- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3635: merge
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/cdd8d520f3c7 changeset: 3635:cdd8d520f3c7 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Apr 13 11:23:19 2010 -0400 description: merge diffstat: static/scripts/checkbox_and_radiobutton.js | 347 ++++ static/scripts/helper_functions.js | 817 ++++++++++ static/scripts/timer.js | 74 + tools/rgenetics/rgGRR.py | 2241 ++++++++++++++------------- tools/rgenetics/rgManQQ.py | 19 +- 5 files changed, 2396 insertions(+), 1102 deletions(-) diffs (truncated from 3540 to 3000 lines): diff -r a6e3f4cae4ce -r cdd8d520f3c7 static/scripts/checkbox_and_radiobutton.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/checkbox_and_radiobutton.js Tue Apr 13 11:23:19 2010 -0400 @@ -0,0 +1,347 @@ +/* +Scripts to create interactive checkboxes and radio buttons in SVG using ECMA script +Copyright (C) <2007> <Andreas Neumann> +Version 1.1.3, 2007-08-09 +neumann(a)karto.baug.ethz.ch +http://www.carto.net/ +http://www.carto.net/neumann/ + +Credits: +* Guy Morton for providing a fix to let users toggle checkboxes by clicking on text labels +* Bruce Rindahl for providing the bugfix described in version 1.1.2 +* Simon Shutter for providing a fix for the ASV in IE crash when reloading the SVG file after calling the .remove() method on a checkbox + +---- + +Documentation: http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/ + +---- + +current version: 1.1.3 + +version history: +1.0 (2006-03-13) +initial version + +1.1 (2006-07-11) +text labels are now clickable (thanks to Guy Morton) +added method .moveTo() to move checkbox to a different location +introduced new constructor parameter labelYOffset to allow more flexible placement of the text label + +1.1.1 (2007-02-06) +added cursor pointer to the text label and use element representing the checkBox + +1.1.2 (2007-04-19) +bug fix: this.selectedIndex was not correctly initialized in method addCheckBox of the radioButtonGroup object + +1.1.3 (2007-08-09) +bug fix: the method .remove() was slightly modified (using removeEventListener) for avoiding a crash related to the method after reloading the SVG file + +------- + + +This ECMA script library is free software; you can redistribute it and/or +modify it under the terms of the GNU Lesser General Public +License as published by the Free Software Foundation; either +version 2.1 of the License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +Lesser General Public License for more details. + +You should have received a copy of the GNU Lesser General Public +License along with this library (lesser_gpl.txt); if not, write to the Free Software +Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +---- + +original document site: http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/ +Please contact the author in case you want to use code or ideas commercially. +If you use this code, please include this copyright header, the included full +LGPL 2.1 text and read the terms provided in the LGPL 2.1 license +(http://www.gnu.org/copyleft/lesser.txt) + +------------------------------- + +Please report bugs and send improvements to neumann(a)karto.baug.ethz.ch +If you use this control, please link to the original (http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/) +somewhere in the source-code-comment or the "about" of your project and give credits, thanks! + +*/ + +function checkBox(id,parentNode,x,y,checkboxId,checkcrossId,checkedStatus,labelText,textStyles,labelDistance,labelYOffset,radioButtonGroup,functionToCall) { + var nrArguments = 13; + var createCheckbox= true; + if (arguments.length == nrArguments) { + this.id = id; //an internal id, this id is not used in the SVG Dom tree + this.parentNode = parentNode; //the parentNode, string or nodeReference + this.x = x; //the center of the checkBox + this.y = y; //the center of the checkBox + this.checkboxId = checkboxId; //the id of the checkbox symbol (background) + this.checkcrossId = checkcrossId; //the id of the checkbox symbol (foreground), pointer-events should be set to "none" + this.checkedStatus = checkedStatus; //a status variable (true|false), indicates if checkbox is on or off + this.labelText = labelText; //the text of the checkbox label to be displayed, use undefined or empty string if you don't need a label text + this.textStyles = textStyles; //an array of literals containing the text settings + if (!this.textStyles["font-size"]) { + this.textStyles["font-size"] = 12; + } + this.labelDistance = labelDistance; //a distance defined from the center of the checkbox to the left of the text of the label + this.labelYOffset = labelYOffset; //a y offset value for the text label in relation to the checkbox symbol center + this.radioButtonGroup = radioButtonGroup; //a reference to a radio button group, if this is a standalone checkBox, just use the parameter undefined + this.functionToCall = functionToCall; //the function to call after triggering checkBox + this.exists = true; //status that indicates if checkbox exists or not, is set to false after method .remove() was called + this.label = undefined; //later a reference to the label text node + } + else { + createCheckbox = false; + alert("Error in checkbox ("+id+"): wrong nr of arguments! You have to pass over "+nrArguments+" parameters."); + } + if (createCheckbox) { + //timer stuff + this.timer = new Timer(this); //a Timer instance for calling the functionToCall + if (this.radioButtonGroup) { + this.timerMs = 0; + } + else { + this.timerMs = 200; //a constant of this object that is used in conjunction with the timer - functionToCall is called after 200 ms + } + //create checkbox + this.createCheckBox(); + } + else { + alert("Could not create checkbox with id '"+id+"' due to errors in the constructor parameters"); + } +} + +//this method creates all necessary checkbox geometry +checkBox.prototype.createCheckBox = function() { + if (typeof(this.parentNode) == "string") { + this.parentNode = document.getElementById(this.parentNode); + } + //create checkbox + this.checkBox = document.createElementNS(svgNS,"use"); + this.checkBox.setAttributeNS(null,"x",this.x); + this.checkBox.setAttributeNS(null,"y",this.y); + this.checkBox.setAttributeNS(xlinkNS,"href","#"+this.checkboxId); + this.checkBox.addEventListener("click",this,false); + this.checkBox.setAttributeNS(null,"cursor","pointer"); + this.parentNode.appendChild(this.checkBox); + //create checkcross + this.checkCross = document.createElementNS(svgNS,"use"); + this.checkCross.setAttributeNS(null,"x",this.x); + this.checkCross.setAttributeNS(null,"y",this.y); + this.checkCross.setAttributeNS(xlinkNS,"href","#"+this.checkcrossId); + this.parentNode.appendChild(this.checkCross); + if (this.checkedStatus == false) { + this.checkCross.setAttributeNS(null,"display","none"); + } + //create label, if any + if (this.labelText) { + if (this.labelText.length > 0) { + this.label = document.createElementNS(svgNS,"text"); + for (var attrib in this.textStyles) { + var value = this.textStyles[attrib]; + if (attrib == "font-size") { + value += "px"; + } + this.label.setAttributeNS(null,attrib,value); + } + this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); + this.label.setAttributeNS(null,"y",(this.y + this.labelYOffset)); + this.label.setAttributeNS(null,"cursor","pointer"); + var labelTextNode = document.createTextNode(this.labelText); + this.label.appendChild(labelTextNode); + this.label.setAttributeNS(null,"pointer-events","all"); + this.label.addEventListener("click",this,false); + this.parentNode.appendChild(this.label); + } + } + if (this.radioButtonGroup) { + this.radioButtonGroup.addCheckBox(this); + } +} + +checkBox.prototype.handleEvent = function(evt) { + if (evt.type == "click") { + if (this.checkedStatus == true) { + this.checkCross.setAttributeNS(null,"display","none"); + this.checkedStatus = false; + } + else { + this.checkCross.setAttributeNS(null,"display","inline"); + this.checkedStatus = true; + } + } + this.timer.setTimeout("fireFunction",this.timerMs); +} + +checkBox.prototype.fireFunction = function() { + if (this.radioButtonGroup) { + this.radioButtonGroup.selectById(this.id,true); + } + else { + if (typeof(this.functionToCall) == "function") { + this.functionToCall(this.id,this.checkedStatus,this.labelText); + } + if (typeof(this.functionToCall) == "object") { + this.functionToCall.checkBoxChanged(this.id,this.checkedStatus,this.labelText); + } + if (typeof(this.functionToCall) == undefined) { + return; + } + } +} + +checkBox.prototype.check = function(FireFunction) { + this.checkCross.setAttributeNS(null,"display","inherit"); + this.checkedStatus = true; + if (FireFunction) { + this.timer.setTimeout("fireFunction",this.timerMs); + } +} + +checkBox.prototype.uncheck = function(FireFunction) { + this.checkCross.setAttributeNS(null,"display","none"); + this.checkedStatus = false; + if (FireFunction) { + this.timer.setTimeout("fireFunction",this.timerMs); + } +} + +//move checkbox to a different position +checkBox.prototype.moveTo = function(moveX,moveY) { + this.x = moveX; + this.y = moveY; + //move checkbox + this.checkBox.setAttributeNS(null,"x",this.x); + this.checkBox.setAttributeNS(null,"y",this.y); + //move checkcross + this.checkCross.setAttributeNS(null,"x",this.x); + this.checkCross.setAttributeNS(null,"y",this.y); + //move text label + if (this.labelText) { + this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); + this.label.setAttributeNS(null,"y",(this.y + this.labelYOffset)); + } +} + +checkBox.prototype.remove = function(FireFunction) { + this.checkBox.removeEventListener("click",this,false); + this.parentNode.removeChild(this.checkBox); + this.parentNode.removeChild(this.checkCross); + if (this.label) { + this.parentNode.removeChild(this.label); + } + this.exists = false; +} + +checkBox.prototype.setLabelText = function(labelText) { + this.labelText = labelText + if (this.label) { + this.label.firstChild.nodeValue = labelText; + } + else { + if (this.labelText.length > 0) { + this.label = document.createElementNS(svgNS,"text"); + for (var attrib in this.textStyles) { + value = this.textStyles[attrib]; + if (attrib == "font-size") { + value += "px"; + } + this.label.setAttributeNS(null,attrib,value); + } + this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); + this.label.setAttributeNS(null,"y",(this.y + this.textStyles["font-size"] * 0.3)); + var labelTextNode = document.createTextNode(this.labelText); + this.label.appendChild(labelTextNode); + this.parentNode.appendChild(this.label); + } + } +} + +/* start of the radioButtonGroup object */ + +function radioButtonGroup(id,functionToCall) { + var nrArguments = 2; + if (arguments.length == nrArguments) { + this.id = id; + if (typeof(functionToCall) == "function" || typeof(functionToCall) == "object" || typeof(functionToCall) == undefined) { + this.functionToCall = functionToCall; + } + else { + alert("Error in radiobutton with ("+id+"): argument functionToCall is not of type 'function', 'object' or undefined!"); + } + this.checkBoxes = new Array(); //this array will hold checkbox objects + this.selectedId = undefined; //holds the id of the active radio button + this.selectedIndex = undefined; //holds the index of the active radio button + //timer stuff + this.timer = new Timer(this); //a Timer instance for calling the functionToCall + this.timerMs = 200; //a constant of this object that is used in conjunction with the timer - functionToCall is called after 200 ms + } + else { + alert("Error in radiobutton with ("+id+"): wrong nr of arguments! You have to pass over "+nrArguments+" parameters."); + } +} + +radioButtonGroup.prototype.addCheckBox = function(checkBoxObj) { + this.checkBoxes.push(checkBoxObj); + if (checkBoxObj.checkedStatus) { + this.selectedId = checkBoxObj.id; + this.selectedIndex = this.checkBoxes.length - 1; + } +} + +//change radio button selection by id +radioButtonGroup.prototype.selectById = function(cbId,fireFunction) { + var found = false; + for (var i=0;i<this.checkBoxes.length;i++) { + if (this.checkBoxes[i].id == cbId) { + this.selectedId = cbId; + this.selectedIndex = i; + if (this.checkBoxes[i].checkedStatus == false) { + this.checkBoxes[i].check(false); + } + found = true; + } + else { + this.checkBoxes[i].uncheck(false); + } + } + if (found) { + if (fireFunction) { + this.timer.setTimeout("fireFunction",this.timerMs); + } + } + else { + alert("Error in radiobutton with ("+this.id+"): could not find checkbox with id '"+cbId+"'"); + } +} + +//change radio button selection by label name +radioButtonGroup.prototype.selectByLabelname = function(labelName,fireFunction) { + var id = -1; + for (var i=0;i<this.checkBoxes.length;i++) { + if (this.checkBoxes[i].labelText == labelName) { + id = this.checkBoxes[i].id; + } + } + if (id == -1) { + alert("Error in radiobutton with ("+this.id+"): could not find checkbox with label '"+labelName+"'"); + } + else { + this.selectById(id,fireFunction); + } +} + +radioButtonGroup.prototype.fireFunction = function() { + if (typeof(this.functionToCall) == "function") { + this.functionToCall(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText); + } + if (typeof(this.functionToCall) == "object") { + this.functionToCall.radioButtonChanged(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText); + } + if (typeof(this.functionToCall) == undefined) { + return; + } +} \ No newline at end of file diff -r a6e3f4cae4ce -r cdd8d520f3c7 static/scripts/helper_functions.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/helper_functions.js Tue Apr 13 11:23:19 2010 -0400 @@ -0,0 +1,817 @@ +/** + * @fileoverview + * + * ECMAScript <a href="http://www.carto.net/papers/svg/resources/helper_functions.html">helper functions</a>, main purpose is to serve in SVG mapping or other SVG based web applications + * + * This ECMA script library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library (http://www.carto.net/papers/svg/resources/lesser_gpl.txt) if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * Please report bugs and send improvements to neumann(a)karto.baug.ethz.ch + * If you use these scripts, please link to the original (http://www.carto.net/papers/svg/resources/helper_functions.html) + * somewhere in the source-code-comment or the "about" of your project and give credits, thanks! + * + * See <a href="js_docs_out/overview-summary-helper_functions.js.html">documentation</a>. + * + * @author Andreas Neumann a.neumann(a)carto.net + * @copyright LGPL 2.1 <a href="http://www.gnu.org/copyleft/lesser.txt">Gnu LGPL 2.1</a> + * @credits Bruce Rindahl, numerous people on svgdevelopers(a)yahoogroups.com + */ + +//global variables necessary to create elements in these namespaces, do not delete them!!!! + +/** + * This variable is a shortcut to the full URL of the SVG namespace + * @final + * @type String + */ +var svgNS = "http://www.w3.org/2000/svg"; + +/** + * This variable is a shortcut to the full URL of the XLink namespace + * @final + * @type String + */ +var xlinkNS = "http://www.w3.org/1999/xlink"; + +/** + * This variable is a shortcut to the full URL of the attrib namespace + * @final + * @type String + */ +var cartoNS = "http://www.carto.net/attrib"; + +/** + * This variable is a alias to the full URL of the attrib namespace + * @final + * @type String + */ +var attribNS = "http://www.carto.net/attrib"; + +/** + * This variable is a alias to the full URL of the Batik extension namespace + * @final + * @type String + */ +var batikNS = "http://xml.apache.org/batik/ext"; + +/** + * Returns the polar direction from a given vector + * @param {Number} xdiff the x-part of the vector + * @param {Number} ydiff the y-part of the vector + * @return direction the direction in radians + * @type Number + * @version 1.0 (2007-04-30) + * @see #toPolarDist + * @see #toRectX + * @see #toRectY + */ +function toPolarDir(xdiff,ydiff) { + var direction = (Math.atan2(ydiff,xdiff)); + return(direction); +} + +/** + * Returns the polar distance from a given vector + * @param {Number} xdiff the x-part of the vector + * @param {Number} ydiff the y-part of the vector + * @return distance the distance + * @type Number + * @version 1.0 (2007-04-30) + * @see #toPolarDir + * @see #toRectX + * @see #toRectY + */ +function toPolarDist(xdiff,ydiff) { + var distance = Math.sqrt(xdiff * xdiff + ydiff * ydiff); + return(distance); +} + +/** + * Returns the x-part of a vector from a given direction and distance + * @param {Number} direction the direction (in radians) + * @param {Number} distance the distance + * @return x the x-part of the vector + * @type Number + * @version 1.0 (2007-04-30) + * @see #toPolarDist + * @see #toPolarDir + * @see #toRectY + */ +function toRectX(direction,distance) { + var x = distance * Math.cos(direction); + return(x); +} + +/** + * Returns the y-part of the vector from a given direction and distance + * @param {Number} direction the direction (in radians) + * @param {Number} distance the distance + * @return y the y-part of the vector + * @type Number + * @version 1.0 (2007-04-30) + * @see #toPolarDist + * @see #toPolarDir + * @see #toRectX + */ +function toRectY(direction,distance) { + y = distance * Math.sin(direction); + return(y); +} + +/** + * Converts degrees to radians + * @param {Number} deg the degree value + * @return rad the radians value + * @type Number + * @version 1.0 (2007-04-30) + * @see #RadToDeg + */ +function DegToRad(deg) { + return (deg / 180.0 * Math.PI); +} + +/** + * Converts radians to degrees + * @param {Number} rad the radians value + * @return deg the degree value + * @type Number + * @version 1.0 (2007-04-30) + * @see #DegToRad + */ +function RadToDeg(rad) { + return (rad / Math.PI * 180.0); +} + +/** + * Converts decimal degrees to degrees, minutes, seconds + * @param {Number} dd the decimal degree value + * @return degrees the degree values in the following notation: {deg:degrees,min:minutes,sec:seconds} + * @type literal + * @version 1.0 (2007-04-30) + * @see #dms2dd + */ +function dd2dms(dd) { + var minutes = (Math.abs(dd) - Math.floor(Math.abs(dd))) * 60; + var seconds = (minutes - Math.floor(minutes)) * 60; + var minutes = Math.floor(minutes); + if (dd >= 0) { + var degrees = Math.floor(dd); + } + else { + var degrees = Math.ceil(dd); + } + return {deg:degrees,min:minutes,sec:seconds}; +} + +/** + * Converts degrees, minutes and seconds to decimal degrees + * @param {Number} deg the degree value + * @param {Number} min the minute value + * @param {Number} sec the second value + * @return deg the decimal degree values + * @type Number + * @version 1.0 (2007-04-30) + * @see #dd2dms + */ +function dms2dd(deg,min,sec) { + if (deg < 0) { + return deg - (min / 60) - (sec / 3600); + } + else { + return deg + (min / 60) + (sec / 3600); + } +} + +/** + * log function, missing in the standard Math object + * @param {Number} x the value where the log function should be applied to + * @param {Number} b the base value for the log function + * @return logResult the result of the log function + * @type Number + * @version 1.0 (2007-04-30) + */ +function log(x,b) { + if(b==null) b=Math.E; + return Math.log(x)/Math.log(b); +} + +/** + * interpolates a value (e.g. elevation) bilinearly based on the position within a cell with 4 corner values + * @param {Number} za the value at the upper left corner of the cell + * @param {Number} zb the value at the upper right corner of the cell + * @param {Number} zc the value at the lower right corner of the cell + * @param {Number} zd the value at the lower left corner of the cell + * @param {Number} xpos the x position of the point where a new value should be interpolated + * @param {Number} ypos the y position of the point where a new value should be interpolated + * @param {Number} ax the x position of the lower left corner of the cell + * @param {Number} ay the y position of the lower left corner of the cell + * @param {Number} cellsize the size of the cell + * @return interpol_value the result of the bilinear interpolation function + * @type Number + * @version 1.0 (2007-04-30) + */ +function intBilinear(za,zb,zc,zd,xpos,ypos,ax,ay,cellsize) { //bilinear interpolation function + var e = (xpos - ax) / cellsize; + var f = (ypos - ay) / cellsize; + + //calculation of weights + var wa = (1 - e) * (1 - f); + var wb = e * (1 - f); + var wc = e * f; + var wd = f * (1 - e); + + var interpol_value = wa * zc + wb * zd + wc * za + wd * zb; + return interpol_value; +} + +/** + * tests if a given point is left or right of a given line + * @param {Number} pointx the x position of the given point + * @param {Number} pointy the y position of the given point + * @param {Number} linex1 the x position of line's start point + * @param {Number} liney1 the y position of line's start point + * @param {Number} linex2 the x position of line's end point + * @param {Number} liney2 the y position of line's end point + * @return leftof the result of the leftOfTest, 1 means leftOf, 0 means rightOf + * @type Number (integer, 0|1) + * @version 1.0 (2007-04-30) + */ +function leftOfTest(pointx,pointy,linex1,liney1,linex2,liney2) { + var result = (liney1 - pointy) * (linex2 - linex1) - (linex1 - pointx) * (liney2 - liney1); + if (result < 0) { + var leftof = 1; //case left of + } + else { + var leftof = 0; //case left of + } + return leftof; +} + +/** + * calculates the distance between a given point and a given line + * @param {Number} pointx the x position of the given point + * @param {Number} pointy the y position of the given point + * @param {Number} linex1 the x position of line's start point + * @param {Number} liney1 the y position of line's start point + * @param {Number} linex2 the x position of line's end point + * @param {Number} liney2 the y position of line's end point + * @return distance the result of the leftOfTest, 1 means leftOf, 0 means rightOf + * @type Number + * @version 1.0 (2007-04-30) + */ +function distFromLine(xpoint,ypoint,linex1,liney1,linex2,liney2) { + var dx = linex2 - linex1; + var dy = liney2 - liney1; + var distance = (dy * (xpoint - linex1) - dx * (ypoint - liney1)) / Math.sqrt(Math.pow(dx,2) + Math.pow(dy,2)); + return distance; +} + +/** + * calculates the angle between two vectors (lines) + * @param {Number} ax