","container","WINDOW_SERVICE_TOKEN","WindowService","DEVICE_PIXEL_RATIO_SERVICE_TOKEN","DevicePixelRatioService","KEYBOARD_SHORTCUT_SERVICE_TOKEN","KeyboardShortcutService","dependencyContainer","CONFIG_TOKEN"],"sources":["../../../src/utils/DependencyContainerUtil/DependencyContainerUtil.ts"],"sourcesContent":["import { container } from 'tsyringe';\nimport type { DependencyContainer } from 'tsyringe';\nimport { WindowService } from '@gen-epix/ui-core/classes/services/WindowService';\nimport { DevicePixelRatioService } from '@gen-epix/ui-core/classes/services/DevicePixelRatioService';\nimport { KeyboardShortcutService } from '@gen-epix/ui-core/classes/services/KeyboardShortcutService';\n\nimport {\n  CONFIG_TOKEN,\n  DEVICE_PIXEL_RATIO_SERVICE_TOKEN,\n  KEYBOARD_SHORTCUT_SERVICE_TOKEN,\n  WINDOW_SERVICE_TOKEN,\n} from '../../constants/config.constants';\nimport type { ConfigBase } from '../../models/config.models';\n\nexport class DependencyContainerUtil {\n  public static createContainer(): DependencyContainer {\n    container.registerInstance(WINDOW_SERVICE_TOKEN, WindowService.getInstance());\n    container.registerInstance(DEVICE_PIXEL_RATIO_SERVICE_TOKEN, DevicePixelRatioService.getInstance());\n    container.registerInstance(KEYBOARD_SHORTCUT_SERVICE_TOKEN, KeyboardShortcutService.getInstance());\n\n    return container;\n  }\n\n  public static resolveConfig<TConfig extends ConfigBase = ConfigBase>(dependencyContainer: DependencyContainer = container): TConfig {\n    return dependencyContainer.resolve(CONFIG_TOKEN) as TConfig;\n  }\n}\n"],"mappings":";;;;;;AAcA,IAAaA,IAAb,MAAqC;CACnC,OAAc,kBAAuC;EAKnD,OAJAC,EAAU,iBAAiBC,GAAsBC,EAAc,YAAY,CAAC,GAC5EF,EAAU,iBAAiBG,GAAkCC,EAAwB,YAAY,CAAC,GAClGJ,EAAU,iBAAiBK,GAAiCC,EAAwB,YAAY,CAAC,GAE1FN;CACT;CAEA,OAAc,cAAuD,IAA2CA,GAAoB;EAClI,OAAOO,EAAoB,QAAQC,CAAY;CACjD;AACF"}

package/dist/utils/ExportUtil/ExportUtil.d.ts

@@ -0,0 +1,6 @@
+export declare class ExportUtil {
+    static downloadCanvasAsImage(canvas: HTMLCanvasElement | null, format: 'jpeg' | 'png', filename?: string): void;
+    static downloadCanvasAsSvg(canvas: HTMLCanvasElement | null, filename?: string): void;
+    static downloadFastaFile(fasta: string, filename?: string): void;
+    static downloadNewickFile(newick: string, filename?: string): void;
+}

package/dist/utils/ExportUtil/index.d.ts

@@ -0,0 +1 @@
+export * from './ExportUtil';

package/dist/utils/ExportUtil/index.js

@@ -0,0 +1,42 @@
+import { DownloadUtil as e } from "@gen-epix/ui-core/utils/DownloadUtil";
+//#region src/utils/ExportUtil/ExportUtil.ts
+var t = class {
+	static downloadCanvasAsImage(t, n, r = "phylogenetic_tree") {
+		if (!t) {
+			console.error("No canvas available for export.");
+			return;
+		}
+		let i = n === "jpeg" ? "image/jpeg" : "image/png", a = n === "jpeg" ? "jpg" : "png", o = t;
+		if (n === "jpeg") {
+			o = document.createElement("canvas"), o.width = t.width, o.height = t.height;
+			let e = o.getContext("2d");
+			e && (e.fillStyle = "#FFFFFF", e.fillRect(0, 0, o.width, o.height), e.drawImage(t, 0, 0));
+		}
+		let s = o.toDataURL(i, .95);
+		e.createDownloadUrl(s, `${r}.${a}`);
+	}
+	static downloadCanvasAsSvg(t, n = "phylogenetic_tree.svg") {
+		if (!t) {
+			console.error("No canvas available for export.");
+			return;
+		}
+		let r = t.toDataURL("image/png"), i = t.width, a = t.height, o = `<?xml version="1.0" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg width="${i}" height="${a}" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+  <image xlink:href="${r}" x="0" y="0" height="${a}" width="${i}" />
+</svg>`, s = new Blob([o], { type: "image/svg+xml;charset=utf-8" }), c = URL.createObjectURL(s);
+		e.createDownloadUrl(c, n), URL.revokeObjectURL(c);
+	}
+	static downloadFastaFile(t, n = "sequence.fasta") {
+		let r = new Blob([t], { type: "text/plain;charset=utf-8" }), i = URL.createObjectURL(r);
+		e.createDownloadUrl(i, n), URL.revokeObjectURL(i);
+	}
+	static downloadNewickFile(t, n = "phylogenetic_tree.nwk") {
+		let r = new Blob([t], { type: "text/plain;charset=utf-8" }), i = URL.createObjectURL(r);
+		e.createDownloadUrl(i, n), URL.revokeObjectURL(i);
+	}
+};
+//#endregion
+export { t as ExportUtil };
+
+//# sourceMappingURL=index.js.map

package/dist/utils/ExportUtil/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":["ExportUtil","canvas","mimeType","format","extension","exportCanvas","ctx","dataUrl","filename","imgData","width","height","svgContent","blob","url","DownloadUtil","fasta","newick"],"sources":["../../../src/utils/ExportUtil/ExportUtil.ts"],"sourcesContent":["import { DownloadUtil } from '@gen-epix/ui-core/utils/DownloadUtil';\n\nexport class ExportUtil {\n  public static downloadCanvasAsImage(\n    canvas: HTMLCanvasElement | null,\n    format: 'jpeg' | 'png',\n    filename = 'phylogenetic_tree',\n  ): void {\n    if (!canvas) {\n      console.error('No canvas available for export.');\n      return;\n    }\n\n    const mimeType = format === 'jpeg' ? 'image/jpeg' : 'image/png';\n    const extension = format === 'jpeg' ? 'jpg' : 'png';\n\n    let exportCanvas = canvas;\n    if (format === 'jpeg') {\n      exportCanvas = document.createElement('canvas');\n      exportCanvas.width = canvas.width;\n      exportCanvas.height = canvas.height;\n      const ctx = exportCanvas.getContext('2d');\n      if (ctx) {\n        ctx.fillStyle = '#FFFFFF';\n        ctx.fillRect(0, 0, exportCanvas.width, exportCanvas.height);\n        ctx.drawImage(canvas, 0, 0);\n      }\n    }\n\n    const dataUrl = exportCanvas.toDataURL(mimeType, 0.95);\n    DownloadUtil.createDownloadUrl(dataUrl, `${filename}.${extension}`);\n  }\n\n  public static downloadCanvasAsSvg(\n    canvas: HTMLCanvasElement | null,\n    filename = 'phylogenetic_tree.svg',\n  ): void {\n    if (!canvas) {\n      console.error('No canvas available for export.');\n      return;\n    }\n\n    const imgData = canvas.toDataURL('image/png');\n    const width = canvas.width;\n    const height = canvas.height;\n\n    const svgContent = `<?xml version=\"1.0\" standalone=\"no\"?>\n<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.1//EN\" \"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd\">\n<svg width=\"${width}\" height=\"${height}\" version=\"1.1\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n  <image xlink:href=\"${imgData}\" x=\"0\" y=\"0\" height=\"${height}\" width=\"${width}\" />\n</svg>`;\n\n    const blob = new Blob([svgContent], { type: 'image/svg+xml;charset=utf-8' });\n    const url = URL.createObjectURL(blob);\n    DownloadUtil.createDownloadUrl(url, filename);\n    URL.revokeObjectURL(url);\n  }\n\n  public static downloadFastaFile(fasta: string, filename = 'sequence.fasta'): void {\n    const blob = new Blob([fasta], { type: 'text/plain;charset=utf-8' });\n    const url = URL.createObjectURL(blob);\n    DownloadUtil.createDownloadUrl(url, filename);\n    URL.revokeObjectURL(url);\n  }\n\n  public static downloadNewickFile(newick: string, filename = 'phylogenetic_tree.nwk'): void {\n    const blob = new Blob([newick], { type: 'text/plain;charset=utf-8' });\n    const url = URL.createObjectURL(blob);\n    DownloadUtil.createDownloadUrl(url, filename);\n    URL.revokeObjectURL(url);\n  }\n}\n"],"mappings":";;AAEA,IAAaA,IAAb,MAAwB;CACtB,OAAc,sBACZ,GACA,GACA,IAAW,qBACL;EACN,IAAI,CAACC,GAAQ;GACX,QAAQ,MAAM,iCAAiC;GAC/C;EACF;EAEA,IAAMC,IAAWC,MAAW,SAAS,eAAe,aAC9CC,IAAYD,MAAW,SAAS,QAAQ,OAE1CE,IAAeJ;EACnB,IAAIE,MAAW,QAAQ;GAGrB,AAFA,IAAe,SAAS,cAAc,QAAQ,GAC9C,EAAa,QAAQF,EAAO,OAC5B,EAAa,SAASA,EAAO;GAC7B,IAAMK,IAAMD,EAAa,WAAW,IAAI;GACxC,AAAIC,MACF,EAAI,YAAY,WAChBA,EAAI,SAAS,GAAG,GAAGD,EAAa,OAAOA,EAAa,MAAM,GAC1DC,EAAI,UAAUL,GAAQ,GAAG,CAAC;EAE9B;EAEA,IAAMM,IAAUF,EAAa,UAAUH,GAAU,GAAI;EACrD,EAAa,kBAAkBK,GAAS,GAAGC,EAAS,GAAGJ,GAAW;CACpE;CAEA,OAAc,oBACZ,GACA,IAAW,yBACL;EACN,IAAI,CAACH,GAAQ;GACX,QAAQ,MAAM,iCAAiC;GAC/C;EACF;EAEA,IAAMQ,IAAUR,EAAO,UAAU,WAAW,GACtCS,IAAQT,EAAO,OACfU,IAASV,EAAO,QAEhBW,IAAa;;cAETF,EAAM,YAAYC,EAAO;uBAChBF,EAAQ,wBAAwBE,EAAO,WAAWD,EAAM;SAGrEG,IAAO,IAAI,KAAK,CAACD,CAAU,GAAG,EAAE,MAAM,8BAA8B,CAAC,GACrEE,IAAM,IAAI,gBAAgBD,CAAI;EAEpC,AADAE,EAAa,kBAAkBD,GAAKN,CAAQ,GAC5C,IAAI,gBAAgBM,CAAG;CACzB;CAEA,OAAc,kBAAkB,GAAe,IAAW,kBAAwB;EAChF,IAAMD,IAAO,IAAI,KAAK,CAACG,CAAK,GAAG,EAAE,MAAM,2BAA2B,CAAC,GAC7DF,IAAM,IAAI,gBAAgBD,CAAI;EAEpC,AADAE,EAAa,kBAAkBD,GAAKN,CAAQ,GAC5C,IAAI,gBAAgBM,CAAG;CACzB;CAEA,OAAc,mBAAmB,GAAgB,IAAW,yBAA+B;EACzF,IAAMD,IAAO,IAAI,KAAK,CAACI,CAAM,GAAG,EAAE,MAAM,2BAA2B,CAAC,GAC9DH,IAAM,IAAI,gBAAgBD,CAAI;EAEpC,AADAE,EAAa,kBAAkBD,GAAKN,CAAQ,GAC5C,IAAI,gBAAgBM,CAAG;CACzB;AACF"}

