Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 326 deletions

diff --git a/web/javascript/svg.js b/web/javascript/svg.js
deleted file mode 100755
index 73523b7b..00000000
--- a/web/javascript/svg.js
+++ /dev/null
@@ -1,326 +0,0 @@
-/*extracted and modified from http://www.carto.net/neumann/cartography/vienna/ */
-var openURL="/webqtl/WebQTL.py?FormID=showDatabase&database=Eye_M2_0906_R&incparentsf1=1&ProbeSetID=";
-var chrLength=[0.0, 491.91598118601547, 946.15708685124116, 1345.2216933525635, 1732.198920660242, 2111.6212086643609, 2484.8595921440615, 2847.1359103053924, 3176.8399906396698, 3486.3641319132003, 3810.7615243606533, 4114.7890532612491, 4415.4830426184499, 4716.5544971256113, 5026.024224847908, 5284.3571135528055, 5529.6098871486292, 5767.1869053349601, 5993.6795668729492, 6146.7463916706538];
-
-var statusObj;
-var zoomVal;
-var svgdoc;
-var zoomValueObj;
-var dispBoxObj;
-var probesetObj;
-var markerObj;
-var xObj;
-var yObj;
-var svgRect;
-var svgMainViewport;
-var overviewViewport;
-
-var allWidth = 8200;
-var allHeight = 8200;
-var xOriginCorner = 0;
-var yOriginCorner = 0;
-
-var evtX;
-var evtY;
-var dataPanelEvtX;
-var dataPanelEvtX;
-var rectUlXCorner;
-var rectUlYCorner
-var pluginPixWidth;
-var pluginPixHeight;
-var mainPixWidth;
-var mainPixHeight;
-var mainX;
-var mainY;
-var scaleFactor = 1;
-var width;
-var height;
-var pressed = 0;
-
-var msgObj;
-
-function initMap(evt) {
-	//initializing values
-	zoomVal = 100; //initial zoomFactor
-	//svgdoc=evt.getTarget().getOwnerDocument();
-	svgdoc = evt.target.ownerDocument;
-   	statusObj = svgdoc.getElementById("statusText");
-	statusObj = statusObj.firstChild;
-
-	zoomValueObj = svgdoc.getElementById("zoomValueObj");
-	zoomValueObj = zoomValueObj.firstChild;
-
-	xObj = svgdoc.getElementById("XLabel");
-	xObj = xObj.firstChild;
-	yObj = svgdoc.getElementById("YLabel");
-	yObj = yObj.firstChild;
-
-	dispBoxObj = svgdoc.getElementById("dispBox");
-	probesetObj = svgdoc.getElementById("_probeset");
-	probesetObj = probesetObj.firstChild;
-	markerObj = svgdoc.getElementById("_marker");
-	markerObj = markerObj.firstChild;
-
-	//dispBoxObj.parent.appendChild(dispBoxObj);
-	svgRect = svgdoc.getElementById("overviewRect");
-	allWidth = svgRect.getAttribute("width");
-	allHeight = svgRect.getAttribute("height");
-	svgMainViewport = svgdoc.getElementById("mainPlot");	
-	mainPixWidth = svgMainViewport.getAttribute("width");
-	mainPixHeight = svgMainViewport.getAttribute("height");
-	mainX = svgMainViewport.getAttribute("x");
-	mainY = svgMainViewport.getAttribute("y");
-	//overviewObjects
-	overviewViewport = svgdoc.getElementById("overviewPlot");		
-	pluginPixWidth = overviewViewport.getAttribute("width");
-	pluginPixHeight = overviewViewport.getAttribute("height");
-	
-	//msgObj = svgdoc.getElementById("msgText")
-	//msgObj = msgObj.firstChild;
-}
-
-//simulating statusbar
-function statusChange(text) {
-	//statusObj.setData(text);
-	statusObj.nodeValue=text;
-}
-
-//magnifier glass mouse-over effects
-function magnify(evt,scaleFact,inOrOut) {
-	if (inOrOut == "in") {
-		if (zoomVal < 1000) {
-			statusChange("click to zoom in");
-			scaleObject(evt,scaleFact);
-		}
-		else {
-			statusChange("maximum zoom factor reached! cannot zoom in any more!");			
-		}
-	}
-	if (inOrOut == "out") {
-		if (zoomVal >= 100) {
-			statusChange("click to zoom out");
-			scaleObject(evt,scaleFact);
-		}
-		else {
-			statusChange("minimum zoom factor reached! cannot zoom out any more!");			
-		}		
-	}
-	if (scaleFact == 1) {
-			statusChange("plot ready");		
-			scaleObject(evt,scaleFact);
-	}	
-}
-
-// Lei Yan
-// 2009/03/26
-
-//scale any object that has a transform-value
-function scaleObject(evt,factor) {
-        //reference to the currently selected object
-        var element = evt.target;
-
-        //query old transform value (we need the translation value)
-        var curTransform = element.getAttribute("transform");
-        curTransform = new String(curTransform); //Wert in ein String umwandeln
-        //no fear from Regular expressions ... just copy it, I copied it either ...