the x part of vector a + * @param {Number} ay the y part of vector a + * @param {Number} bx the x part of vector b + * @param {Number} by the y part of vector b + * @return angle the angle in radians + * @type Number + * @version 1.0 (2007-04-30) + * @credits <a href="http://www.mathe-online.at/mathint/vect2/i.html#Winkel">Mathe Online (Winkel)</a> + */ +function angleBetwTwoLines(ax,ay,bx,by) { + var angle = Math.acos((ax * bx + ay * by) / (Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)) * Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)))); + return angle; +} + +/** + * calculates the bisector vector for two given vectors + * @param {Number} ax the x part of vector a + * @param {Number} ay the y part of vector a + * @param {Number} bx the x part of vector b + * @param {Number} by the y part of vector b + * @return c the resulting vector as an Array, c[0] is the x part of the vector, c[1] is the y part + * @type Array + * @version 1.0 (2007-04-30) + * @credits <a href="http://www.mathe-online.at/mathint/vect1/i.html#Winkelsymmetrale">Mathe Online (Winkelsymmetrale)</a> + * see #calcBisectorAngle + * */ +function calcBisectorVector(ax,ay,bx,by) { + var betraga = Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)); + var betragb = Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)); + var c = new Array(); + c[0] = ax / betraga + bx / betragb; + c[1] = ay / betraga + by / betragb; + return c; +} + +/** + * calculates the bisector angle for two given vectors + * @param {Number} ax the x part of vector a + * @param {Number} ay the y part of vector a + * @param {Number} bx the x part of vector b + * @param {Number} by the y part of vector b + * @return angle the bisector angle in radians + * @type Number + * @version 1.0 (2007-04-30) + * @credits <a href="http://www.mathe-online.at/mathint/vect1/i.html#Winkelsymmetrale">Mathe Online (Winkelsymmetrale)</a> + * see #calcBisectorVector + * */ +function calcBisectorAngle(ax,ay,bx,by) { + var betraga = Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)); + var betragb = Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)); + var c1 = ax / betraga + bx / betragb; + var c2 = ay / betraga + by / betragb; + var angle = toPolarDir(c1,c2); + return angle; +} + +/** + * calculates the intersection point of two given lines + * @param {Number} line1x1 the x the start point of line 1 + * @param {Number} line1y1 the y the start point of line 1 + * @param {Number} line1x2 the x the end point of line 1 + * @param {Number} line1y2 the y the end point of line 1 + * @return interSectPoint the intersection point, interSectPoint.x contains x-part, interSectPoint.y the y-part of the resulting coordinate + * @type Object + * @version 1.0 (2007-04-30) + * @credits <a href="http://astronomy.swin.edu.au/~pbourke/geometry/lineline2d/">P. Bourke</a> + */ +function intersect2lines(line1x1,line1y1,line1x2,line1y2,line2x1,line2y1,line2x2,line2y2) { + var interSectPoint = new Object(); + var denominator = (line2y2 - line2y1)*(line1x2 - line1x1) - (line2x2 - line2x1)*(line1y2 - line1y1); + if (denominator == 0) { + alert("lines are parallel"); + } + else { + var ua = ((line2x2 - line2x1)*(line1y1 - line2y1) - (line2y2 - line2y1)*(line1x1 - line2x1)) / denominator; + var ub = ((line1x2 - line1x1)*(line1y1 - line2y1) - (line1y2 - line1y1)*(line1x1 - line2x1)) / denominator; + } + interSectPoint["x"] = line1x1 + ua * (line1x2 - line1x1); + interSectPoint["y"] = line1y1 + ua * (line1y2 - line1y1); + return interSectPoint; +} + +/** + * reformats a given number to a string by adding separators at every third digit + * @param {String|Number} inputNumber the input number, can be of type number or string + * @param {String} separator the separator, e.g. ' or , + * @return newString the intersection point, interSectPoint.x contains x-part, interSectPoint.y the y-part of the resulting coordinate + * @type String + * @version 1.0 (2007-04-30) + */ +function formatNumberString(inputNumber,separator) { + //check if of type string, if number, convert it to string + if (typeof(inputNumber) == "Number") { + var myTempString = inputNumber.toString(); + } + else { + var myTempString = inputNumber; + } + var newString=""; + //if it contains a comma, it will be split + var splitResults = myTempString.split("."); + var myCounter = splitResults[0].length; + if (myCounter > 3) { + while(myCounter > 0) { + if (myCounter > 3) { + newString = separator + splitResults[0].substr(myCounter - 3,3) + newString; + } + else { + newString = splitResults[0].substr(0,myCounter) + newString; + } + myCounter -= 3; + } + } + else { + newString = splitResults[0]; + } + //concatenate if it contains a comma + if (splitResults[1]) { + newString = newString + "." + splitResults[1]; + } + return newString; +} + +/** + * writes a status text message out to a SVG text element's first child + * @param {String} statusText the text message to be displayed + * @version 1.0 (2007-04-30) + */ + function statusChange(statusText) { + document.getElementById("statusText").firstChild.nodeValue = "Statusbar: " + statusText; +} + +/** + * scales an SVG element, requires that the element has an x and y attribute (e.g. circle, ellipse, use element, etc.) + * @param {dom::Event} evt the evt object that triggered the scaling + * @param {Number} factor the scaling factor + * @version 1.0 (2007-04-30) + */ +function scaleObject(evt,factor) { + //reference to the currently selected object + var element = evt.currentTarget; + var myX = element.getAttributeNS(null,"x"); + var myY = element.getAttributeNS(null,"y"); + var newtransform = "scale(" + factor + ") translate(" + (myX * 1 / factor - myX) + " " + (myY * 1 / factor - myY) +")"; + element.setAttributeNS(null,'transform', newtransform); +} + +/** + * returns the transformation matrix (ctm) for the given node up to the root element + * the basic use case is to provide a wrapper function for the missing SVGLocatable.getTransformToElement method (missing in ASV3) + * @param {svg::SVGTransformable} node the node reference for the SVGElement the ctm is queried + * @return CTM the current transformation matrix from the given node to the root element + * @type svg::SVGMatrix + * @version 1.0 (2007-05-01) + * @credits <a href="http://www.kevlindev.com/tutorials/basics/transformations/toUserSpace/index…">Kevin Lindsey (toUserSpace)</a> + * @see #getTransformToElement + */ +function getTransformToRootElement(node) { + try { + //this part is for fully conformant players (like Opera, Batik, Firefox, Safari ...) + var CTM = node.getTransformToElement(document.documentElement); + } + catch (ex) { + //this part is for ASV3 or other non-conformant players + // Initialize our CTM the node's Current Transformation Matrix + var CTM = node.getCTM(); + // Work our way through the ancestor nodes stopping at the SVG Document + while ( ( node = node.parentNode ) != document ) { + // Multiply the new CTM to the one with what we have accumulated so far + CTM = node.getCTM().multiply(CTM); + } + } + return CTM; +} + +/** + * returns the transformation matrix (ctm) for the given dom::Node up to a different dom::Node + * the basic use case is to provide a wrapper function for the missing SVGLocatable.getTransformToElement method (missing in ASV3) + * @param {svg::SVGTransformable} node the node reference for the element the where the ctm should be calculated from + * @param {svg::SVGTransformable} targetNode the target node reference for the element the ctm should be calculated to + * @return CTM the current transformation matrix from the given node to the target element + * @type svg::SVGMatrix + * @version 1.0 (2007-05-01) + * @credits <a href="http://www.kevlindev.com/tutorials/basics/transformations/toUserSpace/index…">Kevin Lindsey (toUserSpace)</a> + * @see #getTransformToRootElement + */ +function getTransformToElement(node,targetNode) { + try { + //this part is for fully conformant players + var CTM = node.getTransformToElement(targetNode); + } + catch (ex) { + //this part is for ASV3 or other non-conformant players + // Initialize our CTM the node's Current Transformation Matrix + var CTM = node.getCTM(); + // Work our way through the ancestor nodes stopping at the SVG Document + while ( ( node = node.parentNode ) != targetNode ) { + // Multiply the new CTM to the one with what we have accumulated so far + CTM = node.getCTM().multiply(CTM); + } + } + return CTM; +} + +/** + * converts HSV to RGB values + * @param {Number} hue the hue value (between 0 and 360) + * @param {Number} sat the saturation value (between 0 and 1) + * @param {Number} val the value value (between 0 and 1) + * @return rgbArr the rgb values (associative array or object, the keys are: red,green,blue), all values are scaled between 0 and 255 + * @type Object + * @version 1.0 (2007-05-01) + * @see #rgb2hsv + */ +function hsv2rgb(hue,sat,val) { + var rgbArr = new Object(); + if ( sat == 0) { + rgbArr["red"] = Math.round(val * 255); + rgbArr["green"] = Math.round(val * 255); + rgbArr["blue"] = Math.round(val * 255); + } + else { + var h = hue / 60; + var i = Math.floor(h); + var f = h - i; + if (i % 2 == 0) { + f = 1 - f; + } + var m = val * (1 - sat); + var n = val * (1 - sat * f); + switch(i) { + case 0: + rgbArr["red"] = val; + rgbArr["green"] = n; + rgbArr["blue"] = m; + break; + case 1: + rgbArr["red"] = n; + rgbArr["green"] = val; + rgbArr["blue"] = m; + break; + case 2: + rgbArr["red"] = m; + rgbArr["green"] = val; + rgbArr["blue"] = n; + break; + case 3: + rgbArr["red"] = m; + rgbArr["green"] = n; + rgbArr["blue"] = val; + break; + case 4: + rgbArr["red"] = n; + rgbArr["green"] = m; + rgbArr["blue"] = val; + break; + case 5: + rgbArr["red"] = val; + rgbArr["green"] = m; + rgbArr["blue"] = n; + break; + case 6: + rgbArr["red"] = val; + rgbArr["green"] = n; + rgbArr["blue"] = m; + break; + } + rgbArr["red"] = Math.round(rgbArr["red"] * 255); + rgbArr["green"] = Math.round(rgbArr["green"] * 255); + rgbArr["blue"] = Math.round(rgbArr["blue"] * 255); + } + return rgbArr; +} + +/** + * converts RGB to HSV values + * @param {Number} red the hue value (between 0 and 255) + * @param {Number} green the saturation value (between 0 and 255) + * @param {Number} blue the value value (between 0 and 255) + * @return hsvArr the hsv values (associative array or object, the keys are: hue (0-360),sat (0-1),val (0-1)) + * @type Object + * @version 1.0 (2007-05-01) + * @see #hsv2rgb + */ +function rgb2hsv(red,green,blue) { + var hsvArr = new Object(); + red = red / 255; + green = green / 255; + blue = blue / 255; + myMax = Math.max(red, Math.max(green,blue)); + myMin = Math.min(red, Math.min(green,blue)); + v = myMax; + if (myMax > 0) { + s = (myMax - myMin) / myMax; + } + else { + s = 0; + } + if (s > 0) { + myDiff = myMax - myMin; + rc = (myMax - red) / myDiff; + gc = (myMax - green) / myDiff; + bc = (myMax - blue) / myDiff; + if (red == myMax) { + h = (bc - gc) / 6; + } + if (green == myMax) { + h = (2 + rc - bc) / 6; + } + if (blue == myMax) { + h = (4 + gc - rc) / 6; + } + } + else { + h = 0; + } + if (h < 0) { + h += 1; + } + hsvArr["hue"] = Math.round(h * 360); + hsvArr["sat"] = s; + hsvArr["val"] = v; + return hsvArr; +} + +/** + * populates an array such that it can be addressed by both a key or an index nr, + * note that both Arrays need to be of the same length + * @param {Array} arrayKeys the array containing the keys + * @param {Array} arrayValues the array containing the values + * @return returnArray the resulting array containing both associative values and also a regular indexed array + * @type Array + * @version 1.0 (2007-05-01) + */ +function arrayPopulate(arrayKeys,arrayValues) { + var returnArray = new Array(); + if (arrayKeys.length != arrayValues.length) { + alert("error: arrays do not have the same length!"); + } + else { + for (i=0;i<arrayKeys.length;i++) { + returnArray[arrayKeys[i]] = arrayValues[i]; + } + } + return returnArray; +} + +/** + * Wrapper object for network requests, uses getURL or XMLHttpRequest depending on availability + * The callBackFunction receives a XML or text node representing the rootElement + * of the fragment received or the return text, depending on the returnFormat. + * See also the following <a href="http://www.carto.net/papers/svg/network_requests/">documentation</a>. + * @class this is a wrapper object to provide network request functionality (get|post) + * @param {String} url the URL/IRI of the network resource to be called + * @param {Function|Object} callBackFunction the callBack function or object that is called after the data was received, in case of an object, the method 'receiveData' is called; both the function and the object's 'receiveData' method get 2 return parameters: 'node.firstChild'|text (the root element of the XML or text resource), this.additionalParams (if defined) + * @param {String} returnFormat the return format, either 'xml' or 'json' (or text) + * @param {String} method the method of the network request, either 'get' or 'post' + * @param {String|Undefined} postText the String containing the post text (optional) or Undefined (if not a 'post' request) + * @param {Object|Array|String|Number|Undefined} additionalParams additional parameters that will be passed to the callBackFunction or object (optional) or Undefined + * @return a new getData instance + * @type getData + * @constructor + * @version 1.0 (2007-02-23) + */ +function getData(url,callBackFunction,returnFormat,method,postText,additionalParams) { + this.url = url; + this.callBackFunction = callBackFunction; + this.returnFormat = returnFormat; + this.method = method; + this.additionalParams = additionalParams; + if (method != "get" && method != "post") { + alert("Error in network request: parameter 'method' must be 'get' or 'post'"); + } + this.postText = postText; + this.xmlRequest = null; //@private reference to the XMLHttpRequest object +} + +/** + * triggers the network request defined in the constructor + */ +getData.prototype.getData = function() { + //call getURL() if available + if (window.getURL) { + if (this.method == "get") { + getURL(this.url,this); + } + if (this.method == "post") { + postURL(this.url,this.postText,this); + } + } + //or call XMLHttpRequest() if available + else if (window.XMLHttpRequest) { + var _this = this; + this.xmlRequest = new XMLHttpRequest(); + if (this.method == "get") { + if (this.returnFormat == "xml") { + this.xmlRequest.overrideMimeType("text/xml"); + } + this.xmlRequest.open("GET",this.url,true); + } + if (this.method == "post") { + this.xmlRequest.open("POST",this.url,true); + } + this.xmlRequest.onreadystatechange = function() {_this.handleEvent()}; + if (this.method == "get") { + this.xmlRequest.send(null); + } + if (this.method == "post") { + //test if postText exists and is of type string + var reallyPost = true; + if (!this.postText) { + reallyPost = false; + alert("Error in network post request: missing parameter 'postText'!"); + } + if (typeof(this.postText) != "string") { + reallyPost = false; + alert("Error in network post request: parameter 'postText' has to be of type 'string')"); + } + if (reallyPost) { + this.xmlRequest.send(this.postText); + } + } + } + //write an error message if neither method is available + else { + alert("your browser/svg viewer neither supports window.getURL nor window.XMLHttpRequest!"); + } +} + +/** + * this is the callback method for the getURL() or postURL() case + * @private + */ +getData.prototype.operationComplete = function(data) { + //check if data has a success property + if (data.success) { + //parse content of the XML format to the variable "node" + if (this.returnFormat == "xml") { + //convert the text information to an XML node and get the first child + var node = parseXML(data.content,document); + //distinguish between a callback function and an object + if (typeof(this.callBackFunction) == "function") { + this.callBackFunction(node.firstChild,this.additionalParams); + } + if (typeof(this.callBackFunction) == "object") { + this.callBackFunction.receiveData(node.firstChild,this.additionalParams); + } + } + if (this.returnFormat == "json") { + if (typeof(this.callBackFunction) == "function") { + this.callBackFunction(data.content,this.additionalParams); + } + if (typeof(this.callBackFunction) == "object") { + this.callBackFunction.receiveData(data.content,this.additionalParams); + } + } + } + else { + alert("something went wrong with dynamic loading of geometry!"); + } +} + +/** + * this is the callback method for the XMLHttpRequest case + * @private + */ +getData.prototype.handleEvent = function() { + if (this.xmlRequest.readyState == 4) { + if (this.returnFormat == "xml") { + //we need to import the XML node first + var importedNode = document.importNode(this.xmlRequest.responseXML.documentElement,true); + if (typeof(this.callBackFunction) == "function") { + this.callBackFunction(importedNode,this.additionalParams); + } + if (typeof(this.callBackFunction) == "object") { + this.callBackFunction.receiveData(importedNode,this.additionalParams); + } + } + if (this.returnFormat == "json") { + if (typeof(this.callBackFunction) == "function") { + this.callBackFunction(this.xmlRequest.responseText,this.additionalParams); + } + if (typeof(this.callBackFunction) == "object") { + this.callBackFunction.receiveData(this.xmlRequest.responseText,this.additionalParams); + } + } + } +} + +/** + * Serializes an XML node and returns a string representation. Wrapper function to hide implementation differences. + * This can be used for debugging purposes or to post data to a server or network resource. + * @param {dom::Node} node the DOM node reference + * @return textRepresentation the String representation of the XML node + * @type String + * @version 1.0 (2007-05-01) + * @see getData + */ +function serializeNode(node) { + if (typeof XMLSerializer != 'undefined') { + return new XMLSerializer().serializeToString(node); + } + else if (typeof node.xml != 'undefined') { + return node.xml; + } + else if (typeof printNode != 'undefined') { + return printNode(node); + } + else if (typeof Packages != 'undefined') { + try { + var stringWriter = new java.io.StringWriter(); + Packages.org.apache.batik.dom.util.DOMUtilities.writeNode(node,stringWriter); + return stringWriter.toString(); + } + catch (e) { + alert("Sorry, your SVG viewer does not support the printNode/serialize function."); + return ''; + } + } + else { + alert("Sorry, your SVG viewer does not support the printNode/serialize function."); + return ''; + } +} + +/** + * Starts a SMIL animation element with the given id by triggering the '.beginElement()' method. + * This is a convenience (shortcut) function. + * @param {String} id a valid id of a valid SMIL animation element + * @version 1.0 (2007-05-01) + */ +//starts an animtion with the given id +//this function is useful in combination with window.setTimeout() +function startAnimation(id) { + document.getElementById(id).beginElement(); +} diff -r a6e3f4cae4ce -r cdd8d520f3c7 static/scripts/timer.