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note that these are currently put into the style section instead of being\n// defined in classes to aid copy and paste to an external document e.g. word\nexport const intronColor = undefined\nexport const utrColor = 'rgb(200,240,240)'\nexport const proteinColor = 'rgb(220,160,220)'\nexport const cdsColor = 'rgb(220,220,180)'\nexport const updownstreamColor = 'rgba(250,200,200)'\nexport const genomeColor = 'rgb(200,280,200)'\n\nexport function splitString({\n  str,\n  charactersPerRow,\n  showCoordinates,\n  currRemainder = 0,\n  splitSize = 10,\n}: {\n  str: string\n  charactersPerRow: number\n  showCoordinates: boolean\n  currRemainder?: number\n  splitStart?: number\n  splitSize?: number\n}) {\n  const numChunks = Math.ceil(str.length / charactersPerRow)\n  const chunks = new Array(numChunks)\n  let splitStart = currRemainder % 10\n\n  let iter = 0\n  let offset = 0\n  for (; iter < numChunks + 1; ++iter) {\n    const inc = iter === 0 ? charactersPerRow - currRemainder : charactersPerRow\n    const r = str.slice(offset, offset + inc)\n    if (!r) {\n      break\n    }\n    if (showCoordinates) {\n      let res = ''\n      for (let i = 0, j = splitStart; i < r.length; i++, j++) {\n        // note: this adds a space at the start but it causes trouble to try to\n        // say e.g. j%splitSize==0 && j to try to only add non-zero spaces\n        if (j % splitSize === 0) {\n          res += ' '\n          j = 0\n        }\n        res += r[i]\n      }\n      if (res) {\n        chunks[iter] = res\n      }\n    } else {\n      chunks[iter] = r\n    }\n    splitStart = 0 // after newline, reset\n    offset += inc\n  }\n\n  return {\n    segments: chunks,\n    remainder:\n      ((chunks.at(-1)?.replaceAll(' ', '').length || 0) +\n        (iter < 2 ? currRemainder : 0)) %\n      charactersPerRow,\n  }\n}\n","import React from 'react'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport { observer } from 'mobx-react'\n\nconst SequenceDisplay = observer(function ({\n  chunks,\n  start,\n  color,\n  strand = 1,\n  coordStart = start,\n  model,\n}: {\n  chunks: string[]\n  start: number\n  coordStart?: number\n  strand?: number\n  color?: string\n  model: SequenceFeatureDetailsModel\n}) {\n  const { charactersPerRow, showCoordinates } = model\n\n  return chunks.map((chunk, idx) => {\n    const f = coordStart - (start % charactersPerRow)\n    const prefix =\n      (idx === 0 && start % charactersPerRow === 0) || idx > 0\n        ? `${`${f + idx * strand * charactersPerRow}`.padStart(4)}   `\n        : ''\n    const postfix =\n      idx === chunks.length - 1 &&\n      (chunks.at(-1)?.replaceAll(' ', '').length || 0) +\n        (idx === 0 ? start % charactersPerRow : 0) !==\n        charactersPerRow\n        ? null\n        : showCoordinates\n          ? ' \\n'\n          : ''\n    return (\n      /* biome-ignore lint/suspicious/noArrayIndexKey: */\n      <React.Fragment key={`${chunk}-${idx}`}>\n        {showCoordinates ? prefix : null}\n        <span style={{ background: color }}>{chunk}</span>\n        {postfix}\n      </React.Fragment>\n    )\n  })\n})\n\nexport default SequenceDisplay\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { Feat } from '../../util'\nimport { splitString, cdsColor, updownstreamColor, utrColor } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\nimport { SimpleFeatureSerialized } from '../../../util'\n\nconst CDNASequence = observer(function ({\n  utr,\n  cds,\n  exons,\n  sequence,\n  upstream,\n  downstream,\n  feature,\n  includeIntrons,\n  collapseIntron,\n  model,\n}: {\n  utr: Feat[]\n  cds: Feat[]\n  exons: Feat[]\n  sequence: string\n  upstream?: string\n  downstream?: string\n  feature: SimpleFeatureSerialized\n  includeIntrons?: boolean\n  collapseIntron?: boolean\n  model: SequenceFeatureDetailsModel\n}) {\n  const {\n    upperCaseCDS,\n    intronBp,\n    charactersPerRow,\n    showCoordinates,\n    showCoordinatesSetting,\n  } = model\n  const hasCds = cds.length > 0\n  const chunks = (\n    cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons\n  ).filter(f => f.start !