ideogram/src/js/views/chromosome-model.js

Chromosome visualization for the web

function getPixelAndOtherData(bands, chr, hasBands, ideo) {
  var i, band, csLength, width, maxLength,
    pxStop = 0,
    taxid = chr.id.split('-')[1],
    cs = ideo.coordinateSystem,
    chrHeight = ideo.config.chrHeight;

  for (i = 0; i < bands.length; i++) {
    band = bands[i];
    csLength = band[cs].stop - band[cs].start;

    // If ideogram is rotated (and thus showing only one chromosome),
    // then set its width independent of the longest chromosome in this
    // genome.
    if (ideo._layout._isRotated) {
      width = chrHeight * csLength / chr.length;
    } else {
      if (ideo.config.chromosomeScale === 'relative') {
        maxLength = ideo.maxLength[taxid][cs];
      } else {
        maxLength = ideo.maxLength[cs];
      }
      width = chrHeight * chr.length / maxLength * csLength / chr.length;
    }
    bands[i].px = {start: pxStop, stop: pxStop + width, width: width};

    pxStop = bands[i].px.stop;

    if (hasBands && band.stain === 'acen' && band.name[0] === 'p') {
      chr.pcenIndex = i;
    }
  }
  return [bands, chr, pxStop];
}

/**
 * TODO:
 * A chromosome-level scale property is likely
 * nonsensical for any chromosomes that have cytogenetic band data.
 * Different bands tend to have ratios between number of base pairs
 * and physical length.
 *
 * However, a chromosome-level scale property is likely
 * necessary for chromosomes that do not have band data.
 *
 * This needs further review.
 */
function getChrScale(chr, hasBands, ideo) {
  var chrHeight = ideo.config.chrHeight,
    chrLength = chr.length,
    maxLength = ideo.maxLength,
    taxid = chr.id.split('-')[1],
    scale = {};

  scale.bp = chrHeight / maxLength.bp;

  if (ideo.config.multiorganism === true) {
    // chr.scale.bp = band.iscn.stop / band.bp.stop;
    if (ideo.config.chromosomeScale === 'relative') {
      scale.iscn = chrHeight * chrLength / maxLength[taxid].bp;
      scale.bp = chrHeight / maxLength[taxid].bp;
    } else {
      scale.iscn = chrHeight * chrLength / maxLength.bp;
    }
  } else if (hasBands) {
    scale.iscn = chrHeight / maxLength.iscn;
  }

  return scale;
}

function getChromosomePixels(chr) {
  var bands, chrHeight, pxStop, hasBands, maxLength,
    taxid = chr.id.split('-')[1],
    ideo = this;

  bands = chr.bands;
  chrHeight = ideo.config.chrHeight;
  pxStop = 0;
  hasBands = (typeof bands !== 'undefined');

  if (hasBands) {
    [bands, chr, pxStop] = getPixelAndOtherData(bands, chr, hasBands, ideo);
  } else {
    if (ideo.config.chromosomeScale === 'relative') {
      maxLength = ideo.maxLength[taxid][ideo.coordinateSystem];
    } else {
      maxLength = ideo.maxLength[ideo.coordinateSystem];
    }
    pxStop = chrHeight * chr.length / maxLength;
  }

  chr.width = pxStop;
  chr.scale = getChrScale(chr, hasBands, ideo);
  chr.bands = bands;

  return chr;
}

function getChrModelScaffold(chr, bands, chrName, ideo) {
  var hasBands = (typeof bands !== 'undefined');

  if (hasBands) {
    const lastBand = bands[bands.length - 1];
    chr.name = chrName;
    chr.length = lastBand[ideo.coordinateSystem].stop;

    // Accounts for case where this chromosome
    chr.bpLength = lastBand.bp.stop;

    chr.type = 'nuclear';
  } else {
    chr = chrName;
  }

  return chr;
}

/**
 * Encountered when processing an assembly that has chromosomes with
 * centromere data, but this chromosome does not.
 * Example: chromosome F1 in Felis catus.
 */
function deleteExtraneousBands(chr, hasBands) {
  if (hasBands && chr.bands.length === 1) {
    delete chr.bands;
  }
  return chr;
}

function getCentromerePosition(hasBands, bands) {

  if (hasBands === false) return '';

  // As with Macaca mulatta chromosome Y
  const firstBand = bands[0];
  const lastBand = bands.slice(-1)[0];
  const chrLength = lastBand.bp.stop - firstBand.bp.start;
  const smallLength = chrLength/20;

  if (
    // As with almost all mouse chromosome, chimpanzee chr22
    firstBand.name[0] === 'p' && bands[1].name[0] === 'q' &&
    firstBand.bp.stop - firstBand.bp.start < smallLength
  ) {
    return 'telocentric-p';
  }

  const penultimateBand = bands.slice(-2)[0];

  if (
    penultimateBand.name[0] === 'p' && lastBand.name[0] === 'q' &&
    lastBand.bp.stop - lastBand.bp.start < smallLength
  ) {
    // As with Macaca mulatta chromosome Y
    return 'telocentric-q';
  }

  return '';
}

/**
 * Generates a model object for each chromosome containing information on
 * its name, DOM ID, length in base pairs or ISCN coordinates, cytogenetic
 * bands, centromere position, etc.
 */
function getChromosomeModel(bands, chrName, taxid, chrIndex) {
  var hasBands, org,
    chr = {},
    ideo = this;

  hasBands = (typeof bands !== 'undefined');

  chr = getChrModelScaffold(chr, bands, chrName, ideo);

  chr.chrIndex = chrIndex;
  chr.id = 'chr' + chr.name + '-' + taxid;

  if (ideo.config.fullChromosomeLabels === true) {
    org = this.organisms[taxid];
    chr.name = org.scientificName + ' chr' + chr.name;
  }

  chr.bands = bands;
  chr = ideo.getChromosomePixels(chr);
  chr.centromerePosition = getCentromerePosition(hasBands, bands);

  chr = deleteExtraneousBands(chr, hasBands);

  return chr;
}

export {getChromosomeModel, getChromosomePixels};