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/timer.js Tue Apr 13 11:23:19 2010 -0400 @@ -0,0 +1,74 @@ +// source/credits: "Algorithm": http://www.codingforums.com/showthread.php?s=&threadid=10531 +// The constructor should be called with +// the parent object (optional, defaults to window). + +function Timer(){ + this.obj = (arguments.length)?arguments[0]:window; + return this; +} + +// The set functions should be called with: +// - The name of the object method (as a string) (required) +// - The millisecond delay (required) +// - Any number of extra arguments, which will all be +// passed to the method when it is evaluated. + +Timer.prototype.setInterval = function(func, msec){ + var i = Timer.getNew(); + var t = Timer.buildCall(this.obj, i, arguments); + Timer.set[i].timer = window.setInterval(t,msec); + return i; +} +Timer.prototype.setTimeout = function(func, msec){ + var i = Timer.getNew(); + Timer.buildCall(this.obj, i, arguments); + Timer.set[i].timer = window.setTimeout("Timer.callOnce("+i+");",msec); + return i; +} + +// The clear functions should be called with +// the return value from the equivalent set function. + +Timer.prototype.clearInterval = function(i){ + if(!Timer.set[i]) return; + window.clearInterval(Timer.set[i].timer); + Timer.set[i] = null; +} +Timer.prototype.clearTimeout = function(i){ + if(!Timer.set[i]) return; + window.clearTimeout(Timer.set[i].timer); + Timer.set[i] = null; +} + +// Private data + +Timer.set = new Array(); +Timer.buildCall = function(obj, i, args){ + var t = ""; + Timer.set[i] = new Array(); + if(obj != window){ + Timer.set[i].obj = obj; + t = "Timer.set["+i+"].obj."; + } + t += args[0]+"("; + if(args.length > 2){ + Timer.set[i][0] = args[2]; + t += "Timer.set["+i+"][0]"; + for(var j=1; (j+2)<args.length; j++){ + Timer.set[i][j] = args[j+2]; + t += ", Timer.set["+i+"]["+j+"]"; + }} + t += ");"; + Timer.set[i].call = t; + return t; +} +Timer.callOnce = function(i){ + if(!Timer.set[i]) return; + eval(Timer.set[i].call); + Timer.set[i] = null; +} +Timer.getNew = function(){ + var i = 0; + while(Timer.set[i]) i++; + return i; +} \ No newline at end of file diff -r a6e3f4cae4ce -r cdd8d520f3c7 tools/rgenetics/rgGRR.py --- a/tools/rgenetics/rgGRR.py Tue Apr 13 11:17:30 2010 -0400 +++ b/tools/rgenetics/rgGRR.py Tue Apr 13 11:23:19 2010 -0400 @@ -1,1096 +1,1145 @@ -""" -# july 2009: Need to see outliers so need to draw them last? -# could use clustering on the zscores to guess real relationships for unrelateds -# but definitely need to draw last -# added MAX_SHOW_ROWS to limit the length of the main report page -# Changes for Galaxy integration -# added more robust knuth method for one pass mean and sd -# no difference really - let's use scipy.mean() and scipy.std() instead... -# fixed labels and changed to .xls for outlier reports so can open in excel -# interesting - with a few hundred subjects, 5k gives good resolution -# and 100k gives better but not by much -# TODO remove non autosomal markers -# TODO it would be best if label had the zmean and zsd as these are what matter for -# outliers rather than the group mean/sd -# mods to rgGRR.py from channing CVS which John Ziniti has rewritten to produce SVG plots -# to make a Galaxy tool - we need the table of mean and SD for interesting pairs, the SVG and the log -# so the result should be an HTML file - -# rgIBS.py -# use a random subset of markers for a quick ibs -# to identify sample dups and closely related subjects -# try snpMatrix and plink and see which one works best for us? -# abecasis grr plots mean*sd for every subject to show clusters -# mods june 23 rml to avoid non-autosomal markers -# we seem to be distinguishing parent-child by gender - 2 clouds! - - -snpMatrix from David Clayton has: -ibs.stats function to calculate the identity-by-state stats of a group of samples -Description -Given a snp.matrix-class or a X.snp.matrix-class object with N samples, calculates some statistics -about the relatedness of every pair of samples within. - -Usage -ibs.stats(x) -8 ibs.stats -Arguments -x a snp.matrix-class or a X.snp.matrix-class object containing N samples -Details -No-calls are excluded from consideration here. -Value -A data.frame containing N(N - 1)/2 rows, where the row names are the sample name pairs separated -by a comma, and the columns are: -Count count of identical calls, exclusing no-calls -Fraction fraction of identical calls comparied to actual calls being made in both samples -Warning -In some applications, it may be preferable to subset a (random) selection of SNPs first - the -calculation -time increases as N(N - 1)M/2 . Typically for N = 800 samples and M = 3000 SNPs, the -calculation time is about 1 minute. A full GWA scan could take hours, and quite unnecessary for -simple applications such as checking for duplicate or related samples. -Note -This is mostly written to find mislabelled and/or duplicate samples. -Illumina indexes their SNPs in alphabetical order so the mitochondria SNPs comes first - for most -purpose it is undesirable to use these SNPs for IBS purposes. -TODO: Worst-case S4 subsetting seems to make 2 copies of a large object, so one might want to -subset before rbind(), etc; a future version of this routine may contain a built-in subsetting facility -""" -import sys,os,time,random,string,copy,optparse - -try: - set -except NameError: - from Sets import Set as set - -from rgutils import timenow -import plinkbinJZ - - -opts = None -verbose = False - -showPolygons = False - -class NullDevice: - def write(self, s): - pass - -tempstderr = sys.stderr # save -sys.stderr = NullDevice() -# need to avoid blather about deprecation and other strange stuff from scipy -# the current galaxy job runner assumes that -# the job is in error if anything appears on sys.stderr -# grrrrr. James wants to keep it that way instead of using the -# status flag for some strange reason. Presumably he doesn't use R or (in this case, scipy) -import numpy -import scipy -from scipy import weave - - -sys.stderr=tempstderr - - -PROGNAME = os.path.split(sys.argv[0])[-1] -X_AXIS_LABEL = 'Mean Alleles Shared' -Y_AXIS_LABEL = 'SD Alleles Shared' -LEGEND_ALIGN = 'topleft' -LEGEND_TITLE = 'Relationship' -DEFAULT_SYMBOL_SIZE = 1.0 # default symbol size -DEFAULT_SYMBOL_SIZE = 0.5 # default symbol size - -### Some colors for R/rpy -R_BLACK = 1 -R_RED = 2 -R_GREEN = 3 -R_BLUE = 4 -R_CYAN = 5 -R_PURPLE = 6 -R_YELLOW = 7 -R_GRAY = 8 - -### ... and some point-styles - -### -PLOT_HEIGHT = 600 -PLOT_WIDTH = 1150 - - -#SVG_COLORS = ('black', 'darkblue', 'blue', 'deepskyblue', 'firebrick','maroon','crimson') -#SVG_COLORS = ('cyan','dodgerblue','mediumpurple', 'fuchsia', 'red','gold','gray') -SVG_COLORS = ('cyan','dodgerblue','mediumpurple','forestgreen', 'lightgreen','gold','gray') -# dupe,parentchild,sibpair,halfsib,parents,unrel,unkn -#('orange', 'red', 'green', 'chartreuse', 'blue', 'purple', 'gray') - -OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Rel_Mean)\tSdev(Rel_Mean)\tMean(Rel_Sdev)\tSdev(Rel_Sdev)\n' -OUTLIERS_HEADER_list = ['Mean','Sdev','ZMean','ZSdev','FID1','IID1','FID2','IID2', -'RGMean_M','RGMean_SD','RGSD_M','RGSD_SD'] -TABLE_HEADER='fid1 iid1\tfid2 iid2\tmean\tsdev\tzmean\tzsdev\tgeno\trelcode\n' - - -### Relationship codes, text, and lookups/mappings -N_RELATIONSHIP_TYPES = 7 -REL_DUPE, REL_PARENTCHILD, REL_SIBS, REL_HALFSIBS, REL_RELATED, REL_UNRELATED, REL_UNKNOWN = range(N_RELATIONSHIP_TYPES) -REL_LOOKUP = { - REL_DUPE: ('dupe', R_BLUE, 1), - REL_PARENTCHILD: ('parentchild', R_YELLOW, 1), - REL_SIBS: ('sibpairs', R_RED, 1), - REL_HALFSIBS: ('halfsibs', R_GREEN, 1), - REL_RELATED: ('parents', R_PURPLE, 1), - REL_UNRELATED: ('unrelated', R_CYAN, 1), - REL_UNKNOWN: ('unknown', R_GRAY, 1), - } -OUTLIER_STDEVS = { - REL_DUPE: 2, - REL_PARENTCHILD: 2, - REL_SIBS: 2, - REL_HALFSIBS: 2, - REL_RELATED: 2, - REL_UNRELATED: 3, - REL_UNKNOWN: 2, - } -# note now Z can be passed in - -REL_STATES = [REL_LOOKUP[r][0] for r in range(N_RELATIONSHIP_TYPES)] -REL_COLORS = SVG_COLORS -REL_POINTS = [REL_LOOKUP[r][2] for r in range(N_RELATIONSHIP_TYPES)] - -DEFAULT_MAX_SAMPLE_SIZE = 10000 - -REF_COUNT_HOM1 = 3 -REF_COUNT_HET = 2 -REF_COUNT_HOM2 = 1 -MISSING = 0 -MAX_SHOW_ROWS = 100 # framingham has millions - delays showing output page - so truncate and explain -MARKER_PAIRS_PER_SECOND_SLOW = 15000000.0 -MARKER_PAIRS_PER_SECOND_FAST = 70000000.0 - - -galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> -<title></title> -<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> -</head> -<body> -<div class="document"> -""" - - -SVG_HEADER = '''<?xml version="1.0" standalone="no"?> -<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.2//EN" "http://www.w3.org/Graphics/SVG/1.2/DTD/svg12.dtd"> - -<svg width="1280" height="800" - xmlns="http://www.w3.org/2000/svg" version="1.2" - xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()"> - - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/checkbox_and_radiobutton.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/helper_functions.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/timer.js"/> - <script type="text/ecmascript"> - <![CDATA[ - var checkBoxes = new Array(); - var radioGroupBandwidth; - var colours = ['%s','%s','%s','%s','%s','%s','%s']; - function init() { - var style = {"font-family":"Arial,Helvetica", "fill":"black", "font-size":12}; - var dist = 12; - var yOffset = 4; - - //A checkBox for each relationship type dupe,parentchild,sibpair,halfsib,parents,unrel,unkn - checkBoxes["dupe"] = new checkBox("dupe","checkboxes",20,40,"cbRect","cbCross",true,"Duplicate",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["parentchild"] = new checkBox("parentchild","checkboxes",20,60,"cbRect","cbCross",true,"Parent-Child",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["sibpairs"] = new checkBox("sibpairs","checkboxes",20,80,"cbRect","cbCross",true,"Sib-pairs",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["halfsibs"] = new checkBox("halfsibs","checkboxes",20,100,"cbRect","cbCross",true,"Half-sibs",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["parents"] = new checkBox("parents","checkboxes",20,120,"cbRect","cbCross",true,"Parents",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["unrelated"] = new checkBox("unrelated","checkboxes",20,140,"cbRect","cbCross",true,"Unrelated",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["unknown"] = new checkBox("unknown","checkboxes",20,160,"cbRect","cbCross",true,"Unknown",style,dist,yOffset,undefined,hideShowLayer); - - } - - function hideShowLayer(id, status, label) { - var vis = "hidden"; - if (status) { - vis = "visible"; - } - document.getElementById(id).setAttributeNS(null, 'visibility', vis); - } - - function showBTT(evt, rel, mm, dm, md, dd, n, mg, dg, lg, hg) { - var x = parseInt(evt.pageX)-250; - var y = parseInt(evt.pageY)-110; - switch(rel) { - case 0: - fill = colours[rel]; - relt = "dupe"; - break; - case 1: - fill = colours[rel]; - relt = "parentchild"; - break; - case 2: - fill = colours[rel]; - relt = "sibpairs"; - break; - case 3: - fill = colours[rel]; - relt = "halfsibs"; - break; - case 4: - fill = colours[rel]; - relt = "parents"; - break; - case 5: - fill = colours[rel]; - relt = "unrelated"; - break; - case 6: - fill = colours[rel]; - relt = "unknown"; - break; - default: - fill = "cyan"; - relt = "ERROR_CODE: "+rel; - } - - document.getElementById("btRel").textContent = "GROUP: "+relt; - document.getElementById("btMean").textContent = "mean="+mm+" +/- "+dm; - document.getElementById("btSdev").textContent = "sdev="+dm+" +/- "+dd; - document.getElementById("btPair").textContent = "npairs="+n; - document.getElementById("btGeno").textContent = "ngenos="+mg+" +/- "+dg+" (min="+lg+", max="+hg+")"; - document.getElementById("btHead").setAttribute('fill', fill); - - var tt = document.getElementById("btTip"); - tt.setAttribute("transform", "translate("+x+","+y+")"); - tt.setAttribute('visibility', 'visible'); - } - - function showOTT(evt, rel, s1, s2, mean, sdev, ngeno, rmean, rsdev) { - var x = parseInt(evt.pageX)-150; - var y = parseInt(evt.pageY)-180; - - switch(rel) { - case 0: - fill = colours[rel]; - relt = "dupe"; - break; - case 1: - fill = colours[rel]; - relt = "parentchild"; - break; - case 2: - fill = colours[rel]; - relt = "sibpairs"; - break; - case 3: - fill = colours[rel]; - relt = "halfsibs"; - break; - case 4: - fill = colours[rel]; - relt = "parents"; - break; - case 5: - fill = colours[rel]; - relt = "unrelated"; - break; - case 6: - fill = colours[rel]; - relt = "unknown"; - break; - default: - fill = "cyan"; - relt = "ERROR_CODE: "+rel; - } - - document.getElementById("otRel").textContent = "PAIR: "+relt; - document.getElementById("otS1").textContent = "s1="+s1; - document.getElementById("otS2").textContent = "s2="+s2; - document.getElementById("otMean").textContent = "mean="+mean; - document.getElementById("otSdev").textContent = "sdev="+sdev; - document.getElementById("otGeno").textContent = "ngenos="+ngeno; - document.getElementById("otRmean").textContent = "relmean="+rmean; - document.getElementById("otRsdev").textContent = "relsdev="+rsdev; - document.getElementById("otHead").setAttribute('fill', fill); - - var tt = document.getElementById("otTip"); - tt.setAttribute("transform", "translate("+x+","+y+")"); - tt.setAttribute('visibility', 'visible'); - } - - function hideBTT(evt) { - document.getElementById("btTip").setAttributeNS(null, 'visibility', 'hidden'); - } - - function hideOTT(evt) { - document.getElementById("otTip").setAttributeNS(null, 'visibility', 'hidden'); - } - - ]]> - </script> - <defs> -  - <symbol id="cbRect" overflow="visible"> - <rect x="-5" y="-5" width="10" height="10" fill="white" stroke="dimgray" stroke-width="1" cursor="pointer"/> - </symbol> - <symbol id="cbCross" overflow="visible"> - <g pointer-events="none" stroke="black" stroke-width="1"> - <line x1="-3" y1="-3" x2="3" y2="3"/> - <line x1="3" y1="-3" x2="-3" y2="3"/> - </g> - </symbol> - </defs> - -<desc>Developer Works Dynamic Scatter Graph Scaling Example</desc> - - -<g style="stroke-width:1.0; stroke:black; shape-rendering:crispEdges"> -  - <path d="M 100 100 L 1250 100 Z"/> - <path d="M 100 700 L 1250 700 Z"/> - -  - <path d="M 100 100 L 100 700 Z"/> - <path d="M 1250 100 L 1250 700 Z"/> -</g> - -<g transform="translate(100,100)"> - -  - <g style="fill:none; stroke:#dddddd; stroke-width:1; stroke-dasharray:2,2; text-anchor:end; shape-rendering:crispEdges"> - -  - <line x1="125" y1="0" x2="115" y2="600" /> - <line x1="230" y1="0" x2="230" y2="600" /> - <line x1="345" y1="0" x2="345" y2="600" /> - <line x1="460" y1="0" x2="460" y2="600" /> - <line x1="575" y1="0" x2="575" y2="600" style="stroke-dasharray:none;" /> - <line x1="690" y1="0" x2="690" y2="600" /> - <line x1="805" y1="0" x2="805" y2="600" /> - <line x1="920" y1="0" x2="920" y2="600" /> - <line x1="1035" y1="0" x2="1035" y2="600" /> - -  - <line x1="0" y1="60" x2="1150" y2="60" /> - <line x1="0" y1="120" x2="1150" y2="120" /> - <line x1="0" y1="180" x2="1150" y2="180" /> - <line x1="0" y1="240" x2="1150" y2="240" /> - <line x1="0" y1="300" x2="1150" y2="300" style="stroke-dasharray:none;" /> - <line x1="0" y1="360" x2="1150" y2="360" /> - <line x1="0" y1="420" x2="1150" y2="420" /> - <line x1="0" y1="480" x2="1150" y2="480" /> - <line x1="0" y1="540" x2="1150" y2="540" /> - </g> - -  - <g style="fill:black; stroke:none" font-size="12" font-family="Arial" transform="translate(25,25)"> - <rect width="160" height="270" style="fill:none; stroke:black; shape-rendering:crispEdges" /> - <text x="5" y="20" style="fill:black; stroke:none;" font-size="13" font-weight="bold">Given Pair Relationship</text> - <rect x="120" y="35" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="55" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="75" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="95" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="115" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="135" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="155" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <text x="15" y="195" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore gt 15</text> - <circle cx="125" cy="192" r="6" style="stroke:red; fill:gold; fill-opacity:1.0; stroke-width:1;"/> - <text x="15" y="215" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore 4 to 15</text> - <circle cx="125" cy="212" r="3" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/> - <text x="15" y="235" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore lt 4</text> - <circle cx="125" cy="232" r="2" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/> - <g id="checkboxes"> - </g> - </g> - - - <g style='fill:black; stroke:none' font-size="17" font-family="Arial"> -  - <text x="480" y="660">Mean Alleles Shared</text> - <text x="0" y="630" >1.0</text> - <text x="277" y="630" >1.25</text> - <text x="564" y="630" >1.5</text> - <text x="842" y="630" >1.75</text> - <text x="1140" y="630" >2.0</text> - </g> - - <g transform="rotate(270)" style="fill:black; stroke:none" font-size="17" font-family="Arial"> -  - <text x="-350" y="-40">SD Alleles Shared</text> - <text x="-20" y="-10" >1.0</text> - <text x="-165" y="-10" >0.75</text> - <text x="-310" y="-10" >0.5</text> - <text x="-455" y="-10" >0.25</text> - <text x="-600" y="-10" >0.0</text> - </g> - - -<g style="fill:black; stroke:none" font-size="18" font-family="Arial"> - <text x="425" y="-30">%s</text> -</g> - - -''' - -SVG_FOOTER = ''' - -</g> -<g id="btTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial"> - <rect width="250" height="110" style="fill:silver" rx="2" ry="2"/> - <rect id="btHead" width="250" height="20" rx="2" ry="2" /> - <text id="btRel" y="14" x="85">unrelated</text> - <text id="btMean" y="40" x="4">mean=1.5 +/- 0.04</text> - <text id="btSdev" y="60" x="4">sdev=0.7 +/- 0.03</text> - <text id="btPair" y="80" x="4">npairs=1152</text> - <text id="btGeno" y="100" x="4">ngenos=4783 +/- 24 (min=1000, max=5000)</text> -</g> - -<g id="otTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial"> - <rect width="150" height="180" style="fill:silver" rx="2" ry="2"/> - <rect id="otHead" width="150" height="20" rx="2" ry="2" /> - <text id="otRel" y="14" x="40">sibpairs</text> - <text id="otS1" y="40" x="4">s1=fid1,iid1</text> - <text id="otS2" y="60" x="4">s2=fid2,iid2</text> - <text id="otMean" y="80" x="4">mean=1.82</text> - <text id="otSdev" y="100" x="4">sdev=0.7</text> - <text id="otGeno" y="120" x="4">ngeno=4487</text> - <text id="otRmean" y="140" x="4">relmean=1.85</text> - <text id="otRsdev" y="160" x="4">relsdev=0.65</text> -</g> -</svg> -''' - -OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Mean)\tSdev(Mean)\tMean(Sdev)\tSdev(Sdev)\n' - -DEFAULT_MAX_SAMPLE_SIZE = 5000 - -REF_COUNT_HOM1 = 3 -REF_COUNT_HET = 2 -REF_COUNT_HOM2 = 1 -MISSING = 0 - -MARKER_PAIRS_PER_SECOND_SLOW = 15000000 -MARKER_PAIRS_PER_SECOND_FAST = 70000000 - -POLYGONS = { - REL_UNRELATED: ((1.360, 0.655), (1.385, 0.730), (1.620, 0.575), (1.610, 0.505)), - REL_HALFSIBS: ((1.630, 0.500), (1.630, 0.550), (1.648, 0.540), (1.648, 0.490)), - REL_SIBS: ((1.660, 0.510), (1.665, 0.560), (1.820, 0.410), (1.820, 0.390)), - REL_PARENTCHILD: ((1.650, 0.470), (1.650, 0.490), (1.750, 0.440), (1.750, 0.420)), - REL_DUPE: ((1.970, 0.000), (1.970, 0.150), (2.000, 0.150), (2.000, 0.000)), - } - -def distance(point1, point2): - """ Calculate the distance between two points - """ - (x1,y1) = [float(d) for d in point1] - (x2,y2) = [float(d) for d in point2] - dx = abs(x1 - x2) - dy = abs(y1 - y2) - return math.sqrt(dx**2 + dy**2) - -def point_inside_polygon(x, y, poly): - """ Determine if a point (x,y) is inside a given polygon or not - poly is a list of (x,y) pairs. - - Taken from: http://www.ariel.com.au/a/python-point-int-poly.html - """ - - n = len(poly) - inside = False - - p1x,p1y = poly[0] - for i in range(n+1): - p2x,p2y = poly[i % n] - if y > min(p1y,p2y): - if y <= max(p1y,p2y): - if x <= max(p1x,p2x): - if p1y != p2y: - xinters = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x - if p1x == p2x or x <= xinters: - inside = not inside - p1x,p1y = p2x,p2y - return inside - -def readMap(pedfile): - """ - """ - mapfile = pedfile.replace('.ped', '.map') - marker_list = [] - if os.path.exists(mapfile): - print 'readMap: %s' % (mapfile) - fh = file(mapfile, 'r') - for line in fh: - marker_list.append(line.strip().split()) - fh.close() - print 'readMap: %s markers' % (len(marker_list)) - return marker_list - -def calcMeanSD(useme): - """ - A numerically stable algorithm is given below. It also computes the mean. - This algorithm is due to Knuth,[1] who cites Welford.[2] - n = 0 - mean = 0 - M2 = 0 - - foreach x in data: - n = n + 1 - delta = x - mean - mean = mean + delta/n - M2 = M2 + delta*(x - mean) // This expression uses the new value of mean - end for - - variance_n = M2/n - variance = M2/(n - 1) - """ - mean = 0.0 - M2 = 0.0 - sd = 0.0 - n = len(useme) - if n > 1: - for i,x in enumerate(useme): - delta = x - mean - mean = mean + delta/(i+1) # knuth uses n+=1 at start - M2 = M2 + delta*(x - mean) # This expression uses the new value of mean - variance = M2/(n-1) # assume is sample so lose 1 DOF - sd = pow(variance,0.5) - return mean,sd - - -def doIBSpy(inpath='',basename='',outdir=None,logf=None, - nrsSamples=10000,title='title',pdftoo=0,Zcutoff=2.0): - #def doIBS(pedName, title, nrsSamples=None, pdftoo=False): - """ started with snpmatrix but GRR uses actual IBS counts and sd's - """ - repOut = [] # text strings to add to the html display - refallele = {} - tblf = '%s_table.xls' % (title) - tbl = file(os.path.join(outdir,tblf), 'w') - tbl.write(TABLE_HEADER) - svgf = '%s.svg' % (title) - svg = file(os.path.join(outdir,svgf), 'w') - - bedname = '%s.bed' % (inpath) - pedname = '%s.ped' % (inpath) - print 'pedname',pedname - if os.path.exists(bedname): - ped = plinkbinJZ.BPed(inpath) - ped.parse(quick=True) - elif os.path.exists(pedname): - ped = plinkbinJZ.LPed(inpath) - ped.parse() - else: - print >> sys.stdout, '## doIBSpy problem - cannot open %s or %s - cannot run' % (bedname,pedname) - nMarkers = len(ped._markers) - if nMarkers < 5: - print sys.stderr, '### ERROR - %d is too few markers for reliable estimation in %s - terminating' % (nMarkers,PROGNAME) - sys.exit(1) - nSubjects = len(ped._subjects) - nrsSamples = min(nMarkers, nrsSamples) - if opts and opts.use_mito: - markers = range(nMarkers) - nrsSamples = min(len(markers), nrsSamples) - sampleIndexes = sorted(random.sample(markers, nrsSamples)) - else: - autosomals = ped.autosomal_indices() - nrsSamples = min(len(autosomals), nrsSamples) - sampleIndexes = sorted(random.sample(autosomals, nrsSamples)) - - print '' - print 'Getting random.sample of %s from %s total' % (nrsSamples, nMarkers) - npairs = (nSubjects*(nSubjects-1))/2 # total rows in table - newfiles=[svgf,tblf] - explanations = ['rgGRR Plot (requires SVG)','Mean by SD alleles shared - %d rows' % npairs] - # these go with the output file links in the html file - s = 'Reading genotypes for %s subjects and %s markers\n' % (nSubjects, nrsSamples) - logf.write(s) - minUsegenos = nrsSamples/2 # must have half? - nGenotypes = nSubjects*nrsSamples - stime = time.time() - emptyRows = set() - genos = numpy.zeros((nSubjects, nrsSamples), dtype=int) - for s in xrange(nSubjects): - nValid = 0 - #getGenotypesByIndices(self, s, mlist, format) - genos[s] = ped.getGenotypesByIndices(s, sampleIndexes, format='ref') - nValid = sum([1 for g in genos[s] if g]) - if not nValid: - emptyRows.add(s) - sub = ped.getSubject(s) - print 'All missing for row %d (%s)' % (s, sub) - logf.write('All missing for row %d (%s)\n' % (s, sub)) - rtime = time.time() - stime - if verbose: - print '@@Read %s genotypes in %s seconds' % (nGenotypes, rtime) - - - ### Now the expensive part. For each pair of subjects, we get the mean number - ### and standard deviation of shared alleles over all of the markers where both - ### subjects have a known genotype. Identical subjects should have mean shared - ### alleles very close to 2.0 with a standard deviation very close to 0.0. - tot = nSubjects*(nSubjects-1)/2 - nprog = tot/10 - nMarkerpairs = tot * nrsSamples - estimatedTimeSlow = nMarkerpairs/MARKER_PAIRS_PER_SECOND_SLOW - estimatedTimeFast = nMarkerpairs/MARKER_PAIRS_PER_SECOND_FAST - - pairs = [] - pair_data = {} - means = [] ## Mean IBS for each pair - ngenoL = [] ## Count of comparable genotypes for each pair - sdevs = [] ## Standard dev for each pair - rels = [] ## A relationship code for each pair - zmeans = [0.0 for x in xrange(tot)] ## zmean score for each pair for the relgroup - zstds = [0.0 for x in xrange(tot)] ## zstd score for each pair for the relgrp - skip = set() - ndone = 0 ## How many have been done so far - - logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog)) - logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow)) - - t1sum = 0 - t2sum = 0 - t3sum = 0 - now = time.time() - scache = {} - _founder_cache = {} - C_CODE = """ - #include "math.h" - int i; - int sumibs = 0; - int ssqibs = 0; - int ngeno = 0; - float mean = 0; - float M2 = 0; - float delta = 0; - float sdev=0; - float variance=0; - for (i=0; i<nrsSamples; i++) { - int a1 = g1[i]; - int a2 = g2[i]; - if (a1 != 0 && a2 != 0) { - ngeno += 1; - int shared = 2-abs(a1-a2); - delta = shared - mean; - mean = mean + delta/ngeno; - M2 += delta*(shared-mean); - // yes that second time, the updated mean is used see calcmeansd above; - //printf("%d %d %d %d %d %d\\n", i, a1, a2, ngeno, shared, squared); - } - } - if (ngeno > 1) { - variance = M2/(ngeno-1); - sdev = sqrt(variance); - //printf("OK: %d %3.2f %3.2f\\n", ngeno, mean, sdev); - } - //printf("%d %d %d %1.2f %1.2f\\n", ngeno, sumibs, ssqibs, mean, sdev); - result[0] = ngeno; - result[1] = mean; - result[2] = sdev; - return_val = ngeno; - """ - started = time.time() - for s1 in xrange(nSubjects): - if s1 in emptyRows: - continue - (fid1,iid1,did1,mid1,sex1,phe1,iid1,d_sid1,m_sid1) = scache.setdefault(s1, ped.getSubject(s1)) - - isFounder1 = _founder_cache.setdefault(s1, (did1==mid1)) - g1 = genos[s1] - - for s2 in xrange(s1+1, nSubjects): - if s2 in emptyRows: - continue - if nprog and ndone % nprog == 0 and ndone > 1: - dur = time.time() - started - pct = float(ndone)/tot*100.0 - logf.write('%f sec at pair %d of %d (%3.2f%%): %f marker*pairs/sec\n' % (dur, ndone, tot, pct, ndone/dur*nrsSamples)) - t1s = time.time() - - (fid2,iid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache.setdefault(s2, ped.getSubject(s2)) - - g2 = genos[s2] - isFounder2 = _founder_cache.setdefault(s2, (did2==mid2)) - - # Determine the relationship for this pair - relcode = REL_UNKNOWN - if (fid2 == fid1): - if iid1 == iid2: - relcode = REL_DUPE - elif (did2 == did1) and (mid2 == mid1) and did1 != mid1: - relcode = REL_SIBS - elif (iid1 == mid2) or (iid1 == did2) or (iid2 == mid1) or (iid2 == did1): - relcode = REL_PARENTCHILD - elif (str(did1) != '0' and (did2 == did1)) or (str(mid1) != '0' and (mid2 == mid1)): - relcode = REL_HALFSIBS - else: - # People in the same family should be marked as some other - # form of related. In general, these people will have a - # pretty random spread of similarity. This distinction is - # probably not very useful most of the time - relcode = REL_RELATED - else: - ### Different families - relcode = REL_UNRELATED - - t1e = time.time() - t1sum += t1e-t1s - - - ### Calculate sum(2-abs(a1-a2)) and sum((2-abs(a1-a2))**2) and count - ### the number of contributing genotypes. These values are not actually - ### calculated here, but instead are looked up in a table for speed. - ### FIXME: This is still too slow ... - result = [0.0, 0.0, 0.0] - ngeno = weave.inline(C_CODE, ['g1', 'g2', 'nrsSamples', 'result']) - if ngeno >= minUsegenos: - _, mean, sdev = result - means.append(mean) - sdevs.append(sdev) - ngenoL.append(ngeno) - pairs.append((s1, s2)) - rels.append(relcode) - else: - skip.add(ndone) # signal no comparable genotypes for this pair - ndone += 1 - t2e = time.time() - t2sum += t2e-t1e - t3e = time.time() - t3sum += t3e-t2e - - logme = [ 'T1: %s' % (t1sum), 'T2: %s' % (t2sum), 'T3: %s' % (t3sum),'TOT: %s' % (t3e-now), - '%s pairs with no (or not enough) comparable genotypes (%3.1f%%)' % (len(skip), - float(len(skip))/float(tot)*100)] - logf.write('%s\n' % '\t'.join(logme)) - ### Calculate mean and standard deviation of scores on a per relationship - ### type basis, allowing us to flag outliers for each particular relationship - ### type - relstats = {} - relCounts = {} - outlierFiles = {} - for relCode, relInfo in REL_LOOKUP.items(): - relName, relColor, relStyle = relInfo - useme = [means[x] for x in xrange(len(means)) if rels[x] == relCode] - relCounts[relCode] = len(useme) - mm = scipy.mean(useme) - ms = scipy.std(useme) - useme = [sdevs[x] for x in xrange(len(sdevs)) if rels[x] == relCode] - sm = scipy.mean(useme) - ss = scipy.std(useme) - relstats[relCode] = {'sd':(sm,ss), 'mean':(mm,ms)} - logf.write('Relstate %s: mean(mean)=%3.2f sdev(mean)=%3.2f, mean(sdev)=%3.2f sdev(sdev)=%3.2f\n' % (relName, mm, ms, sm, ss)) - - ### now fake z scores for each subject like abecasis recommends max(|zmu|,|zsd|) - ### within each group, for each pair, z=(groupmean-pairmean)/groupsd - available = len(means) - logf.write('%d pairs are available of %d\n' % (available, tot)) - ### s = '\nOutliers:\nrelationship\tzmean\tzsd\tped1\tped2\tmean\tsd\trmeanmean\trmeansd\trsdmean\trsdsd\n' - ### logf.write(s) - pairnum = 0 - offset = 0 - nOutliers = 0 - cexs = [] - outlierRecords = dict([(r, []) for r in range(N_RELATIONSHIP_TYPES)]) - zsdmax = 0 - for s1 in range(nSubjects): - if s1 in emptyRows: - continue - (fid1,iid1,did1,mid1,sex1,aff1,ok1,d_sid1,m_sid1) = scache[s1] - for s2 in range(s1+1, nSubjects): - if s2 in emptyRows: - continue - if pairnum not in skip: - ### Get group stats for this relationship - (fid2,iid2,did2,mid2,sex2,aff2,ok2,d_sid2,m_sid2) = scache[s2] - try: - r = rels[offset] - except IndexError: - logf.write('###OOPS offset %d available %d pairnum %d len(rels) %d', offset, available, pairnum, len(rels)) - rmm,rmd = relstats[r]['mean'] # group mean, group meansd alleles shared - rdm,rdd = relstats[r]['sd'] # group sdmean, group sdsd alleles shared - - try: - zsd = (sdevs[offset] - rdm)/rdd # distance from group mean in group sd units - except: - zsd = 1 - if abs(zsd) > zsdmax: - zsdmax = zsd # keep for sort scaling - try: - zmean = (means[offset] - rmm)/rmd # distance from group mean - except: - zmean = 1 - zmeans[offset] = zmean - zstds[offset] = zsd - pid=(s1,s2) - zrad = max(zsd,zmean) - if zrad < 4: - zrad = 2 - elif 4 < zrad < 15: - zrad = 3 # to 9 - else: # > 15 6=24+ - zrad=zrad/4 - zrad = min(zrad,6) # scale limit - zrad = max(2,max(zsd,zmean)) # as > 2, z grows - pair_data[pid] = (zmean,zsd,r,zrad) - if max(zsd,zmean) > Zcutoff: # is potentially interesting - mean = means[offset] - sdev = sdevs[offset] - outlierRecords[r].append((mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd)) - nOutliers += 1 - tbl.write('%s_%s\t%s_%s\t%f\t%f\t%f\t%f\t%d\t%s\n' % \ - (fid1, iid1, fid2, iid2, mean, sdev, zmean,zsd, ngeno, relcode)) - offset += 1 - pairnum += 1 - logf.write( 'Outliers: %s\n' % (nOutliers)) - - ### Write outlier files for each relationship type - repOut.append('<h2>Outliers in tab delimited files linked above are also listed below</h2>') - lzsd = round(numpy.log10(zsdmax)) + 1 - scalefactor = 10**lzsd - for relCode, relInfo in REL_LOOKUP.items(): - relName, _, _ = relInfo - outliers = outlierRecords[relCode] - if not outliers: - continue - outliers = [(scalefactor*int(abs(x[3]))+ int(abs(x[2])),x) for x in outliers] # decorate - outliers.sort() - logf.write('### outliers after decorated sort=%s' % outliers) - outliers.reverse() # largest deviation first - logf.write('### outliers after decorated sort=%s' % outliers) - outliers = [x[1] for x in outliers] # undecorate - nrows = len(outliers) - truncated = 0 - if nrows > MAX_SHOW_ROWS: - s = '<h3>%s outlying pairs (top %d of %d) from %s</h3><table border="0" cellpadding="3">' % (relName, - MAX_SHOW_ROWS,nrows,title) - truncated = nrows - MAX_SHOW_ROWS - else: - s = '<h3>%s outlying pairs (n=%d) from %s</h3><table border="0" cellpadding="3">' % (relName,nrows,title) - repOut.append(s) - fhname = '%s_rgGRR_%s_outliers.xls' % (title, relName) - fhpath = os.path.join(outdir,fhname) - fh = open(fhpath, 'w') - newfiles.append(fhname) - explanations.append('%s Outlier Pairs %s, N=%d, Cutoff SD=%f' % (relName,title,len(outliers),Zcutoff)) - fh.write(OUTLIERS_HEADER) - s = ''.join(['<th>%s</th>' % x for x in OUTLIERS_HEADER_list]) - repOut.append('<tr align="center">%s</tr>' % s) - for n,rec in enumerate(outliers): - #(mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd) = rec - fh.write('%f\t%f\t%f\t%f\t%s\t%s\t%s\t%s\t%f\t%f\t%f\t%f\n' % tuple(rec)) - # (mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd)) - s = '''<td>%f</td><td>%f</td><td>%f</td><td>%f</td><td>%s</td><td>%s</td> - <td>%s</td><td>%s</td><td>%f</td><td>%f</td><td>%f</td><td>%f</td>''' % tuple(rec) - if n < MAX_SHOW_ROWS: - repOut.append('<tr align="center">%s</tr>' % s) - if truncated > 0: - repOut.append('<H2>WARNING: %d rows truncated - see outlier file for all %d rows</H2>' % (truncated, - nrows)) - fh.close() - repOut.append('</table><p>') - - ### Now, draw the plot in jpeg and svg formats, and optionally in the PDF format - ### if requested - logf.write('Plotting ...') - pointColors = [REL_COLORS[rel] for rel in rels] - pointStyles = [REL_POINTS[rel] for rel in rels] - - mainTitle = '%s (%s subjects, %d snp)' % (title, nSubjects, nrsSamples) - svg.write(SVG_HEADER % (SVG_COLORS[0],SVG_COLORS[1],SVG_COLORS[2],SVG_COLORS[3],SVG_COLORS[4], - SVG_COLORS[5],SVG_COLORS[6],SVG_COLORS[0],SVG_COLORS[0],SVG_COLORS[1],SVG_COLORS[1], - SVG_COLORS[2],SVG_COLORS[2],SVG_COLORS[3],SVG_COLORS[3],SVG_COLORS[4],SVG_COLORS[4], - SVG_COLORS[5],SVG_COLORS[5],SVG_COLORS[6],SVG_COLORS[6],mainTitle)) - #rpy.r.jpeg(filename='%s.jpg' % (title), width=1600, height=1200, pointsize=12, quality=100, bg='white') - #rpy.r.par(mai=(1,1,1,0.5)) - #rpy.r('par(xaxs="i",yaxs="i")') - #rpy.r.plot(means, sdevs, main=mainTitle, ylab=Y_AXIS_LABEL, xlab=X_AXIS_LABEL, cex=cexs, col=pointColors, pch=pointStyles, xlim=(0,2), ylim=(0,2)) - #rpy.r.legend(LEGEND_ALIGN, legend=REL_STATES, pch=REL_POINTS, col=REL_COLORS, title=LEGEND_TITLE) - #rpy.r.grid(nx=10, ny=10, col='lightgray', lty='dotted') - #rpy.r.dev_off() - - ### We will now go through each relationship type to partition plot points - ### into "bulk" and "outlier" groups. Bulk points will represent common - ### mean/sdev pairs and will cover the majority of the points in the plot -- - ### they will use generic tooltip informtion about all of the pairs - ### represented by that point. "Outlier" points will be uncommon pairs, - ### with very specific information in their tooltips. It would be nice to - ### keep hte total number of plotted points in the SVG representation to - ### ~10000 (certainly less than 100000?) - pointMap = {} - orderedRels = [y[1] for y in reversed(sorted([(relCounts.get(x, 0),x) for x in REL_LOOKUP.keys()]))] - # do we really want this? I want out of zone points last and big - for relCode in orderedRels: - svgColor = SVG_COLORS[relCode] - relName, relColor, relStyle = REL_LOOKUP[relCode] - svg.write('<g id="%s" style="stroke:%s; fill:%s; fill-opacity:1.0; stroke-width:1;" cursor="pointer">\n' % (relName, svgColor, svgColor)) - pMap = pointMap.setdefault(relCode, {}) - nPoints = 0 - rpairs=[] - rgenos=[] - rmeans=[] - rsdevs=[] - rz = [] - for x,rel in enumerate(rels): # all pairs - if rel == relCode: - s1,s2 = pairs[x] - pid=(s1,s2) - zmean,zsd,r,zrad = pair_data[pid][:4] - rpairs.append(pairs[x]) - rgenos.append(ngenoL[x]) - rmeans.append(means[x]) - rsdevs.append(sdevs[x]) - rz.append(zrad) - ### Now add the svg point group for this relationship to the svg file - for x in range(len(rmeans)): - svgX = '%d' % ((rmeans[x] - 1.0) * PLOT_WIDTH) # changed so mean scale is 1-2 - svgY = '%d' % (PLOT_HEIGHT - (rsdevs[x] * PLOT_HEIGHT)) # changed so sd scale is 0-1 - s1, s2 = rpairs[x] - (fid1,uid1,did1,mid1,sex1,phe1,iid1,d_sid1,m_sid1) = scache[s1] - (fid2,uid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache[s2] - ngenos = rgenos[x] - nPoints += 1 - point = pMap.setdefault((svgX, svgY), []) - point.append((rmeans[x], rsdevs[x], fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, ngenos,rz[x])) - for (svgX, svgY) in pMap: - points = pMap[(svgX, svgY)] - svgX = int(svgX) - svgY = int(svgY) - if len(points) > 1: - mmean,dmean = calcMeanSD([p[0] for p in points]) - msdev,dsdev = calcMeanSD([p[1] for p in points]) - mgeno,dgeno = calcMeanSD([p[-1] for p in points]) - mingeno = min([p[-1] for p in points]) - maxgeno = max([p[-1] for p in points]) - svg.write("""<circle cx="%d" cy="%d" r="2" - onmouseover="showBTT(evt, %d, %1.2f, %1.2f, %1.2f, %1.2f, %d, %d, %d, %d, %d)" - onmouseout="hideBTT(evt)" />\n""" % (svgX, svgY, relCode, mmean, dmean, msdev, dsdev, len(points), mgeno, dgeno, mingeno, maxgeno)) - else: - mean, sdev, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, ngenos, zrad = points[0][:12] - rmean = float(relstats[relCode]['mean'][0]) - rsdev = float(relstats[relCode]['sd'][0]) - if zrad < 4: - zrad = 2 - elif 4 < zrad < 9: - zrad = 3 # to 9 - else: # > 9 5=15+ - zrad=zrad/3 - zrad = min(zrad,5) # scale limit - if zrad <= 3: - svg.write('<circle cx="%d" cy="%d" r="%s" onmouseover="showOTT(evt, %d, \'%s,%s,%s,%s\', \'%s,%s,%s,%s\', %1.2f, %1.2f, %s, %1.2f, %1.2f)" onmouseout="hideOTT(evt)" />\n' % (svgX, svgY, zrad, relCode, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, mean, sdev, ngenos, rmean, rsdev)) - else: # highlight pairs a long way from expectation by outlining circle in red - svg.write("""<circle cx="%d" cy="%d" r="%s" style="stroke:red; fill:%s; fill-opacity:1.0; stroke-width:1;" - onmouseover="showOTT(evt, %d, \'%s,%s,%s,%s\', \'%s,%s,%s,%s\', %1.2f, %1.2f, %s, %1.2f, %1.2f)" - onmouseout="hideOTT(evt)" />\n""" % \ - (svgX, svgY, zrad, svgColor, relCode, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, mean, sdev, ngenos, rmean, rsdev)) - svg.write('</g>\n') - - ### Create a pdf as well if indicated on the command line - ### WARNING! for framingham share, with about 50M pairs, this is a 5.5GB pdf! -## if pdftoo: -## pdfname = '%s.pdf' % (title) -## rpy.r.pdf(pdfname, 6, 6) -## rpy.r.par(mai=(1,1,1,0.5)) -## rpy.r('par(xaxs="i",yaxs="i")') -## rpy.r.plot(means, sdevs, main='%s, %d snp' % (title, nSamples), ylab=Y_AXIS_LABEL, xlab=X_AXIS_LABEL, cex=cexs, col=pointColors, pch=pointStyles, xlim=(0,2), ylim=(0,2)) -## rpy.r.legend(LEGEND_ALIGN, legend=REL_STATES, pch=REL_POINTS, col=REL_COLORS, title=LEGEND_TITLE) -## rpy.r.grid(nx=10, ny=10, col='lightgray', lty='dotted') -## rpy.r.dev_off() - - ### Draw polygons - if showPolygons: - svg.write('<g id="polygons" cursor="pointer">\n') - for rel, poly in POLYGONS.items(): - points = ' '.join(['%s,%s' % ((p[0]-1.0)*float(PLOT_WIDTH), (PLOT_HEIGHT - p[1]*PLOT_HEIGHT)) for p in poly]) - svg.write('<polygon points="%s" fill="transparent" style="stroke:%s; stroke-width:1"/>\n' % (points, SVG_COLORS[rel])) - svg.write('</g>\n') - - - svg.write(SVG_FOOTER) - svg.close() - return newfiles,explanations,repOut - -def doIBS(n=100): - """parse parameters from galaxy - expect 'input pbed path' 'basename' 'outpath' 'title' 'logpath' 'n' - <command interpreter="python"> - rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" - '$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' - </command> - - """ - u="""<command interpreter="python"> - rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" - '$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' - </command>""" - - if len(sys.argv) < 8: - print >> sys.stdout, 'Need pbed inpath, basename, out_htmlname, outpath, title, logpath, nSNP, Zcutoff on command line please' - print >> sys.stdout, u - sys.exit(1) - ts = '%s%s' % (string.punctuation,string.whitespace) - ptran = string.maketrans(ts,'_'*len(ts)) - inpath = sys.argv[1] - basename = sys.argv[2] - outhtml = sys.argv[3] - newfilepath = sys.argv[4] - try: - os.makedirs(newfilepath) - except: - pass - title = sys.argv[5].translate(ptran) - logfname = 'Log_%s.txt' % title - logpath = os.path.join(newfilepath,logfname) # log was a child - make part of html extra_files_path zoo - n = int(sys.argv[6]) - try: - Zcutoff = float(sys.argv[7]) - except: - Zcutoff = 2.0 - try: - os.makedirs(newfilepath) - except: - pass - logf = file(logpath,'w') - newfiles,explanations,repOut = doIBSpy(inpath=inpath,basename=basename,outdir=newfilepath, - logf=logf,nrsSamples=n,title=title,pdftoo=0,Zcutoff=Zcutoff) - logf.close() - logfs = file(logpath,'r').readlines() - lf = file(outhtml,'w') - lf.write(galhtmlprefix % PROGNAME) - # this is a mess. todo clean up - should each datatype have it's own directory? Yes - # probably. Then titles are universal - but userId libraries are separate. - s = '<div>Output from %s run at %s<br>\n' % (PROGNAME,timenow()) - lf.write('<h4>%s</h4>\n' % s) - fixed = ["'%s'" % x for x in sys.argv] # add quotes just in case - s = 'If you need to rerun this analysis, the command line was\n<pre>%s</pre>\n</div>' % (' '.join(fixed)) - lf.write(s) - #s = """<object data="%s" type="image/svg+xml" width="%d" height="%d"> - # <embed src="%s" type="image/svg+xml" width="%d" height="%d" /> - # </object>""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT,newfiles[0],PLOT_WIDTH,PLOT_HEIGHT) - s = """ <embed src="%s" type="image/svg+xml" width="%d" height="%d" />""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT) - #s = """ <iframe src="%s" type="image/svg+xml" width="%d" height="%d" />""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT) - lf.write(s) - lf.write('<div><h4>Click the links below to save output files and plots</h4><br><ol>\n') - for i in range(len(newfiles)): - if i == 0: - lf.write('<li><a href="%s" type="image/svg+xml" >%s</a></li>\n' % (newfiles[i],explanations[i])) - else: - lf.write('<li><a href="%s">%s</a></li>\n' % (newfiles[i],explanations[i])) - flist = os.listdir(newfilepath) - for fname in flist: - if not fname in newfiles: - lf.write('<li><a href="%s">%s</a></li>\n' % (fname,fname)) - lf.write('</ol></div>') - lf.write('<div>%s</div>' % ('\n'.join(repOut))) # repOut is a list of tables - lf.write('<div><hr><h3>Log from this job (also stored in %s)</h3><pre>%s</pre><hr></div>' % (logfname,'\n'.join(logfs))) - lf.write('</body></html>\n') - lf.close() - logf.close() - -if __name__ == '__main__': - doIBS() - - +""" +# july 2009: Need to see outliers so need to draw them last? +# could use clustering on the zscores to guess real relationships for unrelateds +# but definitely need to draw last +# added MAX_SHOW_ROWS to limit the length of the main report page +# Changes for Galaxy integration +# added more robust knuth method for one pass mean and sd +# no difference really - let's use scipy.mean() and scipy.std() instead... +# fixed labels and changed to .xls for outlier reports so can open in excel +# interesting - with a few hundred subjects, 5k gives good resolution +# and 100k gives better but not by much +# TODO remove non autosomal markers +# TODO it would be best if label had the zmean and zsd as these are what matter for +# outliers rather than the group mean/sd +# mods to rgGRR.py from channing CVS which John Ziniti has rewritten to produce SVG plots +# to make a Galaxy tool - we need the table of mean and SD for interesting pairs, the SVG and the log +# so the result should be an HTML file + +# rgIBS.py +# use a random subset of markers for a quick ibs +# to identify sample dups and closely related subjects +# try snpMatrix and plink and see which one works best for us? +# abecasis grr plots mean*sd for every subject to show clusters +# mods june 23 rml to avoid non-autosomal markers +# we seem to be distinguishing parent-child by gender - 2 clouds! + + +snpMatrix from David Clayton has: +ibs.stats function to calculate the identity-by-state stats of a group of samples +Description +Given a snp.matrix-class or a X.snp.matrix-class object with N samples, calculates some statistics +about the relatedness of every pair of samples within. + +Usage +ibs.stats(x) +8 ibs.stats +Arguments +x a snp.matrix-class or a X.snp.matrix-class object containing N samples +Details +No-calls are excluded from consideration here. +Value +A data.frame containing N(N - 1)/2 rows, where the row names are the sample name pairs separated +by a comma, and the columns are: +Count count of identical calls, exclusing no-calls +Fraction fraction of identical calls comparied to actual calls being made in both samples +Warning +In some applications, it may be preferable to subset a (random) selection of SNPs first - the +calculation +time increases as N(N - 1)M/2 . Typically for N = 800 samples and M = 3000 SNPs, the +calculation time is about 1 minute. A full GWA scan could take hours, and quite unnecessary for +simple applications such as checking for duplicate or related samples. +Note +This is mostly written to find mislabelled and/or duplicate samples. +Illumina indexes their SNPs in alphabetical order so the mitochondria SNPs comes first - for most +purpose it is undesirable to use these SNPs for IBS purposes. +TODO: Worst-case S4 subsetting seems to make 2 copies of a large object, so one might want to +subset before rbind(), etc; a future version of this routine may contain a built-in subsetting facility +""" +import sys,os,time,random,string,copy,optparse + +try: + set +except NameError: + from Sets import Set as set + +from rgutils import timenow,pruneLD,plinke +import plinkbinJZ + + +opts = None +verbose = False + +showPolygons = False + +class NullDevice: + def write(self, s): + pass + +tempstderr = sys.stderr # save +sys.stderr = NullDevice() +# need to avoid blather about deprecation and other strange stuff from scipy +# the current galaxy job runner assumes that +# the job is in error if anything appears on sys.stderr +# grrrrr. James wants to keep it that way instead of using the +# status flag for some strange reason. Presumably he doesn't use R or (in this case, scipy) +import numpy +import scipy +from scipy import weave + + +sys.stderr=tempstderr + + +PROGNAME = os.path.split(sys.argv[0])[-1] +X_AXIS_LABEL = 'Mean Alleles Shared' +Y_AXIS_LABEL = 'SD Alleles Shared' +LEGEND_ALIGN = 'topleft' +LEGEND_TITLE = 'Relationship' +DEFAULT_SYMBOL_SIZE = 1.0 # default symbol size +DEFAULT_SYMBOL_SIZE = 0.5 # default symbol size + +### Some colors for R/rpy +R_BLACK = 1 +R_RED = 2 +R_GREEN = 3 +R_BLUE = 4 +R_CYAN = 5 +R_PURPLE = 6 +R_YELLOW = 7 +R_GRAY = 8 + +### ... and some point-styles + +### +PLOT_HEIGHT = 600 +PLOT_WIDTH = 1150 + + +#SVG_COLORS = ('black', 'darkblue', 'blue', 'deepskyblue', 'firebrick','maroon','crimson') +#SVG_COLORS = ('cyan','dodgerblue','mediumpurple', 'fuchsia', 'red','gold','gray') +SVG_COLORS = ('cyan','dodgerblue','mediumpurple','forestgreen', 'lightgreen','gold','gray') +# dupe,parentchild,sibpair,halfsib,parents,unrel,unkn +#('orange', 'red', 'green', 'chartreuse', 'blue', 'purple', 'gray') + +OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Rel_Mean)\tSdev(Rel_Mean)\tMean(Rel_Sdev)\tSdev(Rel_Sdev)\n' +OUTLIERS_HEADER_list = ['Mean','Sdev','ZMean','ZSdev','FID1','IID1','FID2','IID2', +'RGMean_M','RGMean_SD','RGSD_M','RGSD_SD'] +TABLE_HEADER='fid1 iid1\tfid2 iid2\tmean\tsdev\tzmean\tzsdev\tgeno\trelcode\n' + + +### Relationship codes, text, and lookups/mappings +N_RELATIONSHIP_TYPES = 7 +REL_DUPE, REL_PARENTCHILD, REL_SIBS, REL_HALFSIBS, REL_RELATED, REL_UNRELATED, REL_UNKNOWN = range(N_RELATIONSHIP_TYPES) +REL_LOOKUP = { + REL_DUPE: ('dupe', R_BLUE, 1), + REL_PARENTCHILD: ('parentchild', R_YELLOW, 1), + REL_SIBS: ('sibpairs', R_RED, 1), + REL_HALFSIBS: ('halfsibs', R_GREEN, 1), + REL_RELATED: ('parents', R_PURPLE, 1), + REL_UNRELATED: ('unrelated', R_CYAN, 1), + REL_UNKNOWN: ('unknown', R_GRAY, 1), + } +OUTLIER_STDEVS = { + REL_DUPE: 2, + REL_PARENTCHILD: 2, + REL_SIBS: 2, + REL_HALFSIBS: 2, + REL_RELATED: 2, + REL_UNRELATED: 3, + REL_UNKNOWN: 2, + } +# note now Z can be passed in + +REL_STATES = [REL_LOOKUP[r][0] for r in range(N_RELATIONSHIP_TYPES)] +REL_COLORS = SVG_COLORS +REL_POINTS = [REL_LOOKUP[r][2] for r in range(N_RELATIONSHIP_TYPES)] + +DEFAULT_MAX_SAMPLE_SIZE = 10000 + +REF_COUNT_HOM1 = 3 +REF_COUNT_HET = 2 +REF_COUNT_HOM2 = 1 +MISSING = 0 +MAX_SHOW_ROWS = 100 # framingham has millions - delays showing output page - so truncate and explain +MARKER_PAIRS_PER_SECOND_SLOW = 15000000.0 +MARKER_PAIRS_PER_SECOND_FAST = 70000000.0 + + +galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +""" + + +SVG_HEADER = '''<?xml version="1.0" standalone="no"?