# Source: drawsvg.js

    /**
     * Get the size of the svg based on the no. of rows and row length and other parameter.,.
     * @param {Object} parameters - Contains parameters of width, letter space etc., to draw SVG
     * @param {String} seq - Contains protein Sequence
     */
    function getSvgSize(parameters,seq)
    {
    	let seqLen = seq.length;
    	let num_of_rows = parseInt(seqLen/parameters.row_length) ;
    	let no_of_blocks = parameters.row_length/parameters.block_length - 1 ;
    	let width = parameters.letter_width * (parameters.row_length - 1)+ (no_of_blocks)*parameters.gap_width + parameters.right_margin + parameters.left_margin + 2*parameters.numerical_width;
    	let height = parameters.row_height * num_of_rows + parameters.bottom_margin + parameters.top_margin ;
    	return [width,height];
    }
    /**
     * Draw the sequence on to svg
     * @param {Object} parameters - Contains parameters of width, letter space etc., to draw SVG
     * @param {String} seq - Contains the protein sequence
     * @param {String} id -Contians id of the SVG tag from html.
     * @param {Array} massShiftList - Contains list of all the mass shifts
     * @param {Array} monoMassList - Contains Mono Mass list data
     */
    function buildSvg(parameters,seq,id,massShiftList,monoMassList)
    {
    	let massShiftListLen = massShiftList.length ;
    	d3.selectAll(".residue").remove();
    	let width,height ;
    	[width,height] = getSvgSize(parameters,seq) ;
    	/*create a group under svg with svgId_g*/
    	let id_temp = id + "_g" ;

    	let svgContainer = d3.select("#"+id)
    						.attr("width", width)
    						.attr("height", height)
    						.attr("font-family","'FreeMono',Miltonian,monospace")
    						.attr("font-size","16px")
    						.style("fill", parameters.svgBackground_color)
    	svgContainer = svgContainer.append("g")
    								.attr("id",id_temp)
    								.attr("class",id_temp);
    	text = 	svgContainer.selectAll("text");
    	let x,y ;
    	/*	Get the x and y coordinates of the acid position	*/
    	text.data(seq)
    		.enter()
    		.append("text")
    		.attr("class","residue")
    		.attr("x", function(d,i){
    			x = getX(parameters,i) ;
    			return x ;
    		})
    		.attr("y", function(d,i){
    			y = getY(parameters,i) ;
    			return y ;
    		})
    		.text(function(d,i){
    			for(let k=0;k<massShiftListLen;k++)
    			{
    				if( i == massShiftList[k].position && massShiftList[k].mass != 0)
    				{
    					MassShift(this,massShiftList[k].mass,i);
    					break;
    				}
    				else if(i == massShiftList[k].position && massShiftList[k].mass == 0)
    				{
    					MassShift(this,massShiftList[k].mass,i);
    				}
    			}
    			return d ;
    		})
    		.on("mouseover",function(d,i){
    			d3.select(this).style("cursor","pointer")
    			let id = "massshift_" + i;
    			d3.select("#"+id).attr("font-size","18px");
    		})
    		.on("mouseout",function(d,i){
    			d3.select(this).style("cursor","default")
    			let id = "massshift_" + i;
    			d3.select("#"+id).attr("font-size","11px");
    		})
    		.on("click",function(d,i){
    			handleOnClick(d,i,id,seq,massShiftList,monoMassList)
    		})
    		.style("fill",function(d,i){
    			for(let k=0;k<massShiftListLen;k++)
    			{
    				if( i == massShiftList[k].position )
    				{
    					MassShift(this,massShiftList[k].mass,i);
    					//return "red" ;
    					break;
    				}
    				else if(i == massShiftList[k].position)
    				{
    					MassShift(this,massShiftList[k].mass,i);
    				}
    			}
    			return "black" ;
    		})
    	return parameters;
    }
    /**
     * Handles on click actions.
     * on click of any amino acid, provides a box to enter mass shift.
     * On click of ok, will re calculate and redraws entire page.
     * @param {Char} d Current Amino Acid
     * @param {Integer} i Index or position of the amino acid
     * @param {String} id Contains Id of the SVG on which the sequence is drawn
     * @param {String} seq Sequence of the amino acid
     * @param {Array} massShiftList List of all the amino acids
     * @param {Array} monoMassList List of Mono Mass data
     */
    function handleOnClick(d,i,id,seq,massShiftList,monoMassList){

