@datagrok-libraries/bio 5.65.4 → 6.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/package.json +4 -5
- package/src/helm/consts.d.ts +12 -3
- package/src/helm/consts.d.ts.map +1 -1
- package/src/helm/consts.js +22 -2
- package/src/helm/consts.js.map +1 -1
- package/src/helm/helm-helper.d.ts.map +1 -1
- package/src/helm/helm-helper.js +2 -0
- package/src/helm/helm-helper.js.map +1 -1
- package/src/helm/types.d.ts +66 -24
- package/src/helm/types.d.ts.map +1 -1
- package/src/monomer-works/consts.d.ts +3 -4
- package/src/monomer-works/consts.d.ts.map +1 -1
- package/src/monomer-works/consts.js +4 -3
- package/src/monomer-works/consts.js.map +1 -1
- package/src/monomer-works/monomer-hover.js +2 -1
- package/src/monomer-works/monomer-hover.js.map +1 -1
- package/src/monomer-works/monomer-works.js +6 -6
- package/src/monomer-works/monomer-works.js.map +1 -1
- package/src/monomer-works/seq-to-molfile.js +2 -2
- package/src/monomer-works/seq-to-molfile.js.map +1 -1
- package/src/monomer-works/to-atomic-level-utils.js +6 -6
- package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
- package/src/monomer-works/to-atomic-level.js +10 -9
- package/src/monomer-works/to-atomic-level.js.map +1 -1
- package/src/monomer-works/utils.d.ts +1 -1
- package/src/monomer-works/utils.d.ts.map +1 -1
- package/src/monomer-works/utils.js +3 -2
- package/src/monomer-works/utils.js.map +1 -1
- package/src/unknown.js +2 -1
- package/src/unknown.js.map +1 -1
- package/src/utils/const.d.ts +15 -3
- package/src/utils/const.d.ts.map +1 -1
- package/src/utils/const.js +7 -0
- package/src/utils/const.js.map +1 -1
- package/src/utils/generator.js +2 -1
- package/src/utils/generator.js.map +1 -1
- package/src/utils/macromolecule/utils.d.ts +1 -2
- package/src/utils/macromolecule/utils.d.ts.map +1 -1
- package/src/utils/macromolecule/utils.js +9 -9
- package/src/utils/macromolecule/utils.js.map +1 -1
- package/src/utils/monomer-ui.js +3 -2
- package/src/utils/monomer-ui.js.map +1 -1
- package/src/utils/sequence-position-scroller.d.ts.map +1 -1
- package/src/utils/sequence-position-scroller.js +1 -1
- package/src/utils/sequence-position-scroller.js.map +1 -1
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@@ -3,13 +3,14 @@
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import * as grok from 'datagrok-api/grok';
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import * as DG from 'datagrok-api/dg';
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import wu from 'wu';
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+
import { HELM_MONOMER_TYPE, HELM_POLYMER_TYPE } from '../utils/const';
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import { ALPHABET, NOTATION } from '../utils/macromolecule/consts';
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import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
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import { seqToMolFileWorker } from './seq-to-molfile';
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import { hasMolGraph, NucleotideRole, setMolGraph } from './types';
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import { errInfo } from '../utils/err-info';
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import { alphabetToPolymerType } from './utils';
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-
import { HelmTypes } from '../helm/consts';
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+
import { HelmTypes, PolymerTypes } from '../helm/consts';
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import { monomerWorksConsts as C } from './consts';
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// todo: verify that all functions have return types
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/** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
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@@ -44,7 +45,7 @@ export async function _toAtomicLevel(df, seqCol, monomerLib, seqHelper, rdKitMod
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// We already proved the column is HELM RNA. Pin the polymer type to
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// RNA without leaning on the alphabet detector (which can yield UN
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// when only modified monomers appear).
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-
polymerType =
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polymerType = HELM_POLYMER_TYPE.RNA;
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alphabet = pickRnaAlphabetFromHelm(seqCol, seqHelper);
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}
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else {
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@@ -110,7 +111,7 @@ function isAllHelmRna(seqCol, seqHelper) {
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if (!pts || pts.length !== seqSS.length)
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return false;
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for (const pt of pts)
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-
if (pt !==
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if (pt !== PolymerTypes.RNA)
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return false;
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sawAny = true;
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}
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@@ -160,7 +161,7 @@ function classifyRnaRole(monomerLib, polymerType, symbol) {
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const m = monomerLib.getMonomer(polymerType, symbol);
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if (!m)
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return null;
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-
if (m["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] ===
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if (m["monomerType" /* HELM_FIELDS.MONOMER_TYPE */] === HELM_MONOMER_TYPE.BRANCH)
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return NucleotideRole.BASE;
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const rgroups = m.rgroups ?? [];
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// A chain-end modifier exposes exactly one attachment point.
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@@ -271,7 +272,7 @@ export function getMonomersDictFromLib(monomerSequencesArray, rolesArray, polyme
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// Pre-load default sugar/phosphate when ANY row falls back to bases-only
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// mode (FASTA, separator, or HELM RNA rows the splitter could not split).
