How to use locutus - 10 common examples

var sizes = GenomePlot.chromosomes[ d.toString() ];

					// the space between adjacent chroms
					var space = GenomePlot.MAX_CHROMOSOME_BASE - sizes.chromSizeLeft - sizes.chromSizeRight;

					return GenomePlot.linearGenomicToPaddedPixelScaleX( sizes.chromSizeLeft + space/2 ).toFixed(GenomePlot.FLOAT_PRECISION);
				} )
				.attr( "y1", function( d ) { return GenomePlot.linearWindowPixelToPaddedPixelScaleY( (d === 23 ? 12 : (d-1)) * GenomePlot.pixelsPerLine ).toFixed(GenomePlot.FLOAT_PRECISION); } )
				.attr( "y2", function( d ) { return GenomePlot.linearWindowPixelToPaddedPixelScaleY( (d === 23 ? 13 : (d)) * GenomePlot.pixelsPerLine ).toFixed(GenomePlot.FLOAT_PRECISION); } )
		;

		divs.exit().remove();
	}

	var endTime = performance.now();
	if( GenomePlot.debug ) console.info( sprintf( "%-20s duration: %.4f seconds", "drawVerticalDividers():", ((endTime-startTime)/1000) ) );
}	// drawVerticalDividers

.done (function () {
				GenomePlot.matepairDataStartTime = performance.now();
				console.info( sprintf( "%-20s Started loading Mate Pair data file: %s at %.4fms", "initData():", GenomePlot.matepairDataFile, GenomePlot.matepairDataStartTime ) );

				// load pipeline file, synchronously
				GenomePlot.matepairData = $.ajaxJSONSync (GenomePlot.matepairDataFile);

				var endTime = performance.now();
				console.info( sprintf( "%-20s Finished loading Mate Pair data file: %s at %.4fms (duration: %.4f seconds)", "initData():", GenomePlot.matepairDataFile, endTime, ( ( endTime - GenomePlot.matepairDataStartTime ) / 1000 ) ) );

				// initGUI should be initialized
				if( GenomePlot.matepairData === undefined || GenomePlot.matepairData === null
				||	GenomePlot.gui === undefined )
					return;

				// change the file paths to be relative to the directory the files were copied to
				for( var record in GenomePlot.matepairData ) {
					if( typeof GenomePlot.matepairData[record] !== "string" )
						continue;

					GenomePlot.matepairData[record] =
						GenomePlot.prefixFile + "/" + GenomePlot.matepairData[record].basename();
				}

				GenomePlot.copyNumber30000DataFile = GenomePlot.matepairData["cnvBinned30KJson"];

.call( GenomePlot.axisY_R );

		// fix the resulting text
		yAxisNode_R.selectAll("text")
			.style( {
				"stroke": "none",
				"fill": "black",
				"cursor": "pointer",
			} )
			.each( vCenter( GenomePlot.scale * GenomePlot.pixelsPerLine ) )
			.each( hCenter( GenomePlot.margin.right - 5, 1 ) )
		;
	}

	var endTime = performance.now();
	if( GenomePlot.debug ) console.info( sprintf( "%-20s duration: %.4f seconds", "drawAxis():", ((endTime-startTime)/1000) ) );
};	// drawAxis

console.error( sprintf( "%-20s Rejected loading Cytoband file: %s with %s at %.4fms (duration: %.4f seconds)", "initData():", GenomePlot.cytoBandFile, value, endTime, ( ( endTime - GenomePlot.cytoBandDataStartTime ) / 1000 ) ) );
					},
					function( error ) {
						console.error( sprintf( "%-20s Failed to load Cytoband file: %s with %s", "initData():", GenomePlot.cytoBandFile, error ) );
					}
				);
			} )
			.fail (function () {
				console.error( sprintf( "%-18s Failed to find Cytoband file: %s", "initData():", GenomePlot.cytoBandFile ) );
			} );
	}

	// load alterations data
	GenomePlot.alterationsData = undefined;
	if( GenomePlot.alterationsDataFile === undefined ) {
		console.error( sprintf( "%-18s Undefined Alterations file", "initData():" ) );
	}
	else {
		$.ajaxFileExists (GenomePlot.alterationsDataFile)
			.done (function () {
				GenomePlot.alterationsDataStartTime = performance.now();
				console.info( sprintf( "%-20s Started loading Alterations file: %s at %.4fms", "initData():", GenomePlot.alterationsDataFile, GenomePlot.alterationsDataStartTime ) );
				GenomePlot.loadedResources++;

				d3.text( GenomePlot.alterationsDataFile, "text/csv", function( data )
				{
					var endTime = performance.now();
					console.info( sprintf( "%-20s Finished loading Alterations file: %s at %.4fms (duration: %.4f seconds)", "initData():", GenomePlot.alterationsDataFile, endTime, ( ( endTime - GenomePlot.alterationsDataStartTime ) / 1000 ) ) );
					GenomePlot.loadedResources--;