> +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.2//EN" "http://www.w3.org/Graphics/SVG/1.2/DTD/svg12.dtd"> + +<svg width="1280" height="800" + xmlns="http://www.w3.org/2000/svg" version="1.2" + xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()"> + + <script type="text/ecmascript" xlink:href="/static/scripts/checkbox_and_radiobutton.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/helper_functions.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/timer.js"/> + <script type="text/ecmascript"> + <![CDATA[ + var checkBoxes = new Array(); + var radioGroupBandwidth; + var colours = ['%s','%s','%s','%s','%s','%s','%s']; + function init() { + var style = {"font-family":"Arial,Helvetica", "fill":"black", "font-size":12}; + var dist = 12; + var yOffset = 4; + + //A checkBox for each relationship type dupe,parentchild,sibpair,halfsib,parents,unrel,unkn + checkBoxes["dupe"] = new checkBox("dupe","checkboxes",20,40,"cbRect","cbCross",true,"Duplicate",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["parentchild"] = new checkBox("parentchild","checkboxes",20,60,"cbRect","cbCross",true,"Parent-Child",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["sibpairs"] = new checkBox("sibpairs","checkboxes",20,80,"cbRect","cbCross",true,"Sib-pairs",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["halfsibs"] = new checkBox("halfsibs","checkboxes",20,100,"cbRect","cbCross",true,"Half-sibs",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["parents"] = new checkBox("parents","checkboxes",20,120,"cbRect","cbCross",true,"Parents",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["unrelated"] = new checkBox("unrelated","checkboxes",20,140,"cbRect","cbCross",true,"Unrelated",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["unknown"] = new checkBox("unknown","checkboxes",20,160,"cbRect","cbCross",true,"Unknown",style,dist,yOffset,undefined,hideShowLayer); + + } + + function hideShowLayer(id, status, label) { + var vis = "hidden"; + if (status) { + vis = "visible"; + } + document.getElementById(id).setAttributeNS(null, 'visibility', vis); + } + + function showBTT(evt, rel, mm, dm, md, dd, n, mg, dg, lg, hg) { + var x = parseInt(evt.pageX)-250; + var y = parseInt(evt.pageY)-110; + switch(rel) { + case 0: + fill = colours[rel]; + relt = "dupe"; + break; + case 1: + fill = colours[rel]; + relt = "parentchild"; + break; + case 2: + fill = colours[rel]; + relt = "sibpairs"; + break; + case 3: + fill = colours[rel]; + relt = "halfsibs"; + break; + case 4: + fill = colours[rel]; + relt = "parents"; + break; + case 5: + fill = colours[rel]; + relt = "unrelated"; + break; + case 6: + fill = colours[rel]; + relt = "unknown"; + break; + default: + fill = "cyan"; + relt = "ERROR_CODE: "+rel; + } + + document.getElementById("btRel").textContent = "GROUP: "+relt; + document.getElementById("btMean").textContent = "mean="+mm+" +/- "+dm; + document.getElementById("btSdev").textContent = "sdev="+dm+" +/- "+dd; + document.getElementById("btPair").textContent = "npairs="+n; + document.getElementById("btGeno").textContent = "ngenos="+mg+" +/- "+dg+" (min="+lg+", max="+hg+")"; + document.getElementById("btHead").setAttribute('fill', fill); + + var tt = document.getElementById("btTip"); + tt.setAttribute("transform", "translate("+x+","+y+")"); + tt.setAttribute('visibility', 'visible'); + } + + function showOTT(evt, rel, s1, s2, mean, sdev, ngeno, rmean, rsdev) { + var x = parseInt(evt.pageX)-150; + var y = parseInt(evt.pageY)-180; + + switch(rel) { + case 0: + fill = colours[rel]; + relt = "dupe"; + break; + case 1: + fill = colours[rel]; + relt = "parentchild"; + break; + case 2: + fill = colours[rel]; + relt = "sibpairs"; + break; + case 3: + fill = colours[rel]; + relt = "halfsibs"; + break; + case 4: + fill = colours[rel]; + relt = "parents"; + break; + case 5: + fill = colours[rel]; + relt = "unrelated"; + break; + case 6: + fill = colours[rel]; + relt = "unknown"; + break; + default: + fill = "cyan"; + relt = "ERROR_CODE: "+rel; + } + + document.getElementById("otRel").textContent = "PAIR: "+relt; + document.getElementById("otS1").textContent = "s1="+s1; + document.getElementById("otS2").textContent = "s2="+s2; + document.getElementById("otMean").textContent = "mean="+mean; + document.getElementById("otSdev").textContent = "sdev="+sdev; + document.getElementById("otGeno").textContent = "ngenos="+ngeno; + document.getElementById("otRmean").textContent = "relmean="+rmean; + document.getElementById("otRsdev").textContent = "relsdev="+rsdev; + document.getElementById("otHead").setAttribute('fill', fill); + + var tt = document.getElementById("otTip"); + tt.setAttribute("transform", "translate("+x+","+y+")"); + tt.setAttribute('visibility', 'visible'); + } + + function hideBTT(evt) { + document.getElementById("btTip").setAttributeNS(null, 'visibility', 'hidden'); + } + + function hideOTT(evt) { + document.getElementById("otTip").setAttributeNS(null, 'visibility', 'hidden'); + } + + ]]> + </script> + <defs> +  + <symbol id="cbRect" overflow="visible"> + <rect x="-5" y="-5" width="10" height="10" fill="white" stroke="dimgray" stroke-width="1" cursor="pointer"/> + </symbol> + <symbol id="cbCross" overflow="visible"> + <g pointer-events="none" stroke="black" stroke-width="1"> + <line x1="-3" y1="-3" x2="3" y2="3"/> + <line x1="3" y1="-3" x2="-3" y2="3"/> + </g> + </symbol> + </defs> + +<desc>Developer Works Dynamic Scatter Graph Scaling Example</desc> + + +<g style="stroke-width:1.0; stroke:black; shape-rendering:crispEdges"> +  + <path d="M 100 100 L 1250 100 Z"/> + <path d="M 100 700 L 1250 700 Z"/> + +  + <path d="M 100 100 L 100 700 Z"/> + <path d="M 1250 100 L 1250 700 Z"/> +</g> + +<g transform="translate(100,100)"> + +  + <g style="fill:none; stroke:#dddddd; stroke-width:1; stroke-dasharray:2,2; text-anchor:end; shape-rendering:crispEdges"> + +  + <line x1="125" y1="0" x2="115" y2="600" /> + <line x1="230" y1="0" x2="230" y2="600" /> + <line x1="345" y1="0" x2="345" y2="600" /> + <line x1="460" y1="0" x2="460" y2="600" /> + <line x1="575" y1="0" x2="575" y2="600" style="stroke-dasharray:none;" /> + <line x1="690" y1="0" x2="690" y2="600" /> + <line x1="805" y1="0" x2="805" y2="600" /> + <line x1="920" y1="0" x2="920" y2="600" /> + <line x1="1035" y1="0" x2="1035" y2="600" /> + +  + <line x1="0" y1="60" x2="1150" y2="60" /> + <line x1="0" y1="120" x2="1150" y2="120" /> + <line x1="0" y1="180" x2="1150" y2="180" /> + <line x1="0" y1="240" x2="1150" y2="240" /> + <line x1="0" y1="300" x2="1150" y2="300" style="stroke-dasharray:none;" /> + <line x1="0" y1="360" x2="1150" y2="360" /> + <line x1="0" y1="420" x2="1150" y2="420" /> + <line x1="0" y1="480" x2="1150" y2="480" /> + <line x1="0" y1="540" x2="1150" y2="540" /> + </g> + +  + <g style="fill:black; stroke:none" font-size="12" font-family="Arial" transform="translate(25,25)"> + <rect width="160" height="270" style="fill:none; stroke:black; shape-rendering:crispEdges" /> + <text x="5" y="20" style="fill:black; stroke:none;" font-size="13" font-weight="bold">Given Pair Relationship</text> + <rect x="120" y="35" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="55" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="75" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="95" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="115" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="135" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="155" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <text x="15" y="195" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore gt 15</text> + <circle cx="125" cy="192" r="6" style="stroke:red; fill:gold; fill-opacity:1.0; stroke-width:1;"/> + <text x="15" y="215" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore 4 to 15</text> + <circle cx="125" cy="212" r="3" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/> + <text x="15" y="235" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore lt 4</text> + <circle cx="125" cy="232" r="2" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/> + <g id="checkboxes"> + </g> + </g> + + + <g style='fill:black; stroke:none' font-size="17" font-family="Arial"> +  + <text x="480" y="660">Mean Alleles Shared</text> + <text x="0" y="630" >1.0</text> + <text x="277" y="630" >1.25</text> + <text x="564" y="630" >1.5</text> + <text x="842" y="630" >1.75</text> + <text x="1140" y="630" >2.0</text> + </g> + + <g transform="rotate(270)" style="fill:black; stroke:none" font-size="17" font-family="Arial"> +  + <text x="-350" y="-40">SD Alleles Shared</text> + <text x="-20" y="-10" >1.0</text> + <text x="-165" y="-10" >0.75</text> + <text x="-310" y="-10" >0.5</text> + <text x="-455" y="-10" >0.25</text> + <text x="-600" y="-10" >0.0</text> + </g> + + +<g style="fill:black; stroke:none" font-size="18" font-family="Arial"> + <text x="425" y="-30">%s</text> +</g> + + +''' + +SVG_FOOTER = ''' + +</g> +<g id="btTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial"> + <rect width="250" height="110" style="fill:silver" rx="2" ry="2"/> + <rect id="btHead" width="250" height="20" rx="2" ry="2" /> + <text id="btRel" y="14" x="85">unrelated</text> + <text id="btMean" y="40" x="4">mean=1.5 +/- 0.04</text> + <text id="btSdev" y="60" x="4">sdev=0.7 +/- 0.03</text> + <text id="btPair" y="80" x="4">npairs=1152</text> + <text id="btGeno" y="100" x="4">ngenos=4783 +/- 24 (min=1000, max=5000)</text> +</g> + +<g id="otTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial"> + <rect width="150" height="180" style="fill:silver" rx="2" ry="2"/> + <rect id="otHead" width="150" height="20" rx="2" ry="2" /> + <text id="otRel" y="14" x="40">sibpairs</text> + <text id="otS1" y="40" x="4">s1=fid1,iid1</text> + <text id="otS2" y="60" x="4">s2=fid2,iid2</text> + <text id="otMean" y="80" x="4">mean=1.82</text> + <text id="otSdev" y="100" x="4">sdev=0.7</text> + <text id="otGeno" y="120" x="4">ngeno=4487</text> + <text id="otRmean" y="140" x="4">relmean=1.85</text> + <text id="otRsdev" y="160" x="4">relsdev=0.65</text> +</g> +</svg> +''' + +OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Mean)\tSdev(Mean)\tMean(Sdev)\tSdev(Sdev)\n' + +DEFAULT_MAX_SAMPLE_SIZE = 5000 + +REF_COUNT_HOM1 = 3 +REF_COUNT_HET = 2 +REF_COUNT_HOM2 = 1 +MISSING = 0 + +MARKER_PAIRS_PER_SECOND_SLOW = 15000000 +MARKER_PAIRS_PER_SECOND_FAST = 70000000 + +POLYGONS = { + REL_UNRELATED: ((1.360, 0.655), (1.385, 0.730), (1.620, 0.575), (1.610, 0.505)), + REL_HALFSIBS: ((1.630, 0.500), (1.630, 0.550), (1.648, 0.540), (1.648, 0.490)), + REL_SIBS: ((1.660, 0.510), (1.665, 0.560), (1.820, 0.410), (1.820, 0.390)), + REL_PARENTCHILD: ((1.650, 0.470), (1.650, 0.490), (1.750, 0.440), (1.750, 0.420)), + REL_DUPE: ((1.970, 0.000), (1.970, 0.150), (2.000, 0.150), (2.000, 0.000)), + } + +def distance(point1, point2): + """ Calculate the distance between two points + """ + (x1,y1) = [float(d) for d in point1] + (x2,y2) = [float(d) for d in point2] + dx = abs(x1 - x2) + dy = abs(y1 - y2) + return math.sqrt(dx**2 + dy**2) + +def point_inside_polygon(x, y, poly): + """ Determine if a point (x,y) is inside a given polygon or not + poly is a list of (x,y) pairs. + + Taken from: http://www.ariel.com.au/a/python-point-int-poly.html + """ + + n = len(poly) + inside = False + + p1x,p1y = poly[0] + for i in range(n+1): + p2x,p2y = poly[i % n] + if y > min(p1y,p2y): + if y <= max(p1y,p2y): + if x <= max(p1x,p2x): + if p1y != p2y: + xinters = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x + if p1x == p2x or x <= xinters: + inside = not inside + p1x,p1y = p2x,p2y + return inside + +def readMap(pedfile): + """ + """ + mapfile = pedfile.replace('.ped', '.map') + marker_list = [] + if os.path.exists(mapfile): + print 'readMap: %s' % (mapfile) + fh = file(mapfile, 'r') + for line in fh: + marker_list.append(line.strip().split()) + fh.close() + print 'readMap: %s markers' % (len(marker_list)) + return marker_list + +def calcMeanSD(useme): + """ + A numerically stable algorithm is given below. It also computes the mean. + This algorithm is due to Knuth,[1] who cites Welford.[2] + n = 0 + mean = 0 + M2 = 0 + + foreach x in data: + n = n + 1 + delta = x - mean + mean = mean + delta/n + M2 = M2 + delta*(x - mean) // This expression uses the new value of mean + end for + + variance_n = M2/n + variance = M2/(n - 1) + """ + mean = 0.0 + M2 = 0.0 + sd = 0.0 + n = len(useme) + if n > 1: + for i,x in enumerate(useme): + delta = x - mean + mean = mean + delta/(i+1) # knuth uses n+=1 at start + M2 = M2 + delta*(x - mean) # This expression uses the new value of mean + variance = M2/(n-1) # assume is sample so lose 1 DOF + sd = pow(variance,0.5) + return mean,sd + + +def doIBSpy(ped=None,basename='',outdir=None,logf=None, + nrsSamples=10000,title='title',pdftoo=0,Zcutoff=2.0): + #def doIBS(pedName, title, nrsSamples=None, pdftoo=False): + """ started with snpmatrix but GRR uses actual IBS counts and sd's + """ + repOut = [] # text strings to add to the html display + refallele = {} + tblf = '%s_table.xls' % (title) + tbl = file(os.path.join(outdir,tblf), 'w') + tbl.write(TABLE_HEADER) + svgf = '%s.svg' % (title) + svg = file(os.path.join(outdir,svgf), 'w') + + nMarkers = len(ped._markers) + if nMarkers < 5: + print sys.stderr, '### ERROR - %d is too few markers for reliable estimation in %s - terminating' % (nMarkers,PROGNAME) + sys.exit(1) + nSubjects = len(ped._subjects) + nrsSamples = min(nMarkers, nrsSamples) + if opts and opts.use_mito: + markers = range(nMarkers) + nrsSamples = min(len(markers), nrsSamples) + sampleIndexes = sorted(random.sample(markers, nrsSamples)) + else: + autosomals = ped.autosomal_indices() + nrsSamples = min(len(autosomals), nrsSamples) + sampleIndexes = sorted(random.sample(autosomals, nrsSamples)) + + print '' + print 'Getting random.sample of %s from %s total' % (nrsSamples, nMarkers) + npairs = (nSubjects*(nSubjects-1))/2 # total rows in table + newfiles=[svgf,tblf] + explanations = ['rgGRR Plot (requires SVG)','Mean by SD alleles shared - %d rows' % npairs] + # these go with the output file links in the html file + s = 'Reading genotypes for %s subjects and %s markers\n' % (nSubjects, nrsSamples) + logf.write(s) + minUsegenos = nrsSamples/2 # must have half? + nGenotypes = nSubjects*nrsSamples + stime = time.time() + emptyRows = set() + genos = numpy.zeros((nSubjects, nrsSamples), dtype=int) + for s in xrange(nSubjects): + nValid = 0 + #getGenotypesByIndices(self, s, mlist, format) + genos[s] = ped.getGenotypesByIndices(s, sampleIndexes, format='ref') + nValid = sum([1 for g in genos[s] if g]) + if not nValid: + emptyRows.add(s) + sub = ped.getSubject(s) + print 'All missing for row %d (%s)' % (s, sub) + logf.write('All missing for row %d (%s)\n' % (s, sub)) + rtime = time.time() - stime + if verbose: + print '@@Read %s genotypes in %s seconds' % (nGenotypes, rtime) + + + ### Now the expensive part. For each pair of subjects, we get the mean number + ### and standard deviation of shared alleles over all of the markers where both + ### subjects have a known genotype. Identical subjects should have mean shared + ### alleles very close to 2.0 with a standard deviation very close to 0.0. + tot = nSubjects*(nSubjects-1)/2 + nprog = tot/10 + nMarkerpairs = tot * nrsSamples + estimatedTimeSlow = nMarkerpairs/MARKER_PAIRS_PER_SECOND_SLOW + estimatedTimeFast = nMarkerpairs/MARKER_PAIRS_PER_SECOND_FAST + + pairs = [] + pair_data = {} + means = [] ## Mean IBS for each pair + ngenoL = [] ## Count of comparable genotypes for each pair + sdevs = [] ## Standard dev for each pair + rels = [] ## A relationship code for each pair + zmeans = [0.0 for x in xrange(tot)] ## zmean score for each pair for the relgroup + zstds = [0.0 for x in xrange(tot)] ## zstd score for each pair for the relgrp + skip = set() + ndone = 0 ## How many have been done so far + + logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog)) + logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow)) + + t1sum = 0 + t2sum = 0 + t3sum = 0 + now = time.time() + scache = {}

1 0

[hg] galaxy 3634: Added pound to trimmer list
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a6e3f4cae4ce changeset: 3634:a6e3f4cae4ce user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Apr 13 11:17:30 2010 -0400 description: Added pound to trimmer list diffstat: tools/filters/trimmer.xml | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r 0dc1fc63c945 -r a6e3f4cae4ce tools/filters/trimmer.xml --- a/tools/filters/trimmer.xml Tue Apr 13 10:22:27 2010 -0400 +++ b/tools/filters/trimmer.xml Tue Apr 13 11:17:30 2010 -0400 @@ -28,6 +28,7 @@ <option value="38">&</option> <option value="37">%</option> <option value="94">^</option> + <option value="35">#</option> </param> </inputs> <outputs>

1 0

[hg] galaxy 3633: Add the raw uncompressed .js files needed for ...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0b682d3dd01b changeset: 3633:0b682d3dd01b user: fubar: ross Lazarus at gmail period com date: Tue Apr 13 11:15:35 2010 -0400 description: Add the raw uncompressed .js files needed for rgGRR svg display - the packed ones were already there Fix rgManQQ so the manhattan plot is not called for data without chromosome and offset Use LD reduced data for IBD/GRR for faster performance and better resolution of close relationships Add an LD pruning and thinning step to rgGRR - the target composite pbed or lped has the thinned files permanently added for reuse. This is skipped for small numbers of markers since the plink --thin 0.1 option applied to tinywga.pbed will return an empty file which is not really ideal. diffstat: static/scripts/checkbox_and_radiobutton.js | 347 ++++ static/scripts/helper_functions.js | 817 ++++++++++ static/scripts/timer.js | 74 + tools/rgenetics/rgGRR.py | 2241 ++++++++++++++------------- tools/rgenetics/rgManQQ.py | 19 +- 5 files changed, 2396 insertions(+), 1102 deletions(-) diffs (truncated from 3540 to 3000 lines): diff -r 0dc1fc63c945 -r 0b682d3dd01b static/scripts/checkbox_and_radiobutton.