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// The default monomer adjusters depend on these being present in the dict.
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const anyBasesOnly = polymerType ===
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const anyBasesOnly = polymerType === HELM_POLYMER_TYPE.RNA &&
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rolesArray.some((r) => r === undefined);
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if (anyBasesOnly) {
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const symbols = (alphabet === ALPHABET.RNA) ?
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@@ -290,7 +291,7 @@ export function getMonomersDictFromLib(monomerSequencesArray, rolesArray, polyme
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continue; // Skip gap/empty monomer for MSA
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const role = roles ? roles[posI] : undefined;
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try {
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-
if (polymerType ===
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if (polymerType === HELM_POLYMER_TYPE.RNA && role === undefined &&
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sym.split(/\(|\)/).filter((e) => !!e).length === 3) {
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// legacy: a single token of the form sugar(base)phosphate slipped
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// through unsplit; index just the base.
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@@ -360,7 +361,7 @@ function getMolGraph(monomerSymbol, formattedMonomerLib, moduleRdkit, polymerTyp
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const meta = getMonomerMetadata(atoms, bonds, capGroups, capGroupIdxMap);
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const steabs = getAbsStereocenters(molfileV3K);
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const monomerGraph = { atoms: atoms, bonds: bonds, meta: meta, stereoAtoms: steabs };
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if (polymerType ===
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if (polymerType === HELM_POLYMER_TYPE.PEPTIDE)
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adjustPeptideMonomerGraph(monomerGraph);
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else { // nucleotides
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// Prefer explicit role (HELM-RNA triples mode); fall back to symbol
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@@ -424,7 +425,7 @@ function getAbsStereocenters(molfileV3K) {
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}
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function setShiftsAndTerminalNodes(polymerType, monomerGraph, monomerSymbol, role) {
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// remove the 'rightmost' chain-extending r-group node in the backbone
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if (polymerType ===
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if (polymerType === HELM_POLYMER_TYPE.PEPTIDE) {
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setShifts(monomerGraph, polymerType);
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const removedR2Atom = removeNodeAndBonds(monomerGraph, monomerGraph.meta.rNodes[1]);
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if (removedR2Atom?.removedAtom)
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@@ -632,7 +633,7 @@ function setShifts(molGraph, polymerType) {
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if (molGraph.meta.rNodes.length > 1) {
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molGraph.meta.backboneShift = getShiftBetweenNodes(molGraph, molGraph.meta.rNodes[1] - 1, molGraph.meta.terminalNodes[0] - 1);
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}
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if (polymerType ===
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if (polymerType === HELM_POLYMER_TYPE.RNA && molGraph.meta.rNodes.length > 2) {
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molGraph.meta.branchShift = getShiftBetweenNodes(molGraph, molGraph.meta.rNodes[2] - 1, molGraph.meta.terminalNodes[0] - 1);
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}
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}
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@@ -1 +1 @@
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1
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-
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|
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1
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+
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kBAAkB;QACpB,CAAC,CAAC,kBAAkB;QACpB,CAAC,CAAC,OAAO;KACV,CAAC;IACF,MAAM,gBAAgB,GAAG,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAC/C,iCAAiC;IAEjC,OAAO,gBAAgB,CAAC;AAC1B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,2BAA2B,CAAC,eAAsB;IACtE,IAAI,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,EAAC,CAAC,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzE,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,mEAAmE,CAAC,CAAC;QACxF,OAAO;IACT,CAAC;IAED,MAAM,wBAAwB,GAAG,IAAI,GAAG,EAAkB,CAAC;IAC3D,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;IAErE,KAAK,MAAM,gBAAgB,IAAI,eAAe,EAAE,CAAC;QAC/C,MAAM,aAAa,GAAG,gBAAgB,mCAAoB,CAAC;QAC3D,MAAM,SAAS,GAAG,cAAc,CAAC,gBAAgB,qCAAqB,CAAC,CAAC;QACxE,MAAM,cAAc,GAAG,mBAAmB,CAAC,gBAAgB,qCAAqB,CAAC,CAAC;QAElF,MAAM,UAAU,GAAG,gBAAgB,qCAAqB,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,gBAAgB,qCAAqB,CAAC,CAAC;YAClH,mBAAmB,CAAC,iBAAiB,CAAC,gBAAgB,qCAAqB,CAAC,EAAE,WAAW,CAAC,CAAC;QAC7F,MAAM,MAAM,GAAG,sBAAsB,CAAC,UAAU,CAAC,CAAC;QAElD,MAAM,KAAK,GAAG,cAAc,CAAC,UAAU,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC;QAC3D,MAAM,KAAK,GAAG,cAAc,CAAC,UAAU,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC;QAC3D,MAAM,IAAI,GAAG,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,cAAc,CAAC,CAAC;QAEzE,MAAM,YAAY,GAAa,EAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAC,CAAC;QAExE,cAAc,CAAC,YAAY,CAAC,CAAC;QAC7B,sBAAsB,CAAC,YAAY,CAAC,CAAC;QACrC,MAAM,OAAO,GAAG,2BAA2B,CAAC,YAAY,CAAC,CAAC;QAC1D,wBAAwB,CAAC,GAAG,CAAC,aAAa,EAAE,OAAO,CAAC,CAAC;IACvD,CAAC;IACD,OAAO,wBAAwB,CAAC;AAClC,CAAC;AAED;;iCAEiC;AACjC,MAAM,UAAU,iBAAiB,CAAC,OAAgB;IAChD,MAAM,QAAQ,GAAc,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,gBAAgB,EAAC,CAAC,CAAC;IACpF,MAAM,WAAW,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC;IAExC,MAAM,SAAS,GAAG,cAAc,CAAC,OAAO,qCAAqB,CAAC,CAAC;IAC/D,MAAM,cAAc,GAAG,mBAAmB,CAAC,OAAO,qCAAqB,CAAC,CAAC;IACzE,MAAM,UAAU,GAAG,OAAO,qCAAqB,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,qCAAqB,CAAC,CAAC;QAChG,mBAAmB,CAAC,iBAAiB,CAAC,OAAO,qCAAqB,CAAC,EAAE,WAAW,CAAC,CAAC;IACpF,MAAM,MAAM,GAAG,sBAAsB,CAAC,UAAU,CAAC,CAAC;IAElD,MAAM,KAAK,GAAG,cAAc,CAAC,UAAU,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC;IAC3D,MAAM,KAAK,GAAG,cAAc,CAAC,UAAU,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC;IAC3D,MAAM,IAAI,GAAG,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,cAAc,CAAC,CAAC;IAEzE,MAAM,YAAY,GAAa,EAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAC,CAAC;IAExE,yBAAyB,CAAC,YAAY,CAAC,CAAC;IAExC,MAAM,OAAO,GAAG,2BAA2B,CAAC,YAAY,CAAC,CAAC;IAC1D,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import { ISubstructProvider } from '@datagrok-libraries/chem-meta/src/types';
|
|
3
|
-
import { PolymerType } from '
|
|
3
|
+
import { PolymerType } from '../helm/types';
|
|
4
4
|
import { ISeqMonomer } from '../helm/types';
|
|
5
5
|
import { ALPHABET } from '../utils/macromolecule';
|
|
6
6
|
export type MonomerHoverLink = {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,kBAAkB,EAAC,MAAM,yCAAyC,CAAC;
|
|
1
|
+
{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,OAAO,EAAC,kBAAkB,EAAC,MAAM,yCAAyC,CAAC;AAE3E,OAAO,EAAC,WAAW,EAAC,MAAM,eAAe,CAAC;AAC1C,OAAO,EAAC,WAAW,EAAC,MAAM,eAAe,CAAC;AAE1C,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAEhD,MAAM,MAAM,gBAAgB,GAAG;IAC7B,SAAS,EAAE,EAAE,CAAC,MAAM,CAAC;IACrB,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,QAAQ,EAAE,OAAO,EAAE,WAAW,GAAG,IAAI,EAAE,aAAa,EAAE,EAAE,CAAC,UAAU,GAAG,OAAO,CAAC;CACvG,GAAG,kBAAkB,CAAC;AAEvB,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,GAAG,SAAS,EAAE,OAAO,EAAE,MAAM,GAAG,MAAM,CAGtF;AAED,wBAAgB,aAAa,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,GAAG,SAAS,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,CAEtF;AAED,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,QAAQ,GAAG,WAAW,CAYrE;AAED,+CAA+C;AAC/C,wBAAgB,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,IAAI,CAS5D"}
|
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
import { HELM_POLYMER_TYPE } from '../utils/const';
|
|
1
2
|
import { ALPHABET } from '../utils/macromolecule';
|
|
2
3
|
export function getUnusedColName(df, colName) {
|
|
3
4
|
if (!df)
|
|
@@ -12,9 +13,9 @@ export function alphabetToPolymerType(alphabet) {
|
|
|
12
13
|
let resPolymerType;
|
|
13
14
|
// todo: an exception from dart comes before this check if the alphabet is UN
|
|
14
15
|
if (alphabet === ALPHABET.PT || alphabet === ALPHABET.UN)
|
|
15
|
-
resPolymerType =
|
|
16
|
+
resPolymerType = HELM_POLYMER_TYPE.PEPTIDE;
|
|
16
17
|
else if (alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA)
|
|
17
|
-
resPolymerType =
|
|
18
|
+
resPolymerType = HELM_POLYMER_TYPE.RNA;
|
|
18
19
|
else
|
|
19
20
|
throw new Error(`Unexpected alphabet '${alphabet}'.`);
|
|
20
21
|
return resPolymerType;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"utils.js","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"utils.js","sourceRoot":"","sources":["utils.ts"],"names":[],"mappings":"AAUA,OAAO,EAAC,iBAAiB,EAAC,MAAM,gBAAgB,CAAC;AACjD,OAAO,EAAC,QAAQ,EAAC,MAAM,wBAAwB,CAAC;AAOhD,MAAM,UAAU,gBAAgB,CAAC,EAA4B,EAAE,OAAe;IAC5E,IAAI,CAAC,EAAE;QAAE,OAAO,OAAO,CAAC;IACxB,OAAO,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC;AAC3C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,EAA4B,EAAE,UAAkB;IAC5E,OAAO,gBAAgB,CAAC,EAAE,EAAE,WAAW,UAAU,GAAG,CAAC,CAAC;AACxD,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,QAAkB;IACtD,8DAA8D;IAC9D,IAAI,cAAiC,CAAC;IACtC,6EAA6E;IAC7E,IAAI,QAAQ,KAAK,QAAQ,CAAC,EAAE,IAAI,QAAQ,KAAK,QAAQ,CAAC,EAAE;QACtD,cAAc,GAAG,iBAAiB,CAAC,OAAO,CAAC;SACxC,IAAI,QAAQ,KAAK,QAAQ,CAAC,GAAG,IAAI,QAAQ,KAAK,QAAQ,CAAC,GAAG;QAC7D,cAAc,GAAG,iBAAiB,CAAC,GAAG,CAAC;;QAEvC,MAAM,IAAI,KAAK,CAAC,wBAAwB,QAAQ,IAAI,CAAC,CAAC;IAExD,OAAO,cAAc,CAAC;AACxB,CAAC;AAED,+CAA+C;AAC/C,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,2CAA2C,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;QACvF,uDAAuD,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACpE,OAAO,MAAM,CAAC,CAAC,CAAC;QACd,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG;QAC7B,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG;KACxD,CAAC,CAAC,CAAC,IAAI,CAAC;AACX,CAAC"}
|
package/src/unknown.js
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import { SeqPaletteBase } from './seq-palettes';
|
|
3
3
|
import { getMonomerLibHelper } from './types/monomer-library';
|
|
4
|
+
import { PolymerTypes } from './helm/consts';
|
|
4
5
|
/** makes the color less white, makes the transparency effect always perceptible
|
|
5
6
|
* @param {string} color color in string format either hex or rgb.
|
|
6
7
|
* @param {boolean} scale if scale is needed to 210 brightness.
|
|
