function getMax(values)
{
	var result = 0;
	for (var i = 0; i < values.length; i++)
	{
		if (values[i] > result)
			result = values[i];
	}
	return result;
}

/**
 * This function will first convert the spectrum mass and intensities list in MSP format
 * to the internal lists needed by renderSpectrum function.
 * 
 * @param spectrumMSPString : list of masses and intensities in the following format:
 *  e.g. :  "14 8; 15 15; 27 18; 28 15; 29 15; 30 11; 32 19; 39 32; 40 12; 41 68;"
 */
function renderSpectrumFromMSPString(spectrumMSPString, targetElement)
{
	var spectrum1 = getSpectrumObjectFromMSPString(spectrumMSPString);	
	renderSpectrum(spectrum1, null,targetElement);
}

function endsWith(str, suffix) {
    return str.indexOf(suffix, str.length - suffix.length) !== -1;
}

function getSpectrumObjectFromCouplesString(spectrumCouplesString, couplesSeparator, massAndIntensitySeparator)
{
	var couples = spectrumCouplesString.split(couplesSeparator);
	var masses = new Array();
	var intensities = new Array();
	for (var i = 0; i < couples.length; i++)
	{
		var couple = couples[i].trim().split(massAndIntensitySeparator)
		var mass = parseInt(couple[0])
		var intensity = parseInt(couple[1])
		masses.push(mass);
		intensities.push(intensity);
	}
	var spectrum1 = new Object();
	spectrum1.masses = masses;
	spectrum1.intensities = intensities;
	return spectrum1;
}

function getSpectrumObjectFromMSPString(spectrumMSPString)
{
	spectrumMSPString = spectrumMSPString.trim();
	if (endsWith(spectrumMSPString, ";"))
		spectrumMSPString = spectrumMSPString.substring(0, spectrumMSPString.length - 1);
	return getSpectrumObjectFromCouplesString(spectrumMSPString, ';', ' ');
}


function getSpectrumObjectFromJCAMPString(spectrumJCAMPString)
{
	var spectrum = getSpectrumObjectFromCouplesString(spectrumJCAMPString, ' ', ',');
	for (var i = 0; i < spectrum.intensities.length; i++)
		spectrum.intensities[i] = spectrum.intensities[i]/10;
	return spectrum;
}

/**
 * This function will render a comparison spectrum comparable to 
 * the NIST "head to tail" visualization to compare the measured spectrum 
 * with the matched library spectrum. 
 * 
 * NB: One important detail in this function 
 * is that the library spectrum is not available in NIST output, so 
 * its representative is retrieved from NIST's webbook website in this case.
 * (e.g. http://webbook.nist.gov/cgi/cbook.cgi?JCAMP=C537268&Index=0&Type=Mass
 *  for casNr = "C537268" ) 
 * 
 * 
 * @param spectrumMSPString
 * @param casNr
 * @param targetElement
 */
function renderComparisonSpectrum(spectrumMSPString, casNr, targetElement)
{
	var peakTable;
	try
	{
		//remove dashes:
		casNr = casNr.replace("-", "");
		peakTable = httpGet2("/nist_controller/get_nistdata?casnr="+casNr);
		
	}
	catch(e)
	{
		try
		{
			//workaround for galaxy.wur.nl/galaxy_production/ scenario TODO: make more robust code:
			peakTable = httpGet2("/galaxy_production/nist_controller/get_nistdata?casnr="+casNr);
		}
		catch(e2)
		{
			//assume running locally:
			alert("Error while trying to get data from NIST. Rendering library spectrum with dummy data.");
			peakTable = "55,290 56,240 57,100 58,80"+
						" 63,30 65,150 66,50 67,1271"+
						" 68,370 69,100 70,210 71,10"+
						" 74,50 75,60 76,120 77,2312"+
						" 78,220 79,120 80,190 81,630"+
						" 82,4884 83,2702 84,240 85,20"+
						" 91,180 92,50 93,210 94,3353"+
						" 95,1371 96,1261 97,370 98,120"+
						" 105,1621 106,160 107,70 108,220"+
						" 109,80 110,60 111,30 112,40"+
						" 121,30 122,460 123,940 124,9999";
			//note that the intensities in jcamp response are 10x when compared to MSP format
		}
	}
	var spectrum1 = getSpectrumObjectFromMSPString(spectrumMSPString);
	var spectrum2 = getSpectrumObjectFromJCAMPString(peakTable);
	renderSpectrum(spectrum1, spectrum2,targetElement);	
}

function httpGet2(theUrl)
{
    //Tried many options: the solution was to add a new service to our
	//Galaxy server to act as a proxy to the NIST site and then retrieve the data.
	
