@platforma-sdk/ui-vue 1.45.35 → 1.45.36

package/dist/components/PlMultiSequenceAlignment/Toolbar.vue2.js

@@ -1,228 +0,0 @@
-import { defineComponent as I, useCssModule as K, ref as S, watchEffect as L, computed as x, createElementBlock as w, openBlock as P, Fragment as M, createElementVNode as r, createVNode as o, normalizeClass as m, unref as t, withModifiers as k, withCtx as s, createTextVNode as a, createCommentVNode as U, createBlock as T, withKeys as C } from "vue";
-import { isJsonEqual as q } from "../../lib/util/helpers/dist/objects.js";
-import { PlDropdownMulti as $, PlDropdown as D, PlBtnGhost as V, PlCheckbox as g, PlSlideModal as G, PlNumberField as b, PlBtnPrimary as A, PlBtnSecondary as F } from "@milaboratories/uikit";
-import { defaultSettings as R } from "./settings.js";
-const H = /* @__PURE__ */ I({
-  __name: "Toolbar",
-  props: {
-    settings: {},
-    sequenceColumnOptions: {},
-    labelColumnOptions: {},
-    colorSchemeOptions: {}
-  },
-  emits: ["updateSettings", "export"],
-  setup(B, { emit: O }) {
-    const n = B, y = O, u = K(), f = S(!1);
-    function d(p, e) {
-      y("updateSettings", { [p]: e });
-    }
-    function v(p, e) {
-      d(
-        "widgets",
-        e ? [...n.settings.widgets, p] : n.settings.widgets.filter((l) => p !== l)
-      );
-    }
-    const i = S({ ...n.settings.alignmentParams });
-    L(() => {
-      i.value = { ...n.settings.alignmentParams };
-    });
-    const N = x(
-      () => !q(n.settings.alignmentParams, i.value)
-    ), E = x(
-      () => !q(n.settings.alignmentParams, R.alignmentParams)
-    );
-    return (p, e) => (P(), w(M, null, [
-      r("div", {
-        class: m(t(u).container)
-      }, [
-        r("div", {
-          class: m(t(u).line)
-        }, [
-          r("div", {
-            class: m(t(u).section)
-          }, [
-            o(t($), {
-              label: "Sequence Columns",
-              "model-value": n.settings.sequenceColumnIds ?? [],
-              options: n.sequenceColumnOptions,
-              clearable: "",
-              "onUpdate:modelValue": e[0] || (e[0] = (l) => d("sequenceColumnIds", l))
-            }, null, 8, ["model-value", "options"]),
-            o(t($), {
-              "model-value": n.settings.labelColumnIds ?? [],
-              label: "Label Columns",
-              options: n.labelColumnOptions,
-              clearable: "",
-              "onUpdate:modelValue": e[1] || (e[1] = (l) => d("labelColumnIds", l))
-            }, null, 8, ["model-value", "options"]),
-            o(t(D), {
-              "model-value": n.settings.colorScheme,
-              label: "Color Scheme",
-              options: n.colorSchemeOptions,
-              "onUpdate:modelValue": e[2] || (e[2] = (l) => d("colorScheme", l))
-            }, null, 8, ["model-value", "options"])
-          ], 2),
-          r("div", {
-            class: m(t(u).buttons)
-          }, [
-            o(t(V), {
-              icon: "settings",
-              onClick: e[3] || (e[3] = k((l) => f.value = !0, ["stop"]))
-            }, {
-              default: s(() => e[19] || (e[19] = [
-                a(" Settings ")
-              ])),
-              _: 1
-            }),
-            o(t(V), {
-              icon: "export",
-              onClick: e[4] || (e[4] = k((l) => y("export"), ["stop"]))
-            }, {
-              default: s(() => e[20] || (e[20] = [
-                a(" Export ")
-              ])),
-              _: 1
-            })
-          ], 2)
-        ], 2),
-        r("div", {
-          class: m(t(u).line)
-        }, [
-          r("div", {
-            class: m(t(u).section)
-          }, [
-            o(t(g), {
-              "model-value": n.settings.widgets.includes("seqLogo"),
-              "onUpdate:modelValue": e[5] || (e[5] = (l) => v("seqLogo", l))
-            }, {
-              default: s(() => e[21] || (e[21] = [
-                a(" Seq logo ")
-              ])),
-              _: 1
-            }, 8, ["model-value"]),
-            o(t(g), {
-              "model-value": n.settings.widgets.includes("consensus"),
-              "onUpdate:modelValue": e[6] || (e[6] = (l) => v("consensus", l))
-            }, {
-              default: s(() => e[22] || (e[22] = [
-                a(" Consensus ")
-              ])),
-              _: 1
-            }, 8, ["model-value"]),
-            o(t(g), {
-              "model-value": !1,
-              disabled: ""
-            }, {
-              default: s(() => e[23] || (e[23] = [
-                a("Navigator")
-              ])),
-              _: 1
-            }),
-            o(t(g), {
-              "model-value": n.settings.widgets.includes("tree"),
-              "onUpdate:modelValue": e[7] || (e[7] = (l) => v("tree", l))
-            }, {
-              default: s(() => e[24] || (e[24] = [
-                a(" Tree ")
-              ])),
-              _: 1
-            }, 8, ["model-value"]),
-            o(t(g), {
-              "model-value": n.settings.widgets.includes("legend"),
-              disabled: n.settings.colorScheme.type === "no-color",
-              "onUpdate:modelValue": e[8] || (e[8] = (l) => v("legend", l))
-            }, {
-              default: s(() => e[25] || (e[25] = [
-                a(" Legend ")
-              ])),
-              _: 1
-            }, 8, ["model-value", "disabled"])
-          ], 2)
-        ], 2)
-      ], 2),
-      o(t(G), {
-        modelValue: f.value,
-        "onUpdate:modelValue": e[18] || (e[18] = (l) => f.value = l)
-      }, {
-        title: s(() => e[26] || (e[26] = [
-          a("Settings")
-        ])),
-        default: s(() => [
-          o(t(b), {
-            modelValue: i.value.gpo,
-            "onUpdate:modelValue": e[9] || (e[9] = (l) => i.value.gpo = l),
-            label: "Gap open penalty",
-            step: 0.1,
-            onKeyup: e[10] || (e[10] = C((l) => d("alignmentParams", i.value), ["enter"]))
-          }, {
-            tooltip: s(() => e[27] || (e[27] = [
-              a(" Penalty score assigned to the introduction of a gap in the alignment ")
-            ])),
-            _: 1
-          }, 8, ["modelValue"]),
-          o(t(b), {
-            modelValue: i.value.gpe,
-            "onUpdate:modelValue": e[11] || (e[11] = (l) => i.value.gpe = l),
-            label: "Gap extension penalty",
-            step: 0.1,
-            onKeyup: e[12] || (e[12] = C((l) => d("alignmentParams", i.value), ["enter"]))
-          }, {
-            tooltip: s(() => e[28] || (e[28] = [
-              a(" Penalty score assigned to each additional residue added to an existing gap ")
-            ])),
-            _: 1
-          }, 8, ["modelValue"]),
-          o(t(b), {
-            modelValue: i.value.tgpe,
-            "onUpdate:modelValue": e[13] || (e[13] = (l) => i.value.tgpe = l),
-            label: "Terminal gap extension penalty",
-            step: 0.1,
-            onKeyup: e[14] || (e[14] = C((l) => d("alignmentParams", i.value), ["enter"]))
-          }, {
-            tooltip: s(() => e[29] || (e[29] = [
-              a(" Penalty score assigned to extending gaps at the ends of sequences ")
-            ])),
-            _: 1
-          }, 8, ["modelValue"]),
-          N.value ? (P(), w("div", {
-            key: 0,
-            class: m(t(u).pendingChanges)
-          }, [
-            o(t(A), {
-              onClick: e[15] || (e[15] = (l) => d("alignmentParams", i.value))
-            }, {
-              default: s(() => e[30] || (e[30] = [
-                a(" Apply ")
-              ])),
-              _: 1
-            }),
-            o(t(V), {
-              onClick: e[16] || (e[16] = (l) => i.value = n.settings.alignmentParams)
-            }, {
-              default: s(() => e[31] || (e[31] = [
-                a(" Cancel ")
-              ])),
-              _: 1
-            })
-          ], 2)) : U("", !0),
-          E.value ? (P(), T(t(F), {
-            key: 1,
-            class: m(t(u).resetButton),
-            icon: "reverse",
-            onClick: e[17] || (e[17] = (l) => d("alignmentParams", void 0))
-          }, {
-            default: s(() => e[32] || (e[32] = [
-              a(" Reset to Default ")
-            ])),
-            _: 1
-          }, 8, ["class"])) : U("", !0)
-        ]),
-        _: 1
-      }, 8, ["modelValue"])
-    ], 64));
-  }
-});
-export {
-  H as default
-};
-//# sourceMappingURL=Toolbar.vue2.js.map