== f.end)\n  const toLower = (s: string) => (upperCaseCDS ? s.toLowerCase() : s)\n  const toUpper = (s: string) => (upperCaseCDS ? s.toUpperCase() : s)\n\n  const strand = feature.strand === -1 ? -1 : 1\n  const fullGenomicCoordinates =\n    showCoordinatesSetting === 'genomic' && includeIntrons && !collapseIntron\n\n  const mult = fullGenomicCoordinates ? strand : 1\n  let coordStart = fullGenomicCoordinates\n    ? strand > 0\n      ? feature.start + 1 - (upstream?.length || 0)\n      : feature.end + (upstream?.length || 0)\n    : 0\n  let currStart = 0\n  let currRemainder = 0\n\n  let upstreamChunk = null as React.ReactNode\n  if (upstream) {\n    const { segments, remainder } = splitString({\n      str: toLower(upstream),\n      charactersPerRow,\n      showCoordinates,\n    })\n    upstreamChunk = (\n      <SequenceDisplay\n        model={model}\n        color={updownstreamColor}\n        strand={mult}\n        start={currStart}\n        coordStart={coordStart}\n        chunks={segments}\n      />\n    )\n    currRemainder = remainder\n    currStart = currStart + upstream.length * mult\n    coordStart = coordStart + upstream.length * mult\n  }\n\n  const middleChunks = [] as React.ReactNode[]\n  for (let idx = 0; idx < chunks.length; idx++) {\n    const chunk = chunks[idx]!\n    const intron = sequence.slice(chunk.end, chunks[idx + 1]?.start)\n    const s = sequence.slice(chunk.start, chunk.end)\n    const { segments, remainder } = splitString({\n      str: hasCds\n        ? chunk.type === 'CDS'\n          ? toUpper(s)\n          : toLower(s)\n        : toUpper(s),\n      charactersPerRow,\n      currRemainder,\n      showCoordinates,\n    })\n\n    middleChunks.push(\n      <SequenceDisplay\n        key={`${JSON.stringify(chunk)}-mid`}\n        model={model}\n        color={chunk.type === 'CDS' ? cdsColor : utrColor}\n        strand={mult}\n        start={currStart}\n        coordStart={coordStart}\n        chunks={segments}\n      />,\n    )\n    currRemainder = remainder\n    currStart = currStart + s.length * mult\n    coordStart = coordStart + s.length * mult\n\n    if (intron && includeIntrons && idx < chunks.length - 1) {\n      const str = toLower(\n        collapseIntron && intron.length > intronBp * 2\n          ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`\n          : intron,\n      )\n      const { segments, remainder } = splitString({\n        str,\n        charactersPerRow,\n        currRemainder,\n        showCoordinates,\n      })\n\n      if (segments.length) {\n        middleChunks.push(\n          <SequenceDisplay\n            key={`${JSON.stringify(chunk)}-intron`}\n            model={model}\n            strand={mult}\n            coordStart={coordStart}\n            start={currStart}\n            chunks={segments}\n          />,\n        )\n        currRemainder = remainder\n        currStart = currStart + str.length * mult\n        coordStart = coordStart + str.length * mult\n      }\n    }\n  }\n\n  let downstreamChunk = null as React.ReactNode\n  if (downstream) {\n    const { segments } = splitString({\n      str: toLower(downstream),\n      charactersPerRow,\n      currRemainder,\n      showCoordinates,\n    })\n    downstreamChunk = (\n      <SequenceDisplay\n        start={currStart}\n        model={model}\n        strand={mult}\n        chunks={segments}\n        coordStart={coordStart}\n        color={updownstreamColor}\n      />\n    )\n  }\n  return (\n    <>\n      {upstreamChunk}\n      {middleChunks}\n      {downstreamChunk}\n    </>\n  )\n})\n\nexport default CDNASequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { Feat, stitch } from '../../util'\nimport { proteinColor, splitString } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\n\nconst ProteinSequence = observer(function ({\n  cds,\n  sequence,\n  codonTable,\n  model,\n}: {\n  cds: Feat[]\n  sequence: string\n  codonTable: Record<string, string>\n  model: SequenceFeatureDetailsModel\n}) {\n  const { charactersPerRow, showCoordinates } = model\n  const str = stitch(cds, sequence)\n  let protein = ''\n  for (let i = 0; i < str.length; i += 3) {\n    // use & symbol for undefined codon, or partial slice\n    protein += codonTable[str.slice(i, i + 3)] || '&'\n  }\n  const { segments } = splitString({\n    str: protein,\n    charactersPerRow,\n    showCoordinates,\n  })\n  return (\n    <SequenceDisplay\n      model={model}\n      color={proteinColor}\n      chunks={segments}\n      start={0}\n    />\n  )\n})\n\nexport default ProteinSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { genomeColor, splitString, updownstreamColor } from '../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\nimport { SimpleFeatureSerialized } from '../../../util'\n\nconst GenomicSequence = observer(function ({\n  sequence,\n  upstream,\n  feature,\n  downstream,\n  model,\n}: {\n  sequence: string\n  feature: SimpleFeatureSerialized\n  upstream?: string\n  downstream?: string\n  model: SequenceFeatureDetailsModel\n}) {\n  const { charactersPerRow, showCoordinatesSetting, showCoordinates } = model\n  let currStart = 0\n  let upstreamChunk = null as React.ReactNode\n  let currRemainder = 0\n  const strand = feature.strand === -1 ? -1 : 1\n  const fullGenomicCoordinates = showCoordinatesSetting === 'genomic'\n  const mult = fullGenomicCoordinates ? strand : 1\n  let coordStart = fullGenomicCoordinates\n    ? strand > 0\n      ? feature.start + 1 - (upstream?.length || 0)\n      : feature.end + (upstream?.length || 0)\n    : 0\n  if (upstream) {\n    const { segments, remainder } = splitString({\n      str: upstream,\n      charactersPerRow,\n      showCoordinates,\n    })\n    upstreamChunk = (\n      <SequenceDisplay\n        model={model}\n        color={updownstreamColor}\n        start={currStart}\n        coordStart={coordStart}\n        chunks={segments}\n      />\n    )\n    currRemainder = remainder\n    currStart = currStart + upstream.length * mult\n    coordStart = coordStart + upstream.length * mult\n  }\n\n  const { segments, remainder } = splitString({\n    str: sequence,\n    charactersPerRow,\n    showCoordinates,\n    currRemainder,\n  })\n  const middleChunk = (\n    <SequenceDisplay\n      model={model}\n      color={genomeColor}\n      start={currStart}\n      coordStart={coordStart}\n      chunks={segments}\n    />\n  )\n  currRemainder = remainder\n  currStart += sequence.length * mult\n  coordStart = coordStart + sequence.length * mult\n\n  let downstreamChunk = null as React.ReactNode\n  if (downstream) {\n    const { segments } = splitString({\n      str: downstream,\n      charactersPerRow,\n      currRemainder,\n      showCoordinates,\n    })\n    downstreamChunk = (\n      <SequenceDisplay\n        start={currStart}\n        model={model}\n        chunks={segments}\n        coordStart={coordStart}\n        color={updownstreamColor}\n      />\n    )\n  }\n\n  return (\n    <>\n      {upstreamChunk}\n      {middleChunk}\n      {downstreamChunk}\n    </>\n  )\n})\n\nexport default GenomicSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { cdsColor, splitString } from '../util'\nimport { Feat, stitch } from '../../util'\nimport { SequenceFeatureDetailsModel } from '../model'\nimport SequenceDisplay from './SequenceDisplay'\n\nconst CDSSequence = observer(function ({\n  cds,\n  sequence,\n  model,\n}: {\n  cds: Feat[]\n  sequence: string\n  model: SequenceFeatureDetailsModel\n}) {\n  const { charactersPerRow, showCoordinates } = model\n  const { segments } = splitString({\n    str: stitch(cds, sequence),\n    charactersPerRow,\n    showCoordinates,\n  })\n  return (\n    <SequenceDisplay\n      model={model}\n      color={cdsColor}\n      chunks={segments}\n      start={0}\n    />\n  )\n})\n\nexport default CDSSequence\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport {\n  SimpleFeatureSerialized,\n  