From 911fc4bc3c7a4d31247f6ada01dde4f0e5fb270f Mon Sep 17 00:00:00 2001 From: Hashem Ali Shihab Date: Thu, 21 Mar 2013 12:32:06 +0000 Subject: [PATCH] Incorporated Reviewer Comments --- cancer.html | 437 ++++-- cgi-bin/fathmm.py | 72 +- cgi-bin/results.cgi | 17 +- css/fathmm.css | 2 + index.html | 8 +- inherited.html | 141 +- js/bootstrap.min.js | 2 +- js/jquery.flot.crosshair.js | 167 +++ js/jquery.flot.js | 2599 +++++++++++++++++++++++++++++++++++ parseVCF.py | 67 + 10 files changed, 3303 insertions(+), 209 deletions(-) mode change 100755 => 100644 js/bootstrap.min.js create mode 100644 js/jquery.flot.crosshair.js create mode 100644 js/jquery.flot.js create mode 100644 parseVCF.py diff --git a/cancer.html b/cancer.html index d48385a..0e0ad4c 100755 --- a/cancer.html +++ b/cancer.html @@ -1,8 +1,4 @@ - - - - fathmm - Analyze Cancer-Associated Variants @@ -10,7 +6,7 @@ - + @@ -30,6 +26,8 @@ + + + + + + + diff --git a/cgi-bin/fathmm.py b/cgi-bin/fathmm.py index ea8b3a3..a591032 100755 --- a/cgi-bin/fathmm.py +++ b/cgi-bin/fathmm.py @@ -96,6 +96,13 @@ def process_record(dbSNP, protein, substitution): """ + # throw warning if prediction threshold is invalid + if not isinstance(options.threshold, float): + Predictions.write( + "\t".join([ str(idx), dbSNP, protein, substitution, "", "", "", "Invalid Prediction Threshold (" + str(options.threshold) + ")" ]) + "\n" + ); return False + + # fetch pre-computed sequence record dbCursor.execute("select a.* from Clusters a, Protein b where a.id=b.cluster and b.name='" + protein + "'") SeqRecord = dbCursor.fetchone() @@ -184,24 +191,17 @@ def process_record(dbSNP, protein, substitution): "\t".join([ str(idx), dbSNP, protein, substitution, "", "", "", "No Prediction Available" ]) + "\n" ); return False - if not options.weights.upper() == "UNWEIGHTED": - if options.weights.upper() == "INHERITED": - # "Inherited Disease" predictions ... - Tag = "TOLERATED" - - if float(Score) < -1.50: - Tag = "DAMAGING" - else: - # "Cancer-Associated" predictions ... - Tag = "PASSENGER/OTHER" - - if float(Score) < -1.00: - Tag = "CANCER" - else: - Tag = "TOLERATED" - - if float(Score) < -3.00: + if options.weights.upper() in [ "UNWEIGHTED", "INHERITED" ]: + # "Inherited Disease" predictions ... + Tag = "TOLERATED" + if float(Score) < options.threshold: Tag = "DAMAGING" + else: + # "Cancer-Associated" predictions ... + Tag = "PASSENGER/OTHER" + if float(Score) < options.threshold: + Tag = "CANCER" + Predictions.write( "\t".join([ str(idx), dbSNP, protein, substitution, Tag, Score, "|".join([ x['description'] for x in Phenotypes ]), "" ]) + "\n" @@ -211,14 +211,14 @@ def process_record(dbSNP, protein, substitution): if __name__ == '__main__': # - # PARSE PROGRAM ARGUMENTS + # OPTION PARSER # parser = OptionParser() parser.add_option( "-i", dest = "input", - help = "process dbSNP rs IDs/protein missense mutations from ", + help = "process mutation data from ", metavar = "", default = None ) @@ -234,30 +234,50 @@ def process_record(dbSNP, protein, substitution): dest = "weights", help = "return weighted predictions using pathogenicity weights ", metavar = "", - default = "Inherited" + default = "INHERITED" + ) + parser.add_option( + "-t", + dest = "threshold", + help = "return predictions using as a prediction threshold", + metavar = "", + default = None ) parser.add_option( "-p", dest = "phenotypes", help = "append domain-phenotype associations for mutations using phenotype ontology ", metavar = "", - default = "DO" + default = "" ) (options, args) = parser.parse_args() # - # AUTHENTICATE PROGRAM PARAMETERS + # PARSE/AUTHENTICATE PROGRAM PARAMETERS # if not options.input: - parser.error("No Input File Given (-i parameter)") - + parser.error("Warning: No Input File Specified ") + if not options.output: - parser.error("No Output File Given (-o parameter)") + parser.error("Warning: No Output File Specified ") + if not options.weights: + parser.error("Warning: No Pathogenicity Weights Specified ") + if not options.weights.upper() in [ "UNWEIGHTED", "INHERITED", "CANCER" ]: - parser.error("Invalid Weighting Scheme") + parser.error("Warning: Invalid Pathogenicity Weights ") + + if options.threshold: + try: + options.threshold = float(options.threshold) + except: + pass + else: + if options.weights.upper() == "UNWEIGHTED": options.threshold = -3.00 + if options.weights.upper() == "INHERITED": options.threshold = -1.50 + if options.weights.upper() == "CANCER": options.threshold = -0.75 # # INITIALIZE DATABASE CONNECTION/CURSOR diff --git a/cgi-bin/results.cgi b/cgi-bin/results.cgi index 88b5fba..6db5108 100755 --- a/cgi-bin/results.cgi +++ b/cgi-bin/results.cgi @@ -36,6 +36,7 @@ if __name__ == '__main__': "# Time: " + time.strftime("%H:%M:%S", HTMLTime) + "\n", "# Weights: " + str(HTMLForm['weighted'].value).upper() + "\n", "# Phenotypes: " + str(HTMLForm['phenotypes'].value).upper() + "\n", + "# Threshold: " + str(HTMLForm['threshold'].value) + "\n", str(HTMLForm['batch'].value) ]: open("../tmp/" + HTMLSession + ".txt", "a").write(x) @@ -45,7 +46,8 @@ if __name__ == '__main__': '-i', '../tmp/' + HTMLSession + '.txt', '-o', '../tmp/' + HTMLSession + '.tab', '-w', str(HTMLForm['weighted'].value), - '-p', str(HTMLForm['phenotypes'].value) + '-p', str(HTMLForm['phenotypes'].value), + '-t', str(HTMLForm['threshold'].value) ], stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE) # else: @@ -58,10 +60,6 @@ if __name__ == '__main__': if os.path.exists("../tmp/" + HTMLSession + ".tab"): print """ - - - - fathmm - fathmm Predictions @@ -144,6 +142,7 @@ if __name__ == '__main__':

fathmm Predictions

+

Your request has now been processed and our predictions have been written onto your screen - a "tab-delimited" report of our predictions has been made available below.  In addition, you can retrieve your results at any time using the below Job/Session Identifier. @@ -308,6 +307,7 @@ if __name__ == '__main__':

fathmm Predictions

+

Your request is now being processed and our predictions will be written onto your screen once completed - if you submitted a large batch, please be patient as this may take a while.  Alternatively, you can retrieve your results at any time using the below Job/Session @@ -416,6 +416,7 @@ if __name__ == '__main__':

Unknown Job/Session Identifier

+

You have entered an invalid or unknown Job/Session Identifier - please note, predictions are typically stored on our server for one week before being deleted.

@@ -514,6 +515,7 @@ if __name__ == '__main__':

Server Error

+

It appears there is a problem with our server - please try again and/or report the problem to the system administrator using the following address: fathmm.biocompute.org.uk @@ -551,8 +553,11 @@ if __name__ == '__main__': We welcome any comments and/or suggestions that you may have regarding our software and server - please send an email directly to fathmm@biocompute.org.uk

-
+ + + + """ diff --git a/css/fathmm.css b/css/fathmm.css index 8e8de46..b3ca348 100755 --- a/css/fathmm.css +++ b/css/fathmm.css @@ -34,3 +34,5 @@ a:hover { .modal, .btn-large { outline: none; } + +.tab-content {overflow-x: hidden;} diff --git a/index.html b/index.html index 3a8c3c4..dbd0119 100755 --- a/index.html +++ b/index.html @@ -77,7 +77,7 @@
-

Functional Analysis through Hidden Markov Models (v2.1)

+

Functional Analysis through Hidden Markov Models


A high-throughput web-server capable of predicting the functional, molecular and phenotypic consequences of @@ -96,7 +96,7 @@


- The Functional Analysis through Hidden Markov Models (FATHMM) software and server is a sequence-based algorithm capable of predicting the + The Functional Analysis through Hidden Markov Models (fathmm) software and server is a sequence-based algorithm capable of predicting the functional and phenotypic consequences of protein missense variants via the amalgamation of sequence conservation within hidden Markov models (HMMs), representing the alignment of homologous sequences and conserved protein domains, with 'pathogenicity weights', representing the tolerance of the corresponding model to mutations. @@ -119,7 +119,7 @@

Analyze dbSNP/Protein Missense Variants


-

Obtain instant predictions for the functional, molecular and phenotypic consequences of protein missense variants.

+

Obtain instant predictions describing the functional, molecular and phenotypic consequences of protein missense variants.

go »

@@ -127,7 +127,7 @@

Analyze dbSNP/Protein Missense Variants

Analyze Cancer-Associated Variants


-

Obtain instant disease-specific predictions capable of distinguishing between cancer-promoting/driver and neutral/passsenger mutations.

+

Obtain instant predictions capable of distinguishing between cancer-promoting/driver mutations, passsenger mutations and other germline polymorphisms.

go »

diff --git a/inherited.html b/inherited.html index 3ce4438..78afa6d 100755 --- a/inherited.html +++ b/inherited.html @@ -132,79 +132,98 @@
-

Batch Query:

 - +

Enter Your Mutations:

 + + +
-
+
-
+
-
+
- +
-
- For further information pertaining to the submission format, please click on the 'Example' button above. -
-
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- -
- +
+ + +
+
+
+
+
+ +
+ +
+
+
+
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- -
- +
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+
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+
+ +
+ +
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- - +
+ +
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+ + +
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+
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The "x" mode enables a +vertical crosshair that lets you trace the values on the x axis, "y" +enables a horizontal crosshair and "xy" enables them both. "color" is +the color of the crosshair (default is "rgba(170, 0, 0, 0.80)"), +"lineWidth" is the width of the drawn lines (default is 1). + +The plugin also adds four public methods: + + - setCrosshair(pos) + + Set the position of the crosshair. Note that this is cleared if + the user moves the mouse. "pos" is in coordinates of the plot and + should be on the form { x: xpos, y: ypos } (you can use x2/x3/... + if you're using multiple axes), which is coincidentally the same + format as what you get from a "plothover" event. If "pos" is null, + the crosshair is cleared. + + - clearCrosshair() + + Clear the crosshair. + + - lockCrosshair(pos) + + Cause the crosshair to lock to the current location, no longer + updating if the user moves the mouse. Optionally supply a position + (passed on to setCrosshair()) to move it to. + + Example usage: + var myFlot = $.plot( $("#graph"), ..., { crosshair: { mode: "x" } } }; + $("#graph").bind("plothover", function (evt, position, item) { + if (item) { + // Lock the crosshair to the data point being hovered + myFlot.lockCrosshair({ x: item.datapoint[0], y: item.datapoint[1] }); + } + else { + // Return normal crosshair operation + myFlot.unlockCrosshair(); + } + }); + + - unlockCrosshair() + + Free the crosshair to move again after locking it. +*/ + +(function ($) { + var options = { + crosshair: { + mode: null, // one of null, "x", "y" or "xy", + color: "rgba(170, 0, 0, 0.80)", + lineWidth: 1 + } + }; + + function init(plot) { + // position of crosshair in pixels + var crosshair = { x: -1, y: -1, locked: false }; + + plot.setCrosshair = function setCrosshair(pos) { + if (!pos) + crosshair.x = -1; + else { + var o = plot.p2c(pos); + crosshair.x = Math.max(0, Math.min(o.left, plot.width())); + crosshair.y = Math.max(0, Math.min(o.top, plot.height())); + } + + plot.triggerRedrawOverlay(); + }; + + plot.clearCrosshair = plot.setCrosshair; // passes null for pos + + plot.lockCrosshair = function lockCrosshair(pos) { + if (pos) + plot.setCrosshair(pos); + crosshair.locked = true; + } + + plot.unlockCrosshair = function unlockCrosshair() { + crosshair.locked = false; + } + + function onMouseOut(e) { + if (crosshair.locked) + return; + + if (crosshair.x != -1) { + crosshair.x = -1; + plot.triggerRedrawOverlay(); + } + } + + function onMouseMove(e) { + if (crosshair.locked) + return; + + if (plot.getSelection && plot.getSelection()) { + crosshair.x = -1; // hide the crosshair while selecting + return; + } + + var offset = plot.offset(); + crosshair.x = Math.max(0, Math.min(e.pageX - offset.left, plot.width())); + crosshair.y = Math.max(0, Math.min(e.pageY - offset.top, plot.height())); + plot.triggerRedrawOverlay(); + } + + plot.hooks.bindEvents.push(function (plot, eventHolder) { + if (!plot.getOptions().crosshair.mode) + return; + + eventHolder.mouseout(onMouseOut); + eventHolder.mousemove(onMouseMove); + }); + + plot.hooks.drawOverlay.push(function (plot, ctx) { + var c = plot.getOptions().crosshair; + if (!c.mode) + return; + + var plotOffset = plot.getPlotOffset(); + + ctx.save(); + ctx.translate(plotOffset.left, plotOffset.top); + + if (crosshair.x != -1) { + ctx.strokeStyle = c.color; + ctx.lineWidth = c.lineWidth; + ctx.lineJoin = "round"; + + ctx.beginPath(); + if (c.mode.indexOf("x") != -1) { + ctx.moveTo(crosshair.x, 0); + ctx.lineTo(crosshair.x, plot.height()); + } + if (c.mode.indexOf("y") != -1) { + ctx.moveTo(0, crosshair.y); + ctx.lineTo(plot.width(), crosshair.y); + } + ctx.stroke(); + } + ctx.restore(); + }); + + plot.hooks.shutdown.push(function (plot, eventHolder) { + eventHolder.unbind("mouseout", onMouseOut); + eventHolder.unbind("mousemove", onMouseMove); + }); + } + + $.plot.plugins.push({ + init: init, + options: options, + name: 'crosshair', + version: '1.0' + }); +})(jQuery); diff --git a/js/jquery.flot.js b/js/jquery.flot.js new file mode 100644 index 0000000..aabc544 --- /dev/null +++ b/js/jquery.flot.js @@ -0,0 +1,2599 @@ +/*! Javascript plotting library for jQuery, v. 0.7. + * + * Released under the MIT license by IOLA, December 2007. + * + */ + +// first an inline dependency, jquery.colorhelpers.js, we inline it here +// for convenience + +/* Plugin for jQuery for working with colors. + * + * Version 1.1. + * + * Inspiration from jQuery color animation plugin by John Resig. + * + * Released under the MIT license by Ole Laursen, October 2009. + * + * Examples: + * + * $.color.parse("#fff").scale('rgb', 0.25).add('a', -0.5).toString() + * var c = $.color.extract($("#mydiv"), 'background-color'); + * console.log(c.r, c.g, c.b, c.a); + * $.color.make(100, 50, 25, 0.4).toString() // returns "rgba(100,50,25,0.4)" + * + * Note that .scale() and .add() return the same modified object + * instead of making a new one. + * + * V. 1.1: Fix error handling so e.g. parsing an empty string does + * produce a color rather than just crashing. + */ +(function(B){B.color={};B.color.make=function(F,E,C,D){var G={};G.r=F||0;G.g=E||0;G.b=C||0;G.a=D!=null?D:1;G.add=function(J,I){for(var H=0;H=1){return"rgb("+[G.r,G.g,G.b].join(",")+")"}else{return"rgba("+[G.r,G.g,G.b,G.a].join(",")+")"}};G.normalize=function(){function H(J,K,I){return KI?I:K)}G.r=H(0,parseInt(G.r),255);G.g=H(0,parseInt(G.g),255);G.b=H(0,parseInt(G.b),255);G.a=H(0,G.a,1);return G};G.clone=function(){return B.color.make(G.r,G.b,G.g,G.a)};return G.normalize()};B.color.extract=function(D,C){var E;do{E=D.css(C).toLowerCase();if(E!=""&&E!="transparent"){break}D=D.parent()}while(!B.nodeName(D.get(0),"body"));if(E=="rgba(0, 0, 0, 0)"){E="transparent"}return B.color.parse(E)};B.color.parse=function(F){var E,C=B.color.make;if(E=/rgb\(\s*([0-9]{1,3})\s*,\s*([0-9]{1,3})\s*,\s*([0-9]{1,3})\s*\)/.exec(F)){return C(parseInt(E[1],10),parseInt(E[2],10),parseInt(E[3],10))}if(E=/rgba\(\s*([0-9]{1,3})\s*,\s*([0-9]{1,3})\s*,\s*([0-9]{1,3})\s*,\s*([0-9]+(?:\.[0-9]+)?)\s*\)/.exec(F)){return C(parseInt(E[1],10),parseInt(E[2],10),parseInt(E[3],10),parseFloat(E[4]))}if(E=/rgb\(\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\%\s*\)/.exec(F)){return C(parseFloat(E[1])*2.55,parseFloat(E[2])*2.55,parseFloat(E[3])*2.55)}if(E=/rgba\(\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\%\s*,\s*([0-9]+(?:\.[0-9]+)?)\s*\)/.exec(F)){return C(parseFloat(E[1])*2.55,parseFloat(E[2])*2.55,parseFloat(E[3])*2.55,parseFloat(E[4]))}if(E=/#([a-fA-F0-9]{2})([a-fA-F0-9]{2})([a-fA-F0-9]{2})/.exec(F)){return C(parseInt(E[1],16),parseInt(E[2],16),parseInt(E[3],16))}if(E=/#([a-fA-F0-9])([a-fA-F0-9])([a-fA-F0-9])/.exec(F)){return C(parseInt(E[1]+E[1],16),parseInt(E[2]+E[2],16),parseInt(E[3]+E[3],16))}var D=B.trim(F).toLowerCase();if(D=="transparent"){return C(255,255,255,0)}else{E=A[D]||[0,0,0];return C(E[0],E[1],E[2])}};var A={aqua:[0,255,255],azure:[240,255,255],beige:[245,245,220],black:[0,0,0],blue:[0,0,255],brown:[165,42,42],cyan:[0,255,255],darkblue:[0,0,139],darkcyan:[0,139,139],darkgrey:[169,169,169],darkgreen:[0,100,0],darkkhaki:[189,183,107],darkmagenta:[139,0,139],darkolivegreen:[85,107,47],darkorange:[255,140,0],darkorchid:[153,50,204],darkred:[139,0,0],darksalmon:[233,150,122],darkviolet:[148,0,211],fuchsia:[255,0,255],gold:[255,215,0],green:[0,128,0],indigo:[75,0,130],khaki:[240,230,140],lightblue:[173,216,230],lightcyan:[224,255,255],lightgreen:[144,238,144],lightgrey:[211,211,211],lightpink:[255,182,193],lightyellow:[255,255,224],lime:[0,255,0],magenta:[255,0,255],maroon:[128,0,0],navy:[0,0,128],olive:[128,128,0],orange:[255,165,0],pink:[255,192,203],purple:[128,0,128],violet:[128,0,128],red:[255,0,0],silver:[192,192,192],white:[255,255,255],yellow:[255,255,0]}})(jQuery); + +// the actual Flot code +(function($) { + function Plot(placeholder, data_, options_, plugins) { + // data is on the form: + // [ series1, series2 ... ] + // where series is either just the data as [ [x1, y1], [x2, y2], ... ] + // or { data: [ [x1, y1], [x2, y2], ... ], label: "some label", ... } + + var series = [], + options = { + // the color theme used for graphs + colors: ["#edc240", "#afd8f8", "#cb4b4b", "#4da74d", "#9440ed"], + legend: { + show: true, + noColumns: 1, // number of colums in legend table + labelFormatter: null, // fn: string -> string + labelBoxBorderColor: "#ccc", // border color for the little label boxes + container: null, // container (as jQuery object) to put legend in, null means default on top of graph + position: "ne", // position of default legend container within plot + margin: 5, // distance from grid edge to default legend container within plot + backgroundColor: null, // null means auto-detect + backgroundOpacity: 0.85 // set to 0 to avoid background + }, + xaxis: { + show: null, // null = auto-detect, true = always, false = never + position: "bottom", // or "top" + mode: null, // null or "time" + color: null, // base color, labels, ticks + tickColor: null, // possibly different color of ticks, e.g. "rgba(0,0,0,0.15)" + transform: null, // null or f: number -> number to transform axis + inverseTransform: null, // if transform is set, this should be the inverse function + min: null, // min. value to show, null means set automatically + max: null, // max. value to show, null means set automatically + autoscaleMargin: null, // margin in % to add if auto-setting min/max + ticks: null, // either [1, 3] or [[1, "a"], 3] or (fn: axis info -> ticks) or app. number of ticks for auto-ticks + tickFormatter: null, // fn: number -> string + labelWidth: null, // size of tick labels in pixels + labelHeight: null, + reserveSpace: null, // whether to reserve space even if axis isn't shown + tickLength: null, // size in pixels of ticks, or "full" for whole line + alignTicksWithAxis: null, // axis number or null for no sync + + // mode specific options + tickDecimals: null, // no. of decimals, null means auto + tickSize: null, // number or [number, "unit"] + minTickSize: null, // number or [number, "unit"] + monthNames: null, // list of names of months + timeformat: null, // format string to use + twelveHourClock: false // 12 or 24 time in time mode + }, + yaxis: { + autoscaleMargin: 0.02, + position: "left" // or "right" + }, + xaxes: [], + yaxes: [], + series: { + points: { + show: false, + radius: 3, + lineWidth: 2, // in pixels + fill: true, + fillColor: "#ffffff", + symbol: "circle" // or callback + }, + lines: { + // we don't put in show: false so we can see + // whether lines were actively disabled + lineWidth: 2, // in pixels + fill: false, + fillColor: null, + steps: false + }, + bars: { + show: false, + lineWidth: 2, // in pixels + barWidth: 1, // in units of the x axis + fill: true, + fillColor: null, + align: "left", // or "center" + horizontal: false + }, + shadowSize: 3 + }, + grid: { + show: true, + aboveData: false, + color: "#545454", // primary color used for outline and labels + backgroundColor: null, // null for transparent, else color + borderColor: null, // set if different from the grid color + tickColor: null, // color for the ticks, e.g. "rgba(0,0,0,0.15)" + labelMargin: 5, // in pixels + axisMargin: 8, // in pixels + borderWidth: 2, // in pixels + minBorderMargin: null, // in pixels, null means taken from points radius + markings: null, // array of ranges or fn: axes -> array of ranges + markingsColor: "#f4f4f4", + markingsLineWidth: 2, + // interactive stuff + clickable: false, + hoverable: false, + autoHighlight: true, // highlight in case mouse is near + mouseActiveRadius: 10 // how far the mouse can be away to activate an item + }, + hooks: {} + }, + canvas = null, // the canvas for the plot itself + overlay = null, // canvas for interactive stuff on top of plot + eventHolder = null, // jQuery object that events should be bound to + ctx = null, octx = null, + xaxes = [], yaxes = [], + plotOffset = { left: 0, right: 0, top: 0, bottom: 0}, + canvasWidth = 0, canvasHeight = 0, + plotWidth = 0, plotHeight = 0, + hooks = { + processOptions: [], + processRawData: [], + processDatapoints: [], + drawSeries: [], + draw: [], + bindEvents: [], + drawOverlay: [], + shutdown: [] + }, + plot = this; + + // public functions + plot.setData = setData; + plot.setupGrid = setupGrid; + plot.draw = draw; + plot.getPlaceholder = function() { return placeholder; }; + plot.getCanvas = function() { return canvas; }; + plot.getPlotOffset = function() { return plotOffset; }; + plot.width = function () { return plotWidth; }; + plot.height = function () { return plotHeight; }; + plot.offset = function () { + var o = eventHolder.offset(); + o.left += plotOffset.left; + o.top += plotOffset.top; + return o; + }; + plot.getData = function () { return series; }; + plot.getAxes = function () { + var res = {}, i; + $.each(xaxes.concat(yaxes), function (_, axis) { + if (axis) + res[axis.direction + (axis.n != 1 ? axis.n : "") + "axis"] = axis; + }); + return res; + }; + plot.getXAxes = function () { return xaxes; }; + plot.getYAxes = function () { return yaxes; }; + plot.c2p = canvasToAxisCoords; + plot.p2c = axisToCanvasCoords; + plot.getOptions = function () { return options; }; + plot.highlight = highlight; + plot.unhighlight = unhighlight; + plot.triggerRedrawOverlay = triggerRedrawOverlay; + plot.pointOffset = function(point) { + return { + left: parseInt(xaxes[axisNumber(point, "x") - 1].p2c(+point.x) + plotOffset.left), + top: parseInt(yaxes[axisNumber(point, "y") - 1].p2c(+point.y) + plotOffset.top) + }; + }; + plot.shutdown = shutdown; + plot.resize = function () { + getCanvasDimensions(); + resizeCanvas(canvas); + resizeCanvas(overlay); + }; + + // public attributes + plot.hooks = hooks; + + // initialize + initPlugins(plot); + parseOptions(options_); + setupCanvases(); + setData(data_); + setupGrid(); + draw(); + bindEvents(); + + + function executeHooks(hook, args) { + args = [plot].concat(args); + for (var i = 0; i < hook.length; ++i) + hook[i].apply(this, args); + } + + function initPlugins() { + for (var i = 0; i < plugins.length; ++i) { + var p = plugins[i]; + p.init(plot); + if (p.options) + $.extend(true, options, p.options); + } + } + + function parseOptions(opts) { + var i; + + $.extend(true, options, opts); + + if (options.xaxis.color == null) + options.xaxis.color = options.grid.color; + if (options.yaxis.color == null) + options.yaxis.color = options.grid.color; + + if (options.xaxis.tickColor == null) // backwards-compatibility + options.xaxis.tickColor = options.grid.tickColor; + if (options.yaxis.tickColor == null) // backwards-compatibility + options.yaxis.tickColor = options.grid.tickColor; + + if (options.grid.borderColor == null) + options.grid.borderColor = options.grid.color; + if (options.grid.tickColor == null) + options.grid.tickColor = $.color.parse(options.grid.color).scale('a', 0.22).toString(); + + // fill in defaults in axes, copy at least always the + // first as the rest of the code assumes it'll be there + for (i = 0; i < Math.max(1, options.xaxes.length); ++i) + options.xaxes[i] = $.extend(true, {}, options.xaxis, options.xaxes[i]); + for (i = 0; i < Math.max(1, options.yaxes.length); ++i) + options.yaxes[i] = $.extend(true, {}, options.yaxis, options.yaxes[i]); + + // backwards compatibility, to be removed in future + if (options.xaxis.noTicks && options.xaxis.ticks == null) + options.xaxis.ticks = options.xaxis.noTicks; + if (options.yaxis.noTicks && options.yaxis.ticks == null) + options.yaxis.ticks = options.yaxis.noTicks; + if (options.x2axis) { + options.xaxes[1] = $.extend(true, {}, options.xaxis, options.x2axis); + options.xaxes[1].position = "top"; + } + if (options.y2axis) { + options.yaxes[1] = $.extend(true, {}, options.yaxis, options.y2axis); + options.yaxes[1].position = "right"; + } + if (options.grid.coloredAreas) + options.grid.markings = options.grid.coloredAreas; + if (options.grid.coloredAreasColor) + options.grid.markingsColor = options.grid.coloredAreasColor; + if (options.lines) + $.extend(true, options.series.lines, options.lines); + if (options.points) + $.extend(true, options.series.points, options.points); + if (options.bars) + $.extend(true, options.series.bars, options.bars); + if (options.shadowSize != null) + options.series.shadowSize = options.shadowSize; + + // save options on axes for future reference + for (i = 0; i < options.xaxes.length; ++i) + getOrCreateAxis(xaxes, i + 1).options = options.xaxes[i]; + for (i = 0; i < options.yaxes.length; ++i) + getOrCreateAxis(yaxes, i + 1).options = options.yaxes[i]; + + // add hooks from options + for (var n in hooks) + if (options.hooks[n] && options.hooks[n].length) + hooks[n] = hooks[n].concat(options.hooks[n]); + + executeHooks(hooks.processOptions, [options]); + } + + function setData(d) { + series = parseData(d); + fillInSeriesOptions(); + processData(); + } + + function parseData(d) { + var res = []; + for (var i = 0; i < d.length; ++i) { + var s = $.extend(true, {}, options.series); + + if (d[i].data != null) { + s.data = d[i].data; // move the data instead of deep-copy + delete d[i].data; + + $.extend(true, s, d[i]); + + d[i].data = s.data; + } + else + s.data = d[i]; + res.push(s); + } + + return res; + } + + function axisNumber(obj, coord) { + var a = obj[coord + "axis"]; + if (typeof a == "object") // if we got a real axis, extract number + a = a.n; + if (typeof a != "number") + a = 1; // default to first axis + return a; + } + + function allAxes() { + // return flat array without annoying null entries + return $.grep(xaxes.concat(yaxes), function (a) { return a; }); + } + + function canvasToAxisCoords(pos) { + // return an object with x/y corresponding to all used axes + var res = {}, i, axis; + for (i = 0; i < xaxes.length; ++i) { + axis = xaxes[i]; + if (axis && axis.used) + res["x" + axis.n] = axis.c2p(pos.left); + } + + for (i = 0; i < yaxes.length; ++i) { + axis = yaxes[i]; + if (axis && axis.used) + res["y" + axis.n] = axis.c2p(pos.top); + } + + if (res.x1 !== undefined) + res.x = res.x1; + if (res.y1 !== undefined) + res.y = res.y1; + + return res; + } + + function axisToCanvasCoords(pos) { + // get canvas coords from the first pair of x/y found in pos + var res = {}, i, axis, key; + + for (i = 0; i < xaxes.length; ++i) { + axis = xaxes[i]; + if (axis && axis.used) { + key = "x" + axis.n; + if (pos[key] == null && axis.n == 1) + key = "x"; + + if (pos[key] != null) { + res.left = axis.p2c(pos[key]); + break; + } + } + } + + for (i = 0; i < yaxes.length; ++i) { + axis = yaxes[i]; + if (axis && axis.used) { + key = "y" + axis.n; + if (pos[key] == null && axis.n == 1) + key = "y"; + + if (pos[key] != null) { + res.top = axis.p2c(pos[key]); + break; + } + } + } + + return res; + } + + function getOrCreateAxis(axes, number) { + if (!axes[number - 1]) + axes[number - 1] = { + n: number, // save the number for future reference + direction: axes == xaxes ? "x" : "y", + options: $.extend(true, {}, axes == xaxes ? options.xaxis : options.yaxis) + }; + + return axes[number - 1]; + } + + function fillInSeriesOptions() { + var i; + + // collect what we already got of colors + var neededColors = series.length, + usedColors = [], + assignedColors = []; + for (i = 0; i < series.length; ++i) { + var sc = series[i].color; + if (sc != null) { + --neededColors; + if (typeof sc == "number") + assignedColors.push(sc); + else + usedColors.push($.color.parse(series[i].color)); + } + } + + // we might need to generate more colors if higher indices + // are assigned + for (i = 0; i < assignedColors.length; ++i) { + neededColors = Math.max(neededColors, assignedColors[i] + 1); + } + + // produce colors as needed + var colors = [], variation = 0; + i = 0; + while (colors.length < neededColors) { + var c; + if (options.colors.length == i) // check degenerate case + c = $.color.make(100, 100, 100); + else + c = $.color.parse(options.colors[i]); + + // vary color if needed + var sign = variation % 2 == 1 ? -1 : 1; + c.scale('rgb', 1 + sign * Math.ceil(variation / 2) * 0.2) + + // FIXME: if we're getting to close to something else, + // we should probably skip this one + colors.push(c); + + ++i; + if (i >= options.colors.length) { + i = 0; + ++variation; + } + } + + // fill in the options + var colori = 0, s; + for (i = 0; i < series.length; ++i) { + s = series[i]; + + // assign colors + if (s.color == null) { + s.color = colors[colori].toString(); + ++colori; + } + else if (typeof s.color == "number") + s.color = colors[s.color].toString(); + + // turn on lines automatically in case nothing is set + if (s.lines.show == null) { + var v, show = true; + for (v in s) + if (s[v] && s[v].show) { + show = false; + break; + } + if (show) + s.lines.show = true; + } + + // setup axes + s.xaxis = getOrCreateAxis(xaxes, axisNumber(s, "x")); + s.yaxis = getOrCreateAxis(yaxes, axisNumber(s, "y")); + } + } + + function processData() { + var topSentry = Number.POSITIVE_INFINITY, + bottomSentry = Number.NEGATIVE_INFINITY, + fakeInfinity = Number.MAX_VALUE, + i, j, k, m, length, + s, points, ps, x, y, axis, val, f, p; + + function updateAxis(axis, min, max) { + if (min < axis.datamin && min != -fakeInfinity) + axis.datamin = min; + if (max > axis.datamax && max != fakeInfinity) + axis.datamax = max; + } + + $.each(allAxes(), function (_, axis) { + // init axis + axis.datamin = topSentry; + axis.datamax = bottomSentry; + axis.used = false; + }); + + for (i = 0; i < series.length; ++i) { + s = series[i]; + s.datapoints = { points: [] }; + + executeHooks(hooks.processRawData, [ s, s.data, s.datapoints ]); + } + + // first pass: clean and copy data + for (i = 0; i < series.length; ++i) { + s = series[i]; + + var data = s.data, format = s.datapoints.format; + + if (!format) { + format = []; + // find out how to copy + format.push({ x: true, number: true, required: true }); + format.push({ y: true, number: true, required: true }); + + if (s.bars.show || (s.lines.show && s.lines.fill)) { + format.push({ y: true, number: true, required: false, defaultValue: 0 }); + if (s.bars.horizontal) { + delete format[format.length - 1].y; + format[format.length - 1].x = true; + } + } + + s.datapoints.format = format; + } + + if (s.datapoints.pointsize != null) + continue; // already filled in + + s.datapoints.pointsize = format.length; + + ps = s.datapoints.pointsize; + points = s.datapoints.points; + + insertSteps = s.lines.show && s.lines.steps; + s.xaxis.used = s.yaxis.used = true; + + for (j = k = 0; j < data.length; ++j, k += ps) { + p = data[j]; + + var nullify = p == null; + if (!nullify) { + for (m = 0; m < ps; ++m) { + val = p[m]; + f = format[m]; + + if (f) { + if (f.number && val != null) { + val = +val; // convert to number + if (isNaN(val)) + val = null; + else if (val == Infinity) + val = fakeInfinity; + else if (val == -Infinity) + val = -fakeInfinity; + } + + if (val == null) { + if (f.required) + nullify = true; + + if (f.defaultValue != null) + val = f.defaultValue; + } + } + + points[k + m] = val; + } + } + + if (nullify) { + for (m = 0; m < ps; ++m) { + val = points[k + m]; + if (val != null) { + f = format[m]; + // extract min/max info + if (f.x) + updateAxis(s.xaxis, val, val); + if (f.y) + updateAxis(s.yaxis, val, val); + } + points[k + m] = null; + } + } + else { + // a little bit of line specific stuff that + // perhaps shouldn't be here, but lacking + // better means... + if (insertSteps && k > 0 + && points[k - ps] != null + && points[k - ps] != points[k] + && points[k - ps + 1] != points[k + 1]) { + // copy the point to make room for a middle point + for (m = 0; m < ps; ++m) + points[k + ps + m] = points[k + m]; + + // middle point has same y + points[k + 1] = points[k - ps + 1]; + + // we've added a point, better reflect that + k += ps; + } + } + } + } + + // give the hooks a chance to run + for (i = 0; i < series.length; ++i) { + s = series[i]; + + executeHooks(hooks.processDatapoints, [ s, s.datapoints]); + } + + // second pass: find datamax/datamin for auto-scaling + for (i = 0; i < series.length; ++i) { + s = series[i]; + points = s.datapoints.points, + ps = s.datapoints.pointsize; + + var xmin = topSentry, ymin = topSentry, + xmax = bottomSentry, ymax = bottomSentry; + + for (j = 0; j < points.length; j += ps) { + if (points[j] == null) + continue; + + for (m = 0; m < ps; ++m) { + val = points[j + m]; + f = format[m]; + if (!f || val == fakeInfinity || val == -fakeInfinity) + continue; + + if (f.x) { + if (val < xmin) + xmin = val; + if (val > xmax) + xmax = val; + } + if (f.y) { + if (val < ymin) + ymin = val; + if (val > ymax) + ymax = val; + } + } + } + + if (s.bars.show) { + // make sure we got room for the bar on the dancing floor + var delta = s.bars.align == "left" ? 0 : -s.bars.barWidth/2; + if (s.bars.horizontal) { + ymin += delta; + ymax += delta + s.bars.barWidth; + } + else { + xmin += delta; + xmax += delta + s.bars.barWidth; + } + } + + updateAxis(s.xaxis, xmin, xmax); + updateAxis(s.yaxis, ymin, ymax); + } + + $.each(allAxes(), function (_, axis) { + if (axis.datamin == topSentry) + axis.datamin = null; + if (axis.datamax == bottomSentry) + axis.datamax = null; + }); + } + + function makeCanvas(skipPositioning, cls) { + var c = document.createElement('canvas'); + c.className = cls; + c.width = canvasWidth; + c.height = canvasHeight; + + if (!skipPositioning) + $(c).css({ position: 'absolute', left: 0, top: 0 }); + + $(c).appendTo(placeholder); + + if (!c.getContext) // excanvas hack + c = window.G_vmlCanvasManager.initElement(c); + + // used for resetting in case we get replotted + c.getContext("2d").save(); + + return c; + } + + function getCanvasDimensions() { + canvasWidth = placeholder.width(); + canvasHeight = placeholder.height(); + + if (canvasWidth <= 0 || canvasHeight <= 0) + throw "Invalid dimensions for plot, width = " + canvasWidth + ", height = " + canvasHeight; + } + + function resizeCanvas(c) { + // resizing should reset the state (excanvas seems to be + // buggy though) + if (c.width != canvasWidth) + c.width = canvasWidth; + + if (c.height != canvasHeight) + c.height = canvasHeight; + + // so try to get back to the initial state (even if it's + // gone now, this should be safe according to the spec) + var cctx = c.getContext("2d"); + cctx.restore(); + + // and save again + cctx.save(); + } + + function setupCanvases() { + var reused, + existingCanvas = placeholder.children("canvas.base"), + existingOverlay = placeholder.children("canvas.overlay"); + + if (existingCanvas.length == 0 || existingOverlay == 0) { + // init everything + + placeholder.html(""); // make sure placeholder is clear + + placeholder.css({ padding: 0 }); // padding messes up the positioning + + if (placeholder.css("position") == 'static') + placeholder.css("position", "relative"); // for positioning labels and overlay + + getCanvasDimensions(); + + canvas = makeCanvas(true, "base"); + overlay = makeCanvas(false, "overlay"); // overlay canvas for interactive features + + reused = false; + } + else { + // reuse existing elements + + canvas = existingCanvas.get(0); + overlay = existingOverlay.get(0); + + reused = true; + } + + ctx = canvas.getContext("2d"); + octx = overlay.getContext("2d"); + + // we include the canvas in the event holder too, because IE 7 + // sometimes has trouble with the stacking order + eventHolder = $([overlay, canvas]); + + if (reused) { + // run shutdown in the old plot object + placeholder.data("plot").shutdown(); + + // reset reused canvases + plot.resize(); + + // make sure overlay pixels are cleared (canvas is cleared when we redraw) + octx.clearRect(0, 0, canvasWidth, canvasHeight); + + // then whack any remaining obvious garbage left + eventHolder.unbind(); + placeholder.children().not([canvas, overlay]).remove(); + } + + // save in case we get replotted + placeholder.data("plot", plot); + } + + function bindEvents() { + // bind events + if (options.grid.hoverable) { + eventHolder.mousemove(onMouseMove); + eventHolder.mouseleave(onMouseLeave); + } + + if (options.grid.clickable) + eventHolder.click(onClick); + + executeHooks(hooks.bindEvents, [eventHolder]); + } + + function shutdown() { + if (redrawTimeout) + clearTimeout(redrawTimeout); + + eventHolder.unbind("mousemove", onMouseMove); + eventHolder.unbind("mouseleave", onMouseLeave); + eventHolder.unbind("click", onClick); + + executeHooks(hooks.shutdown, [eventHolder]); + } + + function setTransformationHelpers(axis) { + // set helper functions on the axis, assumes plot area + // has been computed already + + function identity(x) { return x; } + + var s, m, t = axis.options.transform || identity, + it = axis.options.inverseTransform; + + // precompute how much the axis is scaling a point + // in canvas space + if (axis.direction == "x") { + s = axis.scale = plotWidth / Math.abs(t(axis.max) - t(axis.min)); + m = Math.min(t(axis.max), t(axis.min)); + } + else { + s = axis.scale = plotHeight / Math.abs(t(axis.max) - t(axis.min)); + s = -s; + m = Math.max(t(axis.max), t(axis.min)); + } + + // data point to canvas coordinate + if (t == identity) // slight optimization + axis.p2c = function (p) { return (p - m) * s; }; + else + axis.p2c = function (p) { return (t(p) - m) * s; }; + // canvas coordinate to data point + if (!it) + axis.c2p = function (c) { return m + c / s; }; + else + axis.c2p = function (c) { return it(m + c / s); }; + } + + function measureTickLabels(axis) { + var opts = axis.options, i, ticks = axis.ticks || [], labels = [], + l, w = opts.labelWidth, h = opts.labelHeight, dummyDiv; + + function makeDummyDiv(labels, width) { + return $('
      ' + + '
      ' + + labels.join("") + '
      ') + .appendTo(placeholder); + } + + if (axis.direction == "x") { + // to avoid measuring the widths of the labels (it's slow), we + // construct fixed-size boxes and put the labels inside + // them, we don't need the exact figures and the + // fixed-size box content is easy to center + if (w == null) + w = Math.floor(canvasWidth / (ticks.length > 0 ? ticks.length : 1)); + + // measure x label heights + if (h == null) { + labels = []; + for (i = 0; i < ticks.length; ++i) { + l = ticks[i].label; + if (l) + labels.push('
      ' + l + '
      '); + } + + if (labels.length > 0) { + // stick them all in the same div and measure + // collective height + labels.push('
      '); + dummyDiv = makeDummyDiv(labels, "width:10000px;"); + h = dummyDiv.height(); + dummyDiv.remove(); + } + } + } + else if (w == null || h == null) { + // calculate y label dimensions + for (i = 0; i < ticks.length; ++i) { + l = ticks[i].label; + if (l) + labels.push('
      ' + l + '
      '); + } + + if (labels.length > 0) { + dummyDiv = makeDummyDiv(labels, ""); + if (w == null) + w = dummyDiv.children().width(); + if (h == null) + h = dummyDiv.find("div.tickLabel").height(); + dummyDiv.remove(); + } + } + + if (w == null) + w = 0; + if (h == null) + h = 0; + + axis.labelWidth = w; + axis.labelHeight = h; + } + + function allocateAxisBoxFirstPhase(axis) { + // find the bounding box of the axis by looking at label + // widths/heights and ticks, make room by diminishing the + // plotOffset + + var lw = axis.labelWidth, + lh = axis.labelHeight, + pos = axis.options.position, + tickLength = axis.options.tickLength, + axismargin = options.grid.axisMargin, + padding = options.grid.labelMargin, + all = axis.direction == "x" ? xaxes : yaxes, + index; + + // determine axis margin + var samePosition = $.grep(all, function (a) { + return a && a.options.position == pos && a.reserveSpace; + }); + if ($.inArray(axis, samePosition) == samePosition.length - 1) + axismargin = 0; // outermost + + // determine tick length - if we're innermost, we can use "full" + if (tickLength == null) + tickLength = "full"; + + var sameDirection = $.grep(all, function (a) { + return a && a.reserveSpace; + }); + + var innermost = $.inArray(axis, sameDirection) == 0; + if (!innermost && tickLength == "full") + tickLength = 5; + + if (!isNaN(+tickLength)) + padding += +tickLength; + + // compute box + if (axis.direction == "x") { + lh += padding; + + if (pos == "bottom") { + plotOffset.bottom += lh + axismargin; + axis.box = { top: canvasHeight - plotOffset.bottom, height: lh }; + } + else { + axis.box = { top: plotOffset.top + axismargin, height: lh }; + plotOffset.top += lh + axismargin; + } + } + else { + lw += padding; + + if (pos == "left") { + axis.box = { left: plotOffset.left + axismargin, width: lw }; + plotOffset.left += lw + axismargin; + } + else { + plotOffset.right += lw + axismargin; + axis.box = { left: canvasWidth - plotOffset.right, width: lw }; + } + } + + // save for future reference + axis.position = pos; + axis.tickLength = tickLength; + axis.box.padding = padding; + axis.innermost = innermost; + } + + function allocateAxisBoxSecondPhase(axis) { + // set remaining bounding box coordinates + if (axis.direction == "x") { + axis.box.left = plotOffset.left; + axis.box.width = plotWidth; + } + else { + axis.box.top = plotOffset.top; + axis.box.height = plotHeight; + } + } + + function setupGrid() { + var i, axes = allAxes(); + + // first calculate the plot and axis box dimensions + + $.each(axes, function (_, axis) { + axis.show = axis.options.show; + if (axis.show == null) + axis.show = axis.used; // by default an axis is visible if it's got data + + axis.reserveSpace = axis.show || axis.options.reserveSpace; + + setRange(axis); + }); + + allocatedAxes = $.grep(axes, function (axis) { return axis.reserveSpace; }); + + plotOffset.left = plotOffset.right = plotOffset.top = plotOffset.bottom = 0; + if (options.grid.show) { + $.each(allocatedAxes, function (_, axis) { + // make the ticks + setupTickGeneration(axis); + setTicks(axis); + snapRangeToTicks(axis, axis.ticks); + + // find labelWidth/Height for axis + measureTickLabels(axis); + }); + + // with all dimensions in house, we can compute the + // axis boxes, start from the outside (reverse order) + for (i = allocatedAxes.length - 1; i >= 0; --i) + allocateAxisBoxFirstPhase(allocatedAxes[i]); + + // make sure we've got enough space for things that + // might stick out + var minMargin = options.grid.minBorderMargin; + if (minMargin == null) { + minMargin = 0; + for (i = 0; i < series.length; ++i) + minMargin = Math.max(minMargin, series[i].points.radius + series[i].points.lineWidth/2); + } + + for (var a in plotOffset) { + plotOffset[a] += options.grid.borderWidth; + plotOffset[a] = Math.max(minMargin, plotOffset[a]); + } + } + + plotWidth = canvasWidth - plotOffset.left - plotOffset.right; + plotHeight = canvasHeight - plotOffset.bottom - plotOffset.top; + + // now we got the proper plotWidth/Height, we can compute the scaling + $.each(axes, function (_, axis) { + setTransformationHelpers(axis); + }); + + if (options.grid.show) { + $.each(allocatedAxes, function (_, axis) { + allocateAxisBoxSecondPhase(axis); + }); + + insertAxisLabels(); + } + + insertLegend(); + } + + function setRange(axis) { + var opts = axis.options, + min = +(opts.min != null ? opts.min : axis.datamin), + max = +(opts.max != null ? opts.max : axis.datamax), + delta = max - min; + + if (delta == 0.0) { + // degenerate case + var widen = max == 0 ? 1 : 0.01; + + if (opts.min == null) + min -= widen; + // always widen max if we couldn't widen min to ensure we + // don't fall into min == max which doesn't work + if (opts.max == null || opts.min != null) + max += widen; + } + else { + // consider autoscaling + var margin = opts.autoscaleMargin; + if (margin != null) { + if (opts.min == null) { + min -= delta * margin; + // make sure we don't go below zero if all values + // are positive + if (min < 0 && axis.datamin != null && axis.datamin >= 0) + min = 0; + } + if (opts.max == null) { + max += delta * margin; + if (max > 0 && axis.datamax != null && axis.datamax <= 0) + max = 0; + } + } + } + axis.min = min; + axis.max = max; + } + + function setupTickGeneration(axis) { + var opts = axis.options; + + // estimate number of ticks + var noTicks; + if (typeof opts.ticks == "number" && opts.ticks > 0) + noTicks = opts.ticks; + else + // heuristic based on the model a*sqrt(x) fitted to + // some data points that seemed reasonable + noTicks = 0.3 * Math.sqrt(axis.direction == "x" ? canvasWidth : canvasHeight); + + var delta = (axis.max - axis.min) / noTicks, + size, generator, unit, formatter, i, magn, norm; + + if (opts.mode == "time") { + // pretty handling of time + + // map of app. size of time units in milliseconds + var timeUnitSize = { + "second": 1000, + "minute": 60 * 1000, + "hour": 60 * 60 * 1000, + "day": 24 * 60 * 60 * 1000, + "month": 30 * 24 * 60 * 60 * 1000, + "year": 365.2425 * 24 * 60 * 60 * 1000 + }; + + + // the allowed tick sizes, after 1 year we use + // an integer algorithm + var spec = [ + [1, "second"], [2, "second"], [5, "second"], [10, "second"], + [30, "second"], + [1, "minute"], [2, "minute"], [5, "minute"], [10, "minute"], + [30, "minute"], + [1, "hour"], [2, "hour"], [4, "hour"], + [8, "hour"], [12, "hour"], + [1, "day"], [2, "day"], [3, "day"], + [0.25, "month"], [0.5, "month"], [1, "month"], + [2, "month"], [3, "month"], [6, "month"], + [1, "year"] + ]; + + var minSize = 0; + if (opts.minTickSize != null) { + if (typeof opts.tickSize == "number") + minSize = opts.tickSize; + else + minSize = opts.minTickSize[0] * timeUnitSize[opts.minTickSize[1]]; + } + + for (var i = 0; i < spec.length - 1; ++i) + if (delta < (spec[i][0] * timeUnitSize[spec[i][1]] + + spec[i + 1][0] * timeUnitSize[spec[i + 1][1]]) / 2 + && spec[i][0] * timeUnitSize[spec[i][1]] >= minSize) + break; + size = spec[i][0]; + unit = spec[i][1]; + + // special-case the possibility of several years + if (unit == "year") { + magn = Math.pow(10, Math.floor(Math.log(delta / timeUnitSize.year) / Math.LN10)); + norm = (delta / timeUnitSize.year) / magn; + if (norm < 1.5) + size = 1; + else if (norm < 3) + size = 2; + else if (norm < 7.5) + size = 5; + else + size = 10; + + size *= magn; + } + + axis.tickSize = opts.tickSize || [size, unit]; + + generator = function(axis) { + var ticks = [], + tickSize = axis.tickSize[0], unit = axis.tickSize[1], + d = new Date(axis.min); + + var step = tickSize * timeUnitSize[unit]; + + if (unit == "second") + d.setUTCSeconds(floorInBase(d.getUTCSeconds(), tickSize)); + if (unit == "minute") + d.setUTCMinutes(floorInBase(d.getUTCMinutes(), tickSize)); + if (unit == "hour") + d.setUTCHours(floorInBase(d.getUTCHours(), tickSize)); + if (unit == "month") + d.setUTCMonth(floorInBase(d.getUTCMonth(), tickSize)); + if (unit == "year") + d.setUTCFullYear(floorInBase(d.getUTCFullYear(), tickSize)); + + // reset smaller components + d.setUTCMilliseconds(0); + if (step >= timeUnitSize.minute) + d.setUTCSeconds(0); + if (step >= timeUnitSize.hour) + d.setUTCMinutes(0); + if (step >= timeUnitSize.day) + d.setUTCHours(0); + if (step >= timeUnitSize.day * 4) + d.setUTCDate(1); + if (step >= timeUnitSize.year) + d.setUTCMonth(0); + + + var carry = 0, v = Number.NaN, prev; + do { + prev = v; + v = d.getTime(); + ticks.push(v); + if (unit == "month") { + if (tickSize < 1) { + // a bit complicated - we'll divide the month + // up but we need to take care of fractions + // so we don't end up in the middle of a day + d.setUTCDate(1); + var start = d.getTime(); + d.setUTCMonth(d.getUTCMonth() + 1); + var end = d.getTime(); + d.setTime(v + carry * timeUnitSize.hour + (end - start) * tickSize); + carry = d.getUTCHours(); + d.setUTCHours(0); + } + else + d.setUTCMonth(d.getUTCMonth() + tickSize); + } + else if (unit == "year") { + d.setUTCFullYear(d.getUTCFullYear() + tickSize); + } + else + d.setTime(v + step); + } while (v < axis.max && v != prev); + + return ticks; + }; + + formatter = function (v, axis) { + var d = new Date(v); + + // first check global format + if (opts.timeformat != null) + return $.plot.formatDate(d, opts.timeformat, opts.monthNames); + + var t = axis.tickSize[0] * timeUnitSize[axis.tickSize[1]]; + var span = axis.max - axis.min; + var suffix = (opts.twelveHourClock) ? " %p" : ""; + + if (t < timeUnitSize.minute) + fmt = "%h:%M:%S" + suffix; + else if (t < timeUnitSize.day) { + if (span < 2 * timeUnitSize.day) + fmt = "%h:%M" + suffix; + else + fmt = "%b %d %h:%M" + suffix; + } + else if (t < timeUnitSize.month) + fmt = "%b %d"; + else if (t < timeUnitSize.year) { + if (span < timeUnitSize.year) + fmt = "%b"; + else + fmt = "%b %y"; + } + else + fmt = "%y"; + + return $.plot.formatDate(d, fmt, opts.monthNames); + }; + } + else { + // pretty rounding of base-10 numbers + var maxDec = opts.tickDecimals; + var dec = -Math.floor(Math.log(delta) / Math.LN10); + if (maxDec != null && dec > maxDec) + dec = maxDec; + + magn = Math.pow(10, -dec); + norm = delta / magn; // norm is between 1.0 and 10.0 + + if (norm < 1.5) + size = 1; + else if (norm < 3) { + size = 2; + // special case for 2.5, requires an extra decimal + if (norm > 2.25 && (maxDec == null || dec + 1 <= maxDec)) { + size = 2.5; + ++dec; + } + } + else if (norm < 7.5) + size = 5; + else + size = 10; + + size *= magn; + + if (opts.minTickSize != null && size < opts.minTickSize) + size = opts.minTickSize; + + axis.tickDecimals = Math.max(0, maxDec != null ? maxDec : dec); + axis.tickSize = opts.tickSize || size; + + generator = function (axis) { + var ticks = []; + + // spew out all possible ticks + var start = floorInBase(axis.min, axis.tickSize), + i = 0, v = Number.NaN, prev; + do { + prev = v; + v = start + i * axis.tickSize; + ticks.push(v); + ++i; + } while (v < axis.max && v != prev); + return ticks; + }; + + formatter = function (v, axis) { + return v.toFixed(axis.tickDecimals); + }; + } + + if (opts.alignTicksWithAxis != null) { + var otherAxis = (axis.direction == "x" ? xaxes : yaxes)[opts.alignTicksWithAxis - 1]; + if (otherAxis && otherAxis.used && otherAxis != axis) { + // consider snapping min/max to outermost nice ticks + var niceTicks = generator(axis); + if (niceTicks.length > 0) { + if (opts.min == null) + axis.min = Math.min(axis.min, niceTicks[0]); + if (opts.max == null && niceTicks.length > 1) + axis.max = Math.max(axis.max, niceTicks[niceTicks.length - 1]); + } + + generator = function (axis) { + // copy ticks, scaled to this axis + var ticks = [], v, i; + for (i = 0; i < otherAxis.ticks.length; ++i) { + v = (otherAxis.ticks[i].v - otherAxis.min) / (otherAxis.max - otherAxis.min); + v = axis.min + v * (axis.max - axis.min); + ticks.push(v); + } + return ticks; + }; + + // we might need an extra decimal since forced + // ticks don't necessarily fit naturally + if (axis.mode != "time" && opts.tickDecimals == null) { + var extraDec = Math.max(0, -Math.floor(Math.log(delta) / Math.LN10) + 1), + ts = generator(axis); + + // only proceed if the tick interval rounded + // with an extra decimal doesn't give us a + // zero at end + if (!(ts.length > 1 && /\..*0$/.test((ts[1] - ts[0]).toFixed(extraDec)))) + axis.tickDecimals = extraDec; + } + } + } + + axis.tickGenerator = generator; + if ($.isFunction(opts.tickFormatter)) + axis.tickFormatter = function (v, axis) { return "" + opts.tickFormatter(v, axis); }; + else + axis.tickFormatter = formatter; + } + + function setTicks(axis) { + var oticks = axis.options.ticks, ticks = []; + if (oticks == null || (typeof oticks == "number" && oticks > 0)) + ticks = axis.tickGenerator(axis); + else if (oticks) { + if ($.isFunction(oticks)) + // generate the ticks + ticks = oticks({ min: axis.min, max: axis.max }); + else + ticks = oticks; + } + + // clean up/labelify the supplied ticks, copy them over + var i, v; + axis.ticks = []; + for (i = 0; i < ticks.length; ++i) { + var label = null; + var t = ticks[i]; + if (typeof t == "object") { + v = +t[0]; + if (t.length > 1) + label = t[1]; + } + else + v = +t; + if (label == null) + label = axis.tickFormatter(v, axis); + if (!isNaN(v)) + axis.ticks.push({ v: v, label: label }); + } + } + + function snapRangeToTicks(axis, ticks) { + if (axis.options.autoscaleMargin && ticks.length > 0) { + // snap to ticks + if (axis.options.min == null) + axis.min = Math.min(axis.min, ticks[0].v); + if (axis.options.max == null && ticks.length > 1) + axis.max = Math.max(axis.max, ticks[ticks.length - 1].v); + } + } + + function draw() { + ctx.clearRect(0, 0, canvasWidth, canvasHeight); + + var grid = options.grid; + + // draw background, if any + if (grid.show && grid.backgroundColor) + drawBackground(); + + if (grid.show && !grid.aboveData) + drawGrid(); + + for (var i = 0; i < series.length; ++i) { + executeHooks(hooks.drawSeries, [ctx, series[i]]); + drawSeries(series[i]); + } + + executeHooks(hooks.draw, [ctx]); + + if (grid.show && grid.aboveData) + drawGrid(); + } + + function extractRange(ranges, coord) { + var axis, from, to, key, axes = allAxes(); + + for (i = 0; i < axes.length; ++i) { + axis = axes[i]; + if (axis.direction == coord) { + key = coord + axis.n + "axis"; + if (!ranges[key] && axis.n == 1) + key = coord + "axis"; // support x1axis as xaxis + if (ranges[key]) { + from = ranges[key].from; + to = ranges[key].to; + break; + } + } + } + + // backwards-compat stuff - to be removed in future + if (!ranges[key]) { + axis = coord == "x" ? xaxes[0] : yaxes[0]; + from = ranges[coord + "1"]; + to = ranges[coord + "2"]; + } + + // auto-reverse as an added bonus + if (from != null && to != null && from > to) { + var tmp = from; + from = to; + to = tmp; + } + + return { from: from, to: to, axis: axis }; + } + + function drawBackground() { + ctx.save(); + ctx.translate(plotOffset.left, plotOffset.top); + + ctx.fillStyle = getColorOrGradient(options.grid.backgroundColor, plotHeight, 0, "rgba(255, 255, 255, 0)"); + ctx.fillRect(0, 0, plotWidth, plotHeight); + ctx.restore(); + } + + function drawGrid() { + var i; + + ctx.save(); + ctx.translate(plotOffset.left, plotOffset.top); + + // draw markings + var markings = options.grid.markings; + if (markings) { + if ($.isFunction(markings)) { + var axes = plot.getAxes(); + // xmin etc. is backwards compatibility, to be + // removed in the future + axes.xmin = axes.xaxis.min; + axes.xmax = axes.xaxis.max; + axes.ymin = axes.yaxis.min; + axes.ymax = axes.yaxis.max; + + markings = markings(axes); + } + + for (i = 0; i < markings.length; ++i) { + var m = markings[i], + xrange = extractRange(m, "x"), + yrange = extractRange(m, "y"); + + // fill in missing + if (xrange.from == null) + xrange.from = xrange.axis.min; + if (xrange.to == null) + xrange.to = xrange.axis.max; + if (yrange.from == null) + yrange.from = yrange.axis.min; + if (yrange.to == null) + yrange.to = yrange.axis.max; + + // clip + if (xrange.to < xrange.axis.min || xrange.from > xrange.axis.max || + yrange.to < yrange.axis.min || yrange.from > yrange.axis.max) + continue; + + xrange.from = Math.max(xrange.from, xrange.axis.min); + xrange.to = Math.min(xrange.to, xrange.axis.max); + yrange.from = Math.max(yrange.from, yrange.axis.min); + yrange.to = Math.min(yrange.to, yrange.axis.max); + + if (xrange.from == xrange.to && yrange.from == yrange.to) + continue; + + // then draw + xrange.from = xrange.axis.p2c(xrange.from); + xrange.to = xrange.axis.p2c(xrange.to); + yrange.from = yrange.axis.p2c(yrange.from); + yrange.to = yrange.axis.p2c(yrange.to); + + if (xrange.from == xrange.to || yrange.from == yrange.to) { + // draw line + ctx.beginPath(); + ctx.strokeStyle = m.color || options.grid.markingsColor; + ctx.lineWidth = m.lineWidth || options.grid.markingsLineWidth; + ctx.moveTo(xrange.from, yrange.from); + ctx.lineTo(xrange.to, yrange.to); + ctx.stroke(); + } + else { + // fill area + ctx.fillStyle = m.color || options.grid.markingsColor; + ctx.fillRect(xrange.from, yrange.to, + xrange.to - xrange.from, + yrange.from - yrange.to); + } + } + } + + // draw the ticks + var axes = allAxes(), bw = options.grid.borderWidth; + + for (var j = 0; j < axes.length; ++j) { + var axis = axes[j], box = axis.box, + t = axis.tickLength, x, y, xoff, yoff; + if (!axis.show || axis.ticks.length == 0) + continue + + ctx.strokeStyle = axis.options.tickColor || $.color.parse(axis.options.color).scale('a', 0.22).toString(); + ctx.lineWidth = 1; + + // find the edges + if (axis.direction == "x") { + x = 0; + if (t == "full") + y = (axis.position == "top" ? 0 : plotHeight); + else + y = box.top - plotOffset.top + (axis.position == "top" ? box.height : 0); + } + else { + y = 0; + if (t == "full") + x = (axis.position == "left" ? 0 : plotWidth); + else + x = box.left - plotOffset.left + (axis.position == "left" ? box.width : 0); + } + + // draw tick bar + if (!axis.innermost) { + ctx.beginPath(); + xoff = yoff = 0; + if (axis.direction == "x") + xoff = plotWidth; + else + yoff = plotHeight; + + if (ctx.lineWidth == 1) { + x = Math.floor(x) + 0.5; + y = Math.floor(y) + 0.5; + } + + ctx.moveTo(x, y); + ctx.lineTo(x + xoff, y + yoff); + ctx.stroke(); + } + + // draw ticks + ctx.beginPath(); + for (i = 0; i < axis.ticks.length; ++i) { + var v = axis.ticks[i].v; + + xoff = yoff = 0; + + if (v < axis.min || v > axis.max + // skip those lying on the axes if we got a border + || (t == "full" && bw > 0 + && (v == axis.min || v == axis.max))) + continue; + + if (axis.direction == "x") { + x = axis.p2c(v); + yoff = t == "full" ? -plotHeight : t; + + if (axis.position == "top") + yoff = -yoff; + } + else { + y = axis.p2c(v); + xoff = t == "full" ? -plotWidth : t; + + if (axis.position == "left") + xoff = -xoff; + } + + if (ctx.lineWidth == 1) { + if (axis.direction == "x") + x = Math.floor(x) + 0.5; + else + y = Math.floor(y) + 0.5; + } + + ctx.moveTo(x, y); + ctx.lineTo(x + xoff, y + yoff); + } + + ctx.stroke(); + } + + + // draw border + if (bw) { + ctx.lineWidth = bw; + ctx.strokeStyle = options.grid.borderColor; + ctx.strokeRect(-bw/2, -bw/2, plotWidth + bw, plotHeight + bw); + } + + ctx.restore(); + } + + function insertAxisLabels() { + placeholder.find(".tickLabels").remove(); + + var html = ['
      ']; + + var axes = allAxes(); + for (var j = 0; j < axes.length; ++j) { + var axis = axes[j], box = axis.box; + if (!axis.show) + continue; + //debug: html.push('
      ') + html.push('
      '); + for (var i = 0; i < axis.ticks.length; ++i) { + var tick = axis.ticks[i]; + if (!tick.label || tick.v < axis.min || tick.v > axis.max) + continue; + + var pos = {}, align; + + if (axis.direction == "x") { + align = "center"; + pos.left = Math.round(plotOffset.left + axis.p2c(tick.v) - axis.labelWidth/2); + if (axis.position == "bottom") + pos.top = box.top + box.padding; + else + pos.bottom = canvasHeight - (box.top + box.height - box.padding); + } + else { + pos.top = Math.round(plotOffset.top + axis.p2c(tick.v) - axis.labelHeight/2); + if (axis.position == "left") { + pos.right = canvasWidth - (box.left + box.width - box.padding) + align = "right"; + } + else { + pos.left = box.left + box.padding; + align = "left"; + } + } + + pos.width = axis.labelWidth; + + var style = ["position:absolute", "text-align:" + align ]; + for (var a in pos) + style.push(a + ":" + pos[a] + "px") + + html.push('
      ' + tick.label + '
      '); + } + html.push('
      '); + } + + html.push('
      '); + + placeholder.append(html.join("")); + } + + function drawSeries(series) { + if (series.lines.show) + drawSeriesLines(series); + if (series.bars.show) + drawSeriesBars(series); + if (series.points.show) + drawSeriesPoints(series); + } + + function drawSeriesLines(series) { + function plotLine(datapoints, xoffset, yoffset, axisx, axisy) { + var points = datapoints.points, + ps = datapoints.pointsize, + prevx = null, prevy = null; + + ctx.beginPath(); + for (var i = ps; i < points.length; i += ps) { + var x1 = points[i - ps], y1 = points[i - ps + 1], + x2 = points[i], y2 = points[i + 1]; + + if (x1 == null || x2 == null) + continue; + + // clip with ymin + if (y1 <= y2 && y1 < axisy.min) { + if (y2 < axisy.min) + continue; // line segment is outside + // compute new intersection point + x1 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1; + y1 = axisy.min; + } + else if (y2 <= y1 && y2 < axisy.min) { + if (y1 < axisy.min) + continue; + x2 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1; + y2 = axisy.min; + } + + // clip with ymax + if (y1 >= y2 && y1 > axisy.max) { + if (y2 > axisy.max) + continue; + x1 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1; + y1 = axisy.max; + } + else if (y2 >= y1 && y2 > axisy.max) { + if (y1 > axisy.max) + continue; + x2 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1; + y2 = axisy.max; + } + + // clip with xmin + if (x1 <= x2 && x1 < axisx.min) { + if (x2 < axisx.min) + continue; + y1 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1; + x1 = axisx.min; + } + else if (x2 <= x1 && x2 < axisx.min) { + if (x1 < axisx.min) + continue; + y2 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1; + x2 = axisx.min; + } + + // clip with xmax + if (x1 >= x2 && x1 > axisx.max) { + if (x2 > axisx.max) + continue; + y1 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1; + x1 = axisx.max; + } + else if (x2 >= x1 && x2 > axisx.max) { + if (x1 > axisx.max) + continue; + y2 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1; + x2 = axisx.max; + } + + if (x1 != prevx || y1 != prevy) + ctx.moveTo(axisx.p2c(x1) + xoffset, axisy.p2c(y1) + yoffset); + + prevx = x2; + prevy = y2; + ctx.lineTo(axisx.p2c(x2) + xoffset, axisy.p2c(y2) + yoffset); + } + ctx.stroke(); + } + + function plotLineArea(datapoints, axisx, axisy) { + var points = datapoints.points, + ps = datapoints.pointsize, + bottom = Math.min(Math.max(0, axisy.min), axisy.max), + i = 0, top, areaOpen = false, + ypos = 1, segmentStart = 0, segmentEnd = 0; + + // we process each segment in two turns, first forward + // direction to sketch out top, then once we hit the + // end we go backwards to sketch the bottom + while (true) { + if (ps > 0 && i > points.length + ps) + break; + + i += ps; // ps is negative if going backwards + + var x1 = points[i - ps], + y1 = points[i - ps + ypos], + x2 = points[i], y2 = points[i + ypos]; + + if (areaOpen) { + if (ps > 0 && x1 != null && x2 == null) { + // at turning point + segmentEnd = i; + ps = -ps; + ypos = 2; + continue; + } + + if (ps < 0 && i == segmentStart + ps) { + // done with the reverse sweep + ctx.fill(); + areaOpen = false; + ps = -ps; + ypos = 1; + i = segmentStart = segmentEnd + ps; + continue; + } + } + + if (x1 == null || x2 == null) + continue; + + // clip x values + + // clip with xmin + if (x1 <= x2 && x1 < axisx.min) { + if (x2 < axisx.min) + continue; + y1 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1; + x1 = axisx.min; + } + else if (x2 <= x1 && x2 < axisx.min) { + if (x1 < axisx.min) + continue; + y2 = (axisx.min - x1) / (x2 - x1) * (y2 - y1) + y1; + x2 = axisx.min; + } + + // clip with xmax + if (x1 >= x2 && x1 > axisx.max) { + if (x2 > axisx.max) + continue; + y1 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1; + x1 = axisx.max; + } + else if (x2 >= x1 && x2 > axisx.max) { + if (x1 > axisx.max) + continue; + y2 = (axisx.max - x1) / (x2 - x1) * (y2 - y1) + y1; + x2 = axisx.max; + } + + if (!areaOpen) { + // open area + ctx.beginPath(); + ctx.moveTo(axisx.p2c(x1), axisy.p2c(bottom)); + areaOpen = true; + } + + // now first check the case where both is outside + if (y1 >= axisy.max && y2 >= axisy.max) { + ctx.lineTo(axisx.p2c(x1), axisy.p2c(axisy.max)); + ctx.lineTo(axisx.p2c(x2), axisy.p2c(axisy.max)); + continue; + } + else if (y1 <= axisy.min && y2 <= axisy.min) { + ctx.lineTo(axisx.p2c(x1), axisy.p2c(axisy.min)); + ctx.lineTo(axisx.p2c(x2), axisy.p2c(axisy.min)); + continue; + } + + // else it's a bit more complicated, there might + // be a flat maxed out rectangle first, then a + // triangular cutout or reverse; to find these + // keep track of the current x values + var x1old = x1, x2old = x2; + + // clip the y values, without shortcutting, we + // go through all cases in turn + + // clip with ymin + if (y1 <= y2 && y1 < axisy.min && y2 >= axisy.min) { + x1 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1; + y1 = axisy.min; + } + else if (y2 <= y1 && y2 < axisy.min && y1 >= axisy.min) { + x2 = (axisy.min - y1) / (y2 - y1) * (x2 - x1) + x1; + y2 = axisy.min; + } + + // clip with ymax + if (y1 >= y2 && y1 > axisy.max && y2 <= axisy.max) { + x1 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1; + y1 = axisy.max; + } + else if (y2 >= y1 && y2 > axisy.max && y1 <= axisy.max) { + x2 = (axisy.max - y1) / (y2 - y1) * (x2 - x1) + x1; + y2 = axisy.max; + } + + // if the x value was changed we got a rectangle + // to fill + if (x1 != x1old) { + ctx.lineTo(axisx.p2c(x1old), axisy.p2c(y1)); + // it goes to (x1, y1), but we fill that below + } + + // fill triangular section, this sometimes result + // in redundant points if (x1, y1) hasn't changed + // from previous line to, but we just ignore that + ctx.lineTo(axisx.p2c(x1), axisy.p2c(y1)); + ctx.lineTo(axisx.p2c(x2), axisy.p2c(y2)); + + // fill the other rectangle if it's there + if (x2 != x2old) { + ctx.lineTo(axisx.p2c(x2), axisy.p2c(y2)); + ctx.lineTo(axisx.p2c(x2old), axisy.p2c(y2)); + } + } + } + + ctx.save(); + ctx.translate(plotOffset.left, plotOffset.top); + ctx.lineJoin = "round"; + + var lw = series.lines.lineWidth, + sw = series.shadowSize; + // FIXME: consider another form of shadow when filling is turned on + if (lw > 0 && sw > 0) { + // draw shadow as a thick and thin line with transparency + ctx.lineWidth = sw; + ctx.strokeStyle = "rgba(0,0,0,0.1)"; + // position shadow at angle from the mid of line + var angle = Math.PI/18; + plotLine(series.datapoints, Math.sin(angle) * (lw/2 + sw/2), Math.cos(angle) * (lw/2 + sw/2), series.xaxis, series.yaxis); + ctx.lineWidth = sw/2; + plotLine(series.datapoints, Math.sin(angle) * (lw/2 + sw/4), Math.cos(angle) * (lw/2 + sw/4), series.xaxis, series.yaxis); + } + + ctx.lineWidth = lw; + ctx.strokeStyle = series.color; + var fillStyle = getFillStyle(series.lines, series.color, 0, plotHeight); + if (fillStyle) { + ctx.fillStyle = fillStyle; + plotLineArea(series.datapoints, series.xaxis, series.yaxis); + } + + if (lw > 0) + plotLine(series.datapoints, 0, 0, series.xaxis, series.yaxis); + ctx.restore(); + } + + function drawSeriesPoints(series) { + function plotPoints(datapoints, radius, fillStyle, offset, shadow, axisx, axisy, symbol) { + var points = datapoints.points, ps = datapoints.pointsize; + + for (var i = 0; i < points.length; i += ps) { + var x = points[i], y = points[i + 1]; + if (x == null || x < axisx.min || x > axisx.max || y < axisy.min || y > axisy.max) + continue; + + ctx.beginPath(); + x = axisx.p2c(x); + y = axisy.p2c(y) + offset; + if (symbol == "circle") + ctx.arc(x, y, radius, 0, shadow ? Math.PI : Math.PI * 2, false); + else + symbol(ctx, x, y, radius, shadow); + ctx.closePath(); + + if (fillStyle) { + ctx.fillStyle = fillStyle; + ctx.fill(); + } + ctx.stroke(); + } + } + + ctx.save(); + ctx.translate(plotOffset.left, plotOffset.top); + + var lw = series.points.lineWidth, + sw = series.shadowSize, + radius = series.points.radius, + symbol = series.points.symbol; + if (lw > 0 && sw > 0) { + // draw shadow in two steps + var w = sw / 2; + ctx.lineWidth = w; + ctx.strokeStyle = "rgba(0,0,0,0.1)"; + plotPoints(series.datapoints, radius, null, w + w/2, true, + series.xaxis, series.yaxis, symbol); + + ctx.strokeStyle = "rgba(0,0,0,0.2)"; + plotPoints(series.datapoints, radius, null, w/2, true, + series.xaxis, series.yaxis, symbol); + } + + ctx.lineWidth = lw; + ctx.strokeStyle = series.color; + plotPoints(series.datapoints, radius, + getFillStyle(series.points, series.color), 0, false, + series.xaxis, series.yaxis, symbol); + ctx.restore(); + } + + function drawBar(x, y, b, barLeft, barRight, offset, fillStyleCallback, axisx, axisy, c, horizontal, lineWidth) { + var left, right, bottom, top, + drawLeft, drawRight, drawTop, drawBottom, + tmp; + + // in horizontal mode, we start the bar from the left + // instead of from the bottom so it appears to be + // horizontal rather than vertical + if (horizontal) { + drawBottom = drawRight = drawTop = true; + drawLeft = false; + left = b; + right = x; + top = y + barLeft; + bottom = y + barRight; + + // account for negative bars + if (right < left) { + tmp = right; + right = left; + left = tmp; + drawLeft = true; + drawRight = false; + } + } + else { + drawLeft = drawRight = drawTop = true; + drawBottom = false; + left = x + barLeft; + right = x + barRight; + bottom = b; + top = y; + + // account for negative bars + if (top < bottom) { + tmp = top; + top = bottom; + bottom = tmp; + drawBottom = true; + drawTop = false; + } + } + + // clip + if (right < axisx.min || left > axisx.max || + top < axisy.min || bottom > axisy.max) + return; + + if (left < axisx.min) { + left = axisx.min; + drawLeft = false; + } + + if (right > axisx.max) { + right = axisx.max; + drawRight = false; + } + + if (bottom < axisy.min) { + bottom = axisy.min; + drawBottom = false; + } + + if (top > axisy.max) { + top = axisy.max; + drawTop = false; + } + + left = axisx.p2c(left); + bottom = axisy.p2c(bottom); + right = axisx.p2c(right); + top = axisy.p2c(top); + + // fill the bar + if (fillStyleCallback) { + c.beginPath(); + c.moveTo(left, bottom); + c.lineTo(left, top); + c.lineTo(right, top); + c.lineTo(right, bottom); + c.fillStyle = fillStyleCallback(bottom, top); + c.fill(); + } + + // draw outline + if (lineWidth > 0 && (drawLeft || drawRight || drawTop || drawBottom)) { + c.beginPath(); + + // FIXME: inline moveTo is buggy with excanvas + c.moveTo(left, bottom + offset); + if (drawLeft) + c.lineTo(left, top + offset); + else + c.moveTo(left, top + offset); + if (drawTop) + c.lineTo(right, top + offset); + else + c.moveTo(right, top + offset); + if (drawRight) + c.lineTo(right, bottom + offset); + else + c.moveTo(right, bottom + offset); + if (drawBottom) + c.lineTo(left, bottom + offset); + else + c.moveTo(left, bottom + offset); + c.stroke(); + } + } + + function drawSeriesBars(series) { + function plotBars(datapoints, barLeft, barRight, offset, fillStyleCallback, axisx, axisy) { + var points = datapoints.points, ps = datapoints.pointsize; + + for (var i = 0; i < points.length; i += ps) { + if (points[i] == null) + continue; + drawBar(points[i], points[i + 1], points[i + 2], barLeft, barRight, offset, fillStyleCallback, axisx, axisy, ctx, series.bars.horizontal, series.bars.lineWidth); + } + } + + ctx.save(); + ctx.translate(plotOffset.left, plotOffset.top); + + // FIXME: figure out a way to add shadows (for instance along the right edge) + ctx.lineWidth = series.bars.lineWidth; + ctx.strokeStyle = series.color; + var barLeft = series.bars.align == "left" ? 0 : -series.bars.barWidth/2; + var fillStyleCallback = series.bars.fill ? function (bottom, top) { return getFillStyle(series.bars, series.color, bottom, top); } : null; + plotBars(series.datapoints, barLeft, barLeft + series.bars.barWidth, 0, fillStyleCallback, series.xaxis, series.yaxis); + ctx.restore(); + } + + function getFillStyle(filloptions, seriesColor, bottom, top) { + var fill = filloptions.fill; + if (!fill) + return null; + + if (filloptions.fillColor) + return getColorOrGradient(filloptions.fillColor, bottom, top, seriesColor); + + var c = $.color.parse(seriesColor); + c.a = typeof fill == "number" ? fill : 0.4; + c.normalize(); + return c.toString(); + } + + function insertLegend() { + placeholder.find(".legend").remove(); + + if (!options.legend.show) + return; + + var fragments = [], rowStarted = false, + lf = options.legend.labelFormatter, s, label; + for (var i = 0; i < series.length; ++i) { + s = series[i]; + label = s.label; + if (!label) + continue; + + if (i % options.legend.noColumns == 0) { + if (rowStarted) + fragments.push(''); + fragments.push(''); + rowStarted = true; + } + + if (lf) + label = lf(label, s); + + fragments.push( + '
      ' + + '' + label + ''); + } + if (rowStarted) + fragments.push(''); + + if (fragments.length == 0) + return; + + var table = '' + fragments.join("") + '
      '; + if (options.legend.container != null) + $(options.legend.container).html(table); + else { + var pos = "", + p = options.legend.position, + m = options.legend.margin; + if (m[0] == null) + m = [m, m]; + if (p.charAt(0) == "n") + pos += 'top:' + (m[1] + plotOffset.top) + 'px;'; + else if (p.charAt(0) == "s") + pos += 'bottom:' + (m[1] + plotOffset.bottom) + 'px;'; + if (p.charAt(1) == "e") + pos += 'right:' + (m[0] + plotOffset.right) + 'px;'; + else if (p.charAt(1) == "w") + pos += 'left:' + (m[0] + plotOffset.left) + 'px;'; + var legend = $('
      ' + table.replace('style="', 'style="position:absolute;' + pos +';') + '
      ').appendTo(placeholder); + if (options.legend.backgroundOpacity != 0.0) { + // put in the transparent background + // separately to avoid blended labels and + // label boxes + var c = options.legend.backgroundColor; + if (c == null) { + c = options.grid.backgroundColor; + if (c && typeof c == "string") + c = $.color.parse(c); + else + c = $.color.extract(legend, 'background-color'); + c.a = 1; + c = c.toString(); + } + var div = legend.children(); + $('
      ').prependTo(legend).css('opacity', options.legend.backgroundOpacity); + } + } + } + + + // interactive features + + var highlights = [], + redrawTimeout = null; + + // returns the data item the mouse is over, or null if none is found + function findNearbyItem(mouseX, mouseY, seriesFilter) { + var maxDistance = options.grid.mouseActiveRadius, + smallestDistance = maxDistance * maxDistance + 1, + item = null, foundPoint = false, i, j; + + for (i = series.length - 1; i >= 0; --i) { + if (!seriesFilter(series[i])) + continue; + + var s = series[i], + axisx = s.xaxis, + axisy = s.yaxis, + points = s.datapoints.points, + ps = s.datapoints.pointsize, + mx = axisx.c2p(mouseX), // precompute some stuff to make the loop faster + my = axisy.c2p(mouseY), + maxx = maxDistance / axisx.scale, + maxy = maxDistance / axisy.scale; + + // with inverse transforms, we can't use the maxx/maxy + // optimization, sadly + if (axisx.options.inverseTransform) + maxx = Number.MAX_VALUE; + if (axisy.options.inverseTransform) + maxy = Number.MAX_VALUE; + + if (s.lines.show || s.points.show) { + for (j = 0; j < points.length; j += ps) { + var x = points[j], y = points[j + 1]; + if (x == null) + continue; + + // For points and lines, the cursor must be within a + // certain distance to the data point + if (x - mx > maxx || x - mx < -maxx || + y - my > maxy || y - my < -maxy) + continue; + + // We have to calculate distances in pixels, not in + // data units, because the scales of the axes may be different + var dx = Math.abs(axisx.p2c(x) - mouseX), + dy = Math.abs(axisy.p2c(y) - mouseY), + dist = dx * dx + dy * dy; // we save the sqrt + + // use <= to ensure last point takes precedence + // (last generally means on top of) + if (dist < smallestDistance) { + smallestDistance = dist; + item = [i, j / ps]; + } + } + } + + if (s.bars.show && !item) { // no other point can be nearby + var barLeft = s.bars.align == "left" ? 0 : -s.bars.barWidth/2, + barRight = barLeft + s.bars.barWidth; + + for (j = 0; j < points.length; j += ps) { + var x = points[j], y = points[j + 1], b = points[j + 2]; + if (x == null) + continue; + + // for a bar graph, the cursor must be inside the bar + if (series[i].bars.horizontal ? + (mx <= Math.max(b, x) && mx >= Math.min(b, x) && + my >= y + barLeft && my <= y + barRight) : + (mx >= x + barLeft && mx <= x + barRight && + my >= Math.min(b, y) && my <= Math.max(b, y))) + item = [i, j / ps]; + } + } + } + + if (item) { + i = item[0]; + j = item[1]; + ps = series[i].datapoints.pointsize; + + return { datapoint: series[i].datapoints.points.slice(j * ps, (j + 1) * ps), + dataIndex: j, + series: series[i], + seriesIndex: i }; + } + + return null; + } + + function onMouseMove(e) { + if (options.grid.hoverable) + triggerClickHoverEvent("plothover", e, + function (s) { return s["hoverable"] != false; }); + } + + function onMouseLeave(e) { + if (options.grid.hoverable) + triggerClickHoverEvent("plothover", e, + function (s) { return false; }); + } + + function onClick(e) { + triggerClickHoverEvent("plotclick", e, + function (s) { return s["clickable"] != false; }); + } + + // trigger click or hover event (they send the same parameters + // so we share their code) + function triggerClickHoverEvent(eventname, event, seriesFilter) { + var offset = eventHolder.offset(), + canvasX = event.pageX - offset.left - plotOffset.left, + canvasY = event.pageY - offset.top - plotOffset.top, + pos = canvasToAxisCoords({ left: canvasX, top: canvasY }); + + pos.pageX = event.pageX; + pos.pageY = event.pageY; + + var item = findNearbyItem(canvasX, canvasY, seriesFilter); + + if (item) { + // fill in mouse pos for any listeners out there + item.pageX = parseInt(item.series.xaxis.p2c(item.datapoint[0]) + offset.left + plotOffset.left); + item.pageY = parseInt(item.series.yaxis.p2c(item.datapoint[1]) + offset.top + plotOffset.top); + } + + if (options.grid.autoHighlight) { + // clear auto-highlights + for (var i = 0; i < highlights.length; ++i) { + var h = highlights[i]; + if (h.auto == eventname && + !(item && h.series == item.series && + h.point[0] == item.datapoint[0] && + h.point[1] == item.datapoint[1])) + unhighlight(h.series, h.point); + } + + if (item) + highlight(item.series, item.datapoint, eventname); + } + + placeholder.trigger(eventname, [ pos, item ]); + } + + function triggerRedrawOverlay() { + if (!redrawTimeout) + redrawTimeout = setTimeout(drawOverlay, 30); + } + + function drawOverlay() { + redrawTimeout = null; + + // draw highlights + octx.save(); + octx.clearRect(0, 0, canvasWidth, canvasHeight); + octx.translate(plotOffset.left, plotOffset.top); + + var i, hi; + for (i = 0; i < highlights.length; ++i) { + hi = highlights[i]; + + if (hi.series.bars.show) + drawBarHighlight(hi.series, hi.point); + else + drawPointHighlight(hi.series, hi.point); + } + octx.restore(); + + executeHooks(hooks.drawOverlay, [octx]); + } + + function highlight(s, point, auto) { + if (typeof s == "number") + s = series[s]; + + if (typeof point == "number") { + var ps = s.datapoints.pointsize; + point = s.datapoints.points.slice(ps * point, ps * (point + 1)); + } + + var i = indexOfHighlight(s, point); + if (i == -1) { + highlights.push({ series: s, point: point, auto: auto }); + + triggerRedrawOverlay(); + } + else if (!auto) + highlights[i].auto = false; + } + + function unhighlight(s, point) { + if (s == null && point == null) { + highlights = []; + triggerRedrawOverlay(); + } + + if (typeof s == "number") + s = series[s]; + + if (typeof point == "number") + point = s.data[point]; + + var i = indexOfHighlight(s, point); + if (i != -1) { + highlights.splice(i, 1); + + triggerRedrawOverlay(); + } + } + + function indexOfHighlight(s, p) { + for (var i = 0; i < highlights.length; ++i) { + var h = highlights[i]; + if (h.series == s && h.point[0] == p[0] + && h.point[1] == p[1]) + return i; + } + return -1; + } + + function drawPointHighlight(series, point) { + var x = point[0], y = point[1], + axisx = series.xaxis, axisy = series.yaxis; + + if (x < axisx.min || x > axisx.max || y < axisy.min || y > axisy.max) + return; + + var pointRadius = series.points.radius + series.points.lineWidth / 2; + octx.lineWidth = pointRadius; + octx.strokeStyle = $.color.parse(series.color).scale('a', 0.5).toString(); + var radius = 1.5 * pointRadius, + x = axisx.p2c(x), + y = axisy.p2c(y); + + octx.beginPath(); + if (series.points.symbol == "circle") + octx.arc(x, y, radius, 0, 2 * Math.PI, false); + else + series.points.symbol(octx, x, y, radius, false); + octx.closePath(); + octx.stroke(); + } + + function drawBarHighlight(series, point) { + octx.lineWidth = series.bars.lineWidth; + octx.strokeStyle = $.color.parse(series.color).scale('a', 0.5).toString(); + var fillStyle = $.color.parse(series.color).scale('a', 0.5).toString(); + var barLeft = series.bars.align == "left" ? 0 : -series.bars.barWidth/2; + drawBar(point[0], point[1], point[2] || 0, barLeft, barLeft + series.bars.barWidth, + 0, function () { return fillStyle; }, series.xaxis, series.yaxis, octx, series.bars.horizontal, series.bars.lineWidth); + } + + function getColorOrGradient(spec, bottom, top, defaultColor) { + if (typeof spec == "string") + return spec; + else { + // assume this is a gradient spec; IE currently only + // supports a simple vertical gradient properly, so that's + // what we support too + var gradient = ctx.createLinearGradient(0, top, 0, bottom); + + for (var i = 0, l = spec.colors.length; i < l; ++i) { + var c = spec.colors[i]; + if (typeof c != "string") { + var co = $.color.parse(defaultColor); + if (c.brightness != null) + co = co.scale('rgb', c.brightness) + if (c.opacity != null) + co.a *= c.opacity; + c = co.toString(); + } + gradient.addColorStop(i / (l - 1), c); + } + + return gradient; + } + } + } + + $.plot = function(placeholder, data, options) { + //var t0 = new Date(); + var plot = new Plot($(placeholder), data, options, $.plot.plugins); + //(window.console ? console.log : alert)("time used (msecs): " + ((new Date()).getTime() - t0.getTime())); + return plot; + }; + + $.plot.version = "0.7"; + + $.plot.plugins = []; + + // returns a string with the date d formatted according to fmt + $.plot.formatDate = function(d, fmt, monthNames) { + var leftPad = function(n) { + n = "" + n; + return n.length == 1 ? "0" + n : n; + }; + + var r = []; + var escape = false, padNext = false; + var hours = d.getUTCHours(); + var isAM = hours < 12; + if (monthNames == null) + monthNames = ["Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"]; + + if (fmt.search(/%p|%P/) != -1) { + if (hours > 12) { + hours = hours - 12; + } else if (hours == 0) { + hours = 12; + } + } + for (var i = 0; i < fmt.length; ++i) { + var c = fmt.charAt(i); + + if (escape) { + switch (c) { + case 'h': c = "" + hours; break; + case 'H': c = leftPad(hours); break; + case 'M': c = leftPad(d.getUTCMinutes()); break; + case 'S': c = leftPad(d.getUTCSeconds()); break; + case 'd': c = "" + d.getUTCDate(); break; + case 'm': c = "" + (d.getUTCMonth() + 1); break; + case 'y': c = "" + d.getUTCFullYear(); break; + case 'b': c = "" + monthNames[d.getUTCMonth()]; break; + case 'p': c = (isAM) ? ("" + "am") : ("" + "pm"); break; + case 'P': c = (isAM) ? ("" + "AM") : ("" + "PM"); break; + case '0': c = ""; padNext = true; break; + } + if (c && padNext) { + c = leftPad(c); + padNext = false; + } + r.push(c); + if (!padNext) + escape = false; + } + else { + if (c == "%") + escape = true; + else + r.push(c); + } + } + return r.join(""); + }; + + // round to nearby lower multiple of base + function floorInBase(n, base) { + return base * Math.floor(n / base); + } + +})(jQuery); diff --git a/parseVCF.py b/parseVCF.py new file mode 100644 index 0000000..fbd67de --- /dev/null +++ b/parseVCF.py @@ -0,0 +1,67 @@ +#!/usr/bin/python -u + +import os +import argparse + +# +if __name__ == '__main__': + # + + parser = argparse.ArgumentParser( + description = """ +This program will parse the annotations provided by the Ensembl Variant Predictor (VEP) +and create a list of protein consequences which can then be submitted to the +Functional Analysis through Hidden Markov Models (FATHMM) software and server. + """, + epilog = """ +Note: in order for this script to work, the VEP must be called using the additional --protein parameter. + """, + ) + + group = parser.add_argument_group('required arguments') + group.add_argument( + "-i", + dest = "input", + help = "a file containing the VEP annotations to parse", + metavar = "", + default = None, + required = True + ) + group.add_argument( + "-o", + dest = "output", + help = "where the protein consequences should be written to", + metavar = "", + default = None, + required = True + ) + + arguments = parser.parse_args() + + # + + try: + Consequence = {} + + for record in open(arguments.input, "r"): + if record.startswith("#") or not record.find("missense_variant") >= 0: + continue + record = record.strip().split("\t") + + x = record[10].split("/") + Var = x[0] + record[9] + x[1] + Info = dict([ x.split("=") for x in record[-1].split(";") ]) + + if not Info.has_key("ENSP"): + continue + + if not Consequence.has_key(Info['ENSP']): + Consequence[Info['ENSP']] = [] + Consequence[Info['ENSP']].append(Var) + + Processed = open(arguments.output, "w") + for id in Consequence: + Processed.write(id + " " + ",".join(set(Consequence[id])) + "\n") + # + except: + raise