@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

package/dist/maf-POYTGXT4.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../gdc/maf.js"],
-  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\nimport { make_radios, renderTable, sayerror, Menu, table2col } from '#dom'\nimport { fileSize } from '#shared/fileSize.js'\nimport { select } from 'd3-selection'\n\n/*\na UI to list open-access maf files from current cohort\nlet user selects some, for the backend to generate an aggregated maf file and download to user\n\nobj {} TODO convert to class and declare properties\n\n*/\n\nconst tip = new Menu()\n\n// list of columns to show in MAF file table\nconst tableColumns = [\n\t{ label: 'Case', sortable: true },\n\t{ label: 'Project', sortable: true },\n\t{ label: 'Samples' },\n\t{ label: 'File Size', barplot: { tickFormat: '~s' }, sortable: true } // barchart column not sortable yet\n]\n\n// list of gdc maf file columns; selected ones are used for output\nconst mafColumns = [\n\t{ column: 'Hugo_Symbol', selected: true },\n\t{ column: 'Entrez_Gene_Id', selected: true },\n\t{ column: 'Center', selected: true },\n\t{ column: 'NCBI_Build', selected: true },\n\t{ column: 'Chromosome', selected: true },\n\t{ column: 'Start_Position', selected: true },\n\t{ column: 'End_Position', selected: true },\n\t{ column: 'Strand', selected: true },\n\t{ column: 'Variant_Classification', selected: true },\n\t{ column: 'Variant_Type', selected: true },\n\t{ column: 'Reference_Allele', selected: true },\n\t{ column: 'Tumor_Seq_Allele1', selected: true },\n\t{ column: 'Tumor_Seq_Allele2', selected: true },\n\t{ column: 'dbSNP_RS', selected: true },\n\t{ column: 'dbSNP_Val_Status', selected: true },\n\t{ column: 'Tumor_Sample_Barcode', selected: true },\n\t{ column: 'Matched_Norm_Sample_Barcode', selected: true },\n\t{ column: 'Match_Norm_Seq_Allele1', selected: true },\n\t{ column: 'Match_Norm_Seq_Allele2', selected: true },\n\t{ column: 'Tumor_Validation_Allele1', selected: true },\n\t{ column: 'Tumor_Validation_Allele2', selected: true },\n\t{ column: 'Match_Norm_Validation_Allele1', selected: true },\n\t{ column: 'Match_Norm_Validation_Allele2', selected: true },\n\t{ column: 'Verification_Status', selected: true },\n\t{ column: 'Validation_Status', selected: true },\n\t{ column: 'Mutation_Status', selected: true },\n\t{ column: 'Sequencing_Phase', selected: true },\n\t{ column: 'Sequence_Source', selected: true },\n\t{ column: 'Validation_Method', selected: true },\n\t{ column: 'Score', selected: true },\n\t{ column: 'BAM_File', selected: true },\n\t{ column: 'Sequencer', selected: true },\n\t{ column: 'Tumor_Sample_UUID', selected: true },\n\t{ column: 'Matched_Norm_Sample_UUID', selected: true },\n\t{ column: 'HGVSc', selected: true },\n\t{ column: 'HGVSp', selected: true },\n\t{ column: 'HGVSp_Short', selected: true },\n\t{ column: 'Transcript_ID', selected: true },\n\t{ column: 'Exon_Number', selected: true },\n\t{ column: 't_depth', selected: true },\n\t{ column: 't_ref_count', selected: true },\n\t{ column: 't_alt_count', selected: true },\n\t{ column: 'n_depth', selected: true },\n\t{ column: 'n_ref_count', selected: true },\n\t{ column: 'n_alt_count', selected: true },\n\t{ column: 'all_effects', selected: true },\n\t{ column: 'Allele', selected: true },\n\t{ column: 'Gene', selected: true },\n\t{ column: 'Feature', selected: true },\n\t{ column: 'Feature_type', selected: true },\n\t{ column: 'One_Consequence', selected: true },\n\t{ column: 'Consequence', selected: true },\n\t{ column: 'cDNA_position', selected: true },\n\t{ column: 'CDS_position', selected: true },\n\t{ column: 'Protein_position', selected: true },\n\t{ column: 'Amino_acids', selected: true },\n\t{ column: 'Codons', selected: true },\n\t{ column: 'Existing_variation', selected: true },\n\t{ column: 'DISTANCE', selected: true },\n\t{ column: 'TRANSCRIPT_STRAND', selected: true },\n\t{ column: 'SYMBOL', selected: true },\n\t{ column: 'SYMBOL_SOURCE', selected: true },\n\t{ column: 'HGNC_ID', selected: true },\n\t{ column: 'BIOTYPE', selected: true },\n\t{ column: 'CANONICAL', selected: true },\n\t{ column: 'CCDS', selected: true },\n\t{ column: 'ENSP', selected: true },\n\t{ column: 'SWISSPROT', selected: true },\n\t{ column: 'TREMBL', selected: true },\n\t{ column: 'UNIPARC', selected: true },\n\t{ column: 'UNIPROT_ISOFORM', selected: true },\n\t{ column: 'RefSeq', selected: true },\n\t{ column: 'MANE', selected: true },\n\t{ column: 'APPRIS', selected: true },\n\t{ column: 'FLAGS', selected: true },\n\t{ column: 'SIFT', selected: true },\n\t{ column: 'PolyPhen', selected: true },\n\t{ column: 'EXON', selected: true },\n\t{ column: 'INTRON', selected: true },\n\t{ column: 'DOMAINS', selected: true },\n\t{ column: '1000G_AF', selected: true },\n\t{ column: '1000G_AFR_AF', selected: true },\n\t{ column: '1000G_AMR_AF', selected: true },\n\t{ column: '1000G_EAS_AF', selected: true },\n\t{ column: '1000G_EUR_AF', selected: true },\n\t{ column: '1000G_SAS_AF', selected: true },\n\t{ column: 'ESP_AA_AF', selected: true },\n\t{ column: 'ESP_EA_AF', selected: true },\n\t{ column: 'gnomAD_AF', selected: true },\n\t{ column: 'gnomAD_AFR_AF', selected: true },\n\t{ column: 'gnomAD_AMR_AF', selected: true },\n\t{ column: 'gnomAD_ASJ_AF', selected: true },\n\t{ column: 'gnomAD_EAS_AF', selected: true },\n\t{ column: 'gnomAD_FIN_AF', selected: true },\n\t{ column: 'gnomAD_NFE_AF', selected: true },\n\t{ column: 'gnomAD_OTH_AF', selected: true },\n\t{ column: 'gnomAD_SAS_AF', selected: true },\n\t{ column: 'MAX_AF', selected: true },\n\t{ column: 'MAX_AF_POPS', selected: true },\n\t{ column: 'gnomAD_non_cancer_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_AFR_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_AMI_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_AMR_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_ASJ_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_EAS_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_FIN_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_MID_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_NFE_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_OTH_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_SAS_AF', selected: true },\n\t{ column: 'gnomAD_non_cancer_MAX_AF_adj', selected: true },\n\t{ column: 'gnomAD_non_cancer_MAX_AF_POPS_adj', selected: true },\n\t{ column: 'CLIN_SIG', selected: true },\n\t{ column: 'SOMATIC', selected: true },\n\t{ column: 'PUBMED', selected: true },\n\t{ column: 'TRANSCRIPTION_FACTORS', selected: true },\n\t{ column: 'MOTIF_NAME', selected: true },\n\t{ column: 'MOTIF_POS', selected: true },\n\t{ column: 'HIGH_INF_POS', selected: true },\n\t{ column: 'MOTIF_SCORE_CHANGE', selected: true },\n\t{ column: 'miRNA', selected: true },\n\t{ column: 'IMPACT', selected: true },\n\t{ column: 'PICK', selected: true },\n\t{ column: 'VARIANT_CLASS', selected: true },\n\t{ column: 'TSL', selected: true },\n\t{ column: 'HGVS_OFFSET', selected: true },\n\t{ column: 'PHENO', selected: true },\n\t{ column: 'GENE_PHENO', selected: true },\n\t{ column: 'CONTEXT', selected: true },\n\t{ column: 'case_id', selected: true },\n\t{ column: 'GDC_FILTER', selected: true },\n\t{ column: 'COSMIC', selected: true },\n\t{ column: 'hotspot', selected: true },\n\t{ column: 'tumor_bam_uuid', selected: true },\n\t{ column: 'normal_bam_uuid', selected: true },\n\t{ column: 'RNA_Support', selected: true },\n\t{ column: 'RNA_depth', selected: true },\n\t{ column: 'RNA_ref_count', selected: true },\n\t{ column: 'RNA_alt_count', selected: true },\n\t{ column: 'callers', selected: true }\n]\n\nexport async function gdcMAFui({ filter0, callbacks, debugmode = false }, holder) {\n\ttry {\n\t\tif (callbacks) {\n\t\t\t/* due to src/app.js line 100\n\t\t\tdelete this when that is reshaped to app.sjcharts.callbacks={}\n\t\t\t*/\n\t\t\tdelete callbacks.sjcharts\n\t\t\tfor (const n in callbacks) {\n\t\t\t\tif (typeof callbacks[n] != 'function') throw `callbacks.${n} not function`\n\t\t\t}\n\t\t}\n\t\t{\n\t\t\t// validate column names in case of human err\n\t\t\tconst cn = new Set()\n\t\t\tfor (const c of mafColumns) {\n\t\t\t\tif (!c.column) throw '.column missing from an element'\n\t\t\t\tif (cn.has(c.column)) throw 'duplicate column: ' + c.column\n\t\t\t\tcn.add(c.column)\n\t\t\t}\n\t\t}\n\t\tupdate({ filter0 })\n\t} catch (e) {\n\t\tconsole.log(e)\n\t\tsayerror(holder, e.message || e)\n\t}\n\n\tasync function update({ filter0 }) {\n\t\tholder.selectAll('*').remove()\n\t\t// TODO convert obj to class and declare all properties\n\t\tconst obj = {\n\t\t\tholder,\n\t\t\terrDiv: holder.append('div'),\n\t\t\tcontrolDiv: holder.append('div'),\n\t\t\ttableDiv: holder.append('div'),\n\t\t\topts: {\n\t\t\t\tfilter0,\n\t\t\t\texperimentalStrategy: 'WXS'\n\t\t\t},\n\t\t\tmafTableArg: null\n\t\t}\n\t\tmakeControls(obj)\n\t\tawait getFilesAndShowTable(obj)\n\t\tcallbacks?.postRender?.