    	d3.selectAll("#tooltip_pop").remove() ;
    	var div = d3.select("body").append("div")
    	   .attr("class", "tooltip")
    	   .attr("id","tooltip_pop")
    	   .style("opacity", 1);
    	let colorsDropdown = addColorsToDropdown();
    	div.transition()
         .duration(200)
         .style("opacity", .9);
    	div.html(
    			'<input list="browsers" name="myBrowser" type="text" id= "mass_shift" />'+
    			colorsDropdown +
    			'<button id="ok" style = "none" type="button">ok</button>'
    	        )
    	        .style("left", (d3.event.pageX - 30) + "px")
    	        .style("top", (d3.event.pageY - 45) + "px");

    	let shiftPosition = i;

    	d3.select("#ok").on("click",function(){
    	let massShiftVal =  document.getElementById("mass_shift").value ;
    	let tooltipcolor =  document.getElementById("tooltip_color").value ;
    		d3.select("#tooltip_pop").remove() ;
    		massShiftVal = parseFloat(massShiftVal);
    		if(!isNaN(massShiftVal)){
    			let errorType = $(".error_dropdown").val();
    			let errorVal = parseFloat($("#errorval").val().trim());
    			let executionObj = new SeqOfExecution();
    			executionObj.onClickMassShift = {mass:massShiftVal,position:shiftPosition,color:tooltipcolor}
    			executionObj.onClickSequenceOfExecution(errorType,errorVal);
    		}
    	});
    }

    /**
     * Put the numerical positions at the start and end of each row of the sequence
     * @param {Object} para Contains parameters of width, letter space etc., to draw SVG
     * @param {Object} seq Amino Acid Sequence
     * @param {String} id Id of the SVG from html
     */
    function getNumValues(para,seq,id)
    {
    	//remove all the numbers if exist
    	d3.selectAll(".numbers").remove();
    	let svgContainer = d3.select("#"+id+"_g") ;
    	let len = seq.length;
    	for(let i = 0;i < len ;i++ )
    	{
    		let x,y ;
    		let l_position_temp = i ;
    		/*	write the numerical values only at the start position and end position(this is in the
    		 * 	form of 29,59 etc.,. as the data starts with 0 as 1st element) 							*/
    		if(l_position_temp%(para.row_length) ==  0 || l_position_temp%(para.row_length)  ==  (para.row_length-1)
    								|| l_position_temp == len-1)
    		{
    			let id_temp ;
    			let position = i+1 ;
    			if(i%para.row_length ==  0)
    			{
    				/*	Get the coordinates of left numerical	*/
    				[x,y] = calibrateLeftNum(para,l_position_temp) ;
    				x = x ;
    				id_temp = "left_align" ;
    			}
    			else
    			{
    				/*	Get the coordinates of right numerical	*/
    				[x,y] = calibrateRightNum(para,l_position_temp) ;
    				id_temp = "right_align" ;
    			}
    			svgContainer.append("text")
    				.attr("class","numbers")
    				.attr("id", id_temp)
    				.attr("x",x)
    				.attr("y",y)
    				.text(function(d,i){
    					return position ;
    				})
    				.style("text-anchor",function(d,i){
    					/*	Align the left numerical towards left side */
    					if(id_temp == "left_align") return "end" ;
    					return null ;
    				})
    				.style("fill", "black");