-        var translateRegExp=/translate\(([-+]?\d+)(\s*[\s,]\s*)([-+]?\d+)\)\s*/;
-
-        //This part extracts the translation-value from the whole transform-string
-        if (curTransform.length != 0)
-        {
-          var result = curTransform.match(translateRegExp);
-          if (result == null || result.index == -1)
-          {
-             oldTranslateX = 0;
-             oldTranslateY = 0;
-          }
-          else
-          {
-             oldTranslateX = result[1];
-             oldTranslateY = result[3];
-          }
-          //concatenate the string again, add scale-factor
-          var newtransform = "translate(" + oldTranslateX + " " + oldTranslateY + ") " + "scale(" + factor + ")";
-        }
-        //set transform-factor
-        element.setAttribute('transform', newtransform);
-}
-
-function zoomIt(inOrOut) {
-	if (zoomVal>=300) step=100.0;
-	else step=50.0;
-	if (inOrOut == "in") {
-		if (zoomVal < 1000) {
-			statusChange("click to zoom in");
-			zoomVal = zoomVal + step;
-			zoomItReally();
-		}
-		else {
-			statusChange("maximum zoom factor reached! cannot zoom in any more!");
-		}
-	}
-	if (inOrOut == "out") {
-		if (zoomVal > 100) {
-			statusChange("click to zoom out");
-			zoomVal = zoomVal - step;
-			zoomItReally();
-		}
-		else {
-			statusChange("minimum zoom factor reached! cannot zoom out any more!");			
-		}		
-	}
-}
-
-function zoomItReally() {
-	statusChange("panning plot - please be patient ...");
-	
-	//get values from draggable rectangle
-	xulcorner = parseFloat(svgRect.getAttribute("x"));
-	yulcorner = parseFloat(svgRect.getAttribute("y"));
-	width = parseFloat(svgRect.getAttribute("width"));
-	height = parseFloat(svgRect.getAttribute("height"));
-	
-	//calcs
-	xcenter = xulcorner + width / 2;
-	ycenter = yulcorner + height / 2;
-	xnulcorner = xcenter - allWidth / 2 * (100/zoomVal);
-	ynulcorner = ycenter - allHeight / 2 * (100/zoomVal);
-	nWidth = allWidth * (100/zoomVal);
-	nHeight = allHeight * (100/zoomVal);
-
-	if (zoomVal == 100) {
-		xnulcorner = 0;
-		ynulcorner = 0;
-	}		
-	//set values of draggable rectangle
-	svgRect.setAttribute("x",xnulcorner);
-	svgRect.setAttribute("y",ynulcorner);
-	svgRect.setAttribute("width",nWidth);
-	svgRect.setAttribute("height",nHeight);
-	
-	//set viewport of main map
-	newViewport = xnulcorner + " " + ynulcorner + " " + nWidth + " " + nHeight;
-	svgMainViewport.setAttribute("viewBox",newViewport);/**/
-	//zoomValueObj.setData("ZOOM: " + zoomVal+"%");
-	zoomValueObj.nodeValue="ZOOM: " + zoomVal+"%";
-	statusChange("plot ready ...");
-}
-
-function beginPan(evt) {
-	pressed = 1;
-	width = parseFloat(svgRect.getAttribute("width"));
-	height = parseFloat(svgRect.getAttribute("height"));
-	evtX = parseFloat(evt.clientX) * scaleFactor;
-	evtY = parseFloat(evt.clientY) * scaleFactor;
-	rectUlXCorner = parseFloat(svgRect.getAttribute("x"));
-	rectUlYCorner = parseFloat(svgRect.getAttribute("y"));	
-}
-
-function doPan(evt) {
-	if (pressed == 1) {
-		newEvtX = parseFloat(evt.clientX) * scaleFactor; //scaleFactor is because of resizable interface
-		newEvtY = parseFloat(evt.clientY) * scaleFactor;
-		toMoveX = rectUlXCorner + (newEvtX - evtX) * allWidth / pluginPixWidth;
-		toMoveY = rectUlYCorner + (newEvtY - evtY) * allHeight / pluginPixHeight;
-		
-		//restrict to borders of overviewmap
-		if (toMoveX < xOriginCorner) {
-			svgRect.setAttribute("x",xOriginCorner);
-		}
-		else if ((toMoveX + width) > (xOriginCorner + allWidth)) {
-			svgRect.setAttribute("x",xOriginCorner + allWidth - width);				
-		}
-		else {
-			svgRect.setAttribute("x",toMoveX);			
-		}
-		if (toMoveY < yOriginCorner) {
-			svgRect.setAttribute("y",yOriginCorner);
-		}
-		else if ((toMoveY + height) > (yOriginCorner + allHeight)) {
-			svgRect.setAttribute("y",yOriginCorner + allHeight - height);
-		}				
-		else {
-			svgRect.setAttribute("y",toMoveY);
-		}
-		
-		evtX = newEvtX;
-		evtY = newEvtY;
-		rectUlXCorner = parseFloat(svgRect.getAttribute("x"));
-		rectUlYCorner = parseFloat(svgRect.getAttribute("y"));	
-	}	
-}
-
-function endPan() {
-	statusChange("panning plot - please be patient ...");
-	pressed = 0;
-	//set viewport of main plot
-	xulcorner = parseFloat(svgRect.getAttribute("x"));
-	yulcorner = parseFloat(svgRect.getAttribute("y"));
-	width = parseFloat(svgRect.getAttribute("width"));
-	height = parseFloat(svgRect.getAttribute("height"));
-	newViewport = xulcorner + " " + yulcorner + " " + width + " " + height;
-	svgMainViewport.setAttribute("viewBox",newViewport);
-	statusChange("plot ready ...");
-}
-
-function showChr(evt) {
-	xulcorner = parseFloat(svgRect.getAttribute("x"));
-	yulcorner = parseFloat(svgRect.getAttribute("y"));
-	width = parseFloat(svgRect.getAttribute("width"));
-	height = parseFloat(svgRect.getAttribute("height"));
-	myX = parseFloat(evt.clientX-mainX) * scaleFactor;
-	myY = parseFloat(evt.clientY-mainY) * scaleFactor;
-	myX = xulcorner + (myX*100/zoomVal -0.1*mainPixWidth)* allWidth/ mainPixWidth;
-	myY = allHeight*0.8-(yulcorner + (myY*100/zoomVal -0.1*mainPixWidth)* allHeight/ mainPixHeight);
-
-	for (i=0; i<chrLength.length; i++){
-		if (chrLength[i] > myX) break;
-	}
-	i = (i==chrLength.length)? "X":i;
-	//xObj.setData("Marker GMb (Chr "+ i+")");
-	xObj.nodeValue="Marker GMb (Chr "+ i+")";
-
-	for (i=0; i<chrLength.length; i++){
-		if (chrLength[i] > myY) break;
-	}
-	i = (i==chrLength.length)? "X":i;
-	//yObj.setData("Transcript GMb (Chr "+ i+")");
-	yObj.nodeValue="Transcript GMb (Chr "+ i+")";
-}
-
-function showNoChr(evt) {
-	//xObj.setData("Marker GMb");
-	xObj.nodeValue="Marker GMb.";
-	//yObj.setData("Transcript GMb");
-	yObj.nodeValue="Transcript GMb.";
-}
-
-function mvMsgBox(evt) {
-	var element = evt.target;
-	var myX = parseFloat(evt.clientX)+2;
-	var myY = parseFloat(evt.clientY)-2;
-	var newtransform = "translate(" + myX + " " + myY + ") " + "scale(0.8)";
-	dispBoxObj.setAttribute('transform', newtransform);
-	dispBoxObj.setAttribute('visibility', 'visible');
-	//probesetObj.setData("ProbeSet : " + element.getAttribute("ps"));
-	probesetObj.nodeValue="ProbeSet : " + element.getAttribute("ps");
-	//markerObj.setData("Marker : " + element.getAttribute("mk"));
-	markerObj.nodeValue="Marker : " + element.getAttribute("mk");
-}
-
-function hdMsgBox() {
-	dispBoxObj.setAttribute('visibility', 'hidden');
-}
-
-function openPage(evt) {
-	var element = evt.target;
-	var windowName = 'formTarget' + (new Date().getTime());
-	//var openWinString = "openNewWin('"+openURL+element.getAttribute("ps")+"')";
-	//var aURL = "http://www.genenetwork.org"+openURL+element.getAttribute("ps");
-	var aURL = openURL+element.getAttribute("ps");
-	var newWin = window.open(aURL);
-	newWin.focus();
-	return false;
-	
-	//browserEval(openWinString);
-}