(publicApi)\n\t}\n\n\t// return api to be accessible by react wrapper; will call api.update() to auto refresh cohortmaf UI on GFF cohort change\n\tconst publicApi = { update }\n\treturn publicApi\n}\n\nfunction makeControls(obj) {\n\tconst table = table2col({ holder: obj.controlDiv })\n\ttable.addRow('Access', 'Open')\n\ttable.addRow('Workflow Type', 'Aliquot Ensemble Somatic Variant Merging and Masking')\n\t{\n\t\tconst [td1, td2] = table.addRow('Experimental Strategy')\n\t\tmake_radios({\n\t\t\tholder: td2,\n\t\t\toptions: [\n\t\t\t\t{ label: 'WXS', value: 'WXS', checked: obj.opts.experimentalStrategy == 'WXS' },\n\t\t\t\t{\n\t\t\t\t\tlabel: 'Targeted Sequencing',\n\t\t\t\t\tvalue: 'Targeted Sequencing',\n\t\t\t\t\tchecked: obj.opts.experimentalStrategy == 'Targeted Sequencing'\n\t\t\t\t}\n\t\t\t],\n\t\t\tstyles: { display: 'inline' },\n\t\t\tcallback: async value => {\n\t\t\t\tobj.opts.experimentalStrategy = value\n\t\t\t\tawait getFilesAndShowTable(obj)\n\t\t\t}\n\t\t})\n\t}\n\n\t{\n\t\tconst [td1, td2] = table.addRow('Output Columns')\n\t\tconst clickText = td2\n\t\t\t.append('span')\n\t\t\t.attr('class', 'sja_clbtext')\n\t\t\t.on('click', event => {\n\t\t\t\tconst rows = [],\n\t\t\t\t\tselectedRows = []\n\t\t\t\tfor (const [i, c] of mafColumns.entries()) {\n\t\t\t\t\trows.push([{ value: c.column }])\n\t\t\t\t\tif (c.selected) selectedRows.push(i)\n\t\t\t\t}\n\t\t\t\trenderTable({\n\t\t\t\t\tdiv: tip.clear().showunder(event.target).d,\n\t\t\t\t\trows,\n\t\t\t\t\tcolumns: [{ label: 'Column Name' }],\n\t\t\t\t\tselectedRows,\n\t\t\t\t\tnoButtonCallback: (i, n) => {\n\t\t\t\t\t\tmafColumns[i].selected = n.checked\n\t\t\t\t\t\tupdateText()\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t})\n\n\t\tupdateText()\n\n\t\tfunction updateText() {\n\t\t\tclickText.text(\n\t\t\t\t`${mafColumns.reduce((c, i) => c + (i.selected ? 1 : 0), 0)} of ${\n\t\t\t\t\tmafColumns.length\n\t\t\t\t} columns selected. Click to change`\n\t\t\t)\n\t\t}\n\t}\n}\n\nasync function getFilesAndShowTable(obj) {\n\tobj.tableDiv.selectAll('*').remove()\n\tconst wait = obj.tableDiv.append('div').style('margin', '30px 10px 10px 10px').text('Loading...')\n\n\tlet result // convenient for accessing outside of try-catch\n\n\ttry {\n\t\tconst body = {\n\t\t\texperimentalStrategy: obj.opts.experimentalStrategy\n\t\t}\n\t\tif (obj.opts.filter0) body.filter0 = obj.opts.filter0\n\t\tresult = await dofetch3('gdc/maf', { body })\n\t\tif (result.error) throw result.error\n\t\tif (!Array.isArray(result.files)) throw 'result.files[] not array'\n\t\tif (result.files.length == 0) throw 'No MAF files available.'\n\n\t\t// render\n\t\tif (result.filesTotal > result.files.length) {\n\t\t\twait.text(`Showing first ${result.files.length} MAF files out of ${result.filesTotal} total.`)\n\t\t} else {\n\t\t\twait.text(`Showing ${result.files.length} MAF files.`)\n\t\t}\n\n\t\tconst rows = []\n\t\tfor (const f of result.files) {\n\t\t\tconst row = [\n\t\t\t\t{\n\t\t\t\t\thtml: `<a href=https://portal.gdc.cancer.gov/files/${f.id} target=_blank>${f.case_submitter_id}</a>`,\n\t\t\t\t\tvalue: f.case_submitter_id\n\t\t\t\t},\n\t\t\t\t{ value: f.project_id },\n\t\t\t\t{\n\t\t\t\t\thtml: f.sample_types\n\t\t\t\t\t\t.map(i => {\n\t\t\t\t\t\t\treturn (\n\t\t\t\t\t\t\t\t'<span class=\"sja_mcdot\" style=\"padding:1px 8px;background:#ddd;color:black;white-space:nowrap\">' +\n\t\t\t\t\t\t\t\ti +\n\t\t\t\t\t\t\t\t'</span>'\n\t\t\t\t\t\t\t)\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.join(' ')\n\t\t\t\t},\n\t\t\t\t{ value: f.file_size } // do not send in text-formated file size, table sorting won't work\n\t\t\t]\n\t\t\trows.push(row)\n\t\t}\n\n\t\t// tracks table arg, so that the created button DOM element is accessible and can be modified\n\t\tobj.mafTableArg = {\n\t\t\trows,\n\t\t\tcolumns: tableColumns,\n\t\t\tresize: true,\n\t\t\tdiv: obj.tableDiv.append('div'),\n\t\t\tselectAll: true, // comment out for quicker testing\n\t\t\tdataTestId: 'sja_mafFileTable',\n\t\t\theader: { allowSort: true },\n\t\t\tselectedRows: [], //[198], // uncomment out for quicker testing\n\t\t\tbuttonsToLeft: true,\n\t\t\tbuttons: [\n\t\t\t\t{\n\t\t\t\t\ttext: ' ', // table.ts requires this\n\t\t\t\t\tonChange: updateButtonBySelectionChange,\n\t\t\t\t\tcallback: submitSelectedFiles\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\trenderTable(obj.mafTableArg)\n\t} catch (e) {\n\t\twait.text(e.message || e)\n\t\tif (e.stack) console.log(e.stack)\n\t}\n\n\tfunction updateButtonBySelectionChange(lst, button) {\n\t\t// note that button is generated by renderTable()\n\t\tlet sum = 0\n\t\tfor (const i of lst) sum += result.files[i].file_size\n\t\tif (sum == 0) {\n\t\t\tbutton.innerHTML = 'No file selected'\n\t\t\tbutton.disabled = true\n\t\t\treturn\n\t\t}\n\n\t\tbutton.disabled = false\n\t\tbutton.innerHTML =\n\t\t\tsum < result.maxTotalSizeCompressed\n\t\t\t\t? `Download ${fileSize(sum)} compressed MAF data`\n\t\t\t\t: `Download ${fileSize(result.maxTotalSizeCompressed)} compressed MAF data (${fileSize(sum)} selected)`\n\t}\n\n\t/* after table is created, on clicking download btn for first time, create a <span> after download btn,\n\tin order to show server-sent message on problematic files (emtpy, failed, invalid)\n\tscope this <span> for easy access by helpers,\n\tdetect if it is truthy to only create it once\n\t*/\n\tlet serverMessage\n\n\tasync function submitSelectedFiles(lst, button) {\n\t\tconst outColumns = mafColumns.filter(i => i.selected).map(i => i.column)\n\t\tif (outColumns.length == 0) {\n\t\t\twindow.alert('No output columns selected.')