@platforma-open/milaboratories.top-antibodies 3.2.7 → 4.0.0

package/dist/index.js

@@ -10726,7 +10726,7 @@ function matchToColumnId(match, anchorRef) {
 		column: match.column.id
 	};
 }
-const IN_VIVO_SCORE_COLUMN_ID = "pl7.app/vdj/inVivoScore";
+const REPERTOIRE_SCORE_COLUMN_NAME = "pl7.app/vdj/repertoireScore";
 const IN_VIVO_MUTATION_COLUMNS = /* @__PURE__ */ new Set([
 	"pl7.app/vdj/sequence/fractionCDRMutations",
 	"pl7.app/vdj/sequence/nMutations",
@@ -10736,13 +10736,12 @@ const IN_VIVO_MUTATION_COLUMNS = /* @__PURE__ */ new Set([
 const IN_VIVO_FILTER_SPEC_NAMES = /* @__PURE__ */ new Set([
 	"pl7.app/vdj/isProductive",
 	"pl7.app/developabilityRisk",
-	"pl7.app/vdj/developabilityRisk",
-	"pl7.app/vdj/convergence/fastStar"
+	"pl7.app/vdj/developabilityRisk"
 ]);
 const IN_VIVO_RANKING_SPEC_NAMES = /* @__PURE__ */ new Set([
+	"pl7.app/vdj/repertoireScore",
 	"pl7.app/developabilityScore",
-	"pl7.app/vdj/developabilityScore",
-	"pl7.app/vdj/convergence/nbFreq"
+	"pl7.app/vdj/developabilityScore"
 ]);
 const IN_VITRO_FILTER_SPEC_NAMES = /* @__PURE__ */ new Set([
 	"pl7.app/vdj/isProductive",
@@ -10839,23 +10838,20 @@ function computeDefaultFilters(scores, anchorRef) {
 }
 function computePresets(scores, defaultFilters, anchorRef, anchorSpec) {
 	const isPeptide = anchorSpec.axesSpec[1]?.name === "pl7.app/variantKey";
-	const hasInVivoScore = [...IN_VIVO_MUTATION_COLUMNS].every((name) => scores.some((s) => s.column.spec.name === name));
+	const repertoireScore = scores.find((s) => s.column.spec.name === REPERTOIRE_SCORE_COLUMN_NAME);
+	const hasRepertoireScore = repertoireScore !== void 0;
 	const isEnrichmentColumn = (name) => name.startsWith("pl7.app/enrichment") || name.startsWith("pl7.app/vdj/enrichment");
 	const hasEnrichmentScores = scores.some((s) => isEnrichmentColumn(s.column.spec.name));
-	const detectedPreset = isPeptide ? "peptide" : hasInVivoScore ? "in-vivo" : hasEnrichmentScores ? "in-vitro" : void 0;
-	const defaultRankingOrder = scores.filter((s) => s.column.spec.valueType !== "String").filter((s) => !hasInVivoScore || !IN_VIVO_MUTATION_COLUMNS.has(s.column.spec.name)).map((s) => ({
+	const detectedPreset = isPeptide ? "peptide" : hasRepertoireScore ? "in-vivo" : hasEnrichmentScores ? "in-vitro" : void 0;
+	const defaultRankingOrder = scores.filter((s) => s.column.spec.valueType !== "String").filter((s) => !hasRepertoireScore || s.column.spec.name !== "pl7.app/vdj/repertoireScore").filter((s) => !hasRepertoireScore || !IN_VIVO_MUTATION_COLUMNS.has(s.column.spec.name)).map((s) => ({
 		id: `default-rank-${s.column.id}`,
 		value: matchToColumnId(s, anchorRef),
 		rankingOrder: s.column.spec.annotations?.["pl7.app/score/rankingOrder"] ?? "decreasing",
 		isExpanded: false
 	}));
-	if (hasInVivoScore) defaultRankingOrder.unshift({
-		value: {
-			anchorRef,
-			anchorName: "main",
-			column: IN_VIVO_SCORE_COLUMN_ID
-		},
-		rankingOrder: "decreasing"
+	if (repertoireScore) defaultRankingOrder.unshift({
+		value: matchToColumnId(repertoireScore, anchorRef),
+		rankingOrder: repertoireScore.column.spec.annotations?.["pl7.app/score/rankingOrder"] ?? "decreasing"
 	});
 	const specNameByColumnId = new Map(scores.map((s) => [matchToColumnId(s, anchorRef).column, s.column.spec.name]));
 	const inVitroFilters = defaultFilters.filter((f) => {
@@ -10893,13 +10889,12 @@ function computePresets(scores, defaultFilters, anchorRef, anchorSpec) {
 	});
 	return {
 		defaultRankingOrder,
-		hasInVivoScore,
+		hasRepertoireScore,
 		hasEnrichmentScores,
 		detectedPreset,
 		inVivoDefaults: {
 			rankingOrder: defaultRankingOrder.filter((r) => {
 				const col = r.value?.column;
-				if (col === "pl7.app/vdj/inVivoScore") return true;
 				if (col === void 0) return false;
 				const specName = specNameByColumnId.get(col);
 				return specName !== void 0 && IN_VIVO_RANKING_SPEC_NAMES.has(specName);
@@ -11111,23 +11106,14 @@ const platforma$1 = BlockModelV3.create(blockDataModel).args((data) => {
 	const inputAnchor = getInputAnchorRef(ctx.data);
 	const result = buildCollection(ctx, inputAnchor);
 	if (!result) return void 0;
-	const options = deriveLabels(result.collection.findColumns({
-		mode: "enrichment",
-		exclude: commonExcludeSelectors
-	}).filter((m) => isSelectableMatch(m, result.sampleAxisName) && m.column.spec.valueType !== "String"), (m) => m.column.spec, { includeNativeLabel: true }).map(({ value, label }) => ({
-		label,
-		value: matchToColumnId(value, inputAnchor)
-	}));
-	if (result.meta.hasInVivoScore) options.unshift({
-		label: "In Vivo Score",
-		value: {
-			anchorRef: inputAnchor,
-			anchorName: "main",
-			column: IN_VIVO_SCORE_COLUMN_ID
-		}
-	});
 	return {
-		options,
+		options: deriveLabels(result.collection.findColumns({
+			mode: "enrichment",
+			exclude: commonExcludeSelectors
+		}).filter((m) => isSelectableMatch(m, result.sampleAxisName) && m.column.spec.valueType !== "String"), (m) => m.column.spec, { includeNativeLabel: true }).map(({ value, label }) => ({
+			label,
+			value: matchToColumnId(value, inputAnchor)
+		})),
 		defaults: result.meta.defaultRankingOrder,
 		inVivoDefaults: result.meta.inVivoDefaults.rankingOrder,
 		inVitroDefaults: result.meta.inVitroDefaults.rankingOrder,
@@ -11138,7 +11124,7 @@ const platforma$1 = BlockModelV3.create(blockDataModel).args((data) => {
 	if (!result) return void 0;
 	return {
 		detectedPreset: result.meta.detectedPreset,
-		hasInVivoScore: result.meta.hasInVivoScore,
+		hasRepertoireScore: result.meta.hasRepertoireScore,
 		hasEnrichmentScores: result.meta.hasEnrichmentScores
 	};
 }, { retentive: true }).outputWithStatus("pf", (ctx) => {
@@ -11275,7 +11261,7 @@ const platforma$1 = BlockModelV3.create(blockDataModel).args((data) => {
 			],
 			visibility: [
 				{
-					match: (spec) => spec.name === "pl7.app/ranking-order" || spec.name === "pl7.app/vdj/inVivoScore" || isFilterOrRank(spec) || spec.name === Annotation.Label && spec.axesSpec.length === 1 && (spec.axesSpec[0].name === "pl7.app/vdj/clonotypeKey" || spec.axesSpec[0].name === "pl7.app/vdj/scClonotypeKey" || spec.axesSpec[0].name === "pl7.app/variantKey") || spec.annotations?.["pl7.app/vdj/isAssemblingFeature"] === "true" && spec.annotations?.["pl7.app/vdj/isMainSequence"] === "true" && spec.domain?.["pl7.app/alphabet"] === "aminoacid" || spec.annotations?.["pl7.app/isAssemblingFeature"] === "true" && spec.annotations?.["pl7.app/isMainSequence"] === "true" && spec.domain?.["pl7.app/alphabet"] === "aminoacid" || kabatEnabled && spec.name.startsWith("pl7.app/vdj/kabatSequence"),
+					match: (spec) => spec.name === "pl7.app/ranking-order" || isFilterOrRank(spec) || spec.name === Annotation.Label && spec.axesSpec.length === 1 && (spec.axesSpec[0].name === "pl7.app/vdj/clonotypeKey" || spec.axesSpec[0].name === "pl7.app/vdj/scClonotypeKey" || spec.axesSpec[0].name === "pl7.app/variantKey") || spec.annotations?.["pl7.app/vdj/isAssemblingFeature"] === "true" && spec.annotations?.["pl7.app/vdj/isMainSequence"] === "true" && spec.domain?.["pl7.app/alphabet"] === "aminoacid" || spec.annotations?.["pl7.app/isAssemblingFeature"] === "true" && spec.annotations?.["pl7.app/isMainSequence"] === "true" && spec.domain?.["pl7.app/alphabet"] === "aminoacid" || kabatEnabled && spec.name.startsWith("pl7.app/vdj/kabatSequence"),
 					visibility: "default"
 				},
 				{