@platforma-open/milaboratories.clonotype-clustering.model 2.12.1 → 2.13.1

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/clonotype-clustering/clonotype-clustering/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.clonotype-clustering.model@2.12.1 build /home/runner/work/clonotype-clustering/clonotype-clustering/model
+> @platforma-open/milaboratories.clonotype-clustering.model@2.13.1 build /home/runner/work/clonotype-clustering/clonotype-clustering/model
 > tsup && vite build && block-tools build-model
 
 CLI Building entry: src/index.ts
@@ -11,21 +11,21 @@
 CLI Cleaning output folder
 CJS Build start
 ESM Build start
-CJS dist/index.cjs     6.22 KB
-CJS dist/index.cjs.map 15.31 KB
-CJS ⚡️ Build success in 216ms
-ESM dist/index.js     6.23 KB
-ESM dist/index.js.map 15.21 KB
-ESM ⚡️ Build success in 216ms
+CJS dist/index.cjs     6.49 KB
+CJS dist/index.cjs.map 16.05 KB
+CJS ⚡️ Build success in 221ms
+ESM dist/index.js     6.48 KB
+ESM dist/index.js.map 15.96 KB
+ESM ⚡️ Build success in 220ms
 DTS Build start
-DTS ⚡️ Build success in 2845ms
-DTS dist/index.d.cts 5.81 KB
-DTS dist/index.d.ts  5.81 KB
+DTS ⚡️ Build success in 2885ms
+DTS dist/index.d.cts 5.85 KB
+DTS dist/index.d.ts  5.85 KB
 vite v6.3.5 building for production...
 transforming...
-✓ 68 modules transformed.
+✓ 69 modules transformed.
 rendering chunks...
 computing gzip size...
-dist/bundle.js  241.84 kB │ gzip: 46.03 kB │ map: 515.03 kB
-dist/bundle.js  257.09 kB │ gzip: 46.76 kB │ map: 516.70 kB
-✓ built in 1.03s
+dist/bundle.js  242.49 kB │ gzip: 46.09 kB │ map: 516.76 kB
+dist/bundle.js  257.73 kB │ gzip: 46.83 kB │ map: 518.42 kB
+✓ built in 1.30s

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.clonotype-clustering.model
 
+## 2.13.1
+
+### Patch Changes
+
+- 823ff69: Full SDK update
+
+## 2.13.0
+
+### Minor Changes
+
+- c722cfb: Included input sequence trimming option for clustering
+
 ## 2.12.1
 