package/dist/components/PlMultiSequenceAlignment/Toolbar.vue2.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"Toolbar.vue2.js","sources":["../../../src/components/PlMultiSequenceAlignment/Toolbar.vue"],"sourcesContent":["<script setup lang=\"ts\">\nimport { isJsonEqual } from '@milaboratories/helpers';\nimport {\n  type ListOptionNormalized,\n  PlBtnGhost,\n  PlBtnPrimary,\n  PlBtnSecondary,\n  PlCheckbox,\n  PlDropdown,\n  PlDropdownMulti,\n  PlNumberField,\n  PlSlideModal,\n} from '@milaboratories/uikit';\nimport type {\n  PlMultiSequenceAlignmentColorSchemeOption as ColorSchemeOption,\n  PlMultiSequenceAlignmentSettings as Settings,\n  PlMultiSequenceAlignmentWidget,\n  PObjectId,\n  PTableColumnId,\n} from '@platforma-sdk/model';\nimport { computed, ref, useCssModule, watchEffect } from 'vue';\nimport { defaultSettings } from './settings';\n\nconst props = defineProps<{\n  settings: Settings;\n  sequenceColumnOptions: ListOptionNormalized<PObjectId>[] | undefined;\n  labelColumnOptions: ListOptionNormalized<PTableColumnId>[] | undefined;\n  colorSchemeOptions: ListOptionNormalized<ColorSchemeOption>[];\n}>();\n\nconst emit = defineEmits<{\n  updateSettings: [Partial<Settings>];\n  export: [];\n}>();\n\nconst classes = useCssModule();\n\nconst settingsOpen = ref(false);\n\nfunction updateSetting<K extends keyof Settings>(\n  key: K,\n  value: Settings[K] | undefined,\n) {\n  emit('updateSettings', { [key]: value });\n}\n\nfunction toggleWidget(\n  widget: PlMultiSequenceAlignmentWidget,\n  checked: boolean,\n) {\n  updateSetting(\n    'widgets',\n    checked\n      ? [...props.settings.widgets, widget]\n      : props.settings.widgets.filter((w) => widget !== w),\n  );\n}\n\nconst alignmentParams = ref({ ...props.settings.alignmentParams });\nwatchEffect(() => {\n  alignmentParams.value = { ...props.settings.alignmentParams };\n});\n\nconst alignmentParamsChangesPending = computed(() =>\n  !isJsonEqual(props.settings.alignmentParams, alignmentParams.value),\n);\n\nconst canResetAlignmentParams = computed(() =>\n  !isJsonEqual(props.settings.alignmentParams, defaultSettings.alignmentParams),\n);\n</script>\n\n<template>\n  <div :class=\"classes.container\">\n    <div :class=\"classes.line\">\n      <div :class=\"classes.section\">\n        <PlDropdownMulti\n          label=\"Sequence Columns\"\n          :model-value=\"props.settings.sequenceColumnIds ?? []\"\n          :options=\"props.sequenceColumnOptions\"\n          clearable\n          @update:model-value=\"event => updateSetting('sequenceColumnIds', event)\"\n        />\n        <PlDropdownMulti\n          :model-value=\"props.settings.labelColumnIds ?? []\"\n          label=\"Label Columns\"\n          :options=\"props.labelColumnOptions\"\n          clearable\n          @update:model-value=\"event => updateSetting('labelColumnIds', event)\"\n        />\n        <PlDropdown\n          :model-value=\"props.settings.colorScheme\"\n          label=\"Color Scheme\"\n          :options=\"props.colorSchemeOptions\"\n          @update:model-value=\"event => updateSetting('colorScheme', event)\"\n        />\n      </div>\n      <div :class=\"classes.buttons\">\n        <PlBtnGhost icon=\"settings\" @click.stop=\"settingsOpen = true\">\n          Settings\n        </PlBtnGhost>\n        <PlBtnGhost icon=\"export\" @click.stop=\"emit('export')\">\n          Export\n        </PlBtnGhost>\n      </div>\n    </div>\n    <div :class=\"classes.line\">\n      <div :class=\"classes.section\">\n        <PlCheckbox\n          :model-value=\"props.settings.widgets.includes('seqLogo')\"\n          @update:model-value=\"event => toggleWidget('seqLogo', event)\"\n        >\n          Seq logo\n        </PlCheckbox>\n        <PlCheckbox\n          :model-value=\"props.settings.widgets.includes('consensus')\"\n          @update:model-value=\"event => toggleWidget('consensus', event)\"\n        >\n          Consensus\n        </PlCheckbox>\n        <PlCheckbox :model-value=\"false\" disabled>Navigator</PlCheckbox>\n        <PlCheckbox\n          :model-value=\"props.settings.widgets.includes('tree')\"\n          @update:model-value=\"event => toggleWidget('tree', event)\"\n        >\n          Tree\n        </PlCheckbox>\n        <PlCheckbox\n          :model-value=\"props.settings.widgets.includes('legend')\"\n          :disabled=\"props.settings.colorScheme.type === 'no-color'\"\n          @update:model-value=\"event => toggleWidget('legend', event)\"\n        >\n          Legend\n        </PlCheckbox>\n      </div>\n    </div>\n  </div>\n  <PlSlideModal v-model=\"settingsOpen\">\n    <template #title>Settings</template>\n    <PlNumberField\n      v-model=\"alignmentParams.gpo\"\n      label=\"Gap open penalty\"\n      :step=\"0.1\"\n      @keyup.enter=\"updateSetting('alignmentParams', alignmentParams)\"\n    >\n      <template #tooltip>\n        Penalty score assigned to the introduction of a gap in the alignment\n      </template>\n    </PlNumberField>\n    <PlNumberField\n      v-model=\"alignmentParams.gpe\"\n      label=\"Gap extension penalty\"\n      :step=\"0.1\"\n      @keyup.enter=\"updateSetting('alignmentParams', alignmentParams)\"\n    >\n      <template #tooltip>\n        Penalty score assigned to each additional residue added to an existing\n        gap\n      </template>\n    </PlNumberField>\n    <PlNumberField\n      v-model=\"alignmentParams.tgpe\"\n      label=\"Terminal gap extension penalty\"\n      :step=\"0.1\"\n      @keyup.enter=\"updateSetting('alignmentParams', alignmentParams)\"\n    >\n      <template #tooltip>\n        Penalty score assigned to extending gaps at the ends of sequences\n      </template>\n    </PlNumberField>\n    <div\n      v-if=\"alignmentParamsChangesPending\"\n      :class=\"classes.pendingChanges\"\n    >\n      <PlBtnPrimary @click=\"updateSetting('alignmentParams', alignmentParams)\">\n        Apply\n      </PlBtnPrimary>\n      <PlBtnGhost @click=\"alignmentParams = props.settings.alignmentParams\">\n        Cancel\n      </PlBtnGhost>\n    </div>\n    <PlBtnSecondary\n      v-if=\"canResetAlignmentParams\"\n      :class=\"classes.resetButton\"\n      icon=\"reverse\"\n      @click=\"updateSetting('alignmentParams', undefined)\"\n    >\n      Reset to Default\n    </PlBtnSecondary>\n  </PlSlideModal>\n</template>\n\n<style module>\n.container {\n  display: flex;\n  flex-direction: column;\n  gap: 24px;\n}\n\n.line {\n  display: flex;\n  justify-content: space-between;\n}\n\n.section {\n  display: flex;\n  flex-wrap: wrap;\n  gap: 24px;\n}\n\n.buttons {\n  display: flex;\n}\n\n.pendingChanges {\n  display: flex;\n  button {\n    min-width: 160px;\n  }\n}\n\n.resetButton {\n  margin-block-start: auto;\n  span {\n    text-transform: none;\n  }\n}\n</style>\n"],"names":["props","__props","emit","__emit","classes","useCssModule","settingsOpen","ref","updateSetting","key","value","toggleWidget","widget","checked","w","alignmentParams","watchEffect","alignmentParamsChangesPending","computed","isJsonEqual","canResetAlignmentParams","defaultSettings"],"mappings":";;;;;;;;;;;;;;AAuBA,UAAMA,IAAQC,GAORC,IAAOC,GAKPC,IAAUC,EAAA,GAEVC,IAAeC,EAAI,EAAK;AAE9B,aAASC,EACPC,GACAC,GACA;AACA,MAAAR,EAAK,kBAAkB,EAAE,CAACO,CAAG,GAAGC,GAAO;AAAA,IACzC;AAEA,aAASC,EACPC,GACAC,GACA;AACA,MAAAL;AAAA,QACE;AAAA,QACAK,IACI,CAAC,GAAGb,EAAM,SAAS,SAASY,CAAM,IAClCZ,EAAM,SAAS,QAAQ,OAAO,CAACc,MAAMF,MAAWE,CAAC;AAAA,MAAA;AAAA,IAEzD;AAEA,UAAMC,IAAkBR,EAAI,EAAE,GAAGP,EAAM,SAAS,iBAAiB;AACjE,IAAAgB,EAAY,MAAM;AAChB,MAAAD,EAAgB,QAAQ,EAAE,GAAGf,EAAM,SAAS,gBAAA;AAAA,IAC9C,CAAC;AAED,UAAMiB,IAAgCC;AAAA,MAAS,MAC7C,CAACC,EAAYnB,EAAM,SAAS,iBAAiBe,EAAgB,KAAK;AAAA,IAAA,GAG9DK,IAA0BF;AAAA,MAAS,MACvC,CAACC,EAAYnB,EAAM,SAAS,iBAAiBqB,EAAgB,eAAe;AAAA,IAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}