package/dist/utils/FastaUtil/FastaUtil.d.ts

@@ -1,4 +1,4 @@
-import { FastaParseResult } from '../../models/fasta';
+import { FastaParseResult } from '../../models/fasta.models';
 export declare class FastaUtil {
     static parseFasta(content: string): FastaParseResult;
     static stripFastaHeaders(fastaContent: string): string;

package/dist/utils/FastaUtil/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","names":["FastaUtil","content","lines","sequences","currentHeader","currentSeqParts","commitSequence","fullSeq","safeId","sourceLine","line","firstLength","invalidSequences","s","isAligned","fastaContent"],"sources":["../../../src/utils/FastaUtil/FastaUtil.ts"],"sourcesContent":["import type {\n  FastaParseResult,\n  FastaSequence,\n} from '../../models/fasta';\n\nexport class FastaUtil {\n  public static parseFasta(content: string): FastaParseResult {\n    if (!content?.trim()) {\n      return FastaUtil.createErrorResult('The FASTA input is empty.');\n    }\n\n    const lines = content.split(/\\r?\\n/);\n    const sequences: FastaSequence[] = [];\n    let currentHeader = '';\n    let currentSeqParts: string[] = [];\n\n    const commitSequence = (): void => {\n      if (currentHeader) {\n        const fullSeq = currentSeqParts.join('').replace(/\\s/g, '').toUpperCase();\n\n        // Empty records (a header with no following sequence) are retained with\n        // a length of zero rather than being discarded or rejected.\n\n        // Extract ID: part before pipe or tab, sanitized for Newick compatibility\n        const firstPart = currentHeader.split(/[|\\t]/)[0].trim();\n        const safeId = firstPart.replace(/[():;,']/g, '_');\n\n        sequences.push({\n          accessionVersion: safeId,\n          header: currentHeader,\n          id: safeId,\n          length: fullSeq.length,\n          sequence: fullSeq,\n        });\n      }\n    };\n\n    for (const sourceLine of lines) {\n      const line = sourceLine.trim();\n      if (!line) {\n        continue;\n      }\n\n      if (line.startsWith('>')) {\n        commitSequence();\n        currentHeader = line.slice(1).trim();\n        if (!currentHeader) {\n          return FastaUtil.createErrorResult('Every FASTA record needs a non-empty header.');\n        }\n        currentSeqParts = [];\n      } else {\n        if (!currentHeader) {\n          return FastaUtil.createErrorResult('FASTA sequence data appeared before its first header.');\n        }\n        currentSeqParts.push(line);\n      }\n    }\n    commitSequence();\n\n    if (sequences.length === 0) {\n      return FastaUtil.createErrorResult('No FASTA records were found.');\n    }\n\n    // Pre-alignment validation: verify all sequence lengths are equal\n    const firstLength = sequences[0].length;\n    const invalidSequences = sequences.filter((s) => s.length !== firstLength).map((s) => ({ id: s.id, length: s.length }));\n\n    const isAligned = invalidSequences.length === 0;\n\n    return {\n      expectedLength: firstLength,\n      invalidSequences: isAligned ? undefined : invalidSequences,\n      isAligned,\n      sequences,\n    };\n  }\n\n  public static stripFastaHeaders(fastaContent: string): string {\n    const lines = fastaContent.split('\\n');\n    const strippedLines = lines.map((line) => {\n      if (line.startsWith('>')) {\n        const cleanHeader = line.substring(1).trim();\n        const firstPart = cleanHeader.split(/[|\\t]/)[0].trim();\n        const safeId = firstPart.replace(/[():;,']/g, '_');\n        return `>${safeId}`;\n      }\n      return line;\n    });\n    return strippedLines.join('\\n');\n  }\n\n\n  private static createErrorResult(error: string): FastaParseResult {\n    return {\n      error,\n      expectedLength: 0,\n      isAligned: false,\n      sequences: [],\n    };\n  }\n\n}\n"],"mappings":";AAKA,IAAaA,IAAb,MAAaA,EAAU;CACrB,OAAc,WAAW,GAAmC;EAC1D,IAAI,CAACC,GAAS,KAAK,GACjB,OAAOD,EAAU,kBAAkB,2BAA2B;EAGhE,IAAME,IAAQD,EAAQ,MAAM,OAAO,GAC7BE,IAA6B,CAAC,GAChCC,IAAgB,IAChBC,IAA4B,CAAC,GAE3BC,UAA6B;GACjC,IAAIF,GAAe;IACjB,IAAMG,IAAUF,EAAgB,KAAK,EAAE,CAAC,CAAC,QAAQ,OAAO,EAAE,CAAC,CAAC,YAAY,GAOlEG,IADYJ,EAAc,MAAM,OAAO,CAAC,CAAC,EAAE,CAAC,KACnC,CAAA,CAAU,QAAQ,aAAa,GAAG;IAEjD,EAAU,KAAK;KACb,kBAAkBI;KAClB,QAAQJ;KACR,IAAII;KACJ,QAAQD,EAAQ;KAChB,UAAUA;IACZ,CAAC;GACH;EACF;EAEA,KAAK,IAAME,KAAcP,GAAO;GAC9B,IAAMQ,IAAOD,EAAW,KAAK;GAC7B,IAAKC,GAIL;QAAIA,EAAK,WAAW,GAAG,GAAG;KAGxB,IAFAJ,EAAe,GACf,IAAgBI,EAAK,MAAM,CAAC,CAAC,CAAC,KAAK,GAC/B,CAACN,GACH,OAAOJ,EAAU,kBAAkB,8CAA8C;KAEnF,IAAkB,CAAC;IACrB,OAAO;KACL,IAAI,CAACI,GACH,OAAOJ,EAAU,kBAAkB,uDAAuD;KAE5F,EAAgB,KAAKU,CAAI;IAC3B;;EACF;EAGA,IAFAJ,EAAe,GAEXH,EAAU,WAAW,GACvB,OAAOH,EAAU,kBAAkB,8BAA8B;EAInE,IAAMW,IAAcR,EAAU,EAAE,CAAC,QAC3BS,IAAmBT,EAAU,QAAQ,MAAMU,EAAE,WAAWF,CAAW,CAAC,CAAC,KAAK,OAAO;GAAE,IAAIE,EAAE;GAAI,QAAQA,EAAE;EAAO,EAAE,GAEhHC,IAAYF,EAAiB,WAAW;EAE9C,OAAO;GACL,gBAAgBD;GAChB,kBAAkBG,IAAY,KAAA,IAAYF;GAC1C;GACA;EACF;CACF;CAEA,OAAc,kBAAkB,GAA8B;EAW5D,OAVcG,EAAa,MAAM,IACX,CAAA,CAAM,KAAK,MAC3BL,EAAK,WAAW,GAAG,IAId,IAHaA,EAAK,UAAU,CAAC,CAAC,CAAC,KACpB,CAAA,CAAY,MAAM,OAAO,CAAC,CAAC,EAAE,CAAC,KACjC,CAAA,CAAU,QAAQ,aAAa,GACnC,MAENA,CAEF,CAAA,CAAc,KAAK,IAAI;CAChC;CAGA,OAAe,kBAAkB,GAAiC;EAChE,OAAO;GACL;GACA,gBAAgB;GAChB,WAAW;GACX,WAAW,CAAC;EACd;CACF;AAEF"}
+{"version":3,"file":"index.js","names":["FastaUtil","content","lines","sequences","currentHeader","currentSeqParts","commitSequence","fullSeq","safeId","sourceLine","line","firstLength","invalidSequences","s","isAligned","fastaContent"],"sources":["../../../src/utils/FastaUtil/FastaUtil.ts"],"sourcesContent":["import type {\n  FastaParseResult,\n  FastaSequence,\n} from '../../models/fasta.models';\n\nexport class FastaUtil {\n  public static parseFasta(content: string): FastaParseResult {\n    if (!content?.trim()) {\n      return FastaUtil.createErrorResult('The FASTA input is empty.');\n    }\n\n    const lines = content.split(/\\r?\\n/);\n    const sequences: FastaSequence[] = [];\n    let currentHeader = '';\n    let currentSeqParts: string[] = [];\n\n    const commitSequence = (): void => {\n      if (currentHeader) {\n        const fullSeq = currentSeqParts.join('').replace(/\\s/g, '').toUpperCase();\n\n        // Empty records (a header with no following sequence) are retained with\n        // a length of zero rather than being discarded or rejected.\n\n        // Extract ID: part before pipe or tab, sanitized for Newick compatibility\n        const firstPart = currentHeader.split(/[|\\t]/)[0].trim();\n        const safeId = firstPart.replace(/[():;,']/g, '_');\n\n        sequences.push({\n          accessionVersion: safeId,\n          header: currentHeader,\n          id: safeId,\n          length: fullSeq.length,\n          sequence: fullSeq,\n        });\n      }\n    };\n\n    for (const sourceLine of lines) {\n      const line = sourceLine.trim();\n      if (!line) {\n        continue;\n      }\n\n      if (line.startsWith('>')) {\n        commitSequence();\n        currentHeader = line.slice(1).trim();\n        if (!currentHeader) {\n          return FastaUtil.createErrorResult('Every FASTA record needs a non-empty header.');\n        }\n        currentSeqParts = [];\n      } else {\n        if (!currentHeader) {\n          return FastaUtil.createErrorResult('FASTA sequence data appeared before its first header.');\n        }\n        currentSeqParts.push(line);\n      }\n    }\n    commitSequence();\n\n    if (sequences.length === 0) {\n      return FastaUtil.createErrorResult('No FASTA records were found.');\n    }\n\n    // Pre-alignment validation: verify all sequence lengths are equal\n    const firstLength = sequences[0].length;\n    const invalidSequences = sequences.filter((s) => s.length !== firstLength).map((s) => ({ id: s.id, length: s.length }));\n\n    const isAligned = invalidSequences.length === 0;\n\n    return {\n      expectedLength: firstLength,\n      invalidSequences: isAligned ? undefined : invalidSequences,\n      isAligned,\n      sequences,\n    };\n  }\n\n  public static stripFastaHeaders(fastaContent: string): string {\n    const lines = fastaContent.split('\\n');\n    const strippedLines = lines.map((line) => {\n      if (line.startsWith('>')) {\n        const cleanHeader = line.substring(1).trim();\n        const firstPart = cleanHeader.split(/[|\\t]/)[0].trim();\n        const safeId = firstPart.replace(/[():;,']/g, '_');\n        return `>${safeId}`;\n      }\n      return line;\n    });\n    return strippedLines.join('\\n');\n  }\n\n\n  private static createErrorResult(error: string): FastaParseResult {\n    return {\n      error,\n      expectedLength: 0,\n      isAligned: false,\n      sequences: [],\n    };\n  }\n\n}\n"],"mappings":";AAKA,IAAaA,IAAb,MAAaA,EAAU;CACrB,OAAc,WAAW,GAAmC;EAC1D,IAAI,CAACC,GAAS,KAAK,GACjB,OAAOD,EAAU,kBAAkB,2BAA2B;EAGhE,IAAME,IAAQD,EAAQ,MAAM,OAAO,GAC7BE,IAA6B,CAAC,GAChCC,IAAgB,IAChBC,IAA4B,CAAC,GAE3BC,UAA6B;GACjC,IAAIF,GAAe;IACjB,IAAMG,IAAUF,EAAgB,KAAK,EAAE,CAAC,CAAC,QAAQ,OAAO,EAAE,CAAC,CAAC,YAAY,GAOlEG,IADYJ,EAAc,MAAM,OAAO,CAAC,CAAC,EAAE,CAAC,KACnC,CAAA,CAAU,QAAQ,aAAa,GAAG;IAEjD,EAAU,KAAK;KACb,kBAAkBI;KAClB,QAAQJ;KACR,IAAII;KACJ,QAAQD,EAAQ;KAChB,UAAUA;IACZ,CAAC;GACH;EACF;EAEA,KAAK,IAAME,KAAcP,GAAO;GAC9B,IAAMQ,IAAOD,EAAW,KAAK;GAC7B,IAAKC,GAIL;QAAIA,EAAK,WAAW,GAAG,GAAG;KAGxB,IAFAJ,EAAe,GACf,IAAgBI,EAAK,MAAM,CAAC,CAAC,CAAC,KAAK,GAC/B,CAACN,GACH,OAAOJ,EAAU,kBAAkB,8CAA8C;KAEnF,IAAkB,CAAC;IACrB,OAAO;KACL,IAAI,CAACI,GACH,OAAOJ,EAAU,kBAAkB,uDAAuD;KAE5F,EAAgB,KAAKU,CAAI;IAC3B;;EACF;EAGA,IAFAJ,EAAe,GAEXH,EAAU,WAAW,GACvB,OAAOH,EAAU,kBAAkB,8BAA8B;EAInE,IAAMW,IAAcR,EAAU,EAAE,CAAC,QAC3BS,IAAmBT,EAAU,QAAQ,MAAMU,EAAE,WAAWF,CAAW,CAAC,CAAC,KAAK,OAAO;GAAE,IAAIE,EAAE;GAAI,QAAQA,EAAE;EAAO,EAAE,GAEhHC,IAAYF,EAAiB,WAAW;EAE9C,OAAO;GACL,gBAAgBD;GAChB,kBAAkBG,IAAY,KAAA,IAAYF;GAC1C;GACA;EACF;CACF;CAEA,OAAc,kBAAkB,GAA8B;EAW5D,OAVcG,EAAa,MAAM,IACX,CAAA,CAAM,KAAK,MAC3BL,EAAK,WAAW,GAAG,IAId,IAHaA,EAAK,UAAU,CAAC,CAAC,CAAC,KACpB,CAAA,CAAY,MAAM,OAAO,CAAC,CAAC,EAAE,CAAC,KACjC,CAAA,CAAU,QAAQ,aAAa,GACnC,MAENA,CAEF,CAAA,CAAc,KAAK,IAAI;CAChC;CAGA,OAAe,kBAAkB,GAAiC;EAChE,OAAO;GACL;GACA,gBAAgB;GAChB,WAAW;GACX,WAAW,CAAC;EACd;CACF;AAEF"}