    			// When there exist only one number in the last row
    			if(l_position_temp == len-1 && len%(para.row_length) ==  1)
    			{
    				[x,y] = calibrateRightNum(para,l_position_temp) ;
    				id_temp = "right_align" ;
    				svgContainer.append("text")
    				.attr("id", id_temp)
    				.attr("x",x)
    				.attr("y",y)
    				.text(function(d,i){
    					return position ;
    				})
    				.style("fill", "black");
    			}
    		}
    	}
    }
    /**
     * Draw annotations
     * @param {Object} para Contains parameters of width, letter space etc., to draw SVG
     * @param {Array} matchedPeaks Contains Matched List
     * @param {String} id Contains id of the SVG tag from html to draw sequence
     */
    function annotations(para,matchedPeaks,id)
    {
    	// remove all existing polylines with polyline id
    	d3.selectAll("#annoTooltip").remove();
    	d3.selectAll("#polyline").remove();
    	matchedPeaks.forEach(function(matchedPeak,index){
    		let position = matchedPeak.position ;
    		let charge = getIonCharge(matchedPeaks,position);

    		let utilFunctionsObj = new utilFunctions();
    		let tempIon = matchedPeak.ion[0].toLowerCase();
    		let ionType = utilFunctionsObj.getTerminus(tempIon);

    		if("NTERMINUS" == ionType)
    		{
    			drawAnnotation_B(para,position,charge,id) ;
    		}
    		else
    		{
    			drawAnnotation_Y(para,position,charge,id) ;
    		}
    	})
    }
    /**
     * Draw the annotation when the ion type is B
     * @param {Object} para Contains parameters of width, letter space etc., to draw SVG
     * @param {Integer} position Position of the amino acid
     * @param {String} charge Contains the charge at the current position to display on hover of the annotation
     * @param {String} id Contains id of the SVG tag from html to draw sequence
     */
    function drawAnnotation_B(para,position,charge,id)
    {
    	x = getX(para,position-1);
    	y = getY(para,position-1);
    	x = x + (para.letter_width/2) ;
    	let coordinates = (x-2)+","+(y-13)+ " " +(x+4)+","+ (y-11)+" "+(x+4)+","+(y+2);
    	drawAnnotation(position,charge,id,coordinates,x,y);
    }
    /**
     * Draw the annotation when the ion type is Y
     * @param {Object} para Contains parameters of width, letter space etc., to draw SVG
     * @param {Integer} position Position of the amino acid
     * @param {String} charge Contains the charge at the current position to display on hover of the annotation
     * @param {String} id Contains id of the SVG tag from html to draw sequence
     */
    function drawAnnotation_Y(para,position,charge,id)
    {
    	x = getX(para,position-1);
    	y = getY(para,position-1);
    	x = x + (para.letter_width/2);
    	let coordinates = (x+4)+","+ (y-11)+" "+(x+4)+","+(y+2)+ " "+(x+10) + ","+(y+5);
    	drawAnnotation(position,charge,id,coordinates,x,y);
    }
    /**
     * generate cooordinates to dray Y or B annotation
     * @param {Object} para Contains parameters of width, letter space etc., to draw SVG
     * @param {Integer} position Position of the amino acid
     * @param {String} charge Contains the charge at the current position to display on hover of the annotation
     * @param {String} id Contains id of the SVG tag from html to draw sequence
     */
    function drawAnnotation_YB(para,position,charge,id)
    {
    	x = getX(para,position-1);
    	y = getY(para,position-1);
    	x = x + (para.letter_width/2) ;
    	let coordinates =  (x-2)+","+(y-13)+ " " + (x+4)+","+ (y-11)+" "+(x+4)+","+(y+2)+ " "+(x+10) + ","+(y+5);
    	drawAnnotation(position,charge,id,coordinates,x,y);
    }
    /**
     * Draw Annotations
     * @param {Integer} position Position of the amino acid
     * @param {String} charge Contains the charge at the current position to display on hover of the annotation
     * @param {String} id Contains id of the SVG tag from html to draw sequence
     * @param {String} coordinates Contains coordinates to draw the annotaion
     * @param {Integer} x Contains x coordinate of start point to draw the annotation
     * @param {Integer} y Contains y coordinate of start point to draw the annotation
     */
    function drawAnnotation(position,charge,id,coordinates,x,y)
    {
    	let svgContainer = d3.select("#"+id+"_g");
    	let l_polyline = svgContainer.append("polyline")
    							.attr("id","polyline")
    							.attr("points", coordinates)
    							.style("fill", "none")
    							.style("stroke", "1e90ff")
    							.style("stroke-width", 1 );
    	//	Rectangle to have flexible on click and on mouse actions
    	svgContainer.append("rect")
    				.attr("id","annoTooltip")
    				.attr("x", x)
    				.attr("y", y-14)
    				.attr("width", 13)
    				.attr("height", 23)
    				.style("opacity", 0)
    				.attr("cursor", "pointer")
    				.on("click",function(){
    					showIonPeaks(position);
    				})
    				.on("mouseover", function(){
    					appendTooltip(charge);
    				})
    				.on("mouseout", function(d){
    					removeToolTip();
    				});
    }
    /**
     * Append Charge to the tool tip
     * @param {String} charge Contains the charge at the current position to display on hover of the annotation
     */
    function appendTooltip(charge)
    {
    	var div = d3.select("body").append("div")
    								.attr("class", "tooltip annotation_tooltip")
    								.style("opacity", 0);
    		div.transition()
    			.duration(10)
    			.style("opacity", .9);
    		div.html(charge)
    		.style("left", (d3.event.pageX)  + "px")
    		.style("top", (d3.event.pageY - 28)+ "px") ;
    }
    /**
     * Remove tootltip on remove of the mouse from annotation
     */
    function removeToolTip()
    {
    	d3.selectAll(".annotation_tooltip").remove();
    }
    /**
     * Get the charge of the Ion
     * @param {Array} matchedPeaks Array with charge data at all the matched positions
     * @param {Integer} position Position at which the charge data has to be consolidated to show on hover of an annotation
     */
    function getIonCharge(matchedPeaks,position){
    	let l_charge = "";
    	for(let j=0;j<matchedPeaks.length;j++){
    		if(position == matchedPeaks[j].position )
    		{
    			 l_charge = l_charge + matchedPeaks[j].ion
    			 						+" "+matchedPeaks[j].charge+"+ " ;
    		}
    	}
    	return l_charge ;
    }