					GenomePlot.alterationsData = GenomePlot.processAlterationsData(data);

for( var j = 0; j < maskedIndicesRanges.length; j++ )
		{
			GenomePlot.copyNumber30000Data.toLegacy.wdnsMaskedPerChrom[ chrom_id ]
				.push( GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ][ maskedIndicesRanges[ j ] ] );
		}

		// do the same for the end of the chrom. if the last point does not match the expected value it is masked
		// add it directly to the array
		if( GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ][ GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ].length - 1 ] !== (chromosomeEnds - chromosomeStarts) * GenomePlot.copyNumber30000Data.windowSize ) {
			GenomePlot.copyNumber30000Data.toLegacy.wdnsMaskedPerChrom[ chrom_id ]
				.push( GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ][ GenomePlot.copyNumber30000Data.toLegacy.wdnsPerChrom[ chrom_id ].length - 1 ],
						GenomePlot.chromosomes[ (chrom_id+1).toString() ].genomicSize );	// instead of pushing (chromosomeEnds - chromosomeStarts) * GenomePlot.copyNumber30000Data.windowSize push the actual chrom end since we now we are at the end of the chromosome
		}
	}
	console.info( sprintf( "%-20s     Total CNV elements to draw: %s", "initData():", frqCnt.toLocaleString() ) );

	// for the garbage collector
	GenomePlot.copyNumber30000Data.cnv = null;
	GenomePlot.copyNumber30000Data.normalCnv = null;
	GenomePlot.copyNumber30000Data.toLegacy.wdns = null;
	GenomePlot.copyNumber30000Data.toLegacy.frq = null;

	frqGreaterTwoPerChrom = null;
	maskedIndicesArray = null;
	maskedIndicesRanges = null;
};	// processCopyNumber30000Data

GenomePlot.computeChromosomeStartPositions = function ()
{
	if( GenomePlot.graphTypeParams.graphType === "U-Shape" )
	{
		// initialize it every time the function runs; garbage collection will take care of the memory
		GenomePlot.chromPixelStarts = new Array( GenomePlot.NUM_CHROMS );

		GenomePlot.linesPerGraph = 13;

		// height in pixels of one line holding one chromosome (or two)
		GenomePlot.pixelsPerLine = GenomePlot.innerHeight / GenomePlot.linesPerGraph;
		if (GenomePlot.debug) console.log (sprintf ("%-20s pixels/line: %f", "computeChromosomeStartPositions():", GenomePlot.pixelsPerLine));

		// create the start pixels positions of the left chromosomes
		for (var i = 0; i < 13; i++)
		{
			var chrom_id = i+1;

			var cx = 0;
			var cy = (i + 0.5) * GenomePlot.pixelsPerLine;		// computed in the un-padded space

			// x: genomic value; y: pixel value
			if (chrom_id === 13)
				GenomePlot.chromPixelStarts[24-2] = { x: cx, y: cy, adjust: 0 };
			else
				GenomePlot.chromPixelStarts[chrom_id-1] = { x: cx, y: cy, adjust: 0 };
		}

module.exports = function extract (arr, type, prefix)  {
  // From: http://locutusjs.org/php
  // +   original by: Brett Zamir (http://brett-zamir.me)
  // %        note 1: Only works by extracting into global context (whether called in the global scope or
  // %        note 1: within a function); also, the EXTR_REFS flag I believe can't be made to work
  // *     example 1: size = 'large';
  // *     example 1: var_array = {'color' : 'blue', 'size' : 'medium', 'shape' : 'sphere'};
  // *     example 1: extract(var_array, 'EXTR_PREFIX_SAME', 'wddx');
  // *     example 1: color+'-'+size+'-'+shape+'-'+wddx_size;
  // *     returns 1: 'blue-large-sphere-medium'
  if (Object.prototype.toString.call(arr) === '[object Array]' &&
      (type !== 'EXTR_PREFIX_ALL' && type !== 'EXTR_PREFIX_INVALID')) {
    return 0;
  }
  var targetObj = this.window;
  if (this.php_js && this.php_js.ini && this.php_js.ini['locutus.extractTargetObj'] && this.php_js.ini['locutus.extractTargetObj'].local_value) { // Allow designated object to be used instead of window
    targetObj = this.php_js.ini['locutus.extractTargetObj'].local_value;
  }
  var chng = 0;

  for (var i in arr) {
    var validIdent = /^[_a-zA-Z$][\w|$]*$/; // TODO: Refine regexp to allow JS 1.5+ Unicode identifiers
    var prefixed = prefix + '_' + i;
    try {
      switch (type) {
        case 'EXTR_PREFIX_SAME' || 2:
          if (targetObj[i] !== undefined) {
            if (prefixed.match(validIdent) !== null) {
              targetObj[prefixed] = arr[i];
              ++chng;
            }
          } else {

