@platforma-open/milaboratories.immune-assay-data.model 1.5.1 → 1.5.3

package/dist/index.cjs

@@ -1,10 +1,33 @@
 'use strict';
 
 var model$1 = require('@platforma-sdk/model');
+var label = require('./label.cjs');
 
+function getColumns(ctx) {
+    const anchor = ctx.args.datasetRef;
+    if (anchor === undefined)
+        return undefined;
+    const anchorSpec = ctx.resultPool.getPColumnSpecByRef(anchor);
+    if (anchorSpec === undefined)
+        return undefined;
+    // all clone properties
+    const props = (ctx.resultPool.getAnchoredPColumns({ main: anchor }, [
+        {
+            axes: [{ anchor: 'main', idx: 1 }],
+        },
+    ]) ?? [])
+        .filter((p) => p.spec.annotations?.['pl7.app/sequence/isAnnotation'] !== 'true');
+    return {
+        props: props,
+    };
+}
 const model = model$1.BlockModel.create()
     .withArgs({
-    defaultBlockLabel: '',
+    defaultBlockLabel: label.getDefaultBlockLabel({
+        similarityType: 'alignment-score',
+        identity: 0.9,
+        coverageThreshold: 0.95,
+    }),
     customBlockLabel: '',
     settings: {
         coverageThreshold: 0.95, // default value matching MMseqs2 default
@@ -15,6 +38,7 @@ const model = model$1.BlockModel.create()
 })
     .withUiState({
     tableState: model$1.createPlDataTableStateV2(),
+    alignmentModel: {},
 })
     .argsValid((ctx) => ctx.args.datasetRef !== undefined
     && ctx.args.fileHandle !== undefined
@@ -79,6 +103,42 @@ const model = model$1.BlockModel.create()
     if (cols === undefined)
         return undefined;
     return model$1.createPlDataTableV2(ctx, cols, ctx.uiState.tableState);
+})
+    .output('pf', (ctx) => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson()) {
+        return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+        return undefined;
+    return model$1.createPFrameForGraphs(ctx, cols);
+})
+    .output('assaySequenceSpec', (ctx) => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson()) {
+        return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+        return undefined;
+    // Return only sequence column
+    return cols.find((c) => c.spec.name === 'pl7.app/vdj/sequence'
+        && c.spec.axesSpec[0].name === 'pl7.app/vdj/assay/sequenceId')?.spec;
+})
+    .output('msaPf', (ctx) => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson()) {
+        return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+        return undefined;
+    const msaCols = ctx.outputs?.resolve('assayLinkerPframe')?.getPColumns();
+    if (!msaCols)
+        return undefined;
+    const columns = getColumns(ctx);
+    if (columns === undefined) {
+        return undefined;
+    }
+    return model$1.createPFrameForGraphs(ctx, [...msaCols, ...cols, ...columns.props]);
 })
     .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)
     .title(() => 'Immune Assay Data')
@@ -88,5 +148,6 @@ const model = model$1.BlockModel.create()
 ]))
     .done(2);
 
+exports.getDefaultBlockLabel = label.getDefaultBlockLabel;
 exports.model = model;
 //# sourceMappingURL=index.cjs.map