@@ -79,7 +80,7 @@ export class UnknownColorPalette extends UnknownSeqPalette {
|
|
|
79
80
|
get(m, polymerType) {
|
|
80
81
|
const palleteLength = UnknownColorPalette.palette.length;
|
|
81
82
|
const colorObj = UnknownColorPalette.customMonomerColors[m];
|
|
82
|
-
const polType = polymerType ??
|
|
83
|
+
const polType = polymerType ?? PolymerTypes.PEPTIDE;
|
|
83
84
|
if (colorObj && colorObj[polType])
|
|
84
85
|
return colorObj[polType];
|
|
85
86
|
const hash = StringUtils.hashCode(m);
|
package/src/unknown.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"unknown.js","sourceRoot":"","sources":["unknown.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,EAAa,cAAc,EAAC,MAAM,gBAAgB,CAAC;AAC1D,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;
|
|
1
|
+
{"version":3,"file":"unknown.js","sourceRoot":"","sources":["unknown.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,EAAa,cAAc,EAAC,MAAM,gBAAgB,CAAC;AAC1D,OAAO,EAAC,mBAAmB,EAAC,MAAM,yBAAyB,CAAC;AAE5D,OAAO,EAAC,YAAY,EAAC,MAAM,eAAe,CAAC;AAE3C;;;;KAIK;AACL,SAAS,YAAY,CAAC,KAAoB,EAAE,KAAK,GAAG,IAAI;IACtD,IAAI,KAAK,IAAI,IAAI;QACf,OAAO,kBAAkB,CAAC;IAE5B,MAAM,OAAO,GAAW,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;IACjD,IAAI,KAAK,EAAE,CAAC;QACV,MAAM,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC;QAC9B,MAAM,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC;QAC9B,MAAM,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC;QAC9B,wCAAwC;QACxC,MAAM,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;QAC5F,yBAAyB;QACzB,MAAM,KAAK,GAAG,CAAC,GAAG,WAAW,CAAC;QAC9B,MAAM,KAAK,GAAG,CAAC,GAAG,WAAW,CAAC;QAC9B,MAAM,KAAK,GAAG,CAAC,GAAG,WAAW,CAAC;QAC9B,IAAI,WAAW,GAAG,GAAG;YACnB,OAAO,OAAO,KAAK,GAAG,GAAG,IAAI,KAAK,GAAG,GAAG,IAAI,KAAK,GAAG,GAAG,GAAG,CAAC;IAC/D,CAAC;IAED,OAAO,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;AACjC,CAAC;AAED,MAAM,OAAO,WAAW;IACf,MAAM,CAAC,QAAQ,CAAC,CAAS;QAC9B,IAAI,IAAI,GAAW,CAAC,CAAC;QACrB,IAAI,CAAC,CAAC,MAAM,KAAK,CAAC;YAChB,OAAO,IAAI,CAAC;QACd,KAAK,IAAI,CAAC,GAAW,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC1C,MAAM,GAAG,GAAW,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;YACpC,IAAI,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,GAAG,CAAC;YAClC,IAAI,IAAI,CAAC,CAAC,CAAC,2BAA2B;QACxC,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC;CACF;AAED,MAAM,OAAgB,iBAAiB;CAEtC;AAED,MAAM,OAAO,cAAe,SAAQ,iBAAiB;IAC5C,GAAG,CAAC,EAAU,EAAE,YAAqB;QAC1C,OAAO,SAAS,CAAC;IACnB,CAAC;CACF;AAGD,MAAM,OAAO,mBAAoB,SAAQ,iBAAiB;IAEjD,MAAM,KAAK,OAAO;QACvB,IAAI,CAAC,mBAAmB,CAAC,QAAQ;YAC/B,mBAAmB,CAAC,QAAQ,GAAG,mBAAmB,CAAC,YAAY,EAAE,CAAC;QACpE,OAAO,mBAAmB,CAAC,QAAQ,CAAC;IACtC,CAAC;IAMO,MAAM,CAAC,YAAY;QACzB,mBAAmB,EAAE,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE;YAChC,EAAE,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE;gBACjC,MAAM,MAAM,GAAG,EAAE,CAAC,aAAa,EAAE,CAAC;gBAClC,MAAM,CAAC,SAAS,CAAC,SAAS,CAAC,GAAG,EAAE;oBAC9B,mBAAmB,CAAC,mBAAmB,GAAG,EAAE,CAAC;oBAC7C,mBAAmB,CAAC,YAAY,GAAG,MAAM,CAAC,eAAe,EAAE,CAAC;oBAC5D,KAAK,MAAM,WAAW,IAAI,IAAI,CAAC,YAAY,EAAE,CAAC;wBAC5C,MAAM,cAAc,GAAG,MAAM,CAAC,uBAAuB,CAAC,WAA0B,CAAC,CAAC;wBAClF,KAAK,MAAM,aAAa,IAAI,cAAc,EAAE,CAAC;4BAC3C,MAAM,OAAO,GAAG,MAAM,CAAC,UAAU,CAAC,WAA0B,EAAE,aAAa,CAAC,CAAC;4BAC7E,IAAI,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,UAAU,EAAE,CAAC;gCAC/C,IAAI,CAAC,IAAI,CAAC,mBAAmB,CAAC,aAAa,CAAC;oCAC1C,IAAI,CAAC,mBAAmB,CAAC,aAAa,CAAC,GAAG,EAAE,CAAC;gCAE/C,IAAI,CAAC,mBAAmB,CAAC,aAAa,CAAC,CAAC,WAAW,CAAC;oCAClD,YAAY,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC;4BACzD,CAAC;wBACH,CAAC;oBACH,CAAC;gBACH,CAAC,CAAC,CAAC;YACL,CAAC,CAAC,CAAC;QACL,CAAC,CAAC,CAAC;QACH,MAAM,GAAG,GAAI,EAAe,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,cAAc,CAAC,aAAa,CAAC,CAAC,CAAC;QACpF,OAAO,GAAG,CAAC;IACb,CAAC;IAEM,GAAG,CAAC,CAAS,EAAE,WAAoB;QACxC,MAAM,aAAa,GAAG,mBAAmB,CAAC,OAAO,CAAC,MAAM,CAAC;QACzD,MAAM,QAAQ,GAAG,mBAAmB,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC;QAC5D,MAAM,OAAO,GAAG,WAAW,IAAI,YAAY,CAAC,OAAO,CAAC;QACpD,IAAI,QAAQ,IAAI,QAAQ,CAAC,OAAO,CAAC;YAC/B,OAAO,QAAQ,CAAC,OAAO,CAAC,CAAC;QAC3B,MAAM,IAAI,GAAW,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QAC7C,MAAM,EAAE,GAAG,IAAI,GAAG,aAAa,CAAC;QAChC,OAAO,YAAY,CAAC,mBAAmB,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC;IACvD,CAAC;;AA/Cc,4BAAQ,GAAoB,IAAI,CAAC;AAMhD,mEAAmE;AACnE,kFAAkF;AACnE,uCAAmB,GAA4D,EAAE,CAAC;AAClF,gCAAY,GAAa,EAAE,CAAC;AAyC7C,MAAM,OAAO,kBAAmB,SAAQ,cAAc;IAG7C,MAAM,KAAK,IAAI;QACpB,IAAI,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC;YACtB,IAAI,CAAC,IAAI,GAAG,IAAI,cAAc,EAAE,CAAC;QACnC,OAAO,IAAI,CAAC,IAAI,CAAC;IACnB,CAAC;IAIM,MAAM,KAAK,KAAK;QACrB,IAAI,IAAI,CAAC,KAAK,KAAK,KAAK,CAAC;YACvB,IAAI,CAAC,KAAK,GAAG,IAAI,mBAAmB,EAAE,CAAC;QACzC,OAAO,IAAI,CAAC,KAAK,CAAC;IACpB,CAAC;CACF"}
|
package/src/utils/const.d.ts
CHANGED
|
@@ -1,8 +1,20 @@
|
|
|
1
1
|
import { MonomerType, PolymerType } from '../helm/types';
|
|
2
|
-
import { MonomerTypes, PolymerTypes } from '../helm/consts';
|
|
3
|
-
import HELM_POLYMER_TYPE = PolymerTypes;
|
|
4
|
-
import HELM_MONOMER_TYPE = MonomerTypes;
|
|
5
2
|
import { RGroup } from '../types/monomer-library';
|
|
3
|
+
declare const HELM_POLYMER_TYPE: {
|
|
4
|
+
readonly PEPTIDE: "PEPTIDE";
|
|
5
|
+
readonly RNA: "RNA";
|
|
6
|
+
readonly CHEM: "CHEM";
|
|
7
|
+
readonly BLOB: "BLOB";
|
|
8
|
+
readonly G: "G";
|
|
9
|
+
};
|
|
10
|
+
type HELM_POLYMER_TYPE = PolymerType;
|
|
11
|
+
declare const HELM_MONOMER_TYPE: {
|
|
12
|
+
readonly BACKBONE: "Backbone";
|
|
13
|
+
readonly BRANCH: "Branch";
|
|
14
|
+
readonly TERMINAL: "Terminal";
|
|
15
|
+
readonly UNDEFINED: "Undefined";
|
|
16
|
+
};
|
|
17
|
+
type HELM_MONOMER_TYPE = MonomerType;
|
|
6
18
|
export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
|
|
7
19
|
/** Required HELM library monomer fields:
|
|
8
20
|
* https://github.com/PistoiaHELM/HELMMonomerSets/blob/master/HELMmonomerSchema.json */
|
package/src/utils/const.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;
|
|
1
|
+
{"version":3,"file":"const.d.ts","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,WAAW,EAAE,WAAW,EAAC,MAAM,eAAe,CAAC;AAEvD,OAAO,EAAC,MAAM,EAAC,MAAM,0BAA0B,CAAC;AAKhD,QAAA,MAAM,iBAAiB;;;;;;CAAe,CAAC;AACvC,KAAK,iBAAiB,GAAG,WAAW,CAAC;AACrC,QAAA,MAAM,iBAAiB;;;;;CAAe,CAAC;AACvC,KAAK,iBAAiB,GAAG,WAAW,CAAC;AAErC,OAAO,EAAC,iBAAiB,EAAE,iBAAiB,EAAC,CAAC;AAE9C;uFACuF;AACvF,0BAAkB,mBAAmB;IACnC,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,EAAE,OAAO;IACT,OAAO,YAAY;IACnB,MAAM,WAAW;IACjB,YAAY,gBAAgB;IAC5B,YAAY,gBAAgB;IAC5B,WAAW,eAAe;CAC3B;AAGD,0BAAkB,kBAAkB;IAClC,gBAAgB,mBAAmB;IAEnC,0BAA0B,mBAAmB;IAC7C,YAAY,gBAAgB;IAC5B,cAAc,iBAAiB;IAC/B,KAAK,UAAU;CAChB;AAED,0BAAkB,oBAAoB;IACpC,cAAc,kBAAkB;IAChC,IAAI,SAAS;CACd;AAGD,0BAAkB,WAAW;IAC3B,YAAY,gBAAgB;IAC5B,MAAM,WAAW;IACjB,IAAI,SAAS;IACb,MAAM,WAAW;IACjB,OAAO,YAAY;IACnB,cAAc,kBAAkB;IAChC,OAAO,YAAY;IACnB,WAAW,eAAe;IAC1B,EAAE,OAAO;IACT,YAAY,gBAAgB;IAC5B,MAAM,WAAW;CAClB;AAGD,eAAO,MAAM,gBAAgB,eAO5B,CAAC;AAEF,eAAO,MAAM,gBAAgB,gBAAgB,CAAC;AAG9C,eAAO,MAAM,qBAAqB;;;;;;;;;;;;CAYjC,CAAC;AAEF,eAAO,MAAM,aAAa;0BACK,WAAW;;;;;;sBAMvB,MAAM,EAAE;;;0BAGG,WAAW;;CAE/B,CAAC;AAGX,eAAO,MAAM,kBAAkB,MAAQ,CAAC;AACxC,eAAO,MAAM,kBAAkB,OAAQ,CAAC;AAExC,eAAO,MAAM,aAAa,MAAM,CAAC;AACjC,eAAO,MAAM,kBAAkB,MAAM,CAAC;AACtC,eAAO,MAAM,gBAAgB,MAAM,CAAC;AACpC,eAAO,MAAM,oBAAoB,QAGhC,CAAC"}
|
package/src/utils/const.js
CHANGED
|
@@ -1,3 +1,10 @@
|
|
|
1
|
+
import { MonomerTypes, PolymerTypes } from '../helm/consts';
|
|
2
|
+
// hwe exports the HELM type vocabulary as `as const` objects (value-only), not
|
|
3
|
+
// TS enums, so we re-create the value+type duality the old `import X = Enum`
|
|
4
|
+
// aliases provided — consumers use these both as a value (`.RNA`) and as a type.
|
|
5
|
+
const HELM_POLYMER_TYPE = PolymerTypes;
|
|
6
|
+
const HELM_MONOMER_TYPE = MonomerTypes;
|
|
7
|
+
export { HELM_POLYMER_TYPE, HELM_MONOMER_TYPE };
|
|
1
8
|
// core fields of HELM library object used in toAtomicLevel function
|
|
2
9
|
export const HELM_CORE_FIELDS = [
|
|
3
10
|
"symbol" /* HELM_FIELDS.SYMBOL */,
|
package/src/utils/const.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"const.js","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"const.js","sourceRoot":"","sources":["const.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,YAAY,EAAE,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAG1D,+EAA+E;AAC/E,6EAA6E;AAC7E,iFAAiF;AACjF,MAAM,iBAAiB,GAAG,YAAY,CAAC;AAEvC,MAAM,iBAAiB,GAAG,YAAY,CAAC;AAGvC,OAAO,EAAC,iBAAiB,EAAE,iBAAiB,EAAC,CAAC;AA+C9C,oEAAoE;AACpE,MAAM,CAAC,MAAM,gBAAgB,GAAG;;;;;IAK9B,2EAA2E;IAC3E,YAAY;CACb,CAAC;AAEF,MAAM,CAAC,MAAM,gBAAgB,GAAG,aAAa,CAAC;AAE9C,wDAAwD;AACxD,MAAM,CAAC,MAAM,qBAAqB,GAAG;IACnC,aAAa,EAAE,IAAI,EAAE,cAAc;IACnC,QAAQ,EAAE,IAAI;IACd,MAAM,EAAE,MAAM;IACd,QAAQ,EAAE,IAAI;IACd,SAAS,EAAE,UAAU;IACrB,eAAe,EAAE,0BAA0B;IAC3C,SAAS,EAAE,aAAa;IACxB,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,IAAI;IACV,aAAa,EAAE,aAAa;IAC5B,QAAQ,EAAE,aAAa;CACxB,CAAC;AAEF,MAAM,CAAC,MAAM,aAAa,GAAG;IAC3B,aAAa,EAAE,UAAyB;IACxC,QAAQ,EAAE,EAAE;IACZ,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,UAAU;IACpB,SAAS,EAAE,EAAE;IACb,eAAe,EAAE,EAAE;IACnB,SAAS,EAAE,EAAc;IACzB,YAAY,EAAE,IAAI;IAClB,IAAI,EAAE,CAAC;IACP,aAAa,EAAE,SAAwB;IACvC,QAAQ,EAAE,EAAE;CACJ,CAAC;AAEX,gEAAgE;AAChE,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AACxC,MAAM,CAAC,MAAM,kBAAkB,GAAG,KAAK,CAAC;AAExC,MAAM,CAAC,MAAM,aAAa,GAAG,GAAG,CAAC;AACjC,MAAM,CAAC,MAAM,kBAAkB,GAAG,GAAG,CAAC;AACtC,MAAM,CAAC,MAAM,gBAAgB,GAAG,GAAG,CAAC;AACpC,MAAM,CAAC,MAAM,oBAAoB,GAAG,IAAI,MAAM,CAC5C,IAAI,aAAa,GAAG,kBAAkB,eAAe,gBAAgB,GAAG,EACxE,GAAG,CACJ,CAAC"}
|
package/src/utils/generator.js
CHANGED
|
@@ -2,6 +2,7 @@ import * as DG from 'datagrok-api/dg';
|
|
|
2
2
|
import wu from 'wu';
|
|
3
3
|
import { ALPHABET, getAlphabet, NOTATION, TAGS } from './macromolecule';
|
|
4
4
|
import { StringListSeqSplitted } from './macromolecule/utils';
|
|
5
|
+
import { PolymerTypes } from '../helm/consts';
|
|
5
6
|
import { GapOriginals } from './macromolecule/consts';
|
|
6
7
|
export function generateManySequences() {
|
|
7
8
|
const columns = [];
|
|
@@ -25,7 +26,7 @@ export function generateLongSequence(length = 10 ** 4) {
|
|
|
25
26
|
}
|
|
26
27
|
export function generateLongSequence2(seqHelper, notation = NOTATION.SEPARATOR, alphabet = ALPHABET.PT, separator = (notation === NOTATION.SEPARATOR ? '-' : undefined), monomerLib = undefined, colName = 'seq', rowCount = 100, seqLength = 10 ** 6) {
|
|
27
28
|
const alphabetSet = alphabet === ALPHABET.UN ?
|
|
28
|
-
monomerLib?.getMonomerSymbolsByType(
|
|
29
|
+
monomerLib?.getMonomerSymbolsByType(PolymerTypes.PEPTIDE) ?? [] : Array.from(getAlphabet(alphabet));
|
|
29
30
|
const alphabetSize = alphabetSet.length;
|
|
30
31
|
const col = DG.Column.fromType(DG.COLUMN_TYPE.STRING, colName, rowCount);
|
|
31
32
|
col.semType = DG.SEMTYPE.MACROMOLECULE;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"generator.js","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAE,QAAQ,EAAE,IAAI,EAAC,MAAM,iBAAiB,CAAC;AAEtE,OAAO,EAAC,qBAAqB,EAAC,MAAM,uBAAuB,CAAC;
|
|
1
|
+
{"version":3,"file":"generator.js","sourceRoot":"","sources":["generator.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAE,MAAM,IAAI,CAAC;AAEpB,OAAO,EAAC,QAAQ,EAAE,WAAW,EAAE,QAAQ,EAAE,IAAI,EAAC,MAAM,iBAAiB,CAAC;AAEtE,OAAO,EAAC,qBAAqB,EAAC,MAAM,uBAAuB,CAAC;AAE5D,OAAO,EAAC,YAAY,EAAC,MAAM,gBAAgB,CAAC;AAC5C,OAAO,EAAC,YAAY,EAAC,MAAM,wBAAwB,CAAC;AAEpD,MAAM,UAAU,qBAAqB;IACnC,MAAM,OAAO,GAAgB,EAAE,CAAC;IAChC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,QAAQ,EAAE,KAAK,EAC7C,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CACrB,0FAA0F,CAAC,CAAC,CAC/F,CAAC;IACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACrG,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,sGAAsG;AACtG,MAAM,UAAU,oBAAoB,CAAC,SAAiB,EAAE,IAAI,CAAC;IAC3D,MAAM,YAAY,GAChB,4DAA4D,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IAC3G,MAAM,MAAM,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,KAAK,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;IACvG,MAAM,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;IAC1C,MAAM,CAAC,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC;IACvC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;IACnC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE,QAAQ,CAAC,EAAE,CAAC,CAAC;IAC1C,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,mBAAmB,EAAE,MAAM,CAAC,CAAC;IAEhD,MAAM,OAAO,GAAgB,EAAE,CAAC;IAChC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IACrB,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,EAAE,UAAU,EAAE,IAAI,KAAK,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACrG,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,SAAqB,EACzD,WAAqB,QAAQ,CAAC,SAAS,EAAE,WAAqB,QAAQ,CAAC,EAAE,EACzE,YAAgC,CAAC,QAAQ,KAAK,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,EACnF,aAAsC,SAAS,EAC/C,UAAkB,KAAK,EAAE,WAAmB,GAAG,EAAE,YAAoB,EAAE,IAAI,CAAC;IAE5E,MAAM,WAAW,GAAa,QAAQ,KAAK,QAAQ,CAAC,EAAE,CAAC,CAAC;QACtD,UAAU,EAAE,uBAAuB,CAAC,YAAY,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;IACtG,MAAM,YAAY,GAAG,WAAW,CAAC,MAAM,CAAC;IAExC,MAAM,GAAG,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,OAAO,EAAE,QAAQ,CAAC,CAAC;IACzE,GAAG,CAAC,OAAO,GAAG,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;IACvC,GAAG,CAAC,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC;IAC1B,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;IACpC,IAAI,QAAQ,IAAI,QAAQ,CAAC,SAAS;QAAE,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,SAAS,EAAE,SAAU,CAAC,CAAC;IAE3E,MAAM,EAAE,GAAG,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC;IACxC,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,QAAQ,EAAE,IAAI,EAAE,EAAE,CAAC;QAC3C,MAAM,QAAQ,GAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC;aACnD,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;aAC7E,OAAO,EAAE,CAAC;QACb,MAAM,GAAG,GAAG,EAAE,CAAC,MAAM,CAAC,IAAI,qBAAqB,CAAC,QAAQ,EAAE,YAAY,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC;QACnF,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;IACrB,CAAC;IAED,OAAO,GAAG,CAAC;AACb,CAAC"}
|
|
@@ -3,7 +3,6 @@ import { CandidateType, ISeqGraphInfo, ISeqSplitted, MonomerFreqs, SeqColStats,
|
|
|
3
3
|
import { ALPHABET } from './consts';
|
|
4
4
|
import { SeqPalette } from '../../seq-palettes';
|
|
5
5
|
import { ISeqHelper } from '../seq-helper';
|
|
6
|
-
import { PolymerTypes } from '../../helm/consts';
|
|
7
6
|
import { HelmType, PolymerType } from '../../helm/types';
|
|
8
7
|
export declare class StringListSeqSplitted implements ISeqSplitted {
|
|
9
8
|
private readonly mList;
|
|
@@ -28,7 +27,7 @@ export declare class HelmSplitted extends StringListSeqSplitted {
|
|
|
28
27
|
private polymerTypes;
|
|
29
28
|
constructor(mListSeparated: string[][], // list of lists of monomers (separated by | in helm notation
|
|
30
29
|
connections: string, // string part of helm defining connections between monomers
|
|
31
|
-
polymerTypes:
|
|
30
|
+
polymerTypes: PolymerType[], // polymer types for each disjoint sequence part
|
|
32
31
|
gapOriginalMonomer: string);
|
|
33
32
|
protected _graphInfo: ISeqGraphInfo | undefined;
|
|
34
33
|
get graphInfo(): ISeqGraphInfo;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|