 ### Patch Changes

package/dist/bundle.js

@@ -3966,13 +3966,16 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
   });
   z.object({
     /** Included left border. */
-    from: z.number(),
+    from: z.number().min(0),
     /** Excluded right border. */
-    to: z.number()
+    to: z.number().min(1)
   });
   function assertNever(x) {
     throw new Error("Unexpected object: " + x);
   }
+  function uniqueBy(array, makeId) {
+    return [...new Map(array.map((e) => [makeId(e), e])).values()];
+  }
   function isDataInfo(value) {
     if (!value || typeof value !== "object") {
       return false;
@@ -4229,14 +4232,6 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
   function parseJson(value) {
     return JSON.parse(value);
   }
-  const ValueType = {
-    Int: "Int",
-    Long: "Long",
-    Float: "Float",
-    Double: "Double",
-    String: "String",
-    Bytes: "Bytes"
-  };
   function readMetadata(metadata, key) {
     return metadata == null ? void 0 : metadata[key];
   }
@@ -4265,6 +4260,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       IsVirtual: "pl7.app/graph/isVirtual"
     },
     HideDataFromUi: "pl7.app/hideDataFromUi",
+    HideDataFromGraphs: "pl7.app/hideDataFromGraphs",
     IsLinkerColumn: "pl7.app/isLinkerColumn",
     Label: "pl7.app/label",
     Max: "pl7.app/max",
@@ -4282,21 +4278,15 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     },
     Trace: "pl7.app/trace"
   };
-  const AxisSpec = z.object({
-    type: z.nativeEnum(ValueType),
-    name: z.string(),
-    domain: z.record(z.string(), z.string()).optional(),
-    annotations: z.record(z.string(), z.string()).optional(),
-    parentAxes: z.array(z.number()).optional()
-  }).passthrough();
   const AnnotationJson = {
     [Annotation.DiscreteValues]: z.array(z.string()).or(z.array(z.number())),
     [Annotation.Graph.IsVirtual]: z.boolean(),
     [Annotation.HideDataFromUi]: z.boolean(),
+    [Annotation.HideDataFromGraphs]: z.boolean(),
     [Annotation.IsLinkerColumn]: z.boolean(),
     [Annotation.Max]: z.number(),
     [Annotation.Min]: z.number(),
-    [Annotation.Parents]: z.array(AxisSpec),
+    [Annotation.Parents]: z.array(z.string()),
     [Annotation.Sequence.Annotation.Mapping]: z.record(z.string(), z.string()),
     [Annotation.Sequence.IsAnnotation]: z.boolean(),
     [Annotation.Table.OrderPriority]: z.number(),
@@ -4416,7 +4406,8 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       if (axis.parentAxes) {
         modifiedAxis.parentAxesSpec = axis.parentAxes.map((idx2) => modifiedAxes[idx2]);
       } else {
-        modifiedAxis.parentAxesSpec = getNormalizedAxesList(parseParentsFromAnnotations(axis));
+        const parents = parseParentsFromAnnotations(axis).map((name) => modifiedAxes.find((axis2) => axis2.name === name));
+        modifiedAxis.parentAxesSpec = parents.some((p) => p === void 0) ? [] : parents;
         (_a = modifiedAxis.annotations) == null ? true : delete _a[Annotation.Parents];
       }
     });
@@ -6522,7 +6513,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       this.ctx.logError(msg);
     }
   }
-  var version = "1.42.20";
+  var version = "1.42.51";
   const PlatformaSDKVersion = version;
   function isConfigLambda(cfgOrFh) {
     return cfgOrFh.__renderLambda === true;
@@ -6695,6 +6686,9 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     };
   }
   function upgradePlDataTableStateV2(state) {
+    if (!state) {
+      return createPlDataTableStateV2();
+    }
     if (!("version" in state)) {
       state = createPlDataTableStateV2();
     }
@@ -6843,9 +6837,6 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
   function isColumnOptional(spec) {
     return readAnnotation(spec, Annotation.Table.Visibility) === "optional";
   }
-  function uniqueBy(array, makeId) {
-    return [...new Map(array.map((e) => [makeId(e), e])).values()];
-  }
   function createPlDataTableV2(ctx, inputColumns, tableState, ops) {
     if (inputColumns.length === 0)
       return void 0;
@@ -6949,6 +6940,9 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
   function isLinkerColumn(column) {
     return !!readAnnotationJson(column, Annotation.IsLinkerColumn);
   }
+  function isHiddenFromGraphColumn(column) {
+    return !!readAnnotationJson(column, Annotation.HideDataFromGraphs);
+  }
   function getAvailableWithLinkersAxes(linkerColumns, blockAxes) {
     const linkerMap = LinkerMap.fromColumns(linkerColumns.map(getColumnIdAndSpec));
     const startKeys = [];
@@ -7093,14 +7087,9 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
       blockAxes.set(...item);
       allAxes.set(...item);
     }
-    const compatibleWithoutLabels = (columns.getColumns((spec) => spec.axesSpec.some((axisSpec) => {
+    let compatibleWithoutLabels = (columns.getColumns((spec) => !isHiddenFromGraphColumn(spec) && spec.axesSpec.some((axisSpec) => {
       const axisId = getAxisId(axisSpec);
-      for (const selectorAxisSpec of blockAxes.values()) {
-        if (matchAxisId(getAxisId(selectorAxisSpec), axisId)) {
-          return true;
-        }
-      }
-      return false;
+      return Array.from(blockAxes.values()).some((selectorAxisSpec) => matchAxisId(getAxisId(selectorAxisSpec), axisId));
     }), { dontWaitAllData: true, overrideLabelAnnotation: false }) ?? []).filter((column) => !isLabelColumn(column.spec));
     if (!allColumnsReady(compatibleWithoutLabels)) {
       return void 0;
@@ -7111,14 +7100,13 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
         allAxes.set(canonicalizeJson(aid), spec);
       }
     }
-    const compatibleLabels = (columns.getColumns((spec) => spec.axesSpec.some((axisSpec) => {
+    compatibleWithoutLabels = (columns.getColumns((spec) => !isHiddenFromGraphColumn(spec) && spec.axesSpec.every((axisSpec) => {
       const axisId = getAxisId(axisSpec);
-      for (const selectorAxisSpec of allAxes.values()) {
-        if (matchAxisId(getAxisId(selectorAxisSpec), axisId)) {
-          return true;
-        }
-      }
-      return false;
+      return Array.from(allAxes.values()).some((selectorAxisSpec) => matchAxisId(getAxisId(selectorAxisSpec), axisId));
+    }), { dontWaitAllData: true, overrideLabelAnnotation: false }) ?? []).filter((column) => !isLabelColumn(column.spec));
+    const compatibleLabels = (columns.getColumns((spec) => !isHiddenFromGraphColumn(spec) && spec.axesSpec.some((axisSpec) => {
+      const axisId = getAxisId(axisSpec);
+      return Array.from(allAxes.values()).some((selectorAxisSpec) => matchAxisId(getAxisId(selectorAxisSpec), axisId));
     }), { dontWaitAllData: true, overrideLabelAnnotation: false }) ?? []).filter((column) => isLabelColumn(column.spec));
     if (!allColumnsReady(compatibleLabels)) {
       return void 0;
@@ -7198,8 +7186,12 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     similarityType: "sequence-identity",
     coverageThreshold: 0.8,
     // default value matching MMseqs2 default
-    coverageMode: 0
+    coverageMode: 0,
     // default to coverage of query and target
+    trimStart: 0,
+    // default to no trimming from start
+    trimEnd: 0
+    // default to no trimming from end
   }).withUiState({
     title: "Clonotype Clustering",
     tableState: createPlDataTableStateV2(),
@@ -7328,6 +7320,10 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     var _a, _b;
     const msaCols = (_b = (_a = ctx.outputs) == null ? void 0 : _a.resolve("msaPf")) == null ? void 0 : _b.getPColumns();
     if (!msaCols) return void 0;
+    const trimEnabled = (ctx.args.trimStart ?? 0) > 0 || (ctx.args.trimEnd ?? 0) > 0;
+    if (trimEnabled) {
+      return createPFrameForGraphs(ctx, msaCols);
+    }
     const datasetRef = ctx.args.datasetRef;
     if (datasetRef === void 0)
       return void 0;
@@ -7410,7 +7406,7 @@ var __publicField = (obj, key, value) => __defNormalProp(obj, typeof key !== "sy
     { type: "link", href: "/", label: "Main" },
     { type: "link", href: "/bubble", label: "Top Clusters Plot" },
     { type: "link", href: "/histogram", label: "Cluster Size Histogram" }
-  ]).done();
+  ]).done(2);
   exports2.model = model;
   Object.defineProperty(exports2, Symbol.toStringTag, { value: "Module" });
 });