\n\t\t\treturn\n\t\t}\n\n\t\tmayCreateServerMessageSpan(button)\n\n\t\tconst fileIdLst = []\n\t\tfor (const i of lst) {\n\t\t\tfileIdLst.push(result.files[i].id)\n\t\t}\n\t\tif (fileIdLst.length == 0) return\n\n\t\tobj.holder.style('pointer-events', 'none').style('opacity', 0.5)\n\t\tconst oldText = button.innerHTML\n\t\tbutton.innerHTML = 'Loading... Please wait'\n\t\tserverMessage.style('display', 'none')\n\n\t\tlet data\n\t\ttry {\n\t\t\tdata = await dofetch3('gdc/mafBuild', { body: { fileIdLst, columns: outColumns } })\n\t\t\tif (!Object.keys(data).length) throw 'server returned blank multipart'\n\n\t\t\tif (data.errors?.body) {\n\t\t\t\t// expect gdc/mafBuild errors to be an array\n\t\t\t\tconst errors = data.errors.body || []\n\t\t\t\tif (Array.isArray(errors)) {\n\t\t\t\t\tconst fileErrors = errors.filter(d => d.url)\n\t\t\t\t\tif (fileErrors.length) displayRunStatusErrors(fileErrors)\n\t\t\t\t\tconst nonFileErrors = errors.filter(d => !d.url)\n\t\t\t\t\tfor (const e of nonFileErrors) sayerror(obj.errDiv, e.error || e.message)\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// download the file to client\n\t\t\tif (!data.gzfile) throw 'missing gzfile from response'\n\t\t\tconst href = URL.createObjectURL(data.gzfile.body)\n\t\t\tconst a = document.createElement('a')\n\t\t\ta.href = href\n\t\t\ta.download = `cohortMAF.${new Date().toISOString().split('T')[0]}.maf.gz`\n\t\t\ta.style.display = 'none'\n\t\t\tdocument.body.appendChild(a)\n\t\t\ta.click()\n\t\t\tdocument.body.removeChild(a)\n\t\t} catch (e) {\n\t\t\tsayerror(obj.errDiv, e)\n\t\t} finally {\n\t\t\tbutton.innerHTML = oldText\n\t\t\tobj.holder.style('pointer-events', 'auto').style('opacity', 1)\n\t\t}\n\t}\n\n\tfunction mayCreateServerMessageSpan(button) {\n\t\tif (serverMessage) return // message <span> are already created\n\t\tconst holder = select(button.parentElement)\n\t\tserverMessage = holder.append('span').attr('class', 'sja_clbtext').style('display', 'none')\n\t}\n\n\tfunction displayRunStatusErrors(errors) {\n\t\t// errors[] each ele: {error:str, url:str}\n\t\tconst rows = [] // map errors[] to rows[] to show in table of menu\n\t\tfor (const e of errors) {\n\t\t\tif (typeof e.error != 'string') throw '.error=string missing from an entry'\n\t\t\tif (typeof e.url != 'string') throw '.url=string missing from an entry'\n\t\t\t// url should end in file uuid, which can be used to match with original record of that file\n\t\t\tconst l = e.url.split('/')\n\t\t\tconst uuid = l[l.length - 1]\n\t\t\tconst fo = result.files.find(i => i.id == uuid)\n\t\t\tif (fo) {\n\t\t\t\t// record is found for this failed uuid\n\t\t\t\trows.push([\n\t\t\t\t\t{ html: `<a href=${e.url} target=_blank>${fo.case_submitter_id}</a>` },\n\t\t\t\t\t{ value: fo.project_id },\n\t\t\t\t\t{ value: fileSize(fo.file_size) },\n\t\t\t\t\t{ value: e.error }\n\t\t\t\t])\n\t\t\t} else {\n\t\t\t\t// file is not found; could happen in testing when backend hardcodes a uuid not in result.files[], or even gdc backend changes..\n\t\t\t\trows.push([{ value: uuid }, { value: '?' }, { value: '?' }, { value: e.error }])\n\t\t\t}\n\t\t}\n\t\tserverMessage\n\t\t\t.text(`${errors.length} empty/failed file${errors.length > 1 ? 's' : ''}`)\n\t\t\t.style('display', '')\n\t\t\t.on('click', event => {\n\t\t\t\trenderTable({\n\t\t\t\t\trows,\n\t\t\t\t\tcolumns: [{ column: '' }, { column: '' }, { column: '' }, { column: '' }],\n\t\t\t\t\tshowHeader: false,\n\t\t\t\t\tdiv: tip.clear().showunder(event.target).d\n\t\t\t\t})\n\t\t\t})\n\t}\n}\n"],
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-  "names": ["filter0", "updateText"]
-}

package/dist/maftimeline-FOQF6O3X.js

@@ -1,591 +0,0 @@
-import {
-  axisstyle,
-  bulk_badline,
-  disappear2 as disappear,
-  make_table_2col,
-  newpane,
-  newpane3,
-  renderSandboxFormDiv,
-  to_svg
-} from "./chunk-XZZLEHWC.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-CJJ6LDZM.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import "./chunk-QEHUEG4X.js";
-import "./chunk-XDI4UFCZ.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-SEQLC4AD.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-2TIYJ3PH.js";
-import "./chunk-RIGZHHCP.js";
-import "./chunk-AAEXTQT3.js";
-import "./chunk-2UWHV2SB.js";
-import "./chunk-ZLH4PJKX.js";
-import "./chunk-TV74I3Y5.js";
-import {
-  category10_default
-} from "./chunk-IH7ILDJS.js";
-import {
-  axisBottom,
-  axisLeft
-} from "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import {
-  format,
-  linear,
-  log,
-  ordinal,
-  time,
-  timeParse
-} from "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// src/maftimeline.js
-var zerovalue = 1e-5;
-var showcircle = true;
-var maflogscale = true;
-var tip = new Menu();
-function maftimelineui(genomes, holder, sandbox_header) {