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/checkbox_and_radiobutton.js Tue Apr 13 11:15:35 2010 -0400 @@ -0,0 +1,347 @@ +/* +Scripts to create interactive checkboxes and radio buttons in SVG using ECMA script +Copyright (C) <2007> <Andreas Neumann> +Version 1.1.3, 2007-08-09 +neumann(a)karto.baug.ethz.ch +http://www.carto.net/ +http://www.carto.net/neumann/ + +Credits: +* Guy Morton for providing a fix to let users toggle checkboxes by clicking on text labels +* Bruce Rindahl for providing the bugfix described in version 1.1.2 +* Simon Shutter for providing a fix for the ASV in IE crash when reloading the SVG file after calling the .remove() method on a checkbox + +---- + +Documentation: http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/ + +---- + +current version: 1.1.3 + +version history: +1.0 (2006-03-13) +initial version + +1.1 (2006-07-11) +text labels are now clickable (thanks to Guy Morton) +added method .moveTo() to move checkbox to a different location +introduced new constructor parameter labelYOffset to allow more flexible placement of the text label + +1.1.1 (2007-02-06) +added cursor pointer to the text label and use element representing the checkBox + +1.1.2 (2007-04-19) +bug fix: this.selectedIndex was not correctly initialized in method addCheckBox of the radioButtonGroup object + +1.1.3 (2007-08-09) +bug fix: the method .remove() was slightly modified (using removeEventListener) for avoiding a crash related to the method after reloading the SVG file + +------- + + +This ECMA script library is free software; you can redistribute it and/or +modify it under the terms of the GNU Lesser General Public +License as published by the Free Software Foundation; either +version 2.1 of the License, or (at your option) any later version. + +This library is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +Lesser General Public License for more details. + +You should have received a copy of the GNU Lesser General Public +License along with this library (lesser_gpl.txt); if not, write to the Free Software +Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +---- + +original document site: http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/ +Please contact the author in case you want to use code or ideas commercially. +If you use this code, please include this copyright header, the included full +LGPL 2.1 text and read the terms provided in the LGPL 2.1 license +(http://www.gnu.org/copyleft/lesser.txt) + +------------------------------- + +Please report bugs and send improvements to neumann(a)karto.baug.ethz.ch +If you use this control, please link to the original (http://www.carto.net/papers/svg/gui/checkbox_and_radiobutton/) +somewhere in the source-code-comment or the "about" of your project and give credits, thanks! + +*/ + +function checkBox(id,parentNode,x,y,checkboxId,checkcrossId,checkedStatus,labelText,textStyles,labelDistance,labelYOffset,radioButtonGroup,functionToCall) { + var nrArguments = 13; + var createCheckbox= true; + if (arguments.length == nrArguments) { + this.id = id; //an internal id, this id is not used in the SVG Dom tree + this.parentNode = parentNode; //the parentNode, string or nodeReference + this.x = x; //the center of the checkBox + this.y = y; //the center of the checkBox + this.checkboxId = checkboxId; //the id of the checkbox symbol (background) + this.checkcrossId = checkcrossId; //the id of the checkbox symbol (foreground), pointer-events should be set to "none" + this.checkedStatus = checkedStatus; //a status variable (true|false), indicates if checkbox is on or off + this.labelText = labelText; //the text of the checkbox label to be displayed, use undefined or empty string if you don't need a label text + this.textStyles = textStyles; //an array of literals containing the text settings + if (!this.textStyles["font-size"]) { + this.textStyles["font-size"] = 12; + } + this.labelDistance = labelDistance; //a distance defined from the center of the checkbox to the left of the text of the label + this.labelYOffset = labelYOffset; //a y offset value for the text label in relation to the checkbox symbol center + this.radioButtonGroup = radioButtonGroup; //a reference to a radio button group, if this is a standalone checkBox, just use the parameter undefined + this.functionToCall = functionToCall; //the function to call after triggering checkBox + this.exists = true; //status that indicates if checkbox exists or not, is set to false after method .remove() was called + this.label = undefined; //later a reference to the label text node + } + else { + createCheckbox = false; + alert("Error in checkbox ("+id+"): wrong nr of arguments! You have to pass over "+nrArguments+" parameters."); + } + if (createCheckbox) { + //timer stuff + this.timer = new Timer(this); //a Timer instance for calling the functionToCall + if (this.radioButtonGroup) { + this.timerMs = 0; + } + else { + this.timerMs = 200; //a constant of this object that is used in conjunction with the timer - functionToCall is called after 200 ms + } + //create checkbox + this.createCheckBox(); + } + else { + alert("Could not create checkbox with id '"+id+"' due to errors in the constructor parameters"); + } +} + +//this method creates all necessary checkbox geometry +checkBox.prototype.createCheckBox = function() { + if (typeof(this.parentNode) == "string") { + this.parentNode = document.getElementById(this.parentNode); + } + //create checkbox + this.checkBox = document.createElementNS(svgNS,"use"); + this.checkBox.setAttributeNS(null,"x",this.x); + this.checkBox.setAttributeNS(null,"y",this.y); + this.checkBox.setAttributeNS(xlinkNS,"href","#"+this.checkboxId); + this.checkBox.addEventListener("click",this,false); + this.checkBox.setAttributeNS(null,"cursor","pointer"); + this.parentNode.appendChild(this.checkBox); + //create checkcross + this.checkCross = document.createElementNS(svgNS,"use"); + this.checkCross.setAttributeNS(null,"x",this.x); + this.checkCross.setAttributeNS(null,"y",this.y); + this.checkCross.setAttributeNS(xlinkNS,"href","#"+this.checkcrossId); + this.parentNode.appendChild(this.checkCross); + if (this.checkedStatus == false) { + this.checkCross.setAttributeNS(null,"display","none"); + } + //create label, if any + if (this.labelText) { + if (this.labelText.length > 0) { + this.label = document.createElementNS(svgNS,"text"); + for (var attrib in this.textStyles) { + var value = this.textStyles[attrib]; + if (attrib == "font-size") { + value += "px"; + } + this.label.setAttributeNS(null,attrib,value); + } + this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); + this.label.setAttributeNS(null,"y",(this.y + this.labelYOffset)); + this.label.setAttributeNS(null,"cursor","pointer"); + var labelTextNode = document.createTextNode(this.labelText); + this.label.appendChild(labelTextNode); + this.label.setAttributeNS(null,"pointer-events","all"); + this.label.addEventListener("click",this,false); + this.parentNode.appendChild(this.label); + } + } + if (this.radioButtonGroup) { + this.radioButtonGroup.addCheckBox(this); + } +} + +checkBox.prototype.handleEvent = function(evt) { + if (evt.type == "click") { + if (this.checkedStatus == true) { + this.checkCross.setAttributeNS(null,"display","none"); + this.checkedStatus = false; + } + else { + this.checkCross.setAttributeNS(null,"display","inline"); + this.checkedStatus = true; + } + } + this.timer.setTimeout("fireFunction",this.timerMs); +} + +checkBox.prototype.fireFunction = function() { + if (this.radioButtonGroup) { + this.radioButtonGroup.selectById(this.id,true); + } + else { + if (typeof(this.functionToCall) == "function") { + this.functionToCall(this.id,this.checkedStatus,this.labelText); + } + if (typeof(this.functionToCall) == "object") { + this.functionToCall.checkBoxChanged(this.id,this.checkedStatus,this.labelText); + } + if (typeof(this.functionToCall) == undefined) { + return; + } + } +} + +checkBox.prototype.check = function(FireFunction) { + this.checkCross.setAttributeNS(null,"display","inherit"); + this.checkedStatus = true; + if (FireFunction) { + this.timer.setTimeout("fireFunction",this.timerMs); + } +} + +checkBox.prototype.uncheck = function(FireFunction) { + this.checkCross.setAttributeNS(null,"display","none"); + this.checkedStatus = false; + if (FireFunction) { + this.timer.setTimeout("fireFunction",this.timerMs); + } +} + +//move checkbox to a different position +checkBox.prototype.moveTo = function(moveX,moveY) { + this.x = moveX; + this.y = moveY; + //move checkbox + this.checkBox.setAttributeNS(null,"x",this.x); + this.checkBox.setAttributeNS(null,"y",this.y); + //move checkcross + this.checkCross.setAttributeNS(null,"x",this.x); + this.checkCross.setAttributeNS(null,"y",this.y); + //move text label + if (this.labelText) { + this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); + this.label.setAttributeNS(null,"y",(this.y + this.labelYOffset)); + } +} + +checkBox.prototype.remove = function(FireFunction) { + this.checkBox.removeEventListener("click",this,false); + this.parentNode.removeChild(this.checkBox); + this.parentNode.removeChild(this.checkCross); + if (this.label) { + this.parentNode.removeChild(this.label); + } + this.exists = false; +} + +checkBox.prototype.setLabelText = function(labelText) { + this.labelText = labelText + if (this.label) { + this.label.firstChild.nodeValue = labelText; + } + else { + if (this.labelText.length > 0) { + this.label = document.createElementNS(svgNS,"text"); + for (var attrib in this.textStyles) { + value = this.textStyles[attrib]; + if (attrib == "font-size") { + value += "px"; + } + this.label.setAttributeNS(null,attrib,value); + } + this.label.setAttributeNS(null,"x",(this.x + this.labelDistance)); + this.label.setAttributeNS(null,"y",(this.y + this.textStyles["font-size"] * 0.3)); + var labelTextNode = document.createTextNode(this.labelText); + this.label.appendChild(labelTextNode); + this.parentNode.appendChild(this.label); + } + } +} + +/* start of the radioButtonGroup object */ + +function radioButtonGroup(id,functionToCall) { + var nrArguments = 2; + if (arguments.length == nrArguments) { + this.id = id; + if (typeof(functionToCall) == "function" || typeof(functionToCall) == "object" || typeof(functionToCall) == undefined) { + this.functionToCall = functionToCall; + } + else { + alert("Error in radiobutton with ("+id+"): argument functionToCall is not of type 'function', 'object' or undefined!"); + } + this.checkBoxes = new Array(); //this array will hold checkbox objects + this.selectedId = undefined; //holds the id of the active radio button + this.selectedIndex = undefined; //holds the index of the active radio button + //timer stuff + this.timer = new Timer(this); //a Timer instance for calling the functionToCall + this.timerMs = 200; //a constant of this object that is used in conjunction with the timer - functionToCall is called after 200 ms + } + else { + alert("Error in radiobutton with ("+id+"): wrong nr of arguments! You have to pass over "+nrArguments+" parameters."); + } +} + +radioButtonGroup.prototype.addCheckBox = function(checkBoxObj) { + this.checkBoxes.push(checkBoxObj); + if (checkBoxObj.checkedStatus) { + this.selectedId = checkBoxObj.id; + this.selectedIndex = this.checkBoxes.length - 1; + } +} + +//change radio button selection by id +radioButtonGroup.prototype.selectById = function(cbId,fireFunction) { + var found = false; + for (var i=0;i<this.checkBoxes.length;i++) { + if (this.checkBoxes[i].id == cbId) { + this.selectedId = cbId; + this.selectedIndex = i; + if (this.checkBoxes[i].checkedStatus == false) { + this.checkBoxes[i].check(false); + } + found = true; + } + else { + this.checkBoxes[i].uncheck(false); + } + } + if (found) { + if (fireFunction) { + this.timer.setTimeout("fireFunction",this.timerMs); + } + } + else { + alert("Error in radiobutton with ("+this.id+"): could not find checkbox with id '"+cbId+"'"); + } +} + +//change radio button selection by label name +radioButtonGroup.prototype.selectByLabelname = function(labelName,fireFunction) { + var id = -1; + for (var i=0;i<this.checkBoxes.length;i++) { + if (this.checkBoxes[i].labelText == labelName) { + id = this.checkBoxes[i].id; + } + } + if (id == -1) { + alert("Error in radiobutton with ("+this.id+"): could not find checkbox with label '"+labelName+"'"); + } + else { + this.selectById(id,fireFunction); + } +} + +radioButtonGroup.prototype.fireFunction = function() { + if (typeof(this.functionToCall) == "function") { + this.functionToCall(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText); + } + if (typeof(this.functionToCall) == "object") { + this.functionToCall.radioButtonChanged(this.id,this.selectedId,this.checkBoxes[this.selectedIndex].labelText); + } + if (typeof(this.functionToCall) == undefined) { + return; + } +} \ No newline at end of file diff -r 0dc1fc63c945 -r 0b682d3dd01b static/scripts/helper_functions.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/helper_functions.js Tue Apr 13 11:15:35 2010 -0400 @@ -0,0 +1,817 @@ +/** + * @fileoverview + * + * ECMAScript <a href="http://www.carto.net/papers/svg/resources/helper_functions.html">helper functions</a>, main purpose is to serve in SVG mapping or other SVG based web applications + * + * This ECMA script library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library (http://www.carto.net/papers/svg/resources/lesser_gpl.txt) if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * Please report bugs and send improvements to neumann(a)karto.baug.ethz.ch + * If you use these scripts, please link to the original (http://www.carto.net/papers/svg/resources/helper_functions.html) + * somewhere in the source-code-comment or the "about" of your project and give credits, thanks! + * + * See <a href="js_docs_out/overview-summary-helper_functions.js.html">documentation</a>. + * + * @author Andreas Neumann a.neumann(a)carto.net + * @copyright LGPL 2.1 <a href="http://www.gnu.org/copyleft/lesser.txt">Gnu LGPL 2.1</a> + * @credits Bruce Rindahl, numerous people on svgdevelopers(a)yahoogroups.com + */ + +//global variables necessary to create elements in these namespaces, do not delete them!!!! + +/** + * This variable is a shortcut to the full URL of the SVG namespace + * @final + * @type String + */ +var svgNS = "http://www.w3.org/2000/svg"; + +/** + * This variable is a shortcut to the full URL of the XLink namespace + * @final + * @type String + */ +var xlinkNS = "http://www.w3.org/1999/xlink"; + +/** + * This variable is a shortcut to the full URL of the attrib namespace + * @final + * @type String + */ +var cartoNS = "http://www.carto.net/attrib"; + +/** + * This variable is a alias to the full URL of the attrib namespace + * @final + * @type String + */ +var attribNS = "http://www.carto.net/attrib"; + +/** + * This variable is a alias to the full URL of the Batik extension namespace + * @final + * @type String + */ +var batikNS = "http://xml.apache.org/batik/ext"; + +/** + * Returns the polar direction from a given vector + * @param {Number} xdiff the x-part of the vector + * @param {Number} ydiff the y-part of the vector + * @return direction the direction in radians + * @type Number + * @version 1.0 (2007-04-30) + * @see #toPolarDist + * @see #toRectX + * @see #toRectY + */ +function toPolarDir(xdiff,ydiff) { + var direction = (Math.atan2(ydiff,xdiff)); + return(direction); +} + +/** + * Returns the polar distance from a given vector + * @param {Number} xdiff the x-part of the vector + * @param {Number} ydiff the y-part of the vector + * @return distance the distance + * @type Number + * @version 1.0 (2007-04-30) + * @see #toPolarDir + * @see #toRectX + * @see #toRectY + */ +function toPolarDist(xdiff,ydiff) { + var distance = Math.sqrt(xdiff * xdiff + ydiff * ydiff); + return(distance); +} + +/** + * Returns the x-part of a vector from a given direction and distance + * @param {Number} direction the direction (in radians) + * @param {Number} distance the distance + * @return x the x-part of the vector + * @type Number + * @version 1.0 (2007-04-30) + * @see #toPolarDist + * @see #toPolarDir + * @see #toRectY + */ +function toRectX(direction,distance) { + var x = distance * Math.cos(direction); + return(x); +} + +/** + * Returns the y-part of the vector from a given direction and distance + * @param {Number} direction the direction (in radians) + * @param {Number} distance the distance + * @return y the y-part of the vector + * @type Number + * @version 1.0 (2007-04-30) + * @see #toPolarDist + * @see #toPolarDir + * @see #toRectX + */ +function toRectY(direction,distance) { + y = distance * Math.sin(direction); + return(y); +} + +/** + * Converts degrees to radians + * @param {Number} deg the degree value + * @return rad the radians value + * @type Number + * @version 1.0 (2007-04-30) + * @see #RadToDeg + */ +function DegToRad(deg) { + return (deg / 180.0 * Math.PI); +} + +/** + * Converts radians to degrees + * @param {Number} rad the radians value + * @return deg the degree value + * @type Number + * @version 1.0 (2007-04-30) + * @see #DegToRad + */ +function RadToDeg(rad) { + return (rad / Math.PI * 180.0); +} + +/** + * Converts decimal degrees to degrees, minutes, seconds + * @param {Number} dd the decimal degree value + * @return degrees the degree values in the following notation: {deg:degrees,min:minutes,sec:seconds} + * @type literal + * @version 1.0 (2007-04-30) + * @see #dms2dd + */ +function dd2dms(dd) { + var minutes = (Math.abs(dd) - Math.floor(Math.abs(dd))) * 60; + var seconds = (minutes - Math.floor(minutes)) * 60; + var minutes = Math.floor(minutes); + if (dd >= 0) { + var degrees = Math.floor(dd); + } + else { + var degrees = Math.ceil(dd); + } + return {deg:degrees,min:minutes,sec:seconds}; +} + +/** + * Converts degrees, minutes and seconds to decimal degrees + * @param {Number} deg the degree value + * @param {Number} min the minute value + * @param {Number} sec the second value + * @return deg the decimal degree values + * @type Number + * @version 1.0 (2007-04-30) + * @see #dd2dms + */ +function dms2dd(deg,min,sec) { + if (deg < 0) { + return deg - (min / 60) - (sec / 3600); + } + else { + return deg + (min / 60) + (sec / 3600); + } +} + +/** + * log function, missing in the standard Math object + * @param {Number} x the value where the log function should be applied to + * @param {Number} b the base value for the log function + * @return logResult the result of the log function + * @type Number + * @version 1.0 (2007-04-30) + */ +function log(x,b) { + if(b==null) b=Math.E; + return Math.log(x)/Math.log(b); +} + +/** + * interpolates a value (e.g. elevation) bilinearly based on the position within a cell with 4 corner values + * @param {Number} za the value at the upper left corner of the cell + * @param {Number} zb the value at the upper right corner of the cell + * @param {Number} zc the value at the lower right corner of the cell + * @param {Number} zd the value at the lower left corner of the cell + * @param {Number} xpos the x position of the point where a new value should be interpolated + * @param {Number} ypos the y position of the point where a new value should be interpolated + * @param {Number} ax the x position of the lower left corner of the cell + * @param {Number} ay the y position of the lower left corner of the cell + * @param {Number} cellsize the size of the cell + * @return interpol_value the result of the bilinear interpolation function + * @type Number + * @version 1.0 (2007-04-30) + */ +function intBilinear(za,zb,zc,zd,xpos,ypos,ax,ay,cellsize) { //bilinear interpolation function + var e = (xpos - ax) / cellsize; + var f = (ypos - ay) / cellsize; + + //calculation of weights + var wa = (1 - e) * (1 - f); + var wb = e * (1 - f); + var wc = e * f; + var wd = f * (1 - e); + + var interpol_value = wa * zc + wb * zd + wc * za + wd * zb; + return interpol_value; +} + +/** + * tests if a given point is left or right of a given line + * @param {Number} pointx the x position of the given point + * @param {Number} pointy the y position of the given point + * @param {Number} linex1 the x position of line's start point + * @param {Number} liney1 the y position of line's start point + * @param {Number} linex2 the x position of line's end point + * @param {Number} liney2 the y position of line's end point + * @return leftof the result of the leftOfTest, 1 means leftOf, 0 means rightOf + * @type Number (integer, 0|1) + * @version 1.0 (2007-04-30) + */ +function leftOfTest(pointx,pointy,linex1,liney1,linex2,liney2) { + var result = (liney1 - pointy) * (linex2 - linex1) - (linex1 - pointx) * (liney2 - liney1); + if (result < 0) { + var leftof = 1; //case left of + } + else { + var leftof = 0; //case left of + } + return leftof; +} + +/** + * calculates the distance between a given point and a given line + * @param {Number} pointx the x position of the given point + * @param {Number} pointy the y position of the given point + * @param {Number} linex1 the x position of line's start point + * @param {Number} liney1 the y position of line's start point + * @param {Number} linex2 the x position of line's end point + * @param {Number} liney2 the y position of line's end point + * @return distance the result of the leftOfTest, 1 means leftOf, 0 means rightOf + * @type Number + * @version 1.0 (2007-04-30) + */ +function distFromLine(xpoint,ypoint,linex1,liney1,linex2,liney2) { + var dx = linex2 - linex1; + var dy = liney2 - liney1; + var distance = (dy * (xpoint - linex1) - dx * (ypoint - liney1)) / Math.sqrt(Math.pow(dx,2) + Math.pow(dy,2)); + return distance; +} + +/** + * calculates the angle between two vectors (lines) + * @param {Number} ax the x part of vector a + * @param {Number} ay the y part of vector a + * @param {Number} bx the x part of vector b + * @param {Number} by the y part of vector b + * @return angle the angle in radians + * @type Number + * @version 1.0 (2007-04-30) + * @credits <a href="http://www.mathe-online.at/mathint/vect2/i.html#Winkel">Mathe Online (Winkel)</a> + */ +function angleBetwTwoLines(ax,ay,bx,by) { + var angle = Math.acos((ax * bx + ay * by) / (Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)) * Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)))); + return angle; +} + +/** + * calculates the bisector vector for two given vectors + * @param {Number} ax the x part of vector a + * @param {Number} ay the y part of vector a + * @param {Number} bx the x part of vector b + * @param {Number} by the y part of vector b + * @return c the resulting vector as an Array, c[0] is the x part of the vector, c[1] is the y part + * @type Array + * @version 1.0 (2007-04-30) + * @credits <a href="http://www.mathe-online.at/mathint/vect1/i.html#Winkelsymmetrale">Mathe Online (Winkelsymmetrale)</a> + * see #calcBisectorAngle + * */ +function calcBisectorVector(ax,ay,bx,by) { + var betraga = Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)); + var betragb = Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)); + var c = new Array(); + c[0] = ax / betraga + bx / betragb; + c[1] = ay / betraga + by / betragb; + return c; +} + +/** + * calculates the bisector angle for two given vectors + * @param {Number} ax the x part of vector a + * @param {Number} ay the y part of vector a + * @param {Number} bx the x part of vector b + * @param {Number} by the y part of vector b + * @return angle the bisector angle in radians + * @type Number + * @version 1.0 (2007-04-30) + * @credits <a href="http://www.mathe-online.at/mathint/vect1/i.html#Winkelsymmetrale">Mathe Online (Winkelsymmetrale)</a> + * see #calcBisectorVector + * */ +function calcBisectorAngle(ax,ay,bx,by) { + var betraga = Math.sqrt(Math.pow(ax,2) + Math.pow(ay,2)); + var betragb = Math.sqrt(Math.pow(bx,2) + Math.pow(by,2)); + var c1 = ax / betraga + bx / betragb; + var c2 = ay / betraga + by / betragb; + var angle = toPolarDir(c1,c2); + return angle; +} + +/** + * calculates the intersection point of two given lines + * @param {Number} line1x1 the x the start point of line 1 + * @param {Number} line1y1 the y the start point of line 1 + * @param {Number} line1x2 the x the end point of line 1 + * @param {Number} line1y2 the y the end point of line 1 + * @return interSectPoint the intersection point, interSectPoint.x contains x-part, interSectPoint.y the y-part of the resulting coordinate + * @type Object + * @version 1.0 (2007-04-30) + * @credits <a href="http://astronomy.swin.edu.au/~pbourke/geometry/lineline2d/">P. Bourke</a> + */ +function intersect2lines(line1x1,line1y1,line1x2,line1y2,line2x1,line2y1,line2x2,line2y2) { + var interSectPoint = new Object(); + var denominator = (line2y2 - line2y1)*(line1x2 - line1x1) - (line2x2 - line2x1)*(line1y2 - line1y1); + if (denominator == 0) { + alert("lines are parallel"); + } + else { + var ua = ((line2x2 - line2x1)*(line1y1 - line2y1) - (line2y2 - line2y1)*(line1x1 - line2x1)) / denominator; + var ub = ((line1x2 - line1x1)*(line1y1 - line2y1) - (line1y2 - line1y1)*(line1x1 - line2x1)) / denominator; + } + interSectPoint["x"] = line1x1 + ua * (line1x2 - line1x1); + interSectPoint["y"] = line1y1 + ua * (line1y2 - line1y1); + return interSectPoint; +} + +/** + * reformats a given number to a string by adding separators at every third digit + * @param {String|Number} inputNumber the input number, can be of type number or string + * @param {String} separator the separator, e.g. ' or , + * @return newString the intersection point, interSectPoint.x contains x-part, interSectPoint.y the y-part of the resulting coordinate + * @type String + * @version 1.0 (2007-04-30) + */ +function