'IMAGETYPE_JP2': 10,
      'IMAGETYPE_JPX': 11,
      'IMAGETYPE_JB2': 12,
      'IMAGETYPE_SWC': 13,
      'IMAGETYPE_IFF': 14,
      'IMAGETYPE_WBMP': 15,
      'IMAGETYPE_JPEG2000': 9,
      'IMAGETYPE_XBM': 16
    }
  };

  if (this.php_js && this.php_js.ini && this.php_js.ini['locutus.get_defined_constants.setConstants'] && this.php_js.ini['locutus.get_defined_constants.setConstants'].local_value) {
    // Allow us to set a configuration to let this function set global constants
    if (this.php_js.ini['locutus.get_defined_constants.setConstants'].local_value === 'this') {
      win = this;
    } else if (this.php_js.ini['locutus.get_defined_constants.setConstants'].local_value === 'thisExt') {
      win = this;
      thisExt = true;
    } else {
      win = this.window;
    }

    for (ext in constObj) {
      if (thisExt) { // Allows namespacing constants (e.g,. this.pcre.PREG_OFFSET_CAPTURE)
        for (cnst in constObj[ext]) {
          if (!win[ext]) {
            win[ext] = {};
          }
          // These will not be real constants!
          win[ext][cnst] = constObj[ext][cnst];
        }
      } else {

'IMAGETYPE_BMP': 6,
      'IMAGETYPE_TIFF_II': 7,
      'IMAGETYPE_TIFF_MM': 8,
      'IMAGETYPE_JPC': 9,
      'IMAGETYPE_JP2': 10,
      'IMAGETYPE_JPX': 11,
      'IMAGETYPE_JB2': 12,
      'IMAGETYPE_SWC': 13,
      'IMAGETYPE_IFF': 14,
      'IMAGETYPE_WBMP': 15,
      'IMAGETYPE_JPEG2000': 9,
      'IMAGETYPE_XBM': 16
    }
  };

  if (this.php_js && this.php_js.ini && this.php_js.ini['locutus.get_defined_constants.setConstants'] && this.php_js.ini['locutus.get_defined_constants.setConstants'].local_value) {
    // Allow us to set a configuration to let this function set global constants
    if (this.php_js.ini['locutus.get_defined_constants.setConstants'].local_value === 'this') {
      win = this;
    } else if (this.php_js.ini['locutus.get_defined_constants.setConstants'].local_value === 'thisExt') {
      win = this;
      thisExt = true;
    } else {
      win = this.window;
    }

    for (ext in constObj) {
      if (thisExt) { // Allows namespacing constants (e.g,. this.pcre.PREG_OFFSET_CAPTURE)
        for (cnst in constObj[ext]) {
          if (!win[ext]) {
            win[ext] = {};
          }

~i ? Array[i] : Array[Stack.push(that) - 1] = {}
            this.method(that)
              .that = that
            return this.method(that)
          },
          method: function (that) {
            return Array[Stack.indexOf(that)]
          }
        }
      }
      return Relator()
    }())
  }
  // END REDUNDANT

  if (p && p.ini && p.ini['locutus.return_locutus_arrays'].local_value.toLowerCase() === 'on') {
    if (!p.LOCUTUS_Array) {
      // We keep this Relator outside the class in case adding prototype methods below
      // Prototype methods added elsewhere can also use this ArrayRelator to share these "pseudo-global mostly-private" variables
      __ = p.ArrayRelator = p.ArrayRelator || p.Relator.$()
      // We could instead allow arguments of {key:XX, value:YY} but even more cumbersome to write
      p.LOCUTUS_Array = function LOCUTUS_Array () {
        var _ = __.constructor(this),
          args = arguments,
          i = 0,
          argl, p
        args = (args.length === 1 && args[0] && typeof args[0] === 'object' &&
          // If first and only arg is an array, use that (Don't depend on this)
          args[0].length && !args[0].propertyIsEnumerable('length')) ? args[0] : args
        if (!_.objectChain) {
          _.objectChain = args
          _.object = {}