-  let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
-  if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
-  else {
-    ;
-    [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(100, 100, genomes);
-    pane.header.text("MAF timeline plot");
-  }
-  inputdiv.append("p").html(
-    "<a href=https://docs.google.com/document/d/1WXlCVHLq_P2jGiRGJ55uzXCC6p-6Jqn7h406RUID_xo/edit?usp=sharing target=_blank>File format</a>"
-  );
-  inputdiv.append("p").html("<a href=https://www.dropbox.com/s/940wfo6rd1ttlim/example.maftimeline?dl=0 target=_blank>Example file</a>");
-  {
-    const id = Math.random().toString();
-    const p = inputdiv.append("p");
-    p.append("input").attr("type", "checkbox").attr("id", id).property("checked", true).style("margin-right", "5px").on("change", () => {
-      maflogscale = !maflogscale;
-    });
-    p.append("label").attr("for", id).text("Y axis (MAF) log10 scale");
-  }
-  const fileui = () => {
-    filediv.selectAll("*").remove();
-    const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
-      saydiv.text("");
-      const file = event.target.files[0];
-      if (!file) {
-        fileui();
-        return;
-      }
-      if (file.size == 0) {
-        saydiv.text("Wrong file: " + file.name);
-        fileui();
-        return;
-      }
-      const reader = new FileReader();
-      reader.onload = (event2) => {
-        const lines = event2.target.result.trim().split(/\r?\n/);
-        const [err, header] = parseheader(lines[0].trim());
-        if (err) {
-          saydiv.text("File header error: " + err);
-          fileui();
-          return;
-        }
-        const badlines = [];
-        const data = {};
-        let good = 0;
-        for (let i = 1; i < lines.length; i++) {
-          if (lines[i] == "") continue;
-          if (lines[i][0] == "#") continue;
-          const m = parseline(i, lines[i], header, badlines, data);
-          if (m) {
-            good++;
-          }
-        }
-        if (badlines.length) {
-          bulk_badline(header, badlines);
-        }
-        if (good == 0) {
-          fileui();
-          return;
-        }
-        let visual_holder;
-        if (pane) {
-          disappear(pane.pane);
-          const pane2 = newpane({ x: 100, y: 100, toshrink: true });
-          pane2.header.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
-          visual_holder = pane2.body;
-        }
-        if (holder !== void 0) {
-          visual_holder = visualdiv.html('<span style="opacity:.5;font-size:.7em">MAF TIMELINE</span> ' + file.name);
-          inputdiv.selectAll("*").remove();
-          saydiv.text("");
-        }
-        render(data, header, visual_holder);
-      };
-      reader.onerror = function() {
-        saydiv.text("Error reading file " + file.name);
-        fileui();
-        return;
-      };
-      saydiv.text("Parsing file " + file.name + " ...");
-      reader.readAsText(file, "utf8");
-    });
-    setTimeout(() => butt.node().focus(), 1100);
-  };
-  fileui();
-}
-function parseheader(line) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return ["columns must be separated by tab"];
-  const htry = (...lst) => {
-    for (const i2 of lst) {
-      const j = header.indexOf(i2);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("person", "patient", "caseid");
-  if (i == -1) return ["person missing"];
-  header[i] = "patient";
-  i = htry("sample", "sampleid");
-  if (i == -1) return ["sample missing"];
-  header[i] = "sample";
-  i = htry("snv4");
-  if (i == -1) return ["snv4 missing"];
-  header[i] = "snv4";
-  i = htry("date", "dateofsample");
-  if (i == -1) return ["date missing"];
-  header[i] = "date";
-  i = htry("mutant_readcount", "mutantcount");
-  if (i != -1) header[i] = "mutant_readcount";
-  i = htry("ref_readcount", "refcount");
-  if (i != -1) header[i] = "ref_readcount";
-  i = htry("total_readcount", "coveragecount");
-  if (i == -1) return ["total_readcount missing"];
-  header[i] = "coverage";
-  i = htry("maf");
-  if (i == -1) return ["maf missing"];
-  header[i] = "maf";
-  i = htry("call_manual");
-  if (i != -1) header[i] = "call_manual";
-  return [null, header];
-}
-function parseline(i, line, header, badlines, data) {
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.patient) {
-    badlines.push([i, "missing patient", lst]);
-    return;
-  }
-  if (!data[m.patient]) {
-    data[m.patient] = {
-      snv4: {},
-      show: false
-    };
-  }
-  if (!m.snv4) {
-    badlines.push([i, "missing snv4", lst]);
-    return;
-  }
-  if (!data[m.patient].snv4[m.snv4]) {
-    data[m.patient].snv4[m.snv4] = {
-      mutationname: m.snv4,
-      samples: [],
-      subidx: void 0
-    };
-  }
-  if (m.gene) {
-    data[m.patient].snv4[m.snv4].gene = m.gene;
-  }
-  if (!m.maf) {
-    badlines.push([i, "missing maf", lst]);