package/dist/index.cjs.map

@@ -1 +1 @@
-{"version":3,"file":"index.cjs","sources":["../src/index.ts"],"sourcesContent":["import type {\n  ImportFileHandle,\n  PlDataTableStateV2,\n  PlRef,\n  SUniversalPColumnId,\n} from '@platforma-sdk/model';\nimport {\n  BlockModel,\n  createPlDataTableStateV2,\n  createPlDataTableV2,\n} from '@platforma-sdk/model';\n\ntype Settings = {\n  coverageThreshold: number; // fraction of aligned residues required\n  identity: number;\n  similarityType: 'sequence-identity' | 'alignment-score';\n};\n\nexport type ImportColumnInfo = {\n  header: string;\n  type: 'Int' | 'Double' | 'String';\n  /** If this column is a sequence column, the type of the sequence */\n  sequenceType?: 'nucleotide' | 'aminoacid';\n};\n\nexport type BlockArgs = {\n  defaultBlockLabel: string;\n  customBlockLabel: string;\n  datasetRef?: PlRef;\n  targetRef?: SUniversalPColumnId;\n  fileHandle?: ImportFileHandle;\n  fileExtension?: string;\n  importColumns?: ImportColumnInfo[];\n  sequenceColumnHeader?: string;\n  selectedColumns: string[];\n  settings: Settings;\n};\n\nexport type UiState = {\n  fileImportError?: string;\n  tableState: PlDataTableStateV2;\n};\n\nexport const model = BlockModel.create()\n\n  .withArgs<BlockArgs>({\n    defaultBlockLabel: '',\n    customBlockLabel: '',\n    settings: {\n      coverageThreshold: 0.95, // default value matching MMseqs2 default\n      identity: 0.9,\n      similarityType: 'alignment-score',\n    },\n    selectedColumns: [],\n  })\n\n  .withUiState<UiState>({\n    tableState: createPlDataTableStateV2(),\n  })\n\n  .argsValid((ctx) =>\n    ctx.args.datasetRef !== undefined\n    && ctx.args.fileHandle !== undefined\n    && ctx.args.importColumns !== undefined\n    && ctx.args.sequenceColumnHeader !== undefined\n    && ctx.args.targetRef !== undefined\n    && ctx.uiState.fileImportError === undefined,\n  )\n\n  .output('datasetOptions', (ctx) =>\n    ctx.resultPool.getOptions([{\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/clonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }, {\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/scClonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }], { refsWithEnrichments: true }),\n  )\n\n  .output('targetOptions', (ctx) => {\n    const ref = ctx.args.datasetRef;\n    if (ref === undefined) return undefined;\n\n    const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === 'pl7.app/vdj/scClonotypeKey';\n    const sequenceMatchers = [];\n    // const allowedFeatures = ['CDR1', 'CDR2', 'CDR3', 'FR1', 'FR2',\n    //   'FR3', 'FR4', 'VDJRegion'];\n    // for (const feature of allowedFeatures) {\n    if (isSingleCell) {\n      sequenceMatchers.push({\n        axes: [{ anchor: 'main', idx: 1 }],\n        name: 'pl7.app/vdj/sequence',\n        domain: {\n          // 'pl7.app/vdj/feature': feature,\n          'pl7.app/vdj/scClonotypeChain/index': 'primary',\n        },\n      });\n    } else {\n      sequenceMatchers.push({\n        axes: [{ anchor: 'main', idx: 1 }],\n        name: 'pl7.app/vdj/sequence',\n        domain: {\n          // 'pl7.app/vdj/feature': feature,\n        },\n      });\n    }\n\n    return ctx.resultPool.getCanonicalOptions(\n      { main: ref },\n      sequenceMatchers,\n      {\n        ignoreMissingDomains: true,\n        labelOps: {\n          includeNativeLabel: true,\n        },\n      });\n  })\n\n  .output(\n    'dataImportHandle',\n    (ctx) => ctx.outputs?.resolve('dataImportHandle')?.getImportProgress(),\n    { isActive: true },\n  )\n\n  .outputWithStatus('table', (ctx) => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    return createPlDataTableV2(\n      ctx,\n      cols,\n      ctx.uiState.tableState,\n    );\n  })\n\n  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)\n\n  .title(() => 'Immune Assay Data')\n\n  .subtitle((ctx) => ctx.args.customBlockLabel || ctx.args.defaultBlockLabel)\n\n  .sections((_ctx) => ([\n    { type: 'link', href: '/', label: 'Main' },\n  ]))\n\n  .done(2);\n"],"names":["BlockModel","createPlDataTableStateV2","createPlDataTableV2"],"mappings":";;;;AA2CO,MAAM,KAAK,GAAGA,kBAAU,CAAC,MAAM;AAEnC,KAAA,QAAQ,CAAY;AACnB,IAAA,iBAAiB,EAAE,EAAE;AACrB,IAAA,gBAAgB,EAAE,EAAE;AACpB,IAAA,QAAQ,EAAE;QACR,iBAAiB,EAAE,IAAI;AACvB,QAAA,QAAQ,EAAE,GAAG;AACb,QAAA,cAAc,EAAE,iBAAiB;AAClC,KAAA;AACD,IAAA,eAAe,EAAE,EAAE;CACpB;AAEA,KAAA,WAAW,CAAU;IACpB,UAAU,EAAEC,gCAAwB,EAAE;CACvC;AAEA,KAAA,SAAS,CAAC,CAAC,GAAG,KACb,GAAG,CAAC,IAAI,CAAC,UAAU,KAAK;AACrB,OAAA,GAAG,CAAC,IAAI,CAAC,UAAU,KAAK;AACxB,OAAA,GAAG,CAAC,IAAI,CAAC,aAAa,KAAK;AAC3B,OAAA,GAAG,CAAC,IAAI,CAAC,oBAAoB,KAAK;AAClC,OAAA,GAAG,CAAC,IAAI,CAAC,SAAS,KAAK;AACvB,OAAA,GAAG,CAAC,OAAO,CAAC,eAAe,KAAK,SAAS;AAG7C,KAAA,MAAM,CAAC,gBAAgB,EAAE,CAAC,GAAG,KAC5B,GAAG,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC;AACzB,QAAA,IAAI,EAAE;YACJ,EAAE,IAAI,EAAE,kBAAkB,EAAE;YAC5B,EAAE,IAAI,EAAE,0BAA0B,EAAE;AACrC,SAAA;AACD,QAAA,WAAW,EAAE,EAAE,kBAAkB,EAAE,MAAM,EAAE;KAC5C,EAAE;AACD,QAAA,IAAI,EAAE;YACJ,EAAE,IAAI,EAAE,kBAAkB,EAAE;YAC5B,EAAE,IAAI,EAAE,4BAA4B,EAAE;AACvC,SAAA;AACD,QAAA,WAAW,EAAE,EAAE,kBAAkB,EAAE,MAAM,EAAE;AAC5C,KAAA,CAAC,EAAE,EAAE,mBAAmB,EAAE,IAAI,EAAE,CAAC;AAGnC,KAAA,MAAM,CAAC,eAAe,EAAE,CAAC,GAAG,KAAI;AAC/B,IAAA,MAAM,GAAG,GAAG,GAAG,CAAC,IAAI,CAAC,UAAU;IAC/B,IAAI,GAAG,KAAK,SAAS;AAAE,QAAA,OAAO,SAAS;AAEvC,IAAA,MAAM,YAAY,GAAG,GAAG,CAAC,UAAU,CAAC,mBAAmB,CAAC,GAAG,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,4BAA4B;IAC/G,MAAM,gBAAgB,GAAG,EAAE;;;;IAI3B,IAAI,YAAY,EAAE;QAChB,gBAAgB,CAAC,IAAI,CAAC;YACpB,IAAI,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC;AAClC,YAAA,IAAI,EAAE,sBAAsB;AAC5B,YAAA,MAAM,EAAE;;AAEN,gBAAA,oCAAoC,EAAE,SAAS;AAChD,aAAA;AACF,SAAA,CAAC;IACJ;SAAO;QACL,gBAAgB,CAAC,IAAI,CAAC;YACpB,IAAI,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC;AAClC,YAAA,IAAI,EAAE,sBAAsB;AAC5B,YAAA,MAAM,EAAE;;AAEP,aAAA;AACF,SAAA,CAAC;IACJ;AAEA,IAAA,OAAO,GAAG,CAAC,UAAU,CAAC,mBAAmB,CACvC,EAAE,IAAI,EAAE,GAAG,EAAE,EACb,gBAAgB,EAChB;AACE,QAAA,oBAAoB,EAAE,IAAI;AAC1B,QAAA,QAAQ,EAAE;AACR,YAAA,kBAAkB,EAAE,IAAI;AACzB,SAAA;AACF,KAAA,CAAC;AACN,CAAC;KAEA,MAAM,CACL,kBAAkB,EAClB,CAAC,GAAG,KAAK,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,kBAAkB,CAAC,EAAE,iBAAiB,EAAE,EACtE,EAAE,QAAQ,EAAE,IAAI,EAAE;AAGnB,KAAA,gBAAgB,CAAC,OAAO,EAAE,CAAC,GAAG,KAAI;AACjC,IAAA,IAAI,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,cAAc,CAAC,EAAE,aAAa,EAAW,EAAE;AAClE,QAAA,OAAO,SAAS;IAClB;AACA,IAAA,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,EAAE,OAAO,CAAC,OAAO,CAAC,EAAE,WAAW,EAAE;IACzD,IAAI,IAAI,KAAK,SAAS;AACpB,QAAA,OAAO,SAAS;AAElB,IAAA,OAAOC,2BAAmB,CACxB,GAAG,EACH,IAAI,EACJ,GAAG,CAAC,OAAO,CAAC,UAAU,CACvB;AACH,CAAC;AAEA,KAAA,MAAM,CAAC,WAAW,EAAE,CAAC,GAAG,KAAK,GAAG,CAAC,OAAO,EAAE,iBAAiB,EAAE,KAAK,KAAK;AAEvE,KAAA,KAAK,CAAC,MAAM,mBAAmB;AAE/B,KAAA,QAAQ,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,IAAI,CAAC,gBAAgB,IAAI,GAAG,CAAC,IAAI,CAAC,iBAAiB;AAEzE,KAAA,QAAQ,CAAC,CAAC,IAAI,MAAM;IACnB,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE;AAC3C,CAAA,CAAC;KAED,IAAI,CAAC,CAAC;;;;"}