	//way of working: added a new controller to 
	// /home/lukas007/galaxy-dist/lib/galaxy/webapps/galaxy/controllers
	// which gives the service "/nist_controller/get_nistdata?casnr=<casnr>"
	
	var xmlHttp = null;

    xmlHttp = new XMLHttpRequest();
    xmlHttp.open( "GET", theUrl, false );
    xmlHttp.send( null );
    if (xmlHttp.status == 404)
    	throw new Exception("Error while trying to access the data: " + xmlHttp.statusText)
    return xmlHttp.responseText;
}



/**
 * This function will ensure only the local highest peaks get a label 
 * to make the spectrum more readable and avoid all the overlapping labels
 * of minor peaks. 
 * 
 * @param spectrum
 */
function getSpectrumLabels(spectrum)
{
	//TODO - improve logic to include more labels when area of peaks is sparse enough.
	//for now we let all labels, keep only the ones where intensity > 100:
	//and leave the largest/last mass as well:
	var result = new Array();
	for (var i = 0; i < spectrum.masses.length; i++)
	{
		if (spectrum.intensities[i] > 100 || i == spectrum.masses.length-1)
			result.push(spectrum.masses[i]);
		else
			result.push("");
	}
	return result;
}

function renderSpectrum(spectrum1, spectrum2, targetElement)
{
	var maxMassSpectrum1 = getMax(spectrum1.masses);
	var maxX = maxMassSpectrum1;
	spectrum1.labels = getSpectrumLabels(spectrum1)
	var maxMassSpectrum2 = 0;
	if (spectrum2 != null)
	{
		maxMassSpectrum2 = getMax(spectrum2.masses);
		if (maxMassSpectrum2 > maxMassSpectrum1)
			maxX = maxMassSpectrum2;
		spectrum2.labels = getSpectrumLabels(spectrum2)
	}
	maxX += 20;
	
	var margin = {top: 80, right: 80, bottom: 80, left: 80};
	//var width = maxX*2 - margin.left - margin.right;
	//fixed width is better:
	var width = 600 - margin.left - margin.right;
	var zoomFactor = 1;
	
	var height;
	//if (spectrum2 != null)
		//height = 800 - margin.top - margin.bottom;
	//else
		height = 400 - margin.top - margin.bottom;
		
	//var x = d3.scale.ordinal()
	  // .rangeRoundBands([0, width], .1);
	
	var x = d3.scale.linear().domain([0, maxX]).range([0, width]);
	
	var y0 = d3.scale.linear().domain([300, 1100]).range([height, 0]);
	
	var xAxis = d3.svg.axis()
	    .scale(x)
	    .orient("center");
	
	// create left yAxis
	var yAxisLeft = d3.svg.axis().scale(y0).ticks(4).orient("left");
	
	
	var svg = d3.select(targetElement).append("svg")
	    .attr("width", width + margin.left + margin.right)
	    .attr("height", height + margin.top + margin.bottom)
	  .append("g")
	    .attr("class", "graph")
	    .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
	
	
	 //x.domain([0,10,500]);
	 if (spectrum2 != null)
	 {
	 	y0.domain([-999, 999]);
	 }
	 else
 	 {
		y0.domain([0, 999]);
 	 }
	 svg.append("g")
     .attr("class", "x axis")
   	 .append("line")
     .attr("y1", y0(0))
     .attr("y2", y0(0))
     .attr("x2", width);
	 
	 svg.append("g")
	  .attr("class", "y axis axisLeft")
	  .attr("transform", "translate(0,0)")
	  .call(yAxisLeft)
	.append("text")
	  .attr("y", 6)
	  .attr("dy", "-2em")
	  .style("text-anchor", "end")
	  .text("Relative Intensity");
	

	 
	//for each mass in spectrum 1, generate bar:
	for (var i = 0; i < spectrum1.masses.length; i++)
	{
		var heightFactor = 1;
		if (spectrum2 != null)
			heightFactor = 2;
		
		svg.append("rect")
		     .attr("class", "bar1")
		     .attr("x", x(spectrum1.masses[i]*zoomFactor))
		     .attr("width", 1)
		     .attr("y", y0(spectrum1.intensities[i]))
		 	 .attr("height", height/heightFactor - y0(spectrum1.intensities[i]));
		svg.append("text")
		  .attr("x", x(spectrum1.masses[i]*zoomFactor))
		  .attr("y", y0(spectrum1.intensities[i]))
		  .attr("dy", "-1em")
		  .attr("dx", "-1em")
		  .style("text-anchor", "start")
		  .text(spectrum1.labels[i]);
	}
	
	if (spectrum2 != null)
	{
		for (var i = 0; i < spectrum2.masses.length; i++)
		{
			heightFactor = 2;
			
			svg.append("rect")
			     .attr("class", "bar2")
			     .attr("x", x(spectrum2.masses[i]*zoomFactor))
			     .attr("width", 1)
			     .attr("y", y0(0))
			 	 .attr("height", height/heightFactor - y0(spectrum2.intensities[i]));
			svg.append("text")
			  .attr("x", x(spectrum2.masses[i]*zoomFactor))
			  .attr("y", y0(-spectrum2.intensities[i]))
			  .attr("dy", "1.5em")
			  .attr("dx", "-1em")
			  .style("text-anchor", "start")
			  .text(spectrum2.labels[i]);
		}
	}

}