-    return;
-  }
-  let v = Number.parseFloat(m.maf);
-  if (Number.isNaN(v)) {
-    badlines.push([i, "invalid maf", lst]);
-    return;
-  }
-  if (v < zerovalue) {
-    v = zerovalue;
-  }
-  m.maf = v;
-  if (!m.coverage) {
-    badlines.push([i, "missing total_readcount", lst]);
-    return;
-  }
-  if (m.call_manual && m.call_manual == "wildtype") {
-    m.maf = zerovalue;
-  }
-  v = Number.parseInt(m.coverage);
-  if (Number.isNaN(v)) {
-    badlines.push([i, "invalid total_readcount", lst]);
-    return;
-  }
-  m.coverage = v;
-  let date;
-  if (m.date) {
-    const f = timeParse("%m/%d/%Y");
-    date = f(m.date);
-    m.Date = m.date;
-  } else {
-    badlines.push([i, "missing date", lst]);
-    return;
-  }
-  if (date == null) {
-    badlines.push([i, "cannot parse date", lst]);
-    return;
-  }
-  m.date = date;
-  if (!m.sample) {
-    badlines.push([i, "missing sample", lst]);
-    return;
-  }
-  data[m.patient].snv4[m.snv4].samples.push(m);
-  return true;
-}
-function render(data, header, holder) {
-  const table = holder.append("table").style("margin", "20px");
-  const tr1 = table.append("tr");
-  let td = tr1.append("td").style("vertical-align", "top").attr("rowspan", 2);
-  td.append("button").text("Toggle circle visibility").on("click", () => {
-    showcircle = !showcircle;
-    for (const n in data) {
-      if (data[n].show) {
-        data[n].handle.node().click();
-        break;
-      }
-    }
-  });
-  const patientholder = td.append("div").style("margin-top", "10px");
-  const td1 = tr1.append("td").style("vertical-align", "top");
-  const graphholder = td1.append("div").style("display", "inline-block");
-  const controlholder = td1.append("div").style("display", "inline-block").style("vertical-align", "top");
-  const tr2 = table.append("tr");
-  const tiantable = tr2.append("td").append("table").style("border-spacing", "20px").style("border-collapse", "separate");
-  const gtr1 = tiantable.append("tr");
-  td = gtr1.append("td").style("vertical-align", "top");
-  td.append("div").text("Shared").style("font-size", "2em");
-  const graph1holder = td.append("div").style("border", "solid 1px black");
-  td = gtr1.append("td").style("vertical-align", "top");
-  td.append("div").text("Rising").style("font-size", "2em");
-  const graph2holder = td.append("div").style("border", "solid 1px black");
-  const gtr2 = tiantable.append("tr");
-  td = gtr2.append("td").style("vertical-align", "top");
-  td.append("div").text("Falling").style("font-size", "2em");
-  const graph3holder = td.append("div").style("border", "solid 1px black");
-  td = gtr2.append("td").style("vertical-align", "top");
-  td.append("div").text("R-only").style("font-size", "2em");
-  const graph4holder = td.append("div").style("border", "solid 1px black");
-  for (const patient in data) {
-    const snvlst = [];
-    const colors = ordinal(category10_default);
-    for (const x in data[patient].snv4) {
-      const snv = data[patient].snv4[x];
-      snv.show = true;
-      snv.color = colors(snv.mutationname);
-      snv.samples.sort((a, b) => a.date - b.date);
-      for (const s of snv.samples) {
-        s.color = snv.color;
-      }
-      snvlst.push(snv);
-    }
-    const div = patientholder.append("div").classed("sja_menuoption", true).style("color", "black").text(patient).on("click", () => {
-      for (const pn in data) {
-        data[pn].handle.style("color", "black");
-        data[pn].show = false;
-      }
-      data[patient].handle.style("color", "red");
-      data[patient].show = true;
-      makegraph(snvlst, header, graphholder);
-      makesubgraph(snvlst, graph1holder, graph2holder, graph3holder, graph4holder);
-      makecontrol(snvlst, header, controlholder, graphholder, graph1holder, graph2holder, graph3holder, graph4holder);
-    });
-    data[patient].handle = div;
-  }
-  for (const n in data) {
-    data[n].handle.node().click();
-    break;
-  }
-}
-function makesubgraph(snvlst, g1, g2, g3, g4) {
-  g1.selectAll("*").remove();
-  g2.selectAll("*").remove();
-  g3.selectAll("*").remove();
-  g4.selectAll("*").remove();
-  const l1 = [];
-  const l2 = [];
-  const l3 = [];
-  const l4 = [];
-  for (const snv of snvlst) {
-    switch (snv.subidx) {
-      case 1:
-        l1.push(snv);
-        break;
-      case 2:
-        l2.push(snv);
-        break;
-      case 3:
-        l3.push(snv);
-        break;
-      case 4:
-        l4.push(snv);
-        break;
-    }
-  }
-  if (l1.length) {
-    makegraph(l1, null, g1, true);
-  } else {
-    g1.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
-  }
-  if (l2.length) {
-    makegraph(l2, null, g2, true);
-  } else {
-    g2.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
-  }
-  if (l3.length) {
-    makegraph(l3, null, g3, true);
-  } else {