+{"version":3,"file":"index.cjs","sources":["../src/index.ts"],"sourcesContent":["import type {\n  DataInfo,\n  ImportFileHandle,\n  PColumn,\n  PColumnSpec,\n  PColumnValues,\n  PlDataTableStateV2,\n  PlMultiSequenceAlignmentModel,\n  PlRef,\n  RenderCtxLegacy,\n  SUniversalPColumnId,\n  TreeNodeAccessor,\n} from '@platforma-sdk/model';\nimport {\n  BlockModel,\n  createPFrameForGraphs,\n  createPlDataTableStateV2,\n  createPlDataTableV2,\n} from '@platforma-sdk/model';\nimport { getDefaultBlockLabel } from './label';\n\ntype Settings = {\n  coverageThreshold: number; // fraction of aligned residues required\n  identity: number;\n  similarityType: 'sequence-identity' | 'alignment-score';\n};\n\nexport type ImportColumnInfo = {\n  header: string;\n  type: 'Int' | 'Double' | 'String';\n  /** If this column is a sequence column, the type of the sequence */\n  sequenceType?: 'nucleotide' | 'aminoacid';\n};\n\nexport type BlockArgs = {\n  defaultBlockLabel: string;\n  customBlockLabel: string;\n  datasetRef?: PlRef;\n  targetRef?: SUniversalPColumnId;\n  fileHandle?: ImportFileHandle;\n  fileExtension?: string;\n  importColumns?: ImportColumnInfo[];\n  sequenceColumnHeader?: string;\n  selectedColumns: string[];\n  settings: Settings;\n};\n\nexport type UiState = {\n  fileImportError?: string;\n  tableState: PlDataTableStateV2;\n  alignmentModel: PlMultiSequenceAlignmentModel;\n};\n\ntype Column = PColumn<DataInfo<TreeNodeAccessor> | TreeNodeAccessor | PColumnValues>;\n\ntype Columns = {\n  props: Column[];\n};\n\nfunction getColumns(ctx: RenderCtxLegacy<BlockArgs, UiState>): Columns | undefined {\n  const anchor = ctx.args.datasetRef;\n  if (anchor === undefined)\n    return undefined;\n\n  const anchorSpec = ctx.resultPool.getPColumnSpecByRef(anchor);\n  if (anchorSpec === undefined)\n    return undefined;\n\n  // all clone properties\n  const props = (ctx.resultPool.getAnchoredPColumns(\n    { main: anchor },\n    [\n      {\n        axes: [{ anchor: 'main', idx: 1 }],\n      },\n    ]) ?? [])\n    .filter((p) => p.spec.annotations?.['pl7.app/sequence/isAnnotation'] !== 'true');\n\n  return {\n    props: props,\n  };\n}\n\nexport const model = BlockModel.create()\n\n  .withArgs<BlockArgs>({\n    defaultBlockLabel: getDefaultBlockLabel({\n      similarityType: 'alignment-score',\n      identity: 0.9,\n      coverageThreshold: 0.95,\n    }),\n    customBlockLabel: '',\n    settings: {\n      coverageThreshold: 0.95, // default value matching MMseqs2 default\n      identity: 0.9,\n      similarityType: 'alignment-score',\n    },\n    selectedColumns: [],\n  })\n\n  .withUiState<UiState>({\n    tableState: createPlDataTableStateV2(),\n    alignmentModel: {},\n  })\n\n  .argsValid((ctx) =>\n    ctx.args.datasetRef !== undefined\n    && ctx.args.fileHandle !== undefined\n    && ctx.args.importColumns !== undefined\n    && ctx.args.sequenceColumnHeader !== undefined\n    && ctx.args.targetRef !== undefined\n    && ctx.uiState.fileImportError === undefined,\n  )\n\n  .output('datasetOptions', (ctx) =>\n    ctx.resultPool.getOptions([{\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/clonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }, {\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/scClonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }], { refsWithEnrichments: true }),\n  )\n\n  .output('targetOptions', (ctx) => {\n    const ref = ctx.args.datasetRef;\n    if (ref === undefined) return undefined;\n\n    const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === 'pl7.app/vdj/scClonotypeKey';\n    const sequenceMatchers = [];\n    // const allowedFeatures = ['CDR1', 'CDR2', 'CDR3', 'FR1', 'FR2',\n    //   'FR3', 'FR4', 'VDJRegion'];\n    // for (const feature of allowedFeatures) {\n    if (isSingleCell) {\n      sequenceMatchers.push({\n        axes: [{ anchor: 'main', idx: 1 }],\n        name: 'pl7.app/vdj/sequence',\n        domain: {\n          // 'pl7.app/vdj/feature': feature,\n          'pl7.app/vdj/scClonotypeChain/index': 'primary',\n        },\n      });\n    } else {\n      sequenceMatchers.push({\n        axes: [{ anchor: 'main', idx: 1 }],\n        name: 'pl7.app/vdj/sequence',\n        domain: {\n          // 'pl7.app/vdj/feature': feature,\n        },\n      });\n    }\n\n    return ctx.resultPool.getCanonicalOptions(\n      { main: ref },\n      sequenceMatchers,\n      {\n        ignoreMissingDomains: true,\n        labelOps: {\n          includeNativeLabel: true,\n        },\n      });\n  })\n\n  .output(\n    'dataImportHandle',\n    (ctx) => ctx.outputs?.resolve('dataImportHandle')?.getImportProgress(),\n    { isActive: true },\n  )\n\n  .outputWithStatus('table', (ctx) => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    return createPlDataTableV2(\n      ctx,\n      cols,\n      ctx.uiState.tableState,\n    );\n  })\n\n  .output('pf', (ctx) => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    return createPFrameForGraphs(ctx, cols);\n  })\n\n  .output('assaySequenceSpec', (ctx): PColumnSpec | undefined => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n    // Return only sequence column\n    return cols.find((c) => c.spec.name === 'pl7.app/vdj/sequence'\n      && c.spec.axesSpec[0].name === 'pl7.app/vdj/assay/sequenceId')?.spec;\n  })\n\n  .output('msaPf', (ctx) => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    const msaCols = ctx.outputs?.resolve('assayLinkerPframe')?.getPColumns();\n    if (!msaCols) return undefined;\n\n    const columns = getColumns(ctx);\n    if (columns === undefined) {\n      return undefined;\n    }\n\n    return createPFrameForGraphs(ctx, [...msaCols, ...cols, ...columns.props]);\n  })\n\n  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)\n\n  .title(() => 'Immune Assay Data')\n\n  .subtitle((ctx) => ctx.args.customBlockLabel || ctx.args.defaultBlockLabel)\n\n  .sections((_ctx) => ([\n    { type: 'link', href: '/', label: 'Main' },\n  ]))\n\n  .done(2);\n\nexport { getDefaultBlockLabel } from 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package/dist/index.d.ts

@@ -1,4 +1,4 @@
-import type { ImportFileHandle, PlDataTableStateV2, PlRef, SUniversalPColumnId } from '@platforma-sdk/model';
+import type { ImportFileHandle, PlDataTableStateV2, PlMultiSequenceAlignmentModel, PlRef, SUniversalPColumnId } from '@platforma-sdk/model';
 type Settings = {
     coverageThreshold: number;
     identity: number;
@@ -25,9 +25,10 @@ export type BlockArgs = {
 export type UiState = {
     fileImportError?: string;
     tableState: PlDataTableStateV2;
+    alignmentModel: PlMultiSequenceAlignmentModel;
 };
-export declare const model: import("@platforma-sdk/model").PlatformaExtended<import("@platforma-sdk/model").PlatformaV2<BlockArgs, {
-    datasetOptions: import("@platforma-sdk/model").OutputWithStatus<{
+export declare const model: import("@platforma-sdk/model").PlatformaExtended<import("@platforma-sdk/model").PlatformaV2<BlockArgs, import("@platforma-sdk/model").InferOutputsFromConfigs<BlockArgs, {
+    datasetOptions: import("@platforma-sdk/model").ConfigRenderLambda<{
         readonly ref: {
             readonly __isRef: true;
             readonly blockId: string;
@@ -35,28 +36,52 @@ export declare const model: import("@platforma-sdk/model").PlatformaExtended<imp
             readonly requireEnrichments?: true | undefined;
         };
         readonly label: string;
-    }[]> & {
-        __unwrap: true;
-    };
-    targetOptions: import("@platforma-sdk/model").OutputWithStatus<{
+    }[]>;
+} & {
+    targetOptions: import("@platforma-sdk/model").ConfigRenderLambda<{
         label: string;
         value: SUniversalPColumnId;
-    }[] | undefined> & {
-        __unwrap: true;
-    };
-    dataImportHandle: import("@platforma-sdk/model").OutputWithStatus<import("@platforma-sdk/model").ImportProgress | undefined> & {
-        __unwrap: true;
-    };
-    table: import("@platforma-sdk/model").OutputWithStatus<{
+    }[] | undefined>;
+} & {
+    dataImportHandle: import("@platforma-sdk/model").ConfigRenderLambda<import("@platforma-sdk/model").ImportProgress | undefined>;
+} & {
+    table: import("@platforma-sdk/model").ConfigRenderLambda<{
         sourceId: string | null;
         fullTableHandle: import("@platforma-sdk/model").PTableHandle;
         visibleTableHandle: import("@platforma-sdk/model").PTableHandle;
-    }> & {
-        __unwrap: false;
+    } | undefined> & {
+        withStatus: true;
     };
-    isRunning: import("@platforma-sdk/model").OutputWithStatus<boolean> & {
-        __unwrap: true;
-    };
-}, UiState, "/">>;
-export {};
+} & {
+    pf: import("@platforma-sdk/model").ConfigRenderLambda<import("@platforma-sdk/model").PFrameHandle | undefined>;
+} & {
+    assaySequenceSpec: import("@platforma-sdk/model").ConfigRenderLambda<{
+        readonly kind: "PColumn";
+        readonly name: string;
+        readonly domain?: {
+            [x: string]: string;
+        } | undefined;
+        readonly annotations?: {
+            [x: string]: string;
+        } | undefined;
+        readonly valueType: "Int" | "Double" | "String" | "Long" | "Float" | "Bytes";
+        readonly parentAxes?: number[] | undefined;
+        readonly axesSpec: {
+            readonly type: import("@platforma-sdk/model").ValueType;
+            readonly name: string;
+            readonly domain?: {
+                [x: string]: string;
+            } | undefined;
+            readonly annotations?: {
+                [x: string]: string;
+            } | undefined;
+            readonly parentAxes?: number[] | undefined;
+        }[];
+    } | undefined>;
+} & {
+    msaPf: import("@platforma-sdk/model").ConfigRenderLambda<import("@platforma-sdk/model").PFrameHandle | undefined>;
+} & {
+    isRunning: import("@platforma-sdk/model").ConfigRenderLambda<boolean>;
+}, UiState>, UiState, "/">>;
+export { getDefaultBlockLabel } from './label';
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,gBAAgB,EAChB,kBAAkB,EAClB,KAAK,EACL,mBAAmB,EACpB,MAAM,sBAAsB,CAAC;AAO9B,KAAK,QAAQ,GAAG;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,QAAQ,EAAE,MAAM,CAAC;IACjB,cAAc,EAAE,mBAAmB,GAAG,iBAAiB,CAAC;CACzD,CAAC;AAEF,MAAM,MAAM,gBAAgB,GAAG;IAC7B,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,KAAK,GAAG,QAAQ,GAAG,QAAQ,CAAC;IAClC,oEAAoE;IACpE,YAAY,CAAC,EAAE,YAAY,GAAG,WAAW,CAAC;CAC3C,CAAC;AAEF,MAAM,MAAM,SAAS,GAAG;IACtB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,gBAAgB,EAAE,MAAM,CAAC;IACzB,UAAU,CAAC,EAAE,KAAK,CAAC;IACnB,SAAS,CAAC,EAAE,mBAAmB,CAAC;IAChC,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,aAAa,CAAC,EAAE,gBAAgB,EAAE,CAAC;IACnC,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAC9B,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,QAAQ,EAAE,QAAQ,CAAC;CACpB,CAAC;AAEF,MAAM,MAAM,OAAO,GAAG;IACpB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,UAAU,EAAE,kBAAkB,CAAC;CAChC,CAAC;AAEF,eAAO,MAAM,KAAK;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAgHR,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAEV,gBAAgB,EAIhB,kBAAkB,EAClB,6BAA6B,EAC7B,KAAK,EAEL,mBAAmB,EAEpB,MAAM,sBAAsB,CAAC;AAS9B,KAAK,QAAQ,GAAG;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,QAAQ,EAAE,MAAM,CAAC;IACjB,cAAc,EAAE,mBAAmB,GAAG,iBAAiB,CAAC;CACzD,CAAC;AAEF,MAAM,MAAM,gBAAgB,GAAG;IAC7B,MAAM,EAAE,MAAM,CAAC;IACf,IAAI,EAAE,KAAK,GAAG,QAAQ,GAAG,QAAQ,CAAC;IAClC,oEAAoE;IACpE,YAAY,CAAC,EAAE,YAAY,GAAG,WAAW,CAAC;CAC3C,CAAC;AAEF,MAAM,MAAM,SAAS,GAAG;IACtB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,gBAAgB,EAAE,MAAM,CAAC;IACzB,UAAU,CAAC,EAAE,KAAK,CAAC;IACnB,SAAS,CAAC,EAAE,mBAAmB,CAAC;IAChC,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,aAAa,CAAC,EAAE,gBAAgB,EAAE,CAAC;IACnC,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAC9B,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,QAAQ,EAAE,QAAQ,CAAC;CACpB,CAAC;AAEF,MAAM,MAAM,OAAO,GAAG;IACpB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,UAAU,EAAE,kBAAkB,CAAC;IAC/B,cAAc,EAAE,6BAA6B,CAAC;CAC/C,CAAC;AAgCF,eAAO,MAAM,KAAK;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;2BA+JR,CAAC;AAEX,OAAO,EAAE,oBAAoB,EAAE,MAAM,SAAS,CAAC"}

package/dist/index.js

@@ -1,8 +1,31 @@
-import { BlockModel, createPlDataTableStateV2, createPlDataTableV2 } from '@platforma-sdk/model';
+import { BlockModel, createPlDataTableStateV2, createPlDataTableV2, createPFrameForGraphs } from '@platforma-sdk/model';
+import { getDefaultBlockLabel } from './label.js';
 
+function getColumns(ctx) {
+    const anchor = ctx.args.datasetRef;
+    if (anchor === undefined)
+        return undefined;
+    const anchorSpec = ctx.resultPool.getPColumnSpecByRef(anchor);
+    if (anchorSpec === undefined)
+        return undefined;
+    // all clone properties
+    const props = (ctx.resultPool.getAnchoredPColumns({ main: anchor }, [
+        {
+            axes: [{ anchor: 'main', idx: 1 }],
+        },
+    ]) ?? [])
+        .filter((p) => p.spec.annotations?.['pl7.app/sequence/isAnnotation'] !== 'true');
+    return {
+        props: props,
+    };
+}
 const model = BlockModel.create()
     .withArgs({
-    defaultBlockLabel: '',
+    defaultBlockLabel: getDefaultBlockLabel({
+        similarityType: 'alignment-score',
+        identity: 0.9,
+        coverageThreshold: 0.95,
+    }),
     customBlockLabel: '',
     settings: {
         coverageThreshold: 0.95, // default value matching MMseqs2 default
@@ -13,6 +36,7 @@ const model = BlockModel.create()
 })
     .withUiState({
     tableState: createPlDataTableStateV2(),
+    alignmentModel: {},
 })
     .argsValid((ctx) => ctx.args.datasetRef !== undefined
     && ctx.args.fileHandle !== undefined
@@ -77,6 +101,42 @@ const model = BlockModel.create()
     if (cols === undefined)
         return undefined;
     return createPlDataTableV2(ctx, cols, ctx.uiState.tableState);
+})
+    .output('pf', (ctx) => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson()) {
+        return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+        return undefined;
+    return createPFrameForGraphs(ctx, cols);
+})
+    .output('assaySequenceSpec', (ctx) => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson()) {
+        return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+        return undefined;
+    // Return only sequence column
+    return cols.find((c) => c.spec.name === 'pl7.app/vdj/sequence'
+        && c.spec.axesSpec[0].name === 'pl7.app/vdj/assay/sequenceId')?.spec;
+})
+    .output('msaPf', (ctx) => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson()) {
+        return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+        return undefined;
+    const msaCols = ctx.outputs?.resolve('assayLinkerPframe')?.getPColumns();
+    if (!msaCols)
+        return undefined;
+    const columns = getColumns(ctx);
+    if (columns === undefined) {
+        return undefined;
+    }
+    return createPFrameForGraphs(ctx, [...msaCols, ...cols, ...columns.props]);
 })
     .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)
     .title(() => 'Immune Assay Data')
@@ -86,5 +146,5 @@ const model = BlockModel.create()
 ]))
     .done(2);
 
-export { model };
+export { getDefaultBlockLabel, model };
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sources":["../src/index.ts"],"sourcesContent":["import type {\n  ImportFileHandle,\n  PlDataTableStateV2,\n  PlRef,\n  SUniversalPColumnId,\n} from '@platforma-sdk/model';\nimport {\n  BlockModel,\n  createPlDataTableStateV2,\n  createPlDataTableV2,\n} from '@platforma-sdk/model';\n\ntype Settings = {\n  coverageThreshold: number; // fraction of aligned residues required\n  identity: number;\n  similarityType: 'sequence-identity' | 'alignment-score';\n};\n\nexport type ImportColumnInfo = {\n  header: string;\n  type: 'Int' | 'Double' | 'String';\n  /** If this column is a sequence column, the type of the sequence */\n  sequenceType?: 'nucleotide' | 'aminoacid';\n};\n\nexport type BlockArgs = {\n  defaultBlockLabel: string;\n  customBlockLabel: string;\n  datasetRef?: PlRef;\n  targetRef?: SUniversalPColumnId;\n  fileHandle?: ImportFileHandle;\n  fileExtension?: string;\n  importColumns?: ImportColumnInfo[];\n  sequenceColumnHeader?: string;\n  selectedColumns: string[];\n  settings: Settings;\n};\n\nexport type UiState = {\n  fileImportError?: string;\n  tableState: PlDataTableStateV2;\n};\n\nexport const model = BlockModel.create()\n\n  .withArgs<BlockArgs>({\n    defaultBlockLabel: '',\n    customBlockLabel: '',\n    settings: {\n      coverageThreshold: 0.95, // default value matching MMseqs2 default\n      identity: 0.9,\n      similarityType: 'alignment-score',\n    },\n    selectedColumns: [],\n  })\n\n  .withUiState<UiState>({\n    tableState: createPlDataTableStateV2(),\n  })\n\n  .argsValid((ctx) =>\n    ctx.args.datasetRef !== undefined\n    && ctx.args.fileHandle !== undefined\n    && ctx.args.importColumns !== undefined\n    && ctx.args.sequenceColumnHeader !== undefined\n    && ctx.args.targetRef !== undefined\n    && ctx.uiState.fileImportError === undefined,\n  )\n\n  .output('datasetOptions', (ctx) =>\n    ctx.resultPool.getOptions([{\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/clonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }, {\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/scClonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }], { refsWithEnrichments: true }),\n  )\n\n  .output('targetOptions', (ctx) => {\n    const ref = ctx.args.datasetRef;\n    if (ref === undefined) return undefined;\n\n    const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === 'pl7.app/vdj/scClonotypeKey';\n    const sequenceMatchers = [];\n    // const allowedFeatures = ['CDR1', 'CDR2', 'CDR3', 'FR1', 'FR2',\n    //   'FR3', 'FR4', 'VDJRegion'];\n    // for (const feature of allowedFeatures) {\n    if (isSingleCell) {\n      sequenceMatchers.push({\n        axes: [{ anchor: 'main', idx: 1 }],\n        name: 'pl7.app/vdj/sequence',\n        domain: {\n          // 'pl7.app/vdj/feature': feature,\n          'pl7.app/vdj/scClonotypeChain/index': 'primary',\n        },\n      });\n    } else {\n      sequenceMatchers.push({\n        axes: [{ anchor: 'main', idx: 1 }],\n        name: 'pl7.app/vdj/sequence',\n        domain: {\n          // 'pl7.app/vdj/feature': feature,\n        },\n      });\n    }\n\n    return ctx.resultPool.getCanonicalOptions(\n      { main: ref },\n      sequenceMatchers,\n      {\n        ignoreMissingDomains: true,\n        labelOps: {\n          includeNativeLabel: true,\n        },\n      });\n  })\n\n  .output(\n    'dataImportHandle',\n    (ctx) => ctx.outputs?.resolve('dataImportHandle')?.getImportProgress(),\n    { isActive: true },\n  )\n\n  .outputWithStatus('table', (ctx) => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    return createPlDataTableV2(\n      ctx,\n      cols,\n      ctx.uiState.tableState,\n    );\n  })\n\n  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)\n\n  .title(() => 'Immune Assay Data')\n\n  .subtitle((ctx) => ctx.args.customBlockLabel || ctx.args.defaultBlockLabel)\n\n  .sections((_ctx) => ([\n    { type: 'link', href: '/', label: 'Main' },\n  ]))\n\n  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+{"version":3,"file":"index.js","sources":["../src/index.ts"],"sourcesContent":["import type {\n  DataInfo,\n  ImportFileHandle,\n  PColumn,\n  PColumnSpec,\n  PColumnValues,\n  PlDataTableStateV2,\n  PlMultiSequenceAlignmentModel,\n  PlRef,\n  RenderCtxLegacy,\n  SUniversalPColumnId,\n  TreeNodeAccessor,\n} from '@platforma-sdk/model';\nimport {\n  BlockModel,\n  createPFrameForGraphs,\n  createPlDataTableStateV2,\n  createPlDataTableV2,\n} from '@platforma-sdk/model';\nimport { getDefaultBlockLabel } from './label';\n\ntype Settings = {\n  coverageThreshold: number; // fraction of aligned residues required\n  identity: number;\n  similarityType: 'sequence-identity' | 'alignment-score';\n};\n\nexport type ImportColumnInfo = {\n  header: string;\n  type: 'Int' | 'Double' | 'String';\n  /** If this column is a sequence column, the type of the sequence */\n  sequenceType?: 'nucleotide' | 'aminoacid';\n};\n\nexport type BlockArgs = {\n  defaultBlockLabel: string;\n  customBlockLabel: string;\n  datasetRef?: PlRef;\n  targetRef?: SUniversalPColumnId;\n  fileHandle?: ImportFileHandle;\n  fileExtension?: string;\n  importColumns?: ImportColumnInfo[];\n  sequenceColumnHeader?: string;\n  selectedColumns: string[];\n  settings: Settings;\n};\n\nexport type UiState = {\n  fileImportError?: string;\n  tableState: PlDataTableStateV2;\n  alignmentModel: PlMultiSequenceAlignmentModel;\n};\n\ntype Column = PColumn<DataInfo<TreeNodeAccessor> | TreeNodeAccessor | PColumnValues>;\n\ntype Columns = {\n  props: Column[];\n};\n\nfunction getColumns(ctx: RenderCtxLegacy<BlockArgs, UiState>): Columns | undefined {\n  const anchor = ctx.args.datasetRef;\n  if (anchor === undefined)\n    return undefined;\n\n  const anchorSpec = ctx.resultPool.getPColumnSpecByRef(anchor);\n  if (anchorSpec === undefined)\n    return undefined;\n\n  // all clone properties\n  const props = (ctx.resultPool.getAnchoredPColumns(\n    { main: anchor },\n    [\n      {\n        axes: [{ anchor: 'main', idx: 1 }],\n      },\n    ]) ?? [])\n    .filter((p) => p.spec.annotations?.['pl7.app/sequence/isAnnotation'] !== 'true');\n\n  return {\n    props: props,\n  };\n}\n\nexport const model = BlockModel.create()\n\n  .withArgs<BlockArgs>({\n    defaultBlockLabel: getDefaultBlockLabel({\n      similarityType: 'alignment-score',\n      identity: 0.9,\n      coverageThreshold: 0.95,\n    }),\n    customBlockLabel: '',\n    settings: {\n      coverageThreshold: 0.95, // default value matching MMseqs2 default\n      identity: 0.9,\n      similarityType: 'alignment-score',\n    },\n    selectedColumns: [],\n  })\n\n  .withUiState<UiState>({\n    tableState: createPlDataTableStateV2(),\n    alignmentModel: {},\n  })\n\n  .argsValid((ctx) =>\n    ctx.args.datasetRef !== undefined\n    && ctx.args.fileHandle !== undefined\n    && ctx.args.importColumns !== undefined\n    && ctx.args.sequenceColumnHeader !== undefined\n    && ctx.args.targetRef !== undefined\n    && ctx.uiState.fileImportError === undefined,\n  )\n\n  .output('datasetOptions', (ctx) =>\n    ctx.resultPool.getOptions([{\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/clonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }, {\n      axes: [\n        { name: 'pl7.app/sampleId' },\n        { name: 'pl7.app/vdj/scClonotypeKey' },\n      ],\n      annotations: { 'pl7.app/isAnchor': 'true' },\n    }], { refsWithEnrichments: true }),\n  )\n\n  .output('targetOptions', (ctx) => {\n    const ref = ctx.args.datasetRef;\n    if (ref === undefined) return undefined;\n\n    const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === 'pl7.app/vdj/scClonotypeKey';\n    const sequenceMatchers = [];\n    // const allowedFeatures = ['CDR1', 'CDR2', 'CDR3', 'FR1', 'FR2',\n    //   'FR3', 'FR4', 'VDJRegion'];\n    // for (const feature of allowedFeatures) {\n    if (isSingleCell) {\n      sequenceMatchers.push({\n        axes: [{ anchor: 'main', idx: 1 }],\n        name: 'pl7.app/vdj/sequence',\n        domain: {\n          // 'pl7.app/vdj/feature': feature,\n          'pl7.app/vdj/scClonotypeChain/index': 'primary',\n        },\n      });\n    } else {\n      sequenceMatchers.push({\n        axes: [{ anchor: 'main', idx: 1 }],\n        name: 'pl7.app/vdj/sequence',\n        domain: {\n          // 'pl7.app/vdj/feature': feature,\n        },\n      });\n    }\n\n    return ctx.resultPool.getCanonicalOptions(\n      { main: ref },\n      sequenceMatchers,\n      {\n        ignoreMissingDomains: true,\n        labelOps: {\n          includeNativeLabel: true,\n        },\n      });\n  })\n\n  .output(\n    'dataImportHandle',\n    (ctx) => ctx.outputs?.resolve('dataImportHandle')?.getImportProgress(),\n    { isActive: true },\n  )\n\n  .outputWithStatus('table', (ctx) => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    return createPlDataTableV2(\n      ctx,\n      cols,\n      ctx.uiState.tableState,\n    );\n  })\n\n  .output('pf', (ctx) => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    return createPFrameForGraphs(ctx, cols);\n  })\n\n  .output('assaySequenceSpec', (ctx): PColumnSpec | undefined => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n    // Return only sequence column\n    return cols.find((c) => c.spec.name === 'pl7.app/vdj/sequence'\n      && c.spec.axesSpec[0].name === 'pl7.app/vdj/assay/sequenceId')?.spec;\n  })\n\n  .output('msaPf', (ctx) => {\n    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {\n      return undefined;\n    }\n    const cols = ctx.outputs?.resolve('table')?.getPColumns();\n    if (cols === undefined)\n      return undefined;\n\n    const msaCols = ctx.outputs?.resolve('assayLinkerPframe')?.getPColumns();\n    if (!msaCols) return undefined;\n\n    const columns = getColumns(ctx);\n    if (columns === undefined) {\n      return undefined;\n    }\n\n    return createPFrameForGraphs(ctx, [...msaCols, ...cols, ...columns.props]);\n  })\n\n  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)\n\n  .title(() => 'Immune Assay Data')\n\n  .subtitle((ctx) => ctx.args.customBlockLabel || ctx.args.defaultBlockLabel)\n\n  .sections((_ctx) => ([\n    { type: 'link', href: '/', label: 'Main' },\n  ]))\n\n  .done(2);\n\nexport { getDefaultBlockLabel } from 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package/dist/label.cjs

@@ -0,0 +1,22 @@
+'use strict';
+
+function getDefaultBlockLabel(data) {
+    const parts = [];
+    // Add file name if available
+    if (data.fileName) {
+        parts.push(data.fileName);
+    }
+    // Add similarity type label
+    const similarityLabel = data.similarityType === 'alignment-score' ? 'BLOSUM' : 'Exact Match';
+    if (similarityLabel) {
+        parts.push(similarityLabel);
+    }
+    // Add identity threshold
+    parts.push(`ident:${data.identity}`);
+    // Add coverage threshold
+    parts.push(`cov:${data.coverageThreshold}`);
+    return parts.filter(Boolean).join(', ');
+}
+
+exports.getDefaultBlockLabel = getDefaultBlockLabel;
+//# sourceMappingURL=label.cjs.map

package/dist/label.cjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"label.cjs","sources":["../src/label.ts"],"sourcesContent":["export function getDefaultBlockLabel(data: {\n  fileName?: string;\n  similarityType: 'alignment-score' | 'sequence-identity';\n  identity: number;\n  coverageThreshold: number;\n}) {\n  const parts: string[] = [];\n\n  // Add file name if available\n  if (data.fileName) {\n    parts.push(data.fileName);\n  }\n\n  // Add similarity type label\n  const similarityLabel = data.similarityType === 'alignment-score' ? 'BLOSUM' : 'Exact Match';\n  if (similarityLabel) {\n    parts.push(similarityLabel);\n  }\n\n  // Add identity threshold\n  parts.push(`ident:${data.identity}`);\n\n  // Add coverage threshold\n  parts.push(`cov:${data.coverageThreshold}`);\n\n  return parts.filter(Boolean).join(', ');\n}\n"],"names":[],"mappings":";;AAAM,SAAU,oBAAoB,CAAC,IAKpC,EAAA;IACC,MAAM,KAAK,GAAa,EAAE;;AAG1B,IAAA,IAAI,IAAI,CAAC,QAAQ,EAAE;AACjB,QAAA,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC;IAC3B;;AAGA,IAAA,MAAM,eAAe,GAAG,IAAI,CAAC,cAAc,KAAK,iBAAiB,GAAG,QAAQ,GAAG,aAAa;IAC5F,IAAI,eAAe,EAAE;AACnB,QAAA,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC;IAC7B;;IAGA,KAAK,CAAC,IAAI,CAAC,CAAA,MAAA,EAAS,IAAI,CAAC,QAAQ,CAAA,CAAE,CAAC;;IAGpC,KAAK,CAAC,IAAI,CAAC,CAAA,IAAA,EAAO,IAAI,CAAC,iBAAiB,CAAA,CAAE,CAAC;IAE3C,OAAO,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;AACzC;;;;"}

package/dist/label.d.ts

@@ -0,0 +1,7 @@
+export declare function getDefaultBlockLabel(data: {
+    fileName?: string;
+    similarityType: 'alignment-score' | 'sequence-identity';
+    identity: number;
+    coverageThreshold: number;
+}): string;
+//# sourceMappingURL=label.d.ts.map

package/dist/label.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"label.d.ts","sourceRoot":"","sources":["../src/label.ts"],"names":[],"mappings":"AAAA,wBAAgB,oBAAoB,CAAC,IAAI,EAAE;IACzC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,iBAAiB,GAAG,mBAAmB,CAAC;IACxD,QAAQ,EAAE,MAAM,CAAC;IACjB,iBAAiB,EAAE,MAAM,CAAC;CAC3B,UAqBA"}

package/dist/label.js

@@ -0,0 +1,20 @@
+function getDefaultBlockLabel(data) {
+    const parts = [];
+    // Add file name if available
+    if (data.fileName) {
+        parts.push(data.fileName);
+    }
+    // Add similarity type label
+    const similarityLabel = data.similarityType === 'alignment-score' ? 'BLOSUM' : 'Exact Match';
+    if (similarityLabel) {
+        parts.push(similarityLabel);
+    }
+    // Add identity threshold
+    parts.push(`ident:${data.identity}`);
+    // Add coverage threshold
+    parts.push(`cov:${data.coverageThreshold}`);
+    return parts.filter(Boolean).join(', ');
+}
+
+export { getDefaultBlockLabel };
+//# sourceMappingURL=label.js.map

package/dist/label.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"label.js","sources":["../src/label.ts"],"sourcesContent":["export function getDefaultBlockLabel(data: {\n  fileName?: string;\n  similarityType: 'alignment-score' | 'sequence-identity';\n  identity: number;\n  coverageThreshold: number;\n}) {\n  const parts: string[] = [];\n\n  // Add file name if available\n  if (data.fileName) {\n    parts.push(data.fileName);\n  }\n\n  // Add similarity type label\n  const similarityLabel = data.similarityType === 'alignment-score' ? 'BLOSUM' : 'Exact Match';\n  if (similarityLabel) {\n    parts.push(similarityLabel);\n  }\n\n  // Add identity threshold\n  parts.push(`ident:${data.identity}`);\n\n  // Add coverage threshold\n  parts.push(`cov:${data.coverageThreshold}`);\n\n  return parts.filter(Boolean).join(', ');\n}\n"],"names":[],"mappings":"AAAM,SAAU,oBAAoB,CAAC,IAKpC,EAAA;IACC,MAAM,KAAK,GAAa,EAAE;;AAG1B,IAAA,IAAI,IAAI,CAAC,QAAQ,EAAE;AACjB,QAAA,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC;IAC3B;;AAGA,IAAA,MAAM,eAAe,GAAG,IAAI,CAAC,cAAc,KAAK,iBAAiB,GAAG,QAAQ,GAAG,aAAa;IAC5F,IAAI,eAAe,EAAE;AACnB,QAAA,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC;IAC7B;;IAGA,KAAK,CAAC,IAAI,CAAC,CAAA,MAAA,EAAS,IAAI,CAAC,QAAQ,CAAA,CAAE,CAAC;;IAGpC,KAAK,CAAC,IAAI,CAAC,CAAA,IAAA,EAAO,IAAI,CAAC,iBAAiB,CAAA,CAAE,CAAC;IAE3C,OAAO,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;AACzC;;;;"}