defaultCodonTable,\n  generateCodonTable,\n  revcom,\n  toLocale,\n} from '../../util'\nimport {\n  SeqState,\n  calculateUTRs,\n  calculateUTRs2,\n  dedupe,\n  revlist,\n} from '../util'\nimport { SequenceFeatureDetailsModel } from './model'\n// panel types\nimport CDNASequence from './seqtypes/CDNASequence'\nimport ProteinSequence from './seqtypes/ProteinSequence'\nimport GenomicSequence from './seqtypes/GenomicSequence'\nimport CDSSequence from './seqtypes/CDSSequence'\n\ninterface SequencePanelProps {\n  sequence: SeqState\n  feature: SimpleFeatureSerialized\n  model: SequenceFeatureDetailsModel\n}\n\nfunction getStrand(strand: number) {\n  if (strand === -1) {\n    return '(-)'\n  } else if (strand === 1) {\n    return '(+)'\n  } else {\n    return ''\n  }\n}\n\nfunction WordWrap({ children }: { children: React.ReactNode }) {\n  return (\n    <pre\n      style={{\n        /* raw styles instead of className so that html copy works */\n        fontFamily: 'monospace',\n        color: 'black',\n        fontSize: 11,\n      }}\n    >\n      {children}\n    </pre>\n  )\n}\n\nfunction NoWordWrap({ children }: { children: React.ReactNode }) {\n  return (\n    <div\n      style={{\n        /* raw styles instead of className so that html copy works */\n        fontFamily: 'monospace',\n        color: 'black',\n        fontSize: 11,\n        maxWidth: 600,\n        whiteSpace: 'wrap',\n        wordBreak: 'break-all',\n      }}\n    >\n      {children}\n    </div>\n  )\n}\n\nconst SequencePanel = observer(\n  React.forwardRef<HTMLDivElement, SequencePanelProps>(function S(props, ref) {\n    const { model, feature } = props\n    const { showCoordinates, mode } = model\n    let {\n      sequence: { seq, upstream = '', downstream = '' },\n    } = props\n    const { subfeatures = [] } = feature\n\n    const children = subfeatures\n      .sort((a, b) => a.start - b.start)\n      .map(sub => ({\n        ...sub,\n        start: sub.start - feature.start,\n        end: sub.end - feature.start,\n      }))\n\n    // we filter duplicate entries in cds and exon lists duplicate entries\n    // may be rare but was seen in Gencode v36 track NCList, likely a bug\n    // on GFF3 or probably worth ignoring here (produces broken protein\n    // translations if included)\n    //\n    // position 1:224,800,006..225,203,064 gene ENSG00000185842.15 first\n    // transcript ENST00000445597.6\n    //\n    // http://localhost:3000/?config=test_data%2Fconfig.json&session=share-FUl7G1isvF&password=HXh5Y\n\n    let cds = dedupe(children.filter(sub => sub.type === 'CDS'))\n    let utr = dedupe(children.filter(sub => sub.type?.match(/utr/i)))\n    let exons = dedupe(children.filter(sub => sub.type === 'exon'))\n\n    if (!utr.length && cds.length && exons.length) {\n      utr = calculateUTRs(cds, exons)\n    }\n    if (!utr.length && cds.length && !exons.length) {\n      utr = calculateUTRs2(cds, {\n        start: 0,\n        end: feature.end - feature.start,\n        type: 'gene',\n      })\n    }\n\n    if (feature.strand === -1) {\n      // doing this in a single assignment is needed because downstream and\n      // upstream are swapped so this avoids a temp variable\n      ;[seq, upstream, downstream] = [\n        revcom(seq),\n        revcom(downstream),\n        revcom(upstream),\n      ]\n      cds = revlist(cds, seq.length)\n      exons = revlist(exons, seq.length)\n      utr = revlist(utr, seq.length)\n    }\n    const codonTable = generateCodonTable(defaultCodonTable)\n\n    const Container = showCoordinates ? WordWrap : NoWordWrap\n    return (\n      <div\n        data-testid=\"sequence_panel\"\n        ref={ref}\n        style={{ maxHeight: 300, overflow: 'auto' }}\n      >\n        <Container>\n          <div style={{ background: 'white' }}>\n            {`>${[\n              `${feature.name || feature.id}-${mode}`,\n              `${feature.refName}:${toLocale(feature.start + 1)}-${toLocale(feature.end)}${getStrand(feature.strand as number)}`,\n              