-    g3.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
-  }
-  if (l4.length) {
-    makegraph(l4, null, g4, true);
-  } else {
-    g4.append("div").style("padding", "60px").style("background-color", "#ededed").text("no data");
-  }
-}
-function makegraph(snvlst0, header, holder, issub) {
-  holder.selectAll("*").remove();
-  const samples = [];
-  const snvlst = [];
-  for (const snv of snvlst0) {
-    if (!issub && !snv.show) continue;
-    snvlst.push(snv);
-    for (const s of snv.samples) {
-      samples.push(s);
-    }
-  }
-  if (snvlst.length == 0) return;
-  let mindate = snvlst[0].samples[0].date;
-  let maxdate = snvlst[0].samples[0].date;
-  let maxmaf = snvlst[0].samples[0].maf;
-  let maxcoverage = snvlst[0].samples[0].coverage;
-  for (const snv of snvlst) {
-    for (const s of snv.samples) {
-      mindate = Math.min(mindate, s.date);
-      maxdate = Math.max(maxdate, s.date);
-      maxmaf = Math.max(maxmaf, s.maf);
-      maxcoverage = Math.max(maxcoverage, s.coverage);
-    }
-  }
-  const svg = holder.append("svg");
-  const toppad = 30, rightpad = 200, yaxisw = 100, xaxish = 50;
-  let width = 600;
-  let height = 400;
-  let xpad, ypad, minradius;
-  const xaxisg = svg.append("g");
-  const yaxisg = svg.append("g");
-  const drag = svg.append("text").text("drag to resize").attr("class", "sja_clb").attr("text-anchor", "end").on("mousedown", (event) => {
-    event.preventDefault();
-    const x = event.clientX;
-    const y = event.clientY;
-    const w0 = width;
-    const h0 = height;
-    const body = select_default(document.body);
-    body.on("mousemove", (event2) => {
-      setsize(w0 + event2.clientX - x, h0 + event2.clientY - y);
-    }).on("mouseup", () => {
-      body.on("mousemove", null).on("mouseup", null);
-    });
-  });
-  const xscale = time().domain([mindate, maxdate]);
-  const yscale = (maflogscale ? log() : linear()).domain([zerovalue, 1]);
-  const rscale = linear().domain([1, maxcoverage]);
-  const g = svg.append("g");
-  const lines = g.selectAll().data(snvlst).enter().append("path").attr("stroke", (d) => d.color).attr("fill", "none");
-  let circles;
-  if (showcircle) {
-    circles = g.selectAll().data(samples).enter().append("circle").attr("fill", (d) => d.color).attr("fill-opacity", 0.1).on("mouseover", (event, d) => {
-      event.target.setAttribute("fill-opacity", 0.4);
-      tip.clear();
-      tip.show(event.clientX, event.clientY);
-      const lst = [];
-      for (const k in d) {
-        if (k == "color") continue;
-        if (k == "gene") {
-          lst.push({ k: "gene", v: '<span style="color:' + d.color + '">' + d.gene + "</span>" });
-          continue;
-        }
-        if (k == "date") continue;
-        if (k == "url") {
-          lst.push({ k: "URL", v: "<a href=" + d.url + " target=_blank>LINK</a>" });
-          continue;
-        }
-        lst.push({ k, v: d[k] });
-      }
-      make_table_2col(tip.d, lst);
-    }).on("mouseout", (event) => {
-      event.target.setAttribute("fill-opacity", 0.1);
-    });
-  }
-  const legend = svg.append("g");
-  const setsize = (w, h) => {
-    width = w;
-    height = h;
-    minradius = 2;
-    const maxradius = Math.max(width, height) / 30;
-    xpad = maxradius;
-    ypad = maxradius;
-    rscale.range([Math.pow(minradius, 2), Math.pow(maxradius, 2)]);
-    xscale.range([0, width]);
-    yscale.range([height, 0]);
-    svg.attr("width", yaxisw + xpad + width + rightpad).attr("height", toppad + height + ypad + xaxish);
-    xaxisg.attr("transform", "translate(" + (yaxisw + xpad) + "," + (toppad + height + ypad) + ")");
-    yaxisg.attr("transform", "translate(" + yaxisw + "," + toppad + ")");
-    drag.attr("x", yaxisw + xpad + width).attr("y", toppad + height + ypad + xaxish - 4);
-    axisstyle({
-      axis: xaxisg.call(axisBottom().scale(xscale)),
-      showline: true,
-      color: "black",
-      fontsize: Math.max(12, Math.min(20, width / 100))
-    });
-    axisstyle({
-      axis: yaxisg.call(
-        axisLeft().scale(yscale).tickValues([1, 0.1, 0.01, 1e-3, 1e-4, zerovalue]).tickFormat(format(" "))
-      ),
-      showline: true,
-      color: "black",
-      fontsize: Math.max(12, Math.min(20, height / 100))
-    });
-    g.attr("transform", "translate(" + (yaxisw + xpad) + "," + toppad + ")");
-    lines.attr("d", (d) => {
-      const lst = [];
-      for (let i = 0; i < d.samples.length; i++) {
-        const s = d.samples[i];
-        lst.push((i == 0 ? "M" : "L") + " " + xscale(s.date) + " " + yscale(s.maf));
-      }
-      return lst.join(" ");
-    });
-    if (showcircle) {
-      circles.attr("cx", (d) => xscale(d.date)).attr("cy", (d) => yscale(d.maf)).attr("r", (d) => Math.sqrt(rscale(d.coverage)));
-    }
-    legend.attr("transform", "translate(" + (yaxisw + xpad + width + maxradius + 5) + "," + toppad + ")");