package/dist/utils/MetaDataUtil/MetaDataUtil.d.ts

@@ -1,4 +1,4 @@
-import { MetadataParseResult, MetadataRecord } from '../../models/metadata';
+import { MetadataParseResult, MetadataRecord } from '../../models/metadata.models';
 export declare class MetaDataUtil {
     /**
      * Compute the best matching metadata column for the given FASTA sequence IDs.

package/dist/utils/MetaDataUtil/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","names":["MetaDataUtil","matchCounts","columns","recordsByColumn","fastaIds","bestColumn","maxMatches","prioritizedKeys","col","count","currentPriority","newPriority","pKey","found","c","trimmed","query","matched","allAccessions","acc","metadataRecords","matchKeyField","rec","val","colDict","id","metadata","sampleId","\"displayName\"","\"accessionVersion\"","match","content","lines","headerLine","delimiter","records","recordsByAccession","recordsBySampleId","i","line","values","record","colIdx","accessionKey","sampleIdKey"],"sources":["../../../src/utils/MetaDataUtil/MetaDataUtil.ts"],"sourcesContent":["import type {\n  MetadataParseResult,\n  MetadataRecord,\n} from '../../models/metadata';\n\nexport class MetaDataUtil {\n  /**\n   * Compute the best matching metadata column for the given FASTA sequence IDs.\n   */\n  public static findBestMatchingColumn = (\n    columns: string[],\n    recordsByColumn: Record<string, Record<string, MetadataRecord>>,\n    fastaIds: string[],\n  ): { bestColumn: null | string; matchCounts: Record<string, number> } => {\n    const matchCounts = MetaDataUtil.getMatchCounts(columns, recordsByColumn, fastaIds);\n    let bestColumn: null | string = null;\n    let maxMatches = -1;\n\n    if (!columns || !recordsByColumn || !fastaIds || fastaIds.length === 0) {\n      return { bestColumn: null, matchCounts: {} };\n    }\n\n    const prioritizedKeys = [\n      'displayname',\n      'accessionversion',\n      'accession',\n      'sampleid',\n      'sample_id',\n      'id',\n      'strain',\n      'isolate',\n      'submissionid',\n      'name',\n    ];\n\n    for (const col of columns) {\n      const colDict = recordsByColumn[col];\n      if (!colDict) {\n        continue;\n      }\n\n      const count = matchCounts[col];\n\n      if (count > maxMatches) {\n        maxMatches = count;\n        bestColumn = col;\n      } else if (count === maxMatches && count > 0 && bestColumn) {\n        // Tie-breaker: prioritize standard ID column names\n        const currentPriority = prioritizedKeys.indexOf(bestColumn.toLowerCase());\n        const newPriority = prioritizedKeys.indexOf(col.toLowerCase());\n        if (newPriority !== -1 && (currentPriority === -1 || newPriority < currentPriority)) {\n          bestColumn = col;\n        }\n      }\n    }\n\n    if (maxMatches <= 0) {\n      // If no matches, default to highest priority known ID column if available\n      for (const pKey of prioritizedKeys) {\n        const found = columns.find((c) => c.toLowerCase() === pKey);\n        if (found) {\n          bestColumn = found;\n          break;\n        }\n      }\n      if (!bestColumn && columns.length > 0) {\n        bestColumn = columns[0];\n      }\n    }\n\n    return { bestColumn, matchCounts };\n  };\n\n  public static getHighlightedIds(query: string, allAccessions: string[], metadataRecords: MetadataRecord[], matchKeyField: null | string = null): string[] {\n    const trimmed = query.trim().toLowerCase();\n    if (!trimmed) {\n      return [];\n    }\n\n    const matched = new Set<string>();\n\n    // Check accession names / fasta IDs\n    allAccessions.forEach((acc) => {\n      if (acc.toLowerCase().includes(trimmed)) {\n        matched.add(acc);\n      }\n    });\n\n    // Check metadata records\n    metadataRecords.forEach((rec) => {\n      const acc =\n        (matchKeyField && rec[matchKeyField]) ||\n        rec.displayName ||\n        rec.accessionVersion ||\n        rec.accession ||\n        rec.id ||\n        rec.submissionId ||\n        rec.SampleID;\n      if (acc) {\n        const matchesAnyField = Object.values(rec).some(\n          (val) => typeof val === 'string' && val.toLowerCase().includes(trimmed),\n        );\n        if (matchesAnyField) {\n          matched.add(acc);\n        }\n      }\n    });\n\n    return Array.from(matched);\n  }\n  /**\n   * Count FASTA sequence ID matches for each metadata column.\n   */\n  public static getMatchCounts = (\n    columns: string[],\n    recordsByColumn: Record<string, Record<string, MetadataRecord>>,\n    fastaIds: string[],\n  ): Record<string, number> => {\n    const matchCounts: Record<string, number> = {};\n\n    if (!columns || !recordsByColumn || !fastaIds || fastaIds.length === 0) {\n      return matchCounts;\n    }\n\n    for (const col of columns) {\n      const colDict = recordsByColumn[col];\n      if (!colDict) {\n        continue;\n      }\n\n      let count = 0;\n      for (const id of fastaIds) {\n        if (colDict[id]) {\n          count++;\n        }\n      }\n      matchCounts[col] = count;\n    }\n\n    return matchCounts;\n  };\n\n  /**\n   * Retrieve metadata record for a given sample/node name with fallback strategies.\n   */\n  public static readonly getRecordForSample = (\n    metadata: MetadataParseResult | null | undefined,\n    sampleId: string,\n    matchKeyField?: null | string,\n  ): MetadataRecord | undefined => {\n    if (!metadata || !sampleId) {\n      return undefined;\n    }\n\n    // 1. If matchKeyField is specified and exists, check it first\n    if (matchKeyField && metadata.recordsByColumn?.[matchKeyField]) {\n      const rec = metadata.recordsByColumn[matchKeyField][sampleId];\n      if (rec) {\n        return rec;\n      }\n    }\n\n    // 2. Check displayName\n    if (metadata.recordsByColumn?.['displayName']?.[sampleId]) {\n      return metadata.recordsByColumn['displayName'][sampleId];\n    }\n\n    // 3. Check accessionVersion\n    if (metadata.recordsByColumn?.['accessionVersion']?.[sampleId]) {\n      return metadata.recordsByColumn['accessionVersion'][sampleId];\n    }\n\n    // 4. Check accession maps\n    if (metadata.recordsByAccession[sampleId]) {\n      return metadata.recordsByAccession[sampleId];\n    }\n    if (metadata.recordsBySampleId[sampleId]) {\n      return metadata.recordsBySampleId[sampleId];\n    }\n\n    // 5. Broad search through all indexed columns\n    if (metadata.recordsByColumn) {\n      for (const col of Object.keys(metadata.recordsByColumn)) {\n        const match = metadata.recordsByColumn[col][sampleId];\n        if (match) {\n          return match;\n        }\n      }\n    }\n\n    return undefined;\n  };\n\n  public static parseTsv = (content: string): MetadataParseResult => {\n    if (!content?.trim()) {\n      return {\n        columns: [],\n        error: 'Empty metadata content provided.',\n        records: [],\n        recordsByAccession: {},\n        recordsByColumn: {},\n        recordsBySampleId: {},\n      };\n    }\n\n    const lines = content.trim().split('\\n');\n    if (lines.length < 2) {\n      return {\n        columns: [],\n        error: 'Metadata file must contain at least a header row and one data row.',\n        records: [],\n        recordsByAccession: {},\n        recordsByColumn: {},\n        recordsBySampleId: {},\n      };\n    }\n\n    // Parse header row\n    const headerLine = lines[0].trim();\n    let delimiter = '\\t';\n    if (!headerLine.includes('\\t') && headerLine.includes(',')) {\n      delimiter = ',';\n    }\n    const columns = headerLine\n      .split(delimiter)\n      .map((col) => col.trim().replace(/^[\"']|[\"']$/g, ''))\n      .filter((c) => c.length > 0);\n\n    const records: MetadataRecord[] = [];\n    const recordsByAccession: Record<string, MetadataRecord> = {};\n    const recordsBySampleId: Record<string, MetadataRecord> = {};\n    const recordsByColumn: Record<string, Record<string, MetadataRecord>> = {};\n\n    columns.forEach((col) => {\n      recordsByColumn[col] = {};\n    });\n\n    for (let i = 1; i < lines.length; i++) {\n      const line = lines[i].trim();\n      if (!line) {\n        continue;\n      }\n\n      const values = line.split(delimiter).map((val) => val.trim().replace(/^[\"']|[\"']$/g, ''));\n      const record: MetadataRecord = {};\n\n      columns.forEach((col, colIdx) => {\n        const val = values[colIdx] ?? 