mode.endsWith('updownstream')\n                ? `+/- ${toLocale(model.upDownBp)} up/downstream bp`\n                : '',\n            ]\n              .filter(f => !!f)\n              .join(' ')}\\n`}\n          </div>\n          {mode === 'genomic' ? (\n            <GenomicSequence feature={feature} model={model} sequence={seq} />\n          ) : mode === 'genomic_sequence_updownstream' ? (\n            <GenomicSequence\n              model={model}\n              feature={feature}\n              sequence={seq}\n              upstream={upstream}\n              downstream={downstream}\n            />\n          ) : mode === 'cds' ? (\n            <CDSSequence model={model} cds={cds} sequence={seq} />\n          ) : mode === 'cdna' ? (\n            <CDNASequence\n              model={model}\n              exons={exons}\n              feature={feature}\n              cds={cds}\n              utr={utr}\n              sequence={seq}\n            />\n          ) : mode === 'protein' ? (\n            <ProteinSequence\n              model={model}\n              cds={cds}\n              codonTable={codonTable}\n              sequence={seq}\n            />\n          ) : mode === 'gene' ? (\n            <CDNASequence\n              model={model}\n              exons={exons}\n              feature={feature}\n              cds={cds}\n              utr={utr}\n              sequence={seq}\n              includeIntrons\n            />\n          ) : mode === 'gene_collapsed_intron' ? (\n            <CDNASequence\n              model={model}\n              exons={exons}\n              feature={feature}\n              cds={cds}\n              sequence={seq}\n              utr={utr}\n              includeIntrons\n              collapseIntron\n            />\n          ) : mode === 'gene_updownstream' ? (\n            <CDNASequence\n              model={model}\n              exons={exons}\n              feature={feature}\n              cds={cds}\n              sequence={seq}\n              utr={utr}\n              upstream={upstream}\n              downstream={downstream}\n              includeIntrons\n            />\n          ) : mode === 'gene_updownstream_collapsed_intron' ? (\n            <CDNASequence\n              model={model}\n              exons={exons}\n              feature={feature}\n              cds={cds}\n              sequence={seq}\n              utr={utr}\n              upstream={upstream}\n              downstream={downstream}\n              includeIntrons\n              collapseIntron\n            />\n          ) : (\n            <div>Unknown type</div>\n          )}\n        </Container>\n      </div>\n    )\n  }),\n)\n\nexport default SequencePanel\n"],"names":["cdsColor","updownstreamColor","splitString","str","charactersPerRow","showCoordinates","currRemainder","splitSize","numChunks","Math","ceil","length","chunks","Array","splitStart","iter","offset","inc","r","slice","res","i","j","segments","remainder","at","replaceAll","observer","start","color","strand","coordStart","model","map","chunk","idx","prefix","padStart","postfix","React","key","style","background","utr","cds","exons","sequence","upstream","downstream","feature","includeIntrons","collapseIntron","upperCaseCDS","intronBp","showCoordinatesSetting","hasCds","sort","a","b","filter","f","end","toLower","s","toLowerCase","toUpper","toUpperCase","fullGenomicCoordinates","mult","currStart","upstreamChunk","SequenceDisplay","middleChunks","intron","type","push","JSON","stringify","downstreamChunk","codonTable","stitch","protein","middleChunk","WordWrap","children","fontFamily","fontSize","NoWordWrap","maxWidth","whiteSpace","wordBreak","props","ref","mode","seq","subfeatures","sub","dedupe","match","calculateUTRs","calculateUTRs2","revcom","revlist","generateCodonTable","defaultCodonTable","Container","maxHeight","overflow","name","id","refName","toLocale","endsWith","upDownBp","join","GenomicSequence","CDSSequence","CDNASequence","ProteinSequence"],"sourceRoot":""}