-    legend.selectAll("*").remove();
-    let y = minradius;
-    if (showcircle) {
-      legend.append("circle").attr("r", minradius).attr("cx", minradius).attr("cy", y).attr("fill", "#ccc");
-      legend.append("text").text(1).attr("x", minradius * 2 + 10).attr("y", y).attr("font-size", 10).attr("dominant-baseline", "central");
-      y += 5 + minradius + maxradius;
-      legend.append("circle").attr("r", maxradius).attr("cx", maxradius).attr("cy", y).attr("fill", "#ccc");
-      legend.append("text").text(maxcoverage).attr("x", maxradius * 2 + 10).attr("y", y).attr("font-size", 15).attr("dominant-baseline", "central");
-      y += 15 + maxradius;
-    }
-    const fontsize = 12;
-    for (const snv of snvlst) {
-      legend.append("line").attr("x2", 30).attr("y1", y).attr("y2", y).attr("stroke", snv.color);
-      if (showcircle) {
-        legend.append("circle").attr("cx", 15).attr("cy", y).attr("r", 8).attr("fill", snv.color).attr("fill-opacity", 0.1);
-      }
-      legend.append("text").text(snv.gene).attr("dominant-baseline", "central").attr("font-size", fontsize).attr("x", 30 + 10).attr("y", y).attr("fill", snv.color).style("cursor", "default").on("mouseover", (event) => {
-        event.target.setAttribute("font-weight", "bold");
-        lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 3);
-      }).on("mouseout", (event) => {
-        event.target.setAttribute("font-weight", "normal");
-        lines.filter((d) => d.mutationname == snv.mutationname).attr("stroke-width", 1);
-      });
-      y += fontsize + 10;
-    }
-  };
-  setsize(width, height);
-  holder.append("div").style("text-align", "right").append("button").text("SVG").on("click", () => {
-    to_svg(svg.node(), "maf-timeline");
-  });
-}
-function makecontrol(snvlst, header, holder, graphholder, g1, g2, g3, g4) {
-  holder.selectAll("*").remove();
-  const table = holder.append("table");
-  for (const snv of snvlst) {
-    const tr = table.append("tr");
-    const td1 = tr.append("td");
-    td1.text(snv.gene).style("color", snv.color);
-    const td2 = tr.append("td");
-    const checkbox = td2.append("input").attr("type", "checkbox").style("zoom", "150%").property("checked", snv.show);
-    snv.checkbox = checkbox;
-    checkbox.on("change", (event) => {
-      snv.show = event.target.checked;
-      makegraph(snvlst, header, graphholder);
-    });
-    const butt = td2.append("button").style("margin-left", "5px").text("Only").on("click", () => {
-      for (const s2 of snvlst) {
-        s2.show = false;
-        s2.checkbox.property("checked", false);
-      }
-      snv.show = true;
-      snv.checkbox.property("checked", true);
-      makegraph(snvlst, header, graphholder);
-    });
-    let cname = Math.random();
-    const td11 = tr.append("td");
-    const c1 = td11.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(1, event.target));
-    td11.append("label").html("&nbsp;shared").attr("for", cname);
-    cname = Math.random();
-    const td22 = tr.append("td");
-    const c2 = td22.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(2, event.target));
-    td22.append("label").html("&nbsp;rising").attr("for", cname);
-    cname = Math.random();
-    const td33 = tr.append("td");
-    const c3 = td33.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(3, event.target));
-    td33.append("label").html("&nbsp;falling").attr("for", cname);
-    cname = Math.random();
-    const td44 = tr.append("td");
-    const c4 = td44.append("input").attr("type", "checkbox").attr("id", cname).on("change", (event) => cchange(4, event.target));
-    td44.append("label").html("&nbsp;R-only").attr("for", cname);
-    if (snv.subidx == 1) c1.property("checked", true);
-    if (snv.subidx == 2) c2.property("checked", true);
-    if (snv.subidx == 3) c3.property("checked", true);
-    if (snv.subidx == 4) c4.property("checked", true);
-    const cchange = (which, check) => {
-      if (!check.checked) {
-        snv.subidx = -1;
-      } else {
-        snv.subidx = which;
-        if (which == 1) {
-          c2.property("checked", false);
-          c3.property("checked", false);
-          c4.property("checked", false);
-        } else if (which == 2) {
-          c1.property("checked", false);
-          c3.property("checked", false);
-          c4.property("checked", false);
-        } else if (which == 3) {
-          c1.property("checked", false);
-          c2.property("checked", false);
-          c4.property("checked", false);
-        } else {
-          c1.property("checked", false);
-          c2.property("checked", false);
-          c3.property("checked", false);
-        }
-      }
-      makesubgraph(snvlst, g1, g2, g3, g4);
-    };
-  }
-}
-export {
-  maftimelineui as default
-};
-//# sourceMappingURL=maftimeline-FOQF6O3X.js.map