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+{"version":3,"file":"index.js","names":["MetaDataUtil","matchCounts","columns","recordsByColumn","fastaIds","bestColumn","maxMatches","prioritizedKeys","col","count","currentPriority","newPriority","pKey","found","c","trimmed","query","matched","allAccessions","acc","metadataRecords","matchKeyField","rec","val","colDict","id","metadata","sampleId","\"displayName\"","\"accessionVersion\"","match","content","lines","headerLine","delimiter","records","recordsByAccession","recordsBySampleId","i","line","values","record","colIdx","accessionKey","sampleIdKey"],"sources":["../../../src/utils/MetaDataUtil/MetaDataUtil.ts"],"sourcesContent":["import type {\n  MetadataParseResult,\n  MetadataRecord,\n} from '../../models/metadata.models';\n\nexport class MetaDataUtil {\n  /**\n   * Compute the best matching metadata column for the given FASTA sequence IDs.\n   */\n  public static findBestMatchingColumn = (\n    columns: string[],\n    recordsByColumn: Record<string, Record<string, MetadataRecord>>,\n    fastaIds: string[],\n  ): { bestColumn: null | string; matchCounts: Record<string, number> } => {\n    const matchCounts = MetaDataUtil.getMatchCounts(columns, recordsByColumn, fastaIds);\n    let bestColumn: null | string = null;\n    let maxMatches = -1;\n\n    if (!columns || !recordsByColumn || !fastaIds || fastaIds.length === 0) {\n      return { bestColumn: null, matchCounts: {} };\n    }\n\n    const prioritizedKeys = [\n      'displayname',\n      'accessionversion',\n      'accession',\n      'sampleid',\n      'sample_id',\n      'id',\n      'strain',\n      'isolate',\n      'submissionid',\n      'name',\n    ];\n\n    for (const col of columns) {\n      const colDict = recordsByColumn[col];\n      if (!colDict) {\n        continue;\n      }\n\n      const count = matchCounts[col];\n\n      if (count > maxMatches) {\n        maxMatches = count;\n        bestColumn = col;\n      } else if (count === maxMatches && count > 0 && bestColumn) {\n        // Tie-breaker: prioritize standard ID column names\n        const currentPriority = prioritizedKeys.indexOf(bestColumn.toLowerCase());\n        const newPriority = prioritizedKeys.indexOf(col.toLowerCase());\n        if (newPriority !== -1 && (currentPriority === -1 || newPriority < currentPriority)) {\n          bestColumn = col;\n        }\n      }\n    }\n\n    if (maxMatches <= 0) {\n      // If no matches, default to highest priority known ID column if available\n      for (const pKey of prioritizedKeys) {\n        const found = columns.find((c) => c.toLowerCase() === pKey);\n        if (found) {\n          bestColumn = found;\n          break;\n        }\n      }\n      if (!bestColumn && columns.length > 0) {\n        bestColumn = columns[0];\n      }\n    }\n\n    return { bestColumn, matchCounts };\n  };\n\n  public static getHighlightedIds(query: string, allAccessions: string[], metadataRecords: MetadataRecord[], matchKeyField: null | string = null): string[] {\n    const trimmed = query.trim().toLowerCase();\n    if (!trimmed) {\n      return [];\n    }\n\n    const matched = new Set<string>();\n\n    // Check accession names / fasta IDs\n    allAccessions.forEach((acc) => {\n      if (acc.toLowerCase().includes(trimmed)) {\n        matched.add(acc);\n      }\n    });\n\n    // Check metadata records\n    metadataRecords.forEach((rec) => {\n      const acc =\n        (matchKeyField && rec[matchKeyField]) ||\n        rec.displayName ||\n        rec.accessionVersion ||\n        rec.accession ||\n        rec.id ||\n        rec.submissionId ||\n        rec.SampleID;\n      if (acc) {\n        const matchesAnyField = Object.values(rec).some(\n          (val) => typeof val === 'string' && val.toLowerCase().includes(trimmed),\n        );\n        if (matchesAnyField) {\n          matched.add(acc);\n        }\n      }\n    });\n\n    return Array.from(matched);\n  }\n  /**\n   * Count FASTA sequence ID matches for each metadata column.\n   */\n  public static getMatchCounts = (\n    columns: string[],\n    recordsByColumn: Record<string, Record<string, MetadataRecord>>,\n    fastaIds: string[],\n  ): Record<string, number> => {\n    const matchCounts: Record<string, number> = {};\n\n    if (!columns || !recordsByColumn || !fastaIds || fastaIds.length === 0) {\n      return matchCounts;\n    }\n\n    for (const col of columns) {\n      const colDict = recordsByColumn[col];\n      if (!colDict) {\n        continue;\n      }\n\n      let count = 0;\n      for (const id of fastaIds) {\n        if (colDict[id]) {\n          count++;\n        }\n      }\n      matchCounts[col] = count;\n    }\n\n    return matchCounts;\n  };\n\n  /**\n   * Retrieve metadata record for a given sample/node name with fallback strategies.\n   */\n  public static readonly getRecordForSample = (\n    metadata: MetadataParseResult | null | undefined,\n    sampleId: string,\n    matchKeyField?: null | string,\n  ): MetadataRecord | undefined => {\n    if (!metadata || !sampleId) {\n      return undefined;\n    }\n\n    // 1. If matchKeyField is specified and exists, check it first\n    if (matchKeyField && metadata.recordsByColumn?.[matchKeyField]) {\n      const rec = metadata.recordsByColumn[matchKeyField][sampleId];\n      if (rec) {\n        return rec;\n      }\n    }\n\n    // 2. Check displayName\n    if (metadata.recordsByColumn?.['displayName']?.[sampleId]) {\n      return metadata.recordsByColumn['displayName'][sampleId];\n    }\n\n    // 3. Check accessionVersion\n    if (metadata.recordsByColumn?.['accessionVersion']?.[sampleId]) {\n      return metadata.recordsByColumn['accessionVersion'][sampleId];\n    }\n\n    // 4. Check accession maps\n    if (metadata.recordsByAccession[sampleId]) {\n      return metadata.recordsByAccession[sampleId];\n    }\n    if (metadata.recordsBySampleId[sampleId]) {\n      return metadata.recordsBySampleId[sampleId];\n    }\n\n    // 5. Broad search through all indexed columns\n    if (metadata.recordsByColumn) {\n      for (const col of Object.keys(metadata.recordsByColumn)) {\n        const match = metadata.recordsByColumn[col][sampleId];\n        if (match) {\n          return match;\n        }\n      }\n    }\n\n    return undefined;\n  };\n\n  public static parseTsv = (content: string): MetadataParseResult => {\n    if (!content?.trim()) {\n      return {\n        columns: [],\n        error: 'Empty metadata content provided.',\n        records: [],\n        recordsByAccession: {},\n        recordsByColumn: {},\n        recordsBySampleId: {},\n      };\n    }\n\n    const lines = content.trim().split('\\n');\n    if (lines.length < 2) {\n      return {\n        columns: [],\n        error: 'Metadata file must contain at least a header row and one data row.',\n        records: [],\n        recordsByAccession: {},\n        recordsByColumn: {},\n        recordsBySampleId: {},\n      };\n    }\n\n    // Parse header row\n    const headerLine = lines[0].trim();\n    let delimiter = '\\t';\n    if (!headerLine.includes('\\t') && headerLine.includes(',')) {\n      delimiter = ',';\n    }\n    const columns = headerLine\n      .split(delimiter)\n      .map((col) => col.trim().replace(/^[\"']|[\"']$/g, ''))\n      .filter((c) => c.length > 0);\n\n    const records: MetadataRecord[] = [];\n    const recordsByAccession: Record<string, MetadataRecord> = {};\n    const recordsBySampleId: Record<string, MetadataRecord> = {};\n    const recordsByColumn: Record<string, Record<string, MetadataRecord>> = {};\n\n    columns.forEach((col) => {\n      recordsByColumn[col] = {};\n    });\n\n    for (let i = 1; i < lines.length; i++) {\n      const line = lines[i].trim();\n      if (!line) {\n        continue;\n      }\n\n      const values = line.split(delimiter).map((val) => val.trim().replace(/^[\"']|[\"']$/g, ''));\n      const record: MetadataRecord = {};\n\n      columns.forEach((col, colIdx) => {\n        const val = values[colIdx] ?? 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package/dist/utils/StandardConfigUtil/StandardConfigUtil.d.ts

@@ -0,0 +1,4 @@
+import { ConfigBase } from '../../models/config.models';
+export declare class StandardConfigUtil {
+    static createConfig(): Pick<ConfigBase, 'nonce' | 'pageConfig' | 'spinner'>;
+}

package/dist/utils/StandardConfigUtil/index.d.ts

@@ -0,0 +1 @@
+export * from './StandardConfigUtil';

package/dist/utils/StandardConfigUtil/index.js

@@ -0,0 +1,18 @@
+import { WindowService as e } from "@gen-epix/ui-core/classes/services/WindowService";
+//#region src/utils/StandardConfigUtil/StandardConfigUtil.ts
+var t = class {
+	static createConfig() {
+		return {
+			nonce: e.getInstance().document.querySelector("meta[name=\"csp-nonce\"]")?.getAttribute("content") ?? void 0,
+			pageConfig: { appBarHeight: 48 },
+			spinner: {
+				DEFAULT_CIRCULAR_PROGRESS_SIZE: 40,
+				DEFAULT_TAKING_LONGER_TIMEOUT_MS: 5e3
+			}
+		};
+	}
+};
+//#endregion
+export { t as StandardConfigUtil };
+
+//# sourceMappingURL=index.js.map

package/dist/utils/StandardConfigUtil/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":["StandardConfigUtil","WindowService"],"sources":["../../../src/utils/StandardConfigUtil/StandardConfigUtil.ts"],"sourcesContent":["import { WindowService } from '@gen-epix/ui-core/classes/services/WindowService';\n\nimport type { ConfigBase } from '../../models/config.models';\n\nexport class StandardConfigUtil {\n  public static createConfig(): Pick<ConfigBase, 'nonce' | 'pageConfig' | 'spinner'> {\n    return {\n      nonce: WindowService.getInstance().document.querySelector('meta[name=\"csp-nonce\"]')?.getAttribute('content') ?? undefined,\n      pageConfig: {\n        appBarHeight: 48,\n      },\n      spinner: {\n        DEFAULT_CIRCULAR_PROGRESS_SIZE: 40,\n        DEFAULT_TAKING_LONGER_TIMEOUT_MS: 5000,\n      },\n    };\n  }\n}\n"],"mappings":";;AAIA,IAAaA,IAAb,MAAgC;CAC9B,OAAc,eAAqE;EACjF,OAAO;GACL,OAAOC,EAAc,YAAY,CAAC,CAAC,SAAS,cAAc,0BAAwB,CAAC,EAAE,aAAa,SAAS,KAAK,KAAA;GAChH,YAAY,EACV,cAAc,GAChB;GACA,SAAS;IACP,gCAAgC;IAChC,kCAAkC;GACpC;EACF;CACF;AACF"}

package/dist/utils/UrlUtil/index.js

@@ -1,9 +1,10 @@
-import { WindowService as e } from "@gen-epix/ui-core/classes/services/WindowService";
+import { WINDOW_SERVICE_TOKEN as e } from "../../constants/config.constants.js";
+import { container as t } from "tsyringe";
 //#region src/utils/UrlUtil/UrlUtil.ts
-var t = class {
+var n = class {
 	static clearSearchParams() {
-		let t = new URL(e.getInstance().window.location.href);
-		t.search = "", e.getInstance().window.history.replaceState(null, "", t.toString());
+		let n = new URL(t.resolve(e).window.location.href);
+		n.search = "", t.resolve(e).window.history.replaceState(null, "", n.toString());
 	}
 	static fastaLabelFromUrl(e) {
 		try {
@@ -25,6 +26,6 @@ var t = class {
 	}
 };
 //#endregion
-export { t as UrlUtil };
+export { n as UrlUtil };
 
 //# sourceMappingURL=index.js.map

package/dist/utils/UrlUtil/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","names":["UrlUtil","url","WindowService","urlObject","segment"],"sources":["../../../src/utils/UrlUtil/UrlUtil.ts"],"sourcesContent":["import { WindowService } from '@gen-epix/ui-core/classes/services/WindowService';\n\nexport class UrlUtil {\n  public static clearSearchParams(): void {\n    const url = new URL(WindowService.getInstance().window.location.href);\n    url.search = '';\n    WindowService.getInstance().window.history.replaceState(null, '', url.toString());\n  }\n\n  public static fastaLabelFromUrl(url: string): string {\n    try {\n      const urlObject = new URL(url);\n      const segment = urlObject.pathname.split('/').filter(Boolean).pop();\n      if (segment) {\n        return decodeURIComponent(segment);\n      }\n      return `${urlObject.hostname}.fasta`;\n    } catch {\n      return 'remote-alignment.fasta';\n    }\n  }\n\n  public static validateFastaUrl(url: string): string {\n    let urlObject: URL;\n    try {\n      urlObject = new URL(url.trim());\n    } catch {\n      throw new Error('Enter a valid FASTA URL.');\n    }\n    if (urlObject.protocol !== 'http:' && urlObject.protocol !== 'https:') {\n      throw new Error('FASTA URLs must use HTTP or HTTPS.');\n    }\n    return urlObject.href;\n  }\n}\n"],"mappings":";;AAEA,IAAaA,IAAb,MAAqB;CACnB,OAAc,oBAA0B;EACtC,IAAMC,IAAM,IAAI,IAAIC,EAAc,YAAY,CAAC,CAAC,OAAO,SAAS,IAAI;EAEpE,AADA,EAAI,SAAS,IACbA,EAAc,YAAY,CAAC,CAAC,OAAO,QAAQ,aAAa,MAAM,IAAID,EAAI,SAAS,CAAC;CAClF;CAEA,OAAc,kBAAkB,GAAqB;EACnD,IAAI;GACF,IAAME,IAAY,IAAI,IAAIF,CAAG,GACvBG,IAAUD,EAAU,SAAS,MAAM,GAAG,CAAC,CAAC,OAAO,OAAO,CAAC,CAAC,IAAI;GAIlE,OAHIC,IACK,mBAAmBA,CAAO,IAE5B,GAAGD,EAAU,SAAS;EAC/B,QAAQ;GACN,OAAO;EACT;CACF;CAEA,OAAc,iBAAiB,GAAqB;EAClD,IAAIA;EACJ,IAAI;GACF,IAAY,IAAI,IAAIF,EAAI,KAAK,CAAC;EAChC,QAAQ;GACN,MAAU,MAAM,0BAA0B;EAC5C;EACA,IAAIE,EAAU,aAAa,WAAWA,EAAU,aAAa,UAC3D,MAAU,MAAM,oCAAoC;EAEtD,OAAOA,EAAU;CACnB;AACF"}
+{"version":3,"file":"index.js","names":["UrlUtil","url","container","WINDOW_SERVICE_TOKEN","urlObject","segment"],"sources":["../../../src/utils/UrlUtil/UrlUtil.ts"],"sourcesContent":["import { container } from 'tsyringe';\nimport type { WindowService } from '@gen-epix/ui-core/classes/services/WindowService';\n\nimport { WINDOW_SERVICE_TOKEN } from '../../constants/config.constants';\n\nexport class UrlUtil {\n  public static clearSearchParams(): void {\n    const url = new URL(container.resolve<WindowService>(WINDOW_SERVICE_TOKEN).window.location.href);\n    url.search = '';\n    container.resolve<WindowService>(WINDOW_SERVICE_TOKEN).window.history.replaceState(null, '', url.toString());\n  }\n\n  public static fastaLabelFromUrl(url: string): string {\n    try {\n      const urlObject = new URL(url);\n      const segment = urlObject.pathname.split('/').filter(Boolean).pop();\n      if (segment) {\n        return decodeURIComponent(segment);\n      }\n      return `${urlObject.hostname}.fasta`;\n    } catch {\n      return 'remote-alignment.fasta';\n    }\n  }\n\n  public static validateFastaUrl(url: string): string {\n    let urlObject: URL;\n    try {\n      urlObject = new URL(url.trim());\n    } catch {\n      throw new Error('Enter a valid FASTA URL.');\n    }\n    if (urlObject.protocol !== 'http:' && urlObject.protocol !== 'https:') {\n      throw new Error('FASTA URLs must use HTTP or HTTPS.');\n    }\n    return urlObject.href;\n  }\n}\n"],"mappings":";;;AAKA,IAAaA,IAAb,MAAqB;CACnB,OAAc,oBAA0B;EACtC,IAAMC,IAAM,IAAI,IAAIC,EAAU,QAAuBC,CAAoB,CAAC,CAAC,OAAO,SAAS,IAAI;EAE/F,AADA,EAAI,SAAS,IACbD,EAAU,QAAuBC,CAAoB,CAAC,CAAC,OAAO,QAAQ,aAAa,MAAM,IAAIF,EAAI,SAAS,CAAC;CAC7G;CAEA,OAAc,kBAAkB,GAAqB;EACnD,IAAI;GACF,IAAMG,IAAY,IAAI,IAAIH,CAAG,GACvBI,IAAUD,EAAU,SAAS,MAAM,GAAG,CAAC,CAAC,OAAO,OAAO,CAAC,CAAC,IAAI;GAIlE,OAHIC,IACK,mBAAmBA,CAAO,IAE5B,GAAGD,EAAU,SAAS;EAC/B,QAAQ;GACN,OAAO;EACT;CACF;CAEA,OAAc,iBAAiB,GAAqB;EAClD,IAAIA;EACJ,IAAI;GACF,IAAY,IAAI,IAAIH,EAAI,KAAK,CAAC;EAChC,QAAQ;GACN,MAAU,MAAM,0BAA0B;EAC5C;EACA,IAAIG,EAAU,aAAa,WAAWA,EAAU,aAAa,UAC3D,MAAU,MAAM,oCAAoC;EAEtD,OAAOA,EAAU;CACnB;AACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rivm-loculus-tools/common-frontend",
-  "version": "0.2.0",
+  "version": "0.4.0",
   "license": "EUPL-1.2",
   "repository": {
     "type": "git",
@@ -11,9 +11,9 @@
     "@emotion/cache": "*",
     "@emotion/react": "*",
     "@emotion/styled": "*",
-    "@gen-epix/ui-core-components": "^4.4.0",
-    "@gen-epix/ui-core-form": "^4.4.0",
-    "@gen-epix/ui-core": "^3.9.0",
+    "@gen-epix/ui-core-components": "^4.5.0",
+    "@gen-epix/ui-core-form": "^4.4.1",
+    "@gen-epix/ui-core": "^3.9.1",
     "@mui/icons-material": "*",
     "@mui/material": "*",
     "@mui/styled-engine": "*",
@@ -23,7 +23,9 @@
     "react-dom": "*",
     "react-hook-form": "*",
     "react-i18next": "*",
-    "react": "*"
+    "react": "*",
+    "reflect-metadata": "*",
+    "tsyringe": "*"
   },
   "dependencies": {
     "lodash": "4.18.1",
@@ -34,9 +36,9 @@
     "@emotion/react": "11.14.0",
     "@emotion/styled": "11.14.1",
     "@gen-epix/eslint-config": "0.8.0",
-    "@gen-epix/ui-core-components": "4.4.0",
-    "@gen-epix/ui-core-form": "4.4.0",
-    "@gen-epix/ui-core": "3.9.0",
+    "@gen-epix/ui-core-components": "4.5.0",
+    "@gen-epix/ui-core-form": "4.4.1",
+    "@gen-epix/ui-core": "3.9.1",
     "@mui/icons-material": "9.5.0",
     "@mui/material": "9.5.0",
     "@mui/styled-engine": "9.5.0",
@@ -54,6 +56,8 @@
     "react-hook-form": "7.90.0",
     "react-i18next": "17.0.16",
     "react": "19.3.0",
+    "reflect-metadata": "0.2.2",
+    "tsyringe": "4.10.0",
     "typescript": "6.0.3",
     "vite-plugin-dts": "5.1.2",
     "vite-plugin-static-copy": "4.1.1",
@@ -63,61 +67,109 @@
     "dist"
   ],
   "exports": {
+    "./classes/services/EmotionCacheService": {
+      "types": "./dist/classes/services/EmotionCacheService/index.d.ts",
+      "import": "./dist/classes/services/EmotionCacheService/index.js"
+    },
     "./classes/services/FastaDataEventBusService": {
       "types": "./dist/classes/services/FastaDataEventBusService/index.d.ts",
       "import": "./dist/classes/services/FastaDataEventBusService/index.js"
     },
-    "./components/FastaDataImportDialog": {
-      "types": "./dist/components/FastaDataImportDialog/index.d.ts",
-      "import": "./dist/components/FastaDataImportDialog/index.js"
+    "./components/SearchBar": {
+      "types": "./dist/components/SearchBar/index.d.ts",
+      "import": "./dist/components/SearchBar/index.js"
     },
-    "./components/FastaDataImportDialogLoader": {
-      "types": "./dist/components/FastaDataImportDialogLoader/index.d.ts",
-      "import": "./dist/components/FastaDataImportDialogLoader/index.js"
+    "./components/app/App": {
+      "types": "./dist/components/app/App/index.d.ts",
+      "import": "./dist/components/app/App/index.js"
     },
-    "./components/FastaNotLoaded": {
-      "types": "./dist/components/FastaNotLoaded/index.d.ts",
-      "import": "./dist/components/FastaNotLoaded/index.js"
+    "./components/fasta/FastaDataImportDialog": {
+      "types": "./dist/components/fasta/FastaDataImportDialog/index.d.ts",
+      "import": "./dist/components/fasta/FastaDataImportDialog/index.js"
     },
-    "./components/FastaPageHeaderCenterComponent": {
-      "types": "./dist/components/FastaPageHeaderCenterComponent/index.d.ts",
-      "import": "./dist/components/FastaPageHeaderCenterComponent/index.js"
+    "./components/fasta/FastaDataImportDialogLoader": {
+      "types": "./dist/components/fasta/FastaDataImportDialogLoader/index.d.ts",
+      "import": "./dist/components/fasta/FastaDataImportDialogLoader/index.js"
     },
-    "./components/FastaPageHeaderImportButton": {
-      "types": "./dist/components/FastaPageHeaderImportButton/index.d.ts",
-      "import": "./dist/components/FastaPageHeaderImportButton/index.js"
+    "./components/fasta/FastaNotLoaded": {
+      "types": "./dist/components/fasta/FastaNotLoaded/index.d.ts",
+      "import": "./dist/components/fasta/FastaNotLoaded/index.js"
     },
-    "./components/FastaPageHeaderResetButton": {
-      "types": "./dist/components/FastaPageHeaderResetButton/index.d.ts",
-      "import": "./dist/components/FastaPageHeaderResetButton/index.js"
+    "./components/fasta/FastaPageHeaderCenterComponent": {
+      "types": "./dist/components/fasta/FastaPageHeaderCenterComponent/index.d.ts",
+      "import": "./dist/components/fasta/FastaPageHeaderCenterComponent/index.js"
     },
-    "./components/I18nWrapper": {
-      "types": "./dist/components/I18nWrapper/index.d.ts",
-      "import": "./dist/components/I18nWrapper/index.js"
+    "./components/fasta/FastaPageHeaderImportButton": {
+      "types": "./dist/components/fasta/FastaPageHeaderImportButton/index.d.ts",
+      "import": "./dist/components/fasta/FastaPageHeaderImportButton/index.js"
     },
-    "./components/PageHeaderDocumentationButton": {
-      "types": "./dist/components/PageHeaderDocumentationButton/index.d.ts",
-      "import": "./dist/components/PageHeaderDocumentationButton/index.js"
+    "./components/fasta/FastaPageHeaderResetButton": {
+      "types": "./dist/components/fasta/FastaPageHeaderResetButton/index.d.ts",
+      "import": "./dist/components/fasta/FastaPageHeaderResetButton/index.js"
     },
-    "./components/SearchBar": {
-      "types": "./dist/components/SearchBar/index.d.ts",
-      "import": "./dist/components/SearchBar/index.js"
+    "./components/ui/ButtonWithMenu": {
+      "types": "./dist/components/ui/ButtonWithMenu/index.d.ts",
+      "import": "./dist/components/ui/ButtonWithMenu/index.js"
+    },
+    "./components/ui/GenericErrorMessage": {
+      "types": "./dist/components/ui/GenericErrorMessage/index.d.ts",
+      "import": "./dist/components/ui/GenericErrorMessage/index.js"
+    },
+    "./components/ui/I18nWrapper": {
+      "types": "./dist/components/ui/I18nWrapper/index.d.ts",
+      "import": "./dist/components/ui/I18nWrapper/index.js"
+    },
+    "./components/ui/PageCommon": {
+      "types": "./dist/components/ui/PageCommon/index.d.ts",
+      "import": "./dist/components/ui/PageCommon/index.js"
+    },
+    "./components/ui/PageCommonDrawer": {
+      "types": "./dist/components/ui/PageCommonDrawer/index.d.ts",
+      "import": "./dist/components/ui/PageCommonDrawer/index.js"
     },
-    "./components/page": {
-      "types": "./dist/components/page/index.d.ts",
-      "import": "./dist/components/page/index.js"
+    "./components/ui/PageCommonHeader": {
+      "types": "./dist/components/ui/PageCommonHeader/index.d.ts",
+      "import": "./dist/components/ui/PageCommonHeader/index.js"
     },
-    "./constants/page": {
-      "types": "./dist/constants/page.d.ts",
-      "import": "./dist/constants/page.js"
+    "./constants/config.constants": {
+      "types": "./dist/constants/config.constants.d.ts",
+      "import": "./dist/constants/config.constants.js"
     },
-    "./models/fasta": {
-      "types": "./dist/models/fasta.d.ts",
-      "import": "./dist/models/fasta.js"
+    "./constants/page.constants": {
+      "types": "./dist/constants/page.constants.d.ts",
+      "import": "./dist/constants/page.constants.js"
     },
-    "./models/metadata": {
-      "types": "./dist/models/metadata.d.ts",
-      "import": "./dist/models/metadata.js"
+    "./context/commonConfigContext": {
+      "types": "./dist/context/commonConfigContext/index.d.ts",
+      "import": "./dist/context/commonConfigContext/index.js"
+    },
+    "./context/pageCommonContext": {
+      "types": "./dist/context/pageCommonContext/index.d.ts",
+      "import": "./dist/context/pageCommonContext/index.js"
+    },
+    "./hooks/useConfig": {
+      "types": "./dist/hooks/useConfig/index.d.ts",
+      "import": "./dist/hooks/useConfig/index.js"
+    },
+    "./hooks/useUpdateDocumentTitle": {
+      "types": "./dist/hooks/useUpdateDocumentTitle/index.d.ts",
+      "import": "./dist/hooks/useUpdateDocumentTitle/index.js"
+    },
+    "./models/config.models": {
+      "types": "./dist/models/config.models.d.ts",
+      "import": "./dist/models/config.models.js"
+    },
+    "./models/fasta.models": {
+      "types": "./dist/models/fasta.models.d.ts",
+      "import": "./dist/models/fasta.models.js"
+    },
+    "./models/metadata.models": {
+      "types": "./dist/models/metadata.models.d.ts",
+      "import": "./dist/models/metadata.models.js"
+    },
+    "./pages/ErrorPage": {
+      "types": "./dist/pages/ErrorPage/index.d.ts",
+      "import": "./dist/pages/ErrorPage/index.js"
     },
     "./stores/fastaDataStore": {
       "types": "./dist/stores/fastaDataStore/index.d.ts",
@@ -127,6 +179,10 @@
       "types": "./dist/theme/index.d.ts",
       "import": "./dist/theme/index.js"
     },
+    "./utils/DependencyContainerUtil": {
+      "types": "./dist/utils/DependencyContainerUtil/index.d.ts",
+      "import": "./dist/utils/DependencyContainerUtil/index.js"
+    },
     "./utils/DownloadUtil": {
       "types": "./dist/utils/DownloadUtil/index.d.ts",
       "import": "./dist/utils/DownloadUtil/index.js"
@@ -135,6 +191,10 @@
       "types": "./dist/utils/ErrorUtil/index.d.ts",
       "import": "./dist/utils/ErrorUtil/index.js"
     },
+    "./utils/ExportUtil": {
+      "types": "./dist/utils/ExportUtil/index.d.ts",
+      "import": "./dist/utils/ExportUtil/index.js"
+    },
     "./utils/FastaUtil": {
       "types": "./dist/utils/FastaUtil/index.d.ts",
       "import": "./dist/utils/FastaUtil/index.js"
@@ -143,6 +203,10 @@
       "types": "./dist/utils/MetaDataUtil/index.d.ts",
       "import": "./dist/utils/MetaDataUtil/index.js"
     },
+    "./utils/StandardConfigUtil": {
+      "types": "./dist/utils/StandardConfigUtil/index.d.ts",
+      "import": "./dist/utils/StandardConfigUtil/index.js"
+    },
     "./utils/UrlUtil": {
       "types": "./dist/utils/UrlUtil/index.d.ts",
       "import": "./dist/utils/UrlUtil/index.js"

package/dist/_chunks/FastaDataImportDialog.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"FastaDataImportDialog.js","names":["_Fragment","DnaIcon","TableChartIcon","FastaDataImportDialog","withDialog","fastaTab","setFastaTab","useState","fastaFile","setFastaFile","fastaUrl","setFastaUrl","fastaText","setFastaText","metadataTab","setMetadataTab","metadataFile","setMetadataFile","metadataUrl","setMetadataUrl","metadataText","setMetadataText","isLoading","setIsLoading","errorMsg","setErrorMsg","useEffect","openProps","onNoCloseButtonChange","onDisableBackdropClickChange","onCloseError","useCallback","onChangeFastaTab","value","onChangeMetadataTab","onFileSelectedFasta","file","onFileSelectedMetadata","onChangeFastaUrl","event","onChangeFastaText","onChangeMetadataUrl","onChangeMetadataText","onClickLoadData","fastaContent","res","metadataContent","onDataChange","onClose","err","onError","actions","CircularProgress","extraActions","onActionsChange","Fragment","Alert","Box","Paper","Typography","Tabs","Tab","FileDropZone","TextField"],"sources":["../../src/components/FastaDataImportDialog/FastaDataImportDialog.tsx"],"sourcesContent":["import type {\n  ChangeEvent,\n  ReactElement,\n  SyntheticEvent,\n} from 'react';\nimport {\n  useCallback,\n  useEffect,\n  useState,\n} from 'react';\nimport {\n  Alert,\n  Box,\n  CircularProgress,\n  Paper,\n  Tab,\n  Tabs,\n  TextField,\n  Typography,\n} from '@mui/material';\nimport DnaIcon from '@mui/icons-material/Biotech';\nimport TableChartIcon from '@mui/icons-material/TableChart';\nimport { FileDropZone } from '@gen-epix/ui-core-components/components/FileDropZone';\nimport type {\n  WithDialogRefMethods,\n  WithDialogRenderProps,\n} from '@gen-epix/ui-core-components/hoc/withDialog';\nimport { withDialog } from '@gen-epix/ui-core-components/hoc/withDialog';\nimport type { DialogAction } from '@gen-epix/ui-core-components/components/Dialog';\n\n\nenum FASTA_TAB {\n  DROP = 0,\n  URL = 1,\n  PASTE = 2,\n}\n\nenum META_DATA_TAB {\n  DROP = 0,\n  URL = 1,\n  PASTE = 2,\n}\n\nexport interface FastaDataImportDialogOpenProps {\n  initialErrorMessage?: string;\n}\n\nexport interface FastaDataImportDialogProps extends WithDialogRenderProps<FastaDataImportDialogOpenProps> {\n  extraActions?: DialogAction[];\n  onDataChange: (fasta: string, metaData?: string) => void;\n  onError: (error: unknown) => void;\n}\n\nexport type FastaDataImportDialogRefMethods = WithDialogRefMethods<FastaDataImportDialogProps, FastaDataImportDialogOpenProps>;\n\nexport const FastaDataImportDialog = withDialog<FastaDataImportDialogProps, FastaDataImportDialogOpenProps>((\n  {\n    extraActions,\n    onActionsChange,\n    onClose,\n    onDataChange,\n    onDisableBackdropClickChange,\n    onError,\n    onNoCloseButtonChange,\n    openProps,\n  }: FastaDataImportDialogProps,\n): ReactElement => {\n  // FASTA state\n  const [fastaTab, setFastaTab] = useState(FASTA_TAB.DROP);\n  const [fastaFile, setFastaFile] = useState<FileList | null>(null);\n  const [fastaUrl, setFastaUrl] = useState('');\n  const [fastaText, setFastaText] = useState('');\n\n  // Metadata state\n  const [metadataTab, setMetadataTab] = useState(META_DATA_TAB.DROP);\n  const [metadataFile, setMetadataFile] = useState<FileList | null>(null);\n  const [metadataUrl, setMetadataUrl] = useState('');\n  const [metadataText, setMetadataText] = useState('');\n\n  const [isLoading, setIsLoading] = useState(false);\n  const [errorMsg, setErrorMsg] = useState<null | string>(null);\n\n  useEffect(() => {\n    setErrorMsg(openProps?.initialErrorMessage ?? null);\n  }, [openProps]);\n\n  useEffect(() => {\n    if (onNoCloseButtonChange) {\n      onNoCloseButtonChange(!!openProps?.initialErrorMessage);\n    }\n    if (onDisableBackdropClickChange) {\n      onDisableBackdropClickChange(!!openProps?.initialErrorMessage);\n    }\n  }, [onDisableBackdropClickChange, onNoCloseButtonChange, openProps?.initialErrorMessage]);\n\n  const onCloseError = useCallback(() => setErrorMsg(null), []);\n  const onChangeFastaTab = useCallback((_event: SyntheticEvent, value: number) => {\n    setFastaTab(value);\n  }, []);\n  const onChangeMetadataTab = useCallback((_event: SyntheticEvent, value: number) => {\n    setMetadataTab(value);\n  }, []);\n  const onFileSelectedFasta = useCallback((file: FileList) => setFastaFile(file), []);\n  const onFileSelectedMetadata = useCallback((file: FileList) => setMetadataFile(file), []);\n  const onChangeFastaUrl = useCallback((event: ChangeEvent<HTMLInputElement>) => {\n    setFastaUrl(event.target.value);\n  }, []);\n  const onChangeFastaText = useCallback((event: ChangeEvent<HTMLInputElement>) => {\n    setFastaText(event.target.value);\n  }, []);\n  const onChangeMetadataUrl = useCallback((event: ChangeEvent<HTMLInputElement>) => {\n    setMetadataUrl(event.target.value);\n  }, []);\n  const onChangeMetadataText = useCallback((event: ChangeEvent<HTMLInputElement>) => {\n    setMetadataText(event.target.value);\n  }, []);\n\n  const onClickLoadData = useCallback(async () => {\n    setErrorMsg(null);\n    setIsLoading(true);\n\n    try {\n      // 1. Resolve FASTA content\n      let fastaContent = '';\n      if (fastaTab === FASTA_TAB.DROP && fastaFile) {\n        fastaContent = await fastaFile[0].text();\n      } else if (fastaTab === FASTA_TAB.URL && fastaUrl.trim()) {\n        const res = await fetch(fastaUrl.trim());\n        if (!res.ok) {\n          throw new Error(`Failed to fetch FASTA from URL (${res.status} ${res.statusText})`);\n        }\n        fastaContent = await res.text();\n      } else if (fastaTab === FASTA_TAB.PASTE && fastaText.trim()) {\n        fastaContent = fastaText.trim();\n      }\n\n      if (!fastaContent?.trim()) {\n        throw new Error('Please provide FASTA sequence data via file, URL, or paste.');\n      }\n\n      // 2. Resolve Metadata content (optional)\n      let metadataContent = '';\n      if (metadataTab === META_DATA_TAB.DROP && metadataFile) {\n        metadataContent = await metadataFile[0].text();\n      } else if (metadataTab === META_DATA_TAB.URL && metadataUrl.trim()) {\n        const res = await fetch(metadataUrl.trim());\n        if (!res.ok) {\n          throw new Error(`Failed to fetch Metadata from URL (${res.status} ${res.statusText})`);\n        }\n        metadataContent = await res.text();\n      } else if (metadataTab === META_DATA_TAB.PASTE && metadataText.trim()) {\n        metadataContent = metadataText.trim();\n      }\n      onDataChange(fastaContent, metadataContent);\n      if (onClose) {\n        onClose();\n      }\n    } catch (err: unknown) {\n      console.error('Data import failed:', err);\n      onError(err);\n    } finally {\n      setIsLoading(false);\n    }\n  }, [fastaFile, fastaTab, fastaText, fastaUrl, metadataFile, metadataTab, metadataText, metadataUrl, onClose, onDataChange, onError]);\n\n\n  useEffect(() => {\n    const actions: DialogAction[] = [\n      {\n        disabled: isLoading,\n        label: isLoading ? 'Processing...' : 'Load & Calculate',\n        onClick: onClickLoadData,\n        startIcon: isLoading ? (\n          <CircularProgress\n            color={'inherit'}\n            size={18}\n          />\n        ) : undefined,\n        variant: 'contained',\n      },\n    ];\n    if (extraActions?.length) {\n      actions.unshift(...extraActions);\n    }\n    if (onActionsChange) {\n      onActionsChange(actions);\n    }\n  }, [onActionsChange, onClickLoadData, isLoading, extraActions]);\n\n  return (\n    <>\n      {errorMsg && (\n        <Alert\n          onClose={onCloseError}\n          severity={'error'}\n          sx={{\n            marginBottom: 2,\n          }}\n        >\n          {errorMsg}\n        </Alert>\n      )}\n      <Box sx={{ display: 'grid', gap: 3, gridTemplateColumns: { md: '1fr 1fr', xs: '1fr' } }}>\n        {/* FASTA Sequences Group */}\n        <Paper\n          sx={{ borderRadius: 2, p: 2.5 }}\n          variant={'outlined'}\n        >\n          <Box sx={{ alignItems: 'center', display: 'flex', gap: 1, mb: 1.5 }}>\n            <DnaIcon color={'primary'} />\n            <Typography\n              sx={{ fontWeight: 700 }}\n              variant={'subtitle1'}\n            >\n              {'1. FASTA Sequences (Required)'}\n            </Typography>\n          </Box>\n          <Typography\n            color={'text.secondary'}\n            sx={{ display: 'block', mb: 2 }}\n            variant={'caption'}\n          >\n            {'Pre-aligned nucleotide or amino-acid sequence data.'}\n          </Typography>\n          <Tabs\n            onChange={onChangeFastaTab}\n            sx={{ mb: 2, minHeight: 36 }}\n            value={fastaTab}\n          >\n            <Tab\n              label={'File Upload'}\n              sx={{ fontSize: '0.85rem', py: 0.5 }}\n            />\n            <Tab\n              label={'Public URL'}\n              sx={{ fontSize: '0.85rem', py: 0.5 }}\n            />\n            <Tab\n              label={'Direct Paste'}\n              sx={{ fontSize: '0.85rem', py: 0.5 }}\n            />\n          </Tabs>\n          {fastaTab === FASTA_TAB.DROP && (\n            <FileDropZone\n              accept={'.fasta,.fa,.fna,.aln'}\n              files={fastaFile}\n              helperText={'Drag & drop .fasta / .fa alignment file'}\n              onFilesSelected={onFileSelectedFasta}\n            />\n          )}\n          {fastaTab === FASTA_TAB.URL && (\n            <Box sx={{ display: 'flex', flexDirection: 'column', gap: 1.5, justifyContent: 'center', minHeight: 180 }}>\n              <TextField\n                fullWidth\n                helperText={'Enter a publicly accessible URL to a FASTA alignment'}\n                label={'FASTA URL'}\n                onChange={onChangeFastaUrl}\n                placeholder={'https://example.com/sequences.fasta'}\n                value={fastaUrl}\n                variant={'outlined'}\n              />\n            </Box>\n          )}\n          {fastaTab === FASTA_TAB.PASTE && (\n            <Box sx={{ minHeight: 180 }}>\n              <TextField\n                fullWidth\n                label={'Paste FASTA Content'}\n                multiline\n                onChange={onChangeFastaText}\n                placeholder={'>seq1&#10;ACTG...&#10;>seq2&#10;ACTG...'}\n                rows={6}\n                sx={{ fontFamily: 'monospace' }}\n                value={fastaText}\n                variant={'outlined'}\n              />\n            </Box>\n          )}\n        </Paper>\n        {/* TSV Metadata Group */}\n        <Paper\n          sx={{ borderRadius: 2, p: 2.5 }}\n          variant={'outlined'}\n        >\n          <Box sx={{ alignItems: 'center', display: 'flex', gap: 1, mb: 1.5 }}>\n            <TableChartIcon color={'primary'} />\n            <Typography\n              sx={{ fontWeight: 700 }}\n              variant={'subtitle1'}\n            >\n              {'2. TSV Metadata (Optional)'}\n            </Typography>\n          </Box>\n          <Typography\n            color={'text.primary'}\n            sx={{ display: 'block', mb: 2 }}\n            variant={'caption'}\n          >\n            {'Sample attributes for coloring, search & custom leaf labels.'}\n          </Typography>\n          <Tabs\n            onChange={onChangeMetadataTab}\n            sx={{ mb: 2, minHeight: 36 }}\n            value={metadataTab}\n          >\n            <Tab\n              label={'File Upload'}\n              sx={{ fontSize: '0.85rem', py: 0.5 }}\n            />\n            <Tab\n              label={'Public URL'}\n              sx={{ fontSize: '0.85rem', py: 0.5 }}\n            />\n            <Tab\n              label={'Direct Paste'}\n              sx={{ fontSize: '0.85rem', py: 0.5 }}\n            />\n          </Tabs>\n          {metadataTab === META_DATA_TAB.DROP && (\n            <FileDropZone\n              accept={'.tsv,.txt,.csv'}\n              files={metadataFile}\n              label={'TSV Metadata File'}\n              onFilesSelected={onFileSelectedMetadata}\n            />\n          )}\n          {metadataTab === META_DATA_TAB.URL && (\n            <Box sx={{ display: 'flex', flexDirection: 'column', gap: 1.5, justifyContent: 'center', minHeight: 180 }}>\n              <TextField\n                fullWidth\n                helperText={'Enter a publicly accessible URL to a TSV metadata file'}\n                label={'Metadata TSV URL'}\n                onChange={onChangeMetadataUrl}\n                placeholder={'https://example.com/metadata.tsv'}\n                value={metadataUrl}\n                variant={'outlined'}\n              />\n            </Box>\n          )}\n          {metadataTab === META_DATA_TAB.PASTE && (\n            <Box sx={{ minHeight: 180 }}>\n              <TextField\n                fullWidth\n                label={'Paste TSV Content'}\n                multiline\n                onChange={onChangeMetadataText}\n                placeholder={'SampleID&#9;Country&#9;Date&#10;Sample1&#9;NL&#9;2024-01-01'}\n                rows={6}\n                sx={{ fontFamily: 'monospace' }}\n                value={metadataText}\n                variant={'outlined'}\n              />\n            </Box>\n          )}\n        </Paper>\n      </Box>\n    </>\n  );\n}, {\n  defaultTitle: 'Load Phylogenetic Data',\n  fullWidth: true,\n  maxWidth: 'xl',\n  testId: 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package/dist/components/FastaDataImportDialog/index.js

@@ -1 +0,0 @@
-export { t as FastaDataImportDialog } from "../../_chunks/FastaDataImportDialog.js";