    /**
     * MassShift value at the top of the acids
     * @param {Object} thisElem Current element of the amino acid
     * @param {Float} MassShift Value of the mass shift
     * @param {Integer} position Position of the amino acid
     */
    function MassShift(thisElem,MassShift,position)
    {
    	let id = "massshift_" + position;
    	d3.select("#"+id).remove();
    	let dy = -1.2 ;
    	let x = $(thisElem).attr("x");
    	let y = $(thisElem).attr("y");
    	dy = dy+"em" ;
    	let svgContainer = d3.select("#seqsvg");
    	svgContainer.append("text")
    				.attr("class","massshift_class")
    				.attr("id",id)
    			  	.attr("x", x)
    			   	.attr("y", y)
    			   	.attr("dy", dy)
    			   	.text(function(){
    					if(MassShift != 0)
    					{
    						return MassShift ;
    					}
    					return "";
    			   	})
    				//.attr("text-anchor","middle")
    				.attr("fill","black")
    			   .attr("font-size","11px");
    }
    /**
     * Provide a drop down to add different background colors to the mass shifted elements
     */
    function addColorsToDropdown(){
    	let colors = ["white","green","yellow","blue","red"]
    	let startStatement = "<select id=\"tooltip_color\" style=\"background-color:"+colors[0]+"\">";
    	let endStatement = "</select>";
    	let stringyfyingHTML = startStatement;
    	let len = colors.length;
    	for(let i=0;i<len;i++)
    	{
    		stringyfyingHTML += drawRectagleWithColors(colors[i],i);
    	}
    	stringyfyingHTML = stringyfyingHTML + endStatement;
    	console.log("stringyfyingHTML : ", stringyfyingHTML);
    	return stringyfyingHTML;
    }
    /**
     * Add rectagular block with selected color
     * @param {String} color Backgroung color added tot he amino acid
     * @param {Integer} index Position at which the color needed to be added
     */
    function drawRectagleWithColors(color,index){
    	let option = "<option value=\""+color +"\"style=\"width:80px;height:5px;border:1px solid #000;background-color:"+color+"\">";
    	if(index == 0)
    	{
    		option = "<option value=\""+color +"\"style=\"width:80px;height:5px;border:1px solid #000;background-color:"+color+"\""+"selected"+">";
    	}

    	//let div = "<div style=\"width:80px;height:5px;border:1px solid #000;background-color:"+color+"\"></div>";
    	let finalOption = option+color+"</option>";
    	return finalOption;
    }