formatNumberString(inputNumber,separator) { + //check if of type string, if number, convert it to string + if (typeof(inputNumber) == "Number") { + var myTempString = inputNumber.toString(); + } + else { + var myTempString = inputNumber; + } + var newString=""; + //if it contains a comma, it will be split + var splitResults = myTempString.split("."); + var myCounter = splitResults[0].length; + if (myCounter > 3) { + while(myCounter > 0) { + if (myCounter > 3) { + newString = separator + splitResults[0].substr(myCounter - 3,3) + newString; + } + else { + newString = splitResults[0].substr(0,myCounter) + newString; + } + myCounter -= 3; + } + } + else { + newString = splitResults[0]; + } + //concatenate if it contains a comma + if (splitResults[1]) { + newString = newString + "." + splitResults[1]; + } + return newString; +} + +/** + * writes a status text message out to a SVG text element's first child + * @param {String} statusText the text message to be displayed + * @version 1.0 (2007-04-30) + */ + function statusChange(statusText) { + document.getElementById("statusText").firstChild.nodeValue = "Statusbar: " + statusText; +} + +/** + * scales an SVG element, requires that the element has an x and y attribute (e.g. circle, ellipse, use element, etc.) + * @param {dom::Event} evt the evt object that triggered the scaling + * @param {Number} factor the scaling factor + * @version 1.0 (2007-04-30) + */ +function scaleObject(evt,factor) { + //reference to the currently selected object + var element = evt.currentTarget; + var myX = element.getAttributeNS(null,"x"); + var myY = element.getAttributeNS(null,"y"); + var newtransform = "scale(" + factor + ") translate(" + (myX * 1 / factor - myX) + " " + (myY * 1 / factor - myY) +")"; + element.setAttributeNS(null,'transform', newtransform); +} + +/** + * returns the transformation matrix (ctm) for the given node up to the root element + * the basic use case is to provide a wrapper function for the missing SVGLocatable.getTransformToElement method (missing in ASV3) + * @param {svg::SVGTransformable} node the node reference for the SVGElement the ctm is queried + * @return CTM the current transformation matrix from the given node to the root element + * @type svg::SVGMatrix + * @version 1.0 (2007-05-01) + * @credits <a href="http://www.kevlindev.com/tutorials/basics/transformations/toUserSpace/index…">Kevin Lindsey (toUserSpace)</a> + * @see #getTransformToElement + */ +function getTransformToRootElement(node) { + try { + //this part is for fully conformant players (like Opera, Batik, Firefox, Safari ...) + var CTM = node.getTransformToElement(document.documentElement); + } + catch (ex) { + //this part is for ASV3 or other non-conformant players + // Initialize our CTM the node's Current Transformation Matrix + var CTM = node.getCTM(); + // Work our way through the ancestor nodes stopping at the SVG Document + while ( ( node = node.parentNode ) != document ) { + // Multiply the new CTM to the one with what we have accumulated so far + CTM = node.getCTM().multiply(CTM); + } + } + return CTM; +} + +/** + * returns the transformation matrix (ctm) for the given dom::Node up to a different dom::Node + * the basic use case is to provide a wrapper function for the missing SVGLocatable.getTransformToElement method (missing in ASV3) + * @param {svg::SVGTransformable} node the node reference for the element the where the ctm should be calculated from + * @param {svg::SVGTransformable} targetNode the target node reference for the element the ctm should be calculated to + * @return CTM the current transformation matrix from the given node to the target element + * @type svg::SVGMatrix + * @version 1.0 (2007-05-01) + * @credits <a href="http://www.kevlindev.com/tutorials/basics/transformations/toUserSpace/index…">Kevin Lindsey (toUserSpace)</a> + * @see #getTransformToRootElement + */ +function getTransformToElement(node,targetNode) { + try { + //this part is for fully conformant players + var CTM = node.getTransformToElement(targetNode); + } + catch (ex) { + //this part is for ASV3 or other non-conformant players + // Initialize our CTM the node's Current Transformation Matrix + var CTM = node.getCTM(); + // Work our way through the ancestor nodes stopping at the SVG Document + while ( ( node = node.parentNode ) != targetNode ) { + // Multiply the new CTM to the one with what we have accumulated so far + CTM = node.getCTM().multiply(CTM); + } + } + return CTM; +} + +/** + * converts HSV to RGB values + * @param {Number} hue the hue value (between 0 and 360) + * @param {Number} sat the saturation value (between 0 and 1) + * @param {Number} val the value value (between 0 and 1) + * @return rgbArr the rgb values (associative array or object, the keys are: red,green,blue), all values are scaled between 0 and 255 + * @type Object + * @version 1.0 (2007-05-01) + * @see #rgb2hsv + */ +function hsv2rgb(hue,sat,val) { + var rgbArr = new Object(); + if ( sat == 0) { + rgbArr["red"] = Math.round(val * 255); + rgbArr["green"] = Math.round(val * 255); + rgbArr["blue"] = Math.round(val * 255); + } + else { + var h = hue / 60; + var i = Math.floor(h); + var f = h - i; + if (i % 2 == 0) { + f = 1 - f; + } + var m = val * (1 - sat); + var n = val * (1 - sat * f); + switch(i) { + case 0: + rgbArr["red"] = val; + rgbArr["green"] = n; + rgbArr["blue"] = m; + break; + case 1: + rgbArr["red"] = n; + rgbArr["green"] = val; + rgbArr["blue"] = m; + break; + case 2: + rgbArr["red"] = m; + rgbArr["green"] = val; + rgbArr["blue"] = n; + break; + case 3: + rgbArr["red"] = m; + rgbArr["green"] = n; + rgbArr["blue"] = val; + break; + case 4: + rgbArr["red"] = n; + rgbArr["green"] = m; + rgbArr["blue"] = val; + break; + case 5: + rgbArr["red"] = val; + rgbArr["green"] = m; + rgbArr["blue"] = n; + break; + case 6: + rgbArr["red"] = val; + rgbArr["green"] = n; + rgbArr["blue"] = m; + break; + } + rgbArr["red"] = Math.round(rgbArr["red"] * 255); + rgbArr["green"] = Math.round(rgbArr["green"] * 255); + rgbArr["blue"] = Math.round(rgbArr["blue"] * 255); + } + return rgbArr; +} + +/** + * converts RGB to HSV values + * @param {Number} red the hue value (between 0 and 255) + * @param {Number} green the saturation value (between 0 and 255) + * @param {Number} blue the value value (between 0 and 255) + * @return hsvArr the hsv values (associative array or object, the keys are: hue (0-360),sat (0-1),val (0-1)) + * @type Object + * @version 1.0 (2007-05-01) + * @see #hsv2rgb + */ +function rgb2hsv(red,green,blue) { + var hsvArr = new Object(); + red = red / 255; + green = green / 255; + blue = blue / 255; + myMax = Math.max(red, Math.max(green,blue)); + myMin = Math.min(red, Math.min(green,blue)); + v = myMax; + if (myMax > 0) { + s = (myMax - myMin) / myMax; + } + else { + s = 0; + } + if (s > 0) { + myDiff = myMax - myMin; + rc = (myMax - red) / myDiff; + gc = (myMax - green) / myDiff; + bc = (myMax - blue) / myDiff; + if (red == myMax) { + h = (bc - gc) / 6; + } + if (green == myMax) { + h = (2 + rc - bc) / 6; + } + if (blue == myMax) { + h = (4 + gc - rc) / 6; + } + } + else { + h = 0; + } + if (h < 0) { + h += 1; + } + hsvArr["hue"] = Math.round(h * 360); + hsvArr["sat"] = s; + hsvArr["val"] = v; + return hsvArr; +} + +/** + * populates an array such that it can be addressed by both a key or an index nr, + * note that both Arrays need to be of the same length + * @param {Array} arrayKeys the array containing the keys + * @param {Array} arrayValues the array containing the values + * @return returnArray the resulting array containing both associative values and also a regular indexed array + * @type Array + * @version 1.0 (2007-05-01) + */ +function arrayPopulate(arrayKeys,arrayValues) { + var returnArray = new Array(); + if (arrayKeys.length != arrayValues.length) { + alert("error: arrays do not have the same length!"); + } + else { + for (i=0;i<arrayKeys.length;i++) { + returnArray[arrayKeys[i]] = arrayValues[i]; + } + } + return returnArray; +} + +/** + * Wrapper object for network requests, uses getURL or XMLHttpRequest depending on availability + * The callBackFunction receives a XML or text node representing the rootElement + * of the fragment received or the return text, depending on the returnFormat. + * See also the following <a href="http://www.carto.net/papers/svg/network_requests/">documentation</a>. + * @class this is a wrapper object to provide network request functionality (get|post) + * @param {String} url the URL/IRI of the network resource to be called + * @param {Function|Object} callBackFunction the callBack function or object that is called after the data was received, in case of an object, the method 'receiveData' is called; both the function and the object's 'receiveData' method get 2 return parameters: 'node.firstChild'|text (the root element of the XML or text resource), this.additionalParams (if defined) + * @param {String} returnFormat the return format, either 'xml' or 'json' (or text) + * @param {String} method the method of the network request, either 'get' or 'post' + * @param {String|Undefined} postText the String containing the post text (optional) or Undefined (if not a 'post' request) + * @param {Object|Array|String|Number|Undefined} additionalParams additional parameters that will be passed to the callBackFunction or object (optional) or Undefined + * @return a new getData instance + * @type getData + * @constructor + * @version 1.0 (2007-02-23) + */ +function getData(url,callBackFunction,returnFormat,method,postText,additionalParams) { + this.url = url; + this.callBackFunction = callBackFunction; + this.returnFormat = returnFormat; + this.method = method; + this.additionalParams = additionalParams; + if (method != "get" && method != "post") { + alert("Error in network request: parameter 'method' must be 'get' or 'post'"); + } + this.postText = postText; + this.xmlRequest = null; //@private reference to the XMLHttpRequest object +} + +/** + * triggers the network request defined in the constructor + */ +getData.prototype.getData = function() { + //call getURL() if available + if (window.getURL) { + if (this.method == "get") { + getURL(this.url,this); + } + if (this.method == "post") { + postURL(this.url,this.postText,this); + } + } + //or call XMLHttpRequest() if available + else if (window.XMLHttpRequest) { + var _this = this; + this.xmlRequest = new XMLHttpRequest(); + if (this.method == "get") { + if (this.returnFormat == "xml") { + this.xmlRequest.overrideMimeType("text/xml"); + } + this.xmlRequest.open("GET",this.url,true); + } + if (this.method == "post") { + this.xmlRequest.open("POST",this.url,true); + } + this.xmlRequest.onreadystatechange = function() {_this.handleEvent()}; + if (this.method == "get") { + this.xmlRequest.send(null); + } + if (this.method == "post") { + //test if postText exists and is of type string + var reallyPost = true; + if (!this.postText) { + reallyPost = false; + alert("Error in network post request: missing parameter 'postText'!"); + } + if (typeof(this.postText) != "string") { + reallyPost = false; + alert("Error in network post request: parameter 'postText' has to be of type 'string')"); + } + if (reallyPost) { + this.xmlRequest.send(this.postText); + } + } + } + //write an error message if neither method is available + else { + alert("your browser/svg viewer neither supports window.getURL nor window.XMLHttpRequest!"); + } +} + +/** + * this is the callback method for the getURL() or postURL() case + * @private + */ +getData.prototype.operationComplete = function(data) { + //check if data has a success property + if (data.success) { + //parse content of the XML format to the variable "node" + if (this.returnFormat == "xml") { + //convert the text information to an XML node and get the first child + var node = parseXML(data.content,document); + //distinguish between a callback function and an object + if (typeof(this.callBackFunction) == "function") { + this.callBackFunction(node.firstChild,this.additionalParams); + } + if (typeof(this.callBackFunction) == "object") { + this.callBackFunction.receiveData(node.firstChild,this.additionalParams); + } + } + if (this.returnFormat == "json") { + if (typeof(this.callBackFunction) == "function") { + this.callBackFunction(data.content,this.additionalParams); + } + if (typeof(this.callBackFunction) == "object") { + this.callBackFunction.receiveData(data.content,this.additionalParams); + } + } + } + else { + alert("something went wrong with dynamic loading of geometry!"); + } +} + +/** + * this is the callback method for the XMLHttpRequest case + * @private + */ +getData.prototype.handleEvent = function() { + if (this.xmlRequest.readyState == 4) { + if (this.returnFormat == "xml") { + //we need to import the XML node first + var importedNode = document.importNode(this.xmlRequest.responseXML.documentElement,true); + if (typeof(this.callBackFunction) == "function") { + this.callBackFunction(importedNode,this.additionalParams); + } + if (typeof(this.callBackFunction) == "object") { + this.callBackFunction.receiveData(importedNode,this.additionalParams); + } + } + if (this.returnFormat == "json") { + if (typeof(this.callBackFunction) == "function") { + this.callBackFunction(this.xmlRequest.responseText,this.additionalParams); + } + if (typeof(this.callBackFunction) == "object") { + this.callBackFunction.receiveData(this.xmlRequest.responseText,this.additionalParams); + } + } + } +} + +/** + * Serializes an XML node and returns a string representation. Wrapper function to hide implementation differences. + * This can be used for debugging purposes or to post data to a server or network resource. + * @param {dom::Node} node the DOM node reference + * @return textRepresentation the String representation of the XML node + * @type String + * @version 1.0 (2007-05-01) + * @see getData + */ +function serializeNode(node) { + if (typeof XMLSerializer != 'undefined') { + return new XMLSerializer().serializeToString(node); + } + else if (typeof node.xml != 'undefined') { + return node.xml; + } + else if (typeof printNode != 'undefined') { + return printNode(node); + } + else if (typeof Packages != 'undefined') { + try { + var stringWriter = new java.io.StringWriter(); + Packages.org.apache.batik.dom.util.DOMUtilities.writeNode(node,stringWriter); + return stringWriter.toString(); + } + catch (e) { + alert("Sorry, your SVG viewer does not support the printNode/serialize function."); + return ''; + } + } + else { + alert("Sorry, your SVG viewer does not support the printNode/serialize function."); + return ''; + } +} + +/** + * Starts a SMIL animation element with the given id by triggering the '.beginElement()' method. + * This is a convenience (shortcut) function. + * @param {String} id a valid id of a valid SMIL animation element + * @version 1.0 (2007-05-01) + */ +//starts an animtion with the given id +//this function is useful in combination with window.setTimeout() +function startAnimation(id) { + document.getElementById(id).beginElement(); +} diff -r 0dc1fc63c945 -r 0b682d3dd01b static/scripts/timer.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/timer.js Tue Apr 13 11:15:35 2010 -0400 @@ -0,0 +1,74 @@ +// source/credits: "Algorithm": http://www.codingforums.com/showthread.php?s=&threadid=10531 +// The constructor should be called with +// the parent object (optional, defaults to window). + +function Timer(){ + this.obj = (arguments.length)?arguments[0]:window; + return this; +} + +// The set functions should be called with: +// - The name of the object method (as a string) (required) +// - The millisecond delay (required) +// - Any number of extra arguments, which will all be +// passed to the method when it is evaluated. + +Timer.prototype.setInterval = function(func, msec){ + var i = Timer.getNew(); + var t = Timer.buildCall(this.obj, i, arguments); + Timer.set[i].timer = window.setInterval(t,msec); + return i; +} +Timer.prototype.setTimeout = function(func, msec){ + var i = Timer.getNew(); + Timer.buildCall(this.obj, i, arguments); + Timer.set[i].timer = window.setTimeout("Timer.callOnce("+i+");",msec); + return i; +} + +// The clear functions should be called with +// the return value from the equivalent set function. + +Timer.prototype.clearInterval = function(i){ + if(!Timer.set[i]) return; + window.clearInterval(Timer.set[i].timer); + Timer.set[i] = null; +} +Timer.prototype.clearTimeout = function(i){ + if(!Timer.set[i]) return; + window.clearTimeout(Timer.set[i].timer); + Timer.set[i] = null; +} + +// Private data + +Timer.set = new Array(); +Timer.buildCall = function(obj, i, args){ + var t = ""; + Timer.set[i] = new Array(); + if(obj != window){ + Timer.set[i].obj = obj; + t = "Timer.set["+i+"].obj."; + } + t += args[0]+"("; + if(args.length > 2){ + Timer.set[i][0] = args[2]; + t += "Timer.set["+i+"][0]"; + for(var j=1; (j+2)<args.length; j++){ + Timer.set[i][j] = args[j+2]; + t += ", Timer.set["+i+"]["+j+"]"; + }} + t += ");"; + Timer.set[i].call = t; + return t; +} +Timer.callOnce = function(i){ + if(!Timer.set[i]) return; + eval(Timer.set[i].call); + Timer.set[i] = null; +} +Timer.getNew = function(){ + var i = 0; + while(Timer.set[i]) i++; + return i; +} \ No newline at end of file diff -r 0dc1fc63c945 -r 0b682d3dd01b tools/rgenetics/rgGRR.py --- a/tools/rgenetics/rgGRR.py Tue Apr 13 10:22:27 2010 -0400 +++ b/tools/rgenetics/rgGRR.py Tue Apr 13 11:15:35 2010 -0400 @@ -1,1096 +1,1145 @@ -""" -# july 2009: Need to see outliers so need to draw them last? -# could use clustering on the zscores to guess real relationships for unrelateds -# but definitely need to draw last -# added MAX_SHOW_ROWS to limit the length of the main report page -# Changes for Galaxy integration -# added more robust knuth method for one pass mean and sd -# no difference really - let's use scipy.mean() and scipy.std() instead... -# fixed labels and changed to .xls for outlier reports so can open in excel -# interesting - with a few hundred subjects, 5k gives good resolution -# and 100k gives better but not by much -# TODO remove non autosomal markers -# TODO it would be best if label had the zmean and zsd as these are what matter for -# outliers rather than the group mean/sd -# mods to rgGRR.py from channing CVS which John Ziniti has rewritten to produce SVG plots -# to make a Galaxy tool - we need the table of mean and SD for interesting pairs, the SVG and the log -# so the result should be an HTML file - -# rgIBS.py -# use a random subset of markers for a quick ibs -# to identify sample dups and closely related subjects -# try snpMatrix and plink and see which one works best for us? -# abecasis grr plots mean*sd for every subject to show clusters -# mods june 23 rml to avoid non-autosomal markers -# we seem to be distinguishing parent-child by gender - 2 clouds! - - -snpMatrix from David Clayton has: -ibs.stats function to calculate the identity-by-state stats of a group of samples -Description -Given a snp.matrix-class or a X.snp.matrix-class object with N samples, calculates some statistics -about the relatedness of every pair of samples within. - -Usage -ibs.stats(x) -8 ibs.stats -Arguments -x a snp.matrix-class or a X.snp.matrix-class object containing N samples -Details -No-calls are excluded from consideration here. -Value -A data.frame containing N(N - 1)/2 rows, where the row names are the sample name pairs separated -by a comma, and the columns are: -Count count of identical calls, exclusing no-calls -Fraction fraction of identical calls comparied to actual calls being made in both samples -Warning -In some applications, it may be preferable to subset a (random) selection of SNPs first - the -calculation -time increases as N(N - 1)M/2 . Typically for N = 800 samples and M = 3000 SNPs, the -calculation time is about 1 minute. A full GWA scan could take hours, and quite unnecessary for -simple applications such as checking for duplicate or related samples. -Note -This is mostly written to find mislabelled and/or duplicate samples. -Illumina indexes their SNPs in alphabetical order so the mitochondria SNPs comes first - for most -purpose it is undesirable to use these SNPs for IBS purposes. -TODO: Worst-case S4 subsetting seems to make 2 copies of a large object, so one might want to -subset before rbind(), etc; a future version of this routine may contain a built-in subsetting facility -""" -import sys,os,time,random,string,copy,optparse - -try: - set -except NameError: - from Sets import Set as set - -from rgutils import timenow -import plinkbinJZ - - -opts = None -verbose = False - -showPolygons = False - -class NullDevice: - def write(self, s): - pass - -tempstderr = sys.stderr # save -sys.stderr = NullDevice() -# need to avoid blather about deprecation and other strange stuff from scipy -# the current galaxy job runner assumes that -# the job is in error if anything appears on sys.stderr -# grrrrr. James wants to keep it that way instead of using the -# status flag for some strange reason. Presumably he doesn't use R or (in this case, scipy) -import numpy -import scipy -from scipy import weave - - -sys.stderr=tempstderr - - -PROGNAME = os.path.split(sys.argv[0])[-1] -X_AXIS_LABEL = 'Mean Alleles Shared' -Y_AXIS_LABEL = 'SD Alleles Shared' -LEGEND_ALIGN = 'topleft' -LEGEND_TITLE = 'Relationship' -DEFAULT_SYMBOL_SIZE = 1.0 # default symbol size -DEFAULT_SYMBOL_SIZE = 0.5 # default symbol size - -### Some colors for R/rpy -R_BLACK = 1 -R_RED = 2 -R_GREEN = 3 -R_BLUE = 4 -R_CYAN = 5 -R_PURPLE = 6 -R_YELLOW = 7 -R_GRAY = 8 - -### ... and some point-styles - -### -PLOT_HEIGHT = 600 -PLOT_WIDTH = 1150 - - -#SVG_COLORS = ('black', 'darkblue', 'blue', 'deepskyblue', 'firebrick','maroon','crimson') -#SVG_COLORS = ('cyan','dodgerblue','mediumpurple', 'fuchsia', 'red','gold','gray') -SVG_COLORS = ('cyan','dodgerblue','mediumpurple','forestgreen', 'lightgreen','gold','gray') -# dupe,parentchild,sibpair,halfsib,parents,unrel,unkn -#('orange', 'red', 'green', 'chartreuse', 'blue', 'purple', 'gray') - -OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Rel_Mean)\tSdev(Rel_Mean)\tMean(Rel_Sdev)\tSdev(Rel_Sdev)\n' -OUTLIERS_HEADER_list = ['Mean','Sdev','ZMean','ZSdev','FID1','IID1','FID2','IID2', -'RGMean_M','RGMean_SD','RGSD_M','RGSD_SD'] -TABLE_HEADER='fid1 iid1\tfid2 iid2\tmean\tsdev\tzmean\tzsdev\tgeno\trelcode\n' - - -### Relationship codes, text, and lookups/mappings -N_RELATIONSHIP_TYPES = 7 -REL_DUPE, REL_PARENTCHILD, REL_SIBS, REL_HALFSIBS, REL_RELATED, REL_UNRELATED, REL_UNKNOWN = range(N_RELATIONSHIP_TYPES) -REL_LOOKUP = { - REL_DUPE: ('dupe', R_BLUE, 1), - REL_PARENTCHILD: ('parentchild', R_YELLOW, 1), - REL_SIBS: ('sibpairs', R_RED, 1), - REL_HALFSIBS: ('halfsibs', R_GREEN, 1), - REL_RELATED: ('parents', R_PURPLE, 1), - REL_UNRELATED: ('unrelated', R_CYAN, 1), - REL_UNKNOWN: ('unknown', R_GRAY, 1), - } -OUTLIER_STDEVS = { - REL_DUPE: 2, - REL_PARENTCHILD: 2, - REL_SIBS: 2, - REL_HALFSIBS: 2, - REL_RELATED: 2, - REL_UNRELATED: 3, - REL_UNKNOWN: 2, - } -# note now Z can be passed in - -REL_STATES = [REL_LOOKUP[r][0] for r in range(N_RELATIONSHIP_TYPES)] -REL_COLORS = SVG_COLORS -REL_POINTS = [REL_LOOKUP[r][2] for r in range(N_RELATIONSHIP_TYPES)] - -DEFAULT_MAX_SAMPLE_SIZE = 10000 - -REF_COUNT_HOM1 = 3 -REF_COUNT_HET = 2 -REF_COUNT_HOM2 = 1 -MISSING = 0 -MAX_SHOW_ROWS = 100 # framingham has millions - delays showing output page - so truncate and explain -MARKER_PAIRS_PER_SECOND_SLOW = 15000000.0 -MARKER_PAIRS_PER_SECOND_FAST = 70000000.0 - - -galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> -<title></title> -<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> -</head> -<body> -<div class="document"> -""" - - -SVG_HEADER = '''<?xml version="1.0" standalone="no"?> -<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.2//EN" "http://www.w3.org/Graphics/SVG/1.2/DTD/svg12.dtd"> - -<svg width="1280" height="800" - xmlns="http://www.w3.org/2000/svg" version="1.2" - xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()"> - - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/checkbox_and_radiobutton.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/helper_functions.js"/> - <script type="text/ecmascript" xlink:href="/static/scripts/tools/rgenetics/timer.js"/> - <script type="text/ecmascript"> - <![CDATA[ - var checkBoxes = new Array(); - var radioGroupBandwidth; - var colours = ['%s','%s','%s','%s','%s','%s','%s']; - function init() { - var style = {"font-family":"Arial,Helvetica", "fill":"black", "font-size":12}; - var dist = 12; - var yOffset = 4; - - //A checkBox for each relationship type dupe,parentchild,sibpair,halfsib,parents,unrel,unkn - checkBoxes["dupe"] = new checkBox("dupe","checkboxes",20,40,"cbRect","cbCross",true,"Duplicate",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["parentchild"] = new checkBox("parentchild","checkboxes",20,60,"cbRect","cbCross",true,"Parent-Child",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["sibpairs"] = new checkBox("sibpairs","checkboxes",20,80,"cbRect","cbCross",true,"Sib-pairs",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["halfsibs"] = new checkBox("halfsibs","checkboxes",20,100,"cbRect","cbCross",true,"Half-sibs",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["parents"] = new checkBox("parents","checkboxes",20,120,"cbRect","cbCross",true,"Parents",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["unrelated"] = new checkBox("unrelated","checkboxes",20,140,"cbRect","cbCross",true,"Unrelated",style,dist,yOffset,undefined,hideShowLayer); - checkBoxes["unknown"] = new checkBox("unknown","checkboxes",20,160,"cbRect","cbCross",true,"Unknown",style,dist,yOffset,undefined,hideShowLayer); - - } - - function hideShowLayer(id, status, label) { - var vis = "hidden"; - if (status) { - vis = "visible"; - } - document.getElementById(id).setAttributeNS(null, 'visibility', vis); - } - - function showBTT(evt, rel, mm, dm, md, dd, n, mg, dg, lg, hg) { - var x = parseInt(evt.pageX)-250; - var y = parseInt(evt.pageY)-110; - switch(rel) { - case 0: - fill = colours[rel]; - relt = "dupe"; - break; - case 1: - fill = colours[rel]; - relt = "parentchild"; - break; - case 2: - fill = colours[rel]; - relt = "sibpairs"; - break; - case 3: - fill = colours[rel]; - relt = "halfsibs"; - break; - case 4: - fill = colours[rel]; - relt = "parents"; - break; - case 5: - fill = colours[rel]; - relt = "unrelated"; - break; - case 6: - fill = colours[rel]; - relt = "unknown"; - break; - default: - fill = "cyan"; - relt = "ERROR_CODE: "+rel; - } - - document.getElementById("btRel").textContent = "GROUP: "+relt; - document.getElementById("btMean").textContent = "mean="+mm+" +/- "+dm; - document.getElementById("btSdev").textContent = "sdev="+dm+" +/- "+dd; - document.getElementById("btPair").textContent = "npairs="+n; - document.getElementById("btGeno").textContent = "ngenos="+mg+" +/- "+dg+" (min="+lg+", max="+hg+")"; - document.getElementById("btHead").setAttribute('fill', fill); - - var tt = document.getElementById("btTip"); - tt.setAttribute("transform", "translate("+x+","+y+")"); - tt.setAttribute('visibility', 'visible'); - } - - function showOTT(evt, rel, s1, s2, mean, sdev, ngeno, rmean, rsdev) { - var x = parseInt(evt.pageX)-150; - var y = parseInt(evt.pageY)-180; - - switch(rel) { - case 0: - fill = colours[rel]; - relt = "dupe"; - break; - case 1: - fill = colours[rel]; - relt = "parentchild"; - break; - case 2: - fill = colours[rel]; - relt = "sibpairs"; - break; - case 3: - fill = colours[rel]; - relt = "halfsibs"; - break; - case 4: - fill = colours[rel]; - relt = "parents"; - break; - case 5: - fill = colours[rel]; - relt = "unrelated"; - break; - case 6: - fill = colours[rel]; - relt = "unknown"; - break; - default: - fill = "cyan"; - relt = "ERROR_CODE: "+rel; - } - - document.getElementById("otRel").textContent = "PAIR: "+relt; - document.getElementById("otS1").textContent = "s1="+s1; - document.getElementById("otS2").textContent = "s2="+s2; - document.getElementById("otMean").textContent = "mean="+mean; - document.getElementById("otSdev").textContent = "sdev="+sdev; - document.getElementById("otGeno").textContent = "ngenos="+ngeno; - document.getElementById("otRmean").textContent = "relmean="+rmean; - document.getElementById("otRsdev").textContent = "relsdev="+rsdev; - document.getElementById("otHead").setAttribute('fill', fill); - - var tt = document.getElementById("otTip"); - tt.setAttribute("transform", "translate("+x+","+y+")"); - tt.setAttribute('visibility', 'visible'); - } - - function hideBTT(evt) { - document.getElementById("btTip").setAttributeNS(null, 'visibility', 'hidden'); 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stroke:none" font-size="12" font-family="Arial" transform="translate(25,25)"> - <rect width="160" height="270" style="fill:none; stroke:black; shape-rendering:crispEdges" /> - <text x="5" y="20" style="fill:black; stroke:none;" font-size="13" font-weight="bold">Given Pair Relationship</text> - <rect x="120" y="35" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="55" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="75" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="95" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="115" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="135" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <rect x="120" y="155" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> - <text x="15" y="195" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore gt 15</text> - <circle cx="125" cy="192" r="6" style="stroke:red; fill:gold; fill-opacity:1.0; stroke-width:1;"/> - <text x="15" y="215" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore 4 to 15</text> - <circle cx="125" cy="212" r="3" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/> - <text x="15" y="235" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore lt 4</text> - <circle cx="125" cy="232" r="2" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/> - <g id="checkboxes"> - </g> - </g> - - - <g style='fill:black; stroke:none' font-size="17" font-family="Arial"> -  - <text x="480" y="660">Mean Alleles Shared</text> - <text x="0" y="630" >1.0</text> - <text x="277" y="630" >1.25</text> - <text x="564" y="630" >1.5</text> - <text x="842" y="630" >1.75</text> - <text x="1140" y="630" >2.0</text> - </g> - - <g transform="rotate(270)" style="fill:black; stroke:none" font-size="17" font-family="Arial"> -  - <text x="-350" y="-40">SD Alleles Shared</text> - <text x="-20" y="-10" >1.0</text> - <text x="-165" y="-10" >0.75</text> - <text x="-310" y="-10" >0.5</text> - <text x="-455" y="-10" >0.25</text> - <text x="-600" y="-10" >0.0</text> - </g> - - -<g style="fill:black; stroke:none" font-size="18" font-family="Arial"> - <text x="425" y="-30">%s</text> -</g> - - -''' - -SVG_FOOTER = ''' - -</g> -<g id="btTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial"> - <rect width="250" height="110" style="fill:silver" rx="2" ry="2"/> - <rect id="btHead" width="250" height="20" rx="2" ry="2" /> - <text id="btRel" y="14" x="85">unrelated</text> - <text id="btMean" y="40" x="4">mean=1.5 +/- 0.04</text> - <text id="btSdev" y="60" x="4">sdev=0.7 +/- 0.03</text> - <text id="btPair" y="80" x="4">npairs=1152</text> - <text id="btGeno" y="100" x="4">ngenos=4783 +/- 24 (min=1000, max=5000)</text> -</g> - -<g id="otTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial"> - <rect width="150" height="180" style="fill:silver" rx="2" ry="2"/> - <rect id="otHead" width="150" height="20" rx="2" ry="2" /> - <text id="otRel" y="14" x="40">sibpairs</text> - <text id="otS1" y="40" x="4">s1=fid1,iid1</text> - <text id="otS2" y="60" x="4">s2=fid2,iid2</text> - <text id="otMean" y="80" x="4">mean=1.82</text> - <text id="otSdev" y="100" x="4">sdev=0.7</text> - <text id="otGeno" y="120" x="4">ngeno=4487</text> - <text id="otRmean" y="140" x="4">relmean=1.85</text> - <text id="otRsdev" y="160" x="4">relsdev=0.65</text> -</g> -</svg> -''' - -OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Mean)\tSdev(Mean)\tMean(Sdev)\tSdev(Sdev)\n' - -DEFAULT_MAX_SAMPLE_SIZE = 5000 - -REF_COUNT_HOM1 = 3 -REF_COUNT_HET = 2 -REF_COUNT_HOM2 = 1 -MISSING = 0 - -MARKER_PAIRS_PER_SECOND_SLOW = 15000000 -MARKER_PAIRS_PER_SECOND_FAST = 70000000 - -POLYGONS = { - REL_UNRELATED: ((1.360, 0.655), (1.385, 0.730), (1.620, 0.575), (1.610, 0.505)), - REL_HALFSIBS: ((1.630, 0.500), (1.630, 0.550), (1.648, 0.540), (1.648, 0.490)), - REL_SIBS: ((1.660, 0.510), (1.665, 0.560), (1.820, 0.410), (1.820, 0.390)), - REL_PARENTCHILD: ((1.650, 0.470), (1.650, 0.490), (1.750, 0.440), (1.750, 0.420)), - REL_DUPE: ((1.970, 0.000), (1.970, 0.150), (2.000, 0.150), (2.000, 0.000)), - } - -def distance(point1, point2): - """ Calculate the distance between two points - """ - (x1,y1) = [float(d) for d in point1] - (x2,y2) = [float(d) for d in point2] - dx = abs(x1 - x2) - dy = abs(y1 - y2) - return math.sqrt(dx**2 + dy**2) - -def point_inside_polygon(x, y, poly): - """ Determine if a point (x,y) is inside a given polygon or not - poly is a list of (x,y) pairs. - - Taken from: http://www.ariel.com.au/a/python-point-int-poly.html - """ - - n = len(poly) - inside = False - - p1x,p1y = poly[0] - for i in range(n+1): - p2x,p2y = poly[i % n] - if y > min(p1y,p2y): - if y <= max(p1y,p2y): - if x <= max(p1x,p2x): - if p1y != p2y: - xinters = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x - if p1x == p2x or x <= xinters: - inside = not inside - p1x,p1y = p2x,p2y - return inside - -def readMap(pedfile): - """ - """ - mapfile = pedfile.replace('.ped', '.map') - marker_list = [] - if os.path.exists(mapfile): - print 'readMap: %s' % (mapfile) - fh = file(mapfile, 'r') - for line in fh: - marker_list.append(line.strip().split()) - fh.close() - print 'readMap: %s markers' % (len(marker_list)) - return marker_list - -def calcMeanSD(useme): - """ - A numerically stable algorithm is given below. It also computes the mean. - This algorithm is due to Knuth,[1] who cites Welford.[2] - n = 0 - mean = 0 - M2 = 0 - - foreach x in data: - n = n + 1 - delta = x - mean - mean = mean + delta/n - M2 = M2 + delta*(x - mean) // This expression uses the new value of mean - end for - - variance_n = M2/n - variance = M2/(n - 1) - """ - mean = 0.0 - M2 = 0.0 - sd = 0.0 - n = len(useme) - if n > 1: - for i,x in enumerate(useme): - delta = x - mean - mean = mean + delta/(i+1) # knuth uses n+=1 at start - M2 = M2 + delta*(x - mean) # This expression uses the new value of mean - variance = M2/(n-1) # assume is sample so lose 1 DOF - sd = pow(variance,0.5) - return mean,sd - - -def doIBSpy(inpath='',basename='',outdir=None,logf=None, - nrsSamples=10000,title='title',pdftoo=0,Zcutoff=2.0): - #def doIBS(pedName, title, nrsSamples=None, pdftoo=False): - """ started with snpmatrix but GRR uses actual IBS counts and sd's - """ - repOut = [] # text strings to add to the html display - refallele = {} - tblf = '%s_table.xls' % (title) - tbl = file(os.path.join(outdir,tblf), 'w') - tbl.write(TABLE_HEADER) - svgf = '%s.svg' % (title) - svg = file(os.path.join(outdir,svgf), 'w') - - bedname = '%s.bed' % (inpath) - pedname = '%s.ped' % (inpath) - print 'pedname',pedname - if os.path.exists(bedname): - ped = plinkbinJZ.BPed(inpath) - ped.parse(quick=True) - elif os.path.exists(pedname): - ped = plinkbinJZ.LPed(inpath) - ped.parse() - else: - print >> sys.stdout, '## doIBSpy problem - cannot open %s or %s - cannot run' % (bedname,pedname) - nMarkers = len(ped._markers) - if nMarkers < 5: - print sys.stderr, '### ERROR - %d is too few markers for reliable estimation in %s - terminating' % (nMarkers,PROGNAME) - sys.exit(1) - nSubjects = len(ped._subjects) - nrsSamples = min(nMarkers, nrsSamples) - if opts and opts.use_mito: - markers = range(nMarkers) - nrsSamples = min(len(markers), nrsSamples) - sampleIndexes = sorted(random.sample(markers, nrsSamples)) - else: - autosomals = ped.autosomal_indices() - nrsSamples = min(len(autosomals), nrsSamples) - sampleIndexes = sorted(random.sample(autosomals, nrsSamples)) - - print '' - print 'Getting random.sample of %s from %s total' % (nrsSamples, nMarkers) - npairs = (nSubjects*(nSubjects-1))/2 # total rows in table - newfiles=[svgf,tblf] - explanations = ['rgGRR Plot (requires SVG)','Mean by SD alleles shared - %d rows' % npairs] - # these go with the output file links in the html file - s = 'Reading genotypes for %s subjects and %s markers\n' % (nSubjects, nrsSamples) - logf.write(s) - minUsegenos = nrsSamples/2 # must have half? - nGenotypes = nSubjects*nrsSamples - stime = time.time() - emptyRows = set() - genos = numpy.zeros((nSubjects, nrsSamples), dtype=int) - for s in xrange(nSubjects): - nValid = 0 - #getGenotypesByIndices(self, s, mlist, format) - genos[s] = ped.getGenotypesByIndices(s, sampleIndexes, format='ref') - nValid = sum([1 for g in genos[s] if g]) - if not nValid: - emptyRows.add(s) - sub = ped.getSubject(s) - print 'All missing for row %d (%s)' % (s, sub) - logf.write('All missing for row %d (%s)\n' % (s, sub)) - rtime = time.time() - stime - if verbose: - print '@@Read %s genotypes in %s seconds' % (nGenotypes, rtime) - - - ### Now the expensive part. For each pair of subjects, we get the mean number - ### and standard deviation of shared alleles over all of the markers where both - ### subjects have a known genotype. Identical subjects should have mean shared - ### alleles very close to 2.0 with a standard deviation very close to 0.0. - tot = nSubjects*(nSubjects-1)/2 - nprog = tot/10 - nMarkerpairs = tot * nrsSamples - estimatedTimeSlow = nMarkerpairs/MARKER_PAIRS_PER_SECOND_SLOW - estimatedTimeFast = nMarkerpairs/MARKER_PAIRS_PER_SECOND_FAST - - pairs = [] - pair_data = {} - means = [] ## Mean IBS for each pair - ngenoL = [] ## Count of comparable genotypes for each pair - sdevs = [] ## Standard dev for each pair - rels = [] ## A relationship code for each pair - zmeans = [0.0 for x in xrange(tot)] ## zmean score for each pair for the relgroup - zstds = [0.0 for x in xrange(tot)] ## zstd score for each pair for the relgrp - skip = set() - ndone = 0 ## How many have been done so far - - logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog)) - logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow)) - - t1sum = 0 - t2sum = 0 - t3sum = 0 - now = time.time() - scache = {} - _founder_cache = {} - C_CODE = """ - #include "math.h" - int i; - int sumibs = 0; - int ssqibs = 0; - int ngeno = 0; - float mean = 0; - float M2 = 0; - float delta = 0; - float sdev=0; - float variance=0; - for (i=0; i<nrsSamples; i++) { - int a1 = g1[i]; - int a2 = g2[i]; - if (a1 != 0 && a2 != 0) { - ngeno += 1; - int shared = 2-abs(a1-a2); - delta = shared - mean; - mean = mean + delta/ngeno; - M2 += delta*(shared-mean); - // yes that second time, the updated mean is used see calcmeansd above; - //printf("%d %d %d %d %d %d\\n", i, a1, a2, ngeno, shared, squared); - } - } - if (ngeno > 1) { - variance = M2/(ngeno-1); - sdev = sqrt(variance); - //printf("OK: %d %3.2f %3.2f\\n", ngeno, mean, sdev); - } - //printf("%d %d %d %1.2f %1.2f\\n", ngeno, sumibs, ssqibs, mean, sdev); - result[0] = ngeno; - result[1] = mean; - result[2] = sdev; - return_val = ngeno; - """ - started = time.time() - for s1 in xrange(nSubjects): - if s1 in emptyRows: - continue - (fid1,iid1,did1,mid1,sex1,phe1,iid1,d_sid1,m_sid1) = scache.setdefault(s1, ped.getSubject(s1)) - - isFounder1 = _founder_cache.setdefault(s1, (did1==mid1)) - g1 = genos[s1] - - for s2 in xrange(s1+1, nSubjects): - if s2 in emptyRows: - continue - if nprog and ndone % nprog == 0 and ndone > 1: - dur = time.time() - started - pct = float(ndone)/tot*100.0 - logf.write('%f sec at pair %d of %d (%3.2f%%): %f marker*pairs/sec\n' % (dur, ndone, tot, pct, ndone/dur*nrsSamples)) - t1s = time.time() - - (fid2,iid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache.setdefault(s2, ped.getSubject(s2)) - - g2 = genos[s2] - isFounder2 = _founder_cache.setdefault(s2, (did2==mid2)) - - # Determine the relationship for this pair - relcode = REL_UNKNOWN - if (fid2 == fid1): - if iid1 == iid2: - relcode = REL_DUPE - elif (did2 == did1) and (mid2 == mid1) and did1 != mid1: - relcode = REL_SIBS - elif (iid1 == mid2) or (iid1 == did2) or (iid2 == mid1) or (iid2 == did1): - relcode = REL_PARENTCHILD - elif (str(did1) != '0' and (did2 == did1)) or (str(mid1) != '0' and (mid2 == mid1)): - relcode = REL_HALFSIBS - else: - # People in the same family should be marked as some other - # form of related. In general, these people will have a - # pretty random spread of similarity. This distinction is - # probably not very useful most of the time - relcode = REL_RELATED - else: - ### Different families - relcode = REL_UNRELATED - - t1e = time.time() - t1sum += t1e-t1s - - - ### Calculate sum(2-abs(a1-a2)) and sum((2-abs(a1-a2))**2) and count - ### the number of contributing genotypes. These values are not actually - ### calculated here, but instead are looked up in a table for speed. - ### FIXME: This is still too slow ... - result = [0.0, 0.0, 0.0] - ngeno = weave.inline(C_CODE, ['g1', 'g2', 'nrsSamples', 'result']) - if ngeno >= minUsegenos: - _, mean, sdev = result - means.append(mean) - sdevs.append(sdev) - ngenoL.append(ngeno) - pairs.append((s1, s2)) - rels.append(relcode) - else: - skip.add(ndone) # signal no comparable genotypes for this pair - ndone += 1 - t2e = time.time() - t2sum += t2e-t1e - t3e = time.time() - t3sum += t3e-t2e - - logme = [ 'T1: %s' % (t1sum), 'T2: %s' % (t2sum), 'T3: %s' % (t3sum),'TOT: %s' % (t3e-now), - '%s pairs with no (or not enough) comparable genotypes (%3.1f%%)' % (len(skip), - float(len(skip))/float(tot)*100)] - logf.write('%s\n' % '\t'.join(logme)) - ### Calculate mean and standard deviation of scores on a per relationship - ### type basis, allowing us to flag outliers for each particular relationship - ### type - relstats = {} - relCounts = {} - outlierFiles = {} - for relCode, relInfo in REL_LOOKUP.items(): - relName, relColor, relStyle = relInfo - useme = [means[x] for x in xrange(len(means)) if rels[x] == relCode] - relCounts[relCode] = len(useme) - mm = scipy.mean(useme) - ms = scipy.std(useme) - useme = [sdevs[x] for x in xrange(len(sdevs)) if rels[x] == relCode] - sm = scipy.mean(useme) - ss = scipy.std(useme) - relstats[relCode] = {'sd':(sm,ss), 'mean':(mm,ms)} - logf.write('Relstate %s: mean(mean)=%3.2f sdev(mean)=%3.2f, mean(sdev)=%3.2f sdev(sdev)=%3.2f\n' % (relName, mm, ms, sm, ss)) - - ### now fake z scores for each subject like abecasis recommends max(|zmu|,|zsd|) - ### within each group, for each pair, z=(groupmean-pairmean)/groupsd - available = len(means) - logf.write('%d pairs are available of %d\n' % (available, tot)) - ### s = '\nOutliers:\nrelationship\tzmean\tzsd\tped1\tped2\tmean\tsd\trmeanmean\trmeansd\trsdmean\trsdsd\n' - ### logf.write(s) - pairnum = 0 - offset = 0 - nOutliers = 0 - cexs = [] - outlierRecords = dict([(r, []) for r in range(N_RELATIONSHIP_TYPES)]) - zsdmax = 0 - for s1 in range(nSubjects): - if s1 in emptyRows: - continue - (fid1,iid1,did1,mid1,sex1,aff1,ok1,d_sid1,m_sid1) = scache[s1] - for s2 in range(s1+1, nSubjects): - if s2 in emptyRows: - continue - if pairnum not in skip: - ### Get group stats for this relationship - (fid2,iid2,did2,mid2,sex2,aff2,ok2,d_sid2,m_sid2) = scache[s2] - try: - r = rels[offset] - except IndexError: - logf.write('###OOPS offset %d available %d pairnum %d len(rels) %d', offset, available, pairnum, len(rels)) - rmm,rmd = relstats[r]['mean'] # group mean, group meansd alleles shared - rdm,rdd = relstats[r]['sd'] # group sdmean, group sdsd alleles shared - - try: - zsd = (sdevs[offset] - rdm)/rdd # distance from group mean in group sd units - except: - zsd = 1 - if abs(zsd) > zsdmax: - zsdmax = zsd # keep for sort scaling - try: - zmean = (means[offset] - rmm)/rmd # distance from group mean - except: - zmean = 1 - zmeans[offset] = zmean - zstds[offset] = zsd - pid=(s1,s2) - zrad = max(zsd,zmean) - if zrad < 4: - zrad = 2 - elif 4 < zrad < 15: - zrad = 3 # to 9 - else: # > 15 6=24+ - zrad=zrad/4 - zrad = min(zrad,6) # scale limit - zrad = max(2,max(zsd,zmean)) # as > 2, z grows - pair_data[pid] = (zmean,zsd,r,zrad) - if max(zsd,zmean) > Zcutoff: # is potentially interesting - mean = means[offset] - sdev = sdevs[offset] - outlierRecords[r].append((mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd)) - nOutliers += 1 - tbl.write('%s_%s\t%s_%s\t%f\t%f\t%f\t%f\t%d\t%s\n' % \ - (fid1, iid1, fid2, iid2, mean, sdev, zmean,zsd, ngeno, relcode)) - offset += 1 - pairnum += 1 - logf.write( 'Outliers: %s\n' % (nOutliers)) - - ### Write outlier files for each relationship type - repOut.append('<h2>Outliