/* eslint-disable max-len */
import * as DG from 'datagrok-api/dg';
import * as grok from 'datagrok-api/grok';
import * as ui from 'datagrok-api/ui';
import {_package} from '../package';
import {adjustGridcolAfterRender} from '../utils/ui-utils';
import {buildMonomerHoverLink} from '@datagrok-libraries/bio/src/monomer-works/monomer-hover';
import {ChemTags} from '@datagrok-libraries/chem-meta/src/consts';

export async function antibodyDemo() {
  // for some reason the col is not saved in the layout
  const antibodyTags = [
    [
      'units',
      'fasta'
    ],
    [
      'aligned',
      'SEQ.MSA'
    ],
    [
      'alphabet',
      'PT'
    ],
    [
      'cell.renderer',
      'sequence'
    ],
    [
      'quality',
      'Macromolecule'
    ],
    [
      '.semantic-detection-duration',
      '8'
    ],
    [
      '.annotations',
      '[{"id":"deamid-ng","name":"Deamidation (NG)","description":"deamidation liability pattern (111 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"high","motifPattern":"NG","autoGenerated":true},{"id":"deamid-ns","name":"Deamidation (NS)","description":"deamidation liability pattern (859 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"medium","motifPattern":"NS","autoGenerated":true},{"id":"deamid-na","name":"Deamidation (NA)","description":"deamidation liability pattern (69 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"low","motifPattern":"NA","autoGenerated":true},{"id":"deamid-nd","name":"Deamidation (ND)","description":"deamidation liability pattern (18 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"low","motifPattern":"ND","autoGenerated":true},{"id":"deamid-nt","name":"Deamidation (NT)","description":"deamidation liability pattern (546 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#E53935","severity":"low","motifPattern":"NT","autoGenerated":true},{"id":"isom-dg","name":"Isomerization (DG)","description":"isomerization liability pattern (118 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#FF9800","severity":"high","motifPattern":"DG","autoGenerated":true},{"id":"isom-ds","name":"Isomerization (DS)","description":"isomerization liability pattern (306 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#FF9800","severity":"medium","motifPattern":"DS","autoGenerated":true},{"id":"oxid-m","name":"Oxidation (Met)","description":"oxidation liability pattern (1220 hits)","start":null,"end":null,"visualType":"point","category":"liability","color":"#9C27B0","severity":"medium","motifPattern":"M","autoGenerated":true},{"id":"oxid-w","name":"Oxidation (Trp)","description":"oxidation liability pattern (2593 hits)","start":null,"end":null,"visualType":"point","category":"liability","color":"#9C27B0","severity":"low","motifPattern":"W","autoGenerated":true},{"id":"glyco-nxst","name":"N-glycosylation","description":"glycosylation liability pattern (38 hits)","start":null,"end":null,"visualType":"motif","category":"liability","color":"#4CAF50","severity":"high","motifPattern":"N[^P][ST]","autoGenerated":true},{"id":"free-cys","name":"Free Cysteine","description":"freeCysteine liability pattern (2327 hits)","start":null,"end":null,"visualType":"point","category":"liability","color":"#607D8B","severity":"info","motifPattern":"C","autoGenerated":true},{"id":"kabat-heavy-fr1","name":"FR1","description":"FR1 (KABAT 1-30)","start":"1","end":"30","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-cdr1","name":"CDR1","description":"CDR1 (KABAT 31-35)","start":"31","end":"35","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-fr2","name":"FR2","description":"FR2 (KABAT 36-49)","start":"36","end":"49","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-cdr2","name":"CDR2","description":"CDR2 (KABAT 50-65)","start":"50","end":"65","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-fr3","name":"FR3","description":"FR3 (KABAT 66-94)","start":"66","end":"94","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-cdr3","name":"CDR3","description":"CDR3 (KABAT 95-102)","start":"95","end":"102","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true},{"id":"kabat-heavy-fr4","name":"FR4","description":"FR4 (KABAT 103-113)","start":"103","end":"113","visualType":"region","category":"structure","sourceScheme":"KABAT","autoGenerated":true}]'
    ],
    [
      '.annotationColumnName',
      '~AntibodyHC_annotations'
    ],
    [
      '.id',
      '750dcca0-48b0-11f1-e663-211b32f9e20c'
    ],
    [
      '.numberingScheme',
      'kabat'
    ],
    [
      '.regions',
      '[{"name":"FR1","description":"FR1 (KABAT 1-30)","start":"1","end":"30"},{"name":"CDR1","description":"CDR1 (KABAT 31-35)","start":"31","end":"35"},{"name":"FR2","description":"FR2 (KABAT 36-49)","start":"36","end":"49"},{"name":"CDR2","description":"CDR2 (KABAT 50-65)","start":"50","end":"65"},{"name":"FR3","description":"FR3 (KABAT 66-94)","start":"66","end":"94"},{"name":"CDR3","description":"CDR3 (KABAT 95-102)","start":"95","end":"102"},{"name":"FR4","description":"FR4 (KABAT 103-113)","start":"103","end":"113"}]'
    ],
    [
      '.positionShift',
      '42.10943057774151'
    ]
  ];
  const df = await _package.files.readCsv('demo-files/Antibody_HC.csv');
  const orCol = df.col('AntibodyHC')!;
  antibodyTags.forEach(([k, v]) => orCol.setTag(k, v));
  const clustCol = df.col('cluster (dbscan)')!;
  const stCol = clustCol.convertTo(DG.TYPE.STRING);
  df.columns.remove(clustCol.name);
  df.columns.add(stCol);
  const layoutTXT = await _package.files.readAsText('demo-files/Antibody_HC.layout');
  const layout = DG.ViewLayout.fromJson(layoutTXT);
  layout.columns.forEach((c) => {
    const col = df.col(c.name);
    if (col)
      Object.entries(c.tags).forEach(([k, v]) => col.setTag(k, v));
  });
  const tv = grok.shell.addTableView(df);
  await DG.delay(100);
  tv.loadLayout(layout, true);
}

export async function atomicLevelDemo() {
  const df = await _package.files.readCsv('demo-files/Atomic_Level.csv');
  await df.meta.detectSemanticTypes();
  const tv = grok.shell.addTableView(df);
  await DG.delay(100);
  await buildMonomerHoverLink(df.col('helm')!, df.col('molfile(helm)')!, _package.monomerLib, _package.seqHelper, _package.rdKitModule, true);
  adjustGridcolAfterRender(tv.grid, 'molfile(HELM)', 500, 300, true);
  adjustGridcolAfterRender(tv.grid, 'HELM', 500, undefined, true);
  df.col('molfile(helm)')!.setTag(ChemTags.SEQUENCE_SRC_HL_MONOMERS, 'false');
  df.col('molfile(helm)')!.setTag(ChemTags.SEQUENCE_SRC_COL, 'HELM');
  grok.shell.info('Hover over monomers in HELM column to highlight them in molecular structure.', {timeout: 10});
}

export async function sirnaDemo() {
  const df = await _package.files.readCsv('demo-files/SIRNA.csv');
  const layoutTXT = await _package.files.readAsText('demo-files/SIRNA.layout');
  const layout = DG.ViewLayout.fromJson(layoutTXT);
  df.col('sense_seq')!.setTag('aligned', 'SEQ.MSA');
  df.col('antisense_seq')!.setTag('aligned', 'SEQ.MSA');
  const tv = grok.shell.addTableView(df);
  await DG.delay(100);
  tv.loadLayout(layout, true);
  await df.meta.detectSemanticTypes();
  grok.shell.info('Hover over the oligo structrues to see modifications to different sugars, linkers and residues.', {timeout: 10});
  setTimeout(() => {
    df.currentCell = df.cell(0, 'oligo_helm');
  }, 300);
}