ideogram/src/js/ploidy.js

Chromosome visualization with D3.js

export class Ploidy {

  constructor(config) {
    this._config = config;
    this._description = this._normalize(this._config.ploidyDesc);
  }

  // Get number of chromosomes in a chromosome set
  getChromosomesNumber(setNumber) {
    if (this._config.ploidyDesc) {
      var chrSetCode = this._config.ploidyDesc[setNumber];
      if (chrSetCode instanceof Object) {
        return Object.keys(chrSetCode)[0].length;
      } else {
        return chrSetCode.length;
      }
    } else {
      return this._config.ploidy || 1;
    }
  }

  // Normalize use defined description
  _normalize(description) {
    var normalized, key, descValue;

    // Return the same if no description provided
    if (!description) {
      return description;
    }

    // Array of normalized description objects
    normalized = [];

    // Loop through description and normalize
    for (key in description) {
      descValue = description[key];
      if (typeof descValue === 'string') {
        if (this._config.orientation === 'vertical') {
          descValue = descValue.split('').reverse();
        }
        normalized.push({
          ancestors: descValue,
          existence: this._getexistenceArray(descValue.length)
        });
      } else {
        normalized.push({
          ancestors: Object.keys(descValue)[0],
          existence: descValue[Object.keys(descValue)[0]]
        });
      }
    }

    return normalized;
  }

  // Get array filled by '11' elements
  _getexistenceArray(length) {
    var array = [];

    for (var i = 0; i < length; i++) {
      array.push('11');
    }

    return array;
  }

  getSetSize(chrSetNumber) {
    if (this._description) {
      return this._description[chrSetNumber].ancestors.length;
    } else {
      return 1;
    }
  }

  // Get ancestor letter
  getAncestor(chrSetNumber, chrNumber) {
    if (this._description) {
      return this._description[chrSetNumber].ancestors[chrNumber];
    } else {
      return '';
    }
  }

  // Check if chromosome's arm should be rendered.
  // If no description was provided, method returns true and
  // something another depending on user provided description.
  exists(chrSetNumber, chrNumber, armNumber) {
    if (this._description) {
      var desc =
        this._description[chrSetNumber].existence[chrNumber][armNumber];
      return Number(desc) > 0;
    } else {
      return true;
    }
  }

}