package/dist/components/PlMultiSequenceAlignment/Toolbar.vue3.js

@@ -1,19 +0,0 @@
-(function(){"use strict";try{if(typeof document<"u"){var e=document.createElement("style");e.appendChild(document.createTextNode("._container_ypn45_2{display:flex;flex-direction:column;gap:24px}._line_ypn45_8{display:flex;justify-content:space-between}._section_ypn45_13{display:flex;flex-wrap:wrap;gap:24px}._buttons_ypn45_19,._pendingChanges_ypn45_23{display:flex}._pendingChanges_ypn45_23 button{min-width:160px}._resetButton_ypn45_30{margin-block-start:auto}._resetButton_ypn45_30 span{text-transform:none}")),document.head.appendChild(e)}}catch(n){console.error("vite-plugin-css-injected-by-js",n)}})();
-const n = "_container_ypn45_2", t = "_line_ypn45_8", e = "_section_ypn45_13", s = "_buttons_ypn45_19", o = "_pendingChanges_ypn45_23", _ = "_resetButton_ypn45_30", c = {
-  container: n,
-  line: t,
-  section: e,
-  buttons: s,
-  pendingChanges: o,
-  resetButton: _
-};
-export {
-  s as buttons,
-  n as container,
-  c as default,
-  t as line,
-  o as pendingChanges,
-  _ as resetButton,
-  e as section
-};
-//# sourceMappingURL=Toolbar.vue3.js.map

package/dist/components/PlMultiSequenceAlignment/Toolbar.vue3.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"Toolbar.vue3.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;"}

package/dist/components/PlMultiSequenceAlignment/cell-size.d.ts

@@ -1,4 +0,0 @@
-export declare const cellSize: {
-    inline: number;
-    block: number;
-};

package/dist/components/PlMultiSequenceAlignment/cell-size.js

@@ -1,8 +0,0 @@
-const e = {
-  inline: 20,
-  block: 24
-};
-export {
-  e as cellSize
-};
-//# sourceMappingURL=cell-size.js.map

package/dist/components/PlMultiSequenceAlignment/cell-size.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"cell-size.js","sources":["../../../src/components/PlMultiSequenceAlignment/cell-size.ts"],"sourcesContent":["export const cellSize = {\n  inline: 20,\n  block: 24,\n};\n"],"names":["cellSize"],"mappings":"AAAO,MAAMA,IAAW;AAAA,EACtB,QAAQ;AAAA,EACR,OAAO;AACT;"}

package/dist/components/PlMultiSequenceAlignment/chemical-properties.d.ts

@@ -1,44 +0,0 @@
-import { HighlightLegend, ResidueCounts } from './types';
-export declare function highlightByChemicalProperties({ sequences, residueCounts }: {
-    sequences: string[];
-    residueCounts: ResidueCounts;
-}): {
-    blob: Blob;
-    legend: HighlightLegend;
-};
-declare const chemicalPropertiesColorScheme: {
-    hydrophobic: {
-        label: string;
-        color: string;
-    };
-    positiveCharge: {
-        label: string;
-        color: string;
-    };
-    negativeCharge: {
-        label: string;
-        color: string;
-    };
-    polar: {
-        label: string;
-        color: string;
-    };
-    cysteine: {
-        label: string;
-        color: string;
-    };
-    glycine: {
-        label: string;
-        color: string;
-    };
-    proline: {
-        label: string;
-        color: string;
-    };
-    aromatic: {
-        label: string;
-        color: string;
-    };
-};
-export type ChemicalCategory = keyof typeof chemicalPropertiesColorScheme;
-export {};

package/dist/components/PlMultiSequenceAlignment/chemical-properties.js

@@ -1,132 +0,0 @@
-function E({ sequences: t, residueCounts: g }) {
-  var C, h, u;
-  const i = [], c = v({
-    residueCounts: g,
-    rowCount: t.length
-  }), n = ((C = t.at(0)) == null ? void 0 : C.length) ?? 0, l = t.length;
-  for (let e = 0; e < n; e += 1)
-    for (let o = 0; o < l; o += 1) {
-      const F = t[o][e], d = (u = (h = c.at(e)) == null ? void 0 : h.find(({ residues: a }) => a.includes(F))) == null ? void 0 : u.category;
-      if (!d) continue;
-      const r = i.at(-1);
-      r && r.category === d && r.column === e && r.start + r.length === o ? r.length += 1 : i.push({ category: d, column: e, start: o, length: 1 });
-    }
-  const s = Map.groupBy(i, ({ category: e }) => e), y = new Blob(
-    function* () {
-      var o;
-      yield `<svg xmlns="http://www.w3.org/2000/svg" viewBox="${`0 0 ${n * 2} ${l}`}" stroke-width="2" preserveAspectRatio="none">`;
-      for (const [F, d] of s) {
-        const r = (o = P[F]) == null ? void 0 : o.color;
-        if (!r) continue;
-        yield `<path stroke="${r}" d="`;
-        let a = 0, A = 0;
-        for (const { column: m, start: b, length: f } of d)
-          yield `m${m * 2 + 1 - a},${b - A}v${f}`, a = m * 2 + 1, A = b + f;
-        yield '"/>';
-      }
-      yield "</svg>";
-    }().toArray(),
-    { type: "image/svg+xml" }
-  ), p = Object.fromEntries(
-    Object.entries(P).filter(([e]) => s.has(e))
-  );
-  return { blob: y, legend: p };
-}
-const v = ({ residueCounts: t, rowCount: g }) => t.map((i) => {
-  const c = /* @__PURE__ */ new Set();
-  return D.filter(
-    ({ residues: n, rules: l }) => n.split("").some((s) => s in i) && (!l || l.split("").map(
-      (s) => [s, w[s]]
-    ).some(([s, { residues: y, threshold: p }]) => {
-      if (c.has(s)) return !0;
-      const h = y.split("").reduce((u, e) => u + (i[e] ?? 0), 0) >= g * p;
-      return h && c.add(s), h;
-    }))
-  );
-}), P = {
-  hydrophobic: {
-    label: "Hydrophobic",
-    color: "#99CCFF"
-  },
-  positiveCharge: {
-    label: "Positive Charged",
-    color: "#FFA2A3"
-  },
-  negativeCharge: {
-    label: "Negative Charged",
-    color: "#C1ADFF"
-  },
-  polar: {
-    label: "Polar",
-    color: "#99E099"
-  },
-  cysteine: {
-    label: "Cysteines",
-    color: "#FAAAFA"
-  },
-  glycine: {
-    label: "Glycines",
-    color: "#F7BC5D"
-  },
-  proline: {
-    label: "Prolines",
-    color: "#FFFF8F"
-  },
-  aromatic: {
-    label: "Aromatic",
-    color: "#A2F5FA"
-  }
-}, w = {
-  "%": { residues: "WLVIMAFCYHP", threshold: 0.6 },
-  "#": { residues: "WLVIMAFCYHP", threshold: 0.8 },
-  "-": { residues: "ED", threshold: 0.5 },
-  "+": { residues: "KR", threshold: 0.6 },
-  g: { residues: "G", threshold: 0.5 },
-  n: { residues: "N", threshold: 0.5 },
-  q: { residues: "QE", threshold: 0.5 },
-  p: { residues: "P", threshold: 0.5 },
-  t: { residues: "TS", threshold: 0.5 },
-  A: { residues: "A", threshold: 0.85 },
-  C: { residues: "C", threshold: 0.85 },
-  D: { residues: "D", threshold: 0.85 },
-  E: { residues: "E", threshold: 0.85 },
-  F: { residues: "F", threshold: 0.85 },
-  G: { residues: "G", threshold: 0.85 },
-  H: { residues: "H", threshold: 0.85 },
-  I: { residues: "I", threshold: 0.85 },
-  K: { residues: "K", threshold: 0.85 },
-  L: { residues: "L", threshold: 0.85 },
-  M: { residues: "M", threshold: 0.85 },
-  N: { residues: "N", threshold: 0.85 },
-  P: { residues: "P", threshold: 0.85 },
-  Q: { residues: "Q", threshold: 0.85 },
-  R: { residues: "R", threshold: 0.85 },
-  S: { residues: "S", threshold: 0.85 },
-  T: { residues: "T", threshold: 0.85 },
-  V: { residues: "V", threshold: 0.85 },
-  W: { residues: "W", threshold: 0.85 },
-  Y: { residues: "Y", threshold: 0.85 }
-}, D = [
-  { residues: "G", category: "glycine", rules: "" },
-  { residues: "P", category: "proline", rules: "" },
-  { residues: "T", category: "polar", rules: "tST%#" },
-  { residues: "S", category: "polar", rules: "tST#" },
-  { residues: "N", category: "polar", rules: "nND" },
-  { residues: "Q", category: "polar", rules: "qQE+KR" },
-  // criteria below has to go before the other criteria for C,
-  // otherwise it will never match
-  { residues: "C", category: "cysteine", rules: "C" },
-  { residues: "WLVIMF", category: "hydrophobic", rules: "%#ACFHILMVWYPp" },
-  // below there was an 's' rule too,
-  // but no definition of such rule was provided
-  { residues: "A", category: "hydrophobic", rules: "%#ACFHILMVWYPpTSG" },
-  { residues: "C", category: "hydrophobic", rules: "%#AFHILMVWYSPp" },
-  { residues: "HY", category: "aromatic", rules: "%#ACFHILMVWYPp" },
-  { residues: "E", category: "negativeCharge", rules: "-DEqQ" },
-  { residues: "D", category: "negativeCharge", rules: "-DEnN" },
-  { residues: "KR", category: "positiveCharge", rules: "+KRQ" }
-];
-export {
-  E as highlightByChemicalProperties
-};
-//# sourceMappingURL=chemical-properties.js.map

package/dist/components/PlMultiSequenceAlignment/chemical-properties.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"chemical-properties.js","sources":["../../../src/components/PlMultiSequenceAlignment/chemical-properties.ts"],"sourcesContent":["import type { HighlightLegend, ResidueCounts } from './types';\n\nexport function highlightByChemicalProperties(\n  { sequences, residueCounts }: {\n    sequences: string[];\n    residueCounts: ResidueCounts;\n  },\n): { blob: Blob; legend: HighlightLegend } {\n  const lines: {\n    category: ChemicalCategory;\n    column: number;\n    start: number;\n    length: number;\n  }[] = [];\n  const chemicalProperties = getAlignmentChemicalProperties({\n    residueCounts,\n    rowCount: sequences.length,\n  });\n  const width = sequences.at(0)?.length ?? 0;\n  const height = sequences.length;\n  for (let column = 0; column < width; column += 1) {\n    for (let row = 0; row < height; row += 1) {\n      const residue = sequences[row][column];\n      const category = chemicalProperties\n        .at(column)\n        ?.find(({ residues }) => residues.includes(residue))\n        ?.category;\n      if (!category) continue;\n      const lastLine = lines.at(-1);\n      if (\n        lastLine\n        && lastLine.category === category\n        && lastLine.column === column\n        && lastLine.start + lastLine.length === row\n      ) {\n        lastLine.length += 1;\n      } else {\n        lines.push({ category, column, start: row, length: 1 });\n      }\n    }\n  }\n  const linesByCategory = Map.groupBy(lines, ({ category }) => category);\n  const blob = new Blob(\n    (function*() {\n      const viewBox = `0 0 ${width * 2} ${height}`;\n      yield `<svg xmlns=\"http://www.w3.org/2000/svg\" viewBox=\"${viewBox}\" stroke-width=\"2\" preserveAspectRatio=\"none\">`;\n      for (const [category, lines] of linesByCategory) {\n        const color = chemicalPropertiesColorScheme[category]?.color;\n        if (!color) continue;\n        yield `<path stroke=\"${color}\" d=\"`;\n        let x = 0, y = 0;\n        for (const { column, start, length } of lines) {\n          yield `m${column * 2 + 1 - x},${start - y}v${length}`;\n          x = column * 2 + 1;\n          y = start + length;\n        }\n        yield '\"/>';\n      }\n      yield '</svg>';\n    })().toArray(),\n    { type: 'image/svg+xml' },\n  );\n  const legend = Object.fromEntries(\n    Object.entries(chemicalPropertiesColorScheme)\n      .filter(([color]) => linesByCategory.has(color as ChemicalCategory)),\n  );\n  return { blob, legend };\n}\n\nconst getAlignmentChemicalProperties = (\n  { residueCounts, rowCount }: {\n    residueCounts: ResidueCounts;\n    rowCount: number;\n  },\n): ColumnChemicalProperties[] =>\n  residueCounts.map((column) => {\n    const matchedRules = new Set<string>();\n    return categoryCriterion.filter(({ residues, rules }) =>\n      residues.split('').some((residue) => residue in column)\n      && (!rules || rules.split('').map((ruleName) =>\n        [ruleName, ruleDefinitions[ruleName as RuleName]] as const,\n      ).some(([ruleName, { residues, threshold }]) => {\n        if (matchedRules.has(ruleName)) return true;\n        const groupCount = residues.split('')\n          .reduce((acc, residue) => acc + (column[residue] ?? 0), 0);\n        const matches = groupCount >= rowCount * threshold;\n        if (matches) matchedRules.add(ruleName);\n        return matches;\n      })),\n    );\n  });\n\ntype ColumnChemicalProperties = {\n  residues: string;\n  category: ChemicalCategory;\n}[];\n\nconst chemicalPropertiesColorScheme = {\n  hydrophobic: {\n    label: 'Hydrophobic',\n    color: '#99CCFF',\n  },\n  positiveCharge: {\n    label: 'Positive Charged',\n    color: '#FFA2A3',\n  },\n  negativeCharge: {\n    label: 'Negative Charged',\n    color: '#C1ADFF',\n  },\n  polar: {\n    label: 'Polar',\n    color: '#99E099',\n  },\n  cysteine: {\n    label: 'Cysteines',\n    color: '#FAAAFA',\n  },\n  glycine: {\n    label: 'Glycines',\n    color: '#F7BC5D',\n  },\n  proline: {\n    label: 'Prolines',\n    color: '#FFFF8F',\n  },\n  aromatic: {\n    label: 'Aromatic',\n    color: '#A2F5FA',\n  },\n} satisfies HighlightLegend;\n\nexport type ChemicalCategory = keyof typeof chemicalPropertiesColorScheme;\n\n/*\n * Below taken mostly from\n * https://www.rbvi.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/multalignviewer/colprot.par}\n */\n\nconst ruleDefinitions = {\n  '%': { residues: 'WLVIMAFCYHP', threshold: 0.6 },\n  '#': { residues: 'WLVIMAFCYHP', threshold: 0.8 },\n  '-': { residues: 'ED', threshold: 0.5 },\n  '+': { residues: 'KR', threshold: 0.6 },\n  'g': { residues: 'G', threshold: 0.5 },\n  'n': { residues: 'N', threshold: 0.5 },\n  'q': { residues: 'QE', threshold: 0.5 },\n  'p': { residues: 'P', threshold: 0.5 },\n  't': { residues: 'TS', threshold: 0.5 },\n  'A': { residues: 'A', threshold: 0.85 },\n  'C': { residues: 'C', threshold: 0.85 },\n  'D': { residues: 'D', threshold: 0.85 },\n  'E': { residues: 'E', threshold: 0.85 },\n  'F': { residues: 'F', threshold: 0.85 },\n  'G': { residues: 'G', threshold: 0.85 },\n  'H': { residues: 'H', threshold: 0.85 },\n  'I': { residues: 'I', threshold: 0.85 },\n  'K': { residues: 'K', threshold: 0.85 },\n  'L': { residues: 'L', threshold: 0.85 },\n  'M': { residues: 'M', threshold: 0.85 },\n  'N': { residues: 'N', threshold: 0.85 },\n  'P': { residues: 'P', threshold: 0.85 },\n  'Q': { residues: 'Q', threshold: 0.85 },\n  'R': { residues: 'R', threshold: 0.85 },\n  'S': { residues: 'S', threshold: 0.85 },\n  'T': { residues: 'T', threshold: 0.85 },\n  'V': { residues: 'V', threshold: 0.85 },\n  'W': { residues: 'W', threshold: 0.85 },\n  'Y': { residues: 'Y', threshold: 0.85 },\n};\n\ntype RuleName = keyof typeof ruleDefinitions;\n\nconst categoryCriterion: Criteria[] = [\n  { residues: 'G', category: 'glycine', rules: '' },\n  { residues: 'P', category: 'proline', rules: '' },\n  { residues: 'T', category: 'polar', rules: 'tST%#' },\n  { residues: 'S', category: 'polar', rules: 'tST#' },\n  { residues: 'N', 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package/dist/components/PlMultiSequenceAlignment/data.d.ts

@@ -1,61 +0,0 @@
-import { ListOptionNormalized } from '@milaboratories/uikit';
-import { PColumnIdAndSpec, PFrameHandle, PlMultiSequenceAlignmentColorSchemeOption, PlMultiSequenceAlignmentSettings, PlSelectionModel, PObjectId, PTableColumnId } from '@platforma-sdk/model';
-import { HighlightLegend, ResidueCounts } from './types';
-import type * as PhylogeneticTreeWorker from './phylogenetic-tree.worker';
-export declare const SEQUENCE_LIMIT = 1000;
-export declare const useSequenceColumnsOptions: (paramsGetter: () => {
-    pFrame: PFrameHandle | undefined;
-    sequenceColumnPredicate: (column: PColumnIdAndSpec) => boolean;
-}) => {
-    data: import('vue').Ref<OptionsWithDefaults<PObjectId> | undefined, OptionsWithDefaults<PObjectId> | undefined>;
-    isLoading: import('vue').Ref<boolean, boolean>;
-    error: import('vue').Ref<Error | undefined, Error | undefined>;
-};
-export declare const useLabelColumnsOptions: (paramsGetter: () => {
-    pFrame: PFrameHandle | undefined;
-    sequenceColumnIds: PObjectId[] | undefined;
-}) => {
-    data: import('vue').Ref<OptionsWithDefaults<PTableColumnId> | undefined, OptionsWithDefaults<PTableColumnId> | undefined>;
-    isLoading: import('vue').Ref<boolean, boolean>;
-    error: import('vue').Ref<Error | undefined, Error | undefined>;
-};
-export declare const useMarkupColumnsOptions: (paramsGetter: () => {
-    pFrame: PFrameHandle | undefined;
-    sequenceColumnIds: PObjectId[] | undefined;
-}) => {
-    data: import('vue').Ref<ListOptionNormalized<PObjectId[]>[] | undefined, ListOptionNormalized<PObjectId[]>[] | undefined>;
-    isLoading: import('vue').Ref<boolean, boolean>;
-    error: import('vue').Ref<Error | undefined, Error | undefined>;
-};
-export declare const useMultipleAlignmentData: (paramsGetter: () => {
-    pFrame: PFrameHandle | undefined;
-    sequenceColumnIds: PObjectId[] | undefined;
-    labelColumnIds: PTableColumnId[] | undefined;
-    selection: PlSelectionModel | undefined;
-    colorScheme: PlMultiSequenceAlignmentColorSchemeOption;
-    alignmentParams: PlMultiSequenceAlignmentSettings["alignmentParams"];
-    shouldBuildPhylogeneticTree: boolean;
-}) => {
-    data: import('vue').Ref<MultipleAlignmentData | undefined, MultipleAlignmentData | undefined>;
-    isLoading: import('vue').Ref<boolean, boolean>;
-    error: import('vue').Ref<Error | undefined, Error | undefined>;
-};
-type MultipleAlignmentData = {
-    sequences: {
-        name: string;
-        rows: string[];
-        residueCounts: ResidueCounts;
-        highlightImageUrl?: string;
-    }[];
-    labels: {
-        rows: string[];
-    }[];
-    highlightLegend?: HighlightLegend;
-    phylogeneticTree?: PhylogeneticTreeWorker.TreeNodeData[];
-    exceedsLimit: boolean;
-};
-type OptionsWithDefaults<T> = {
-    options: ListOptionNormalized<T>[];
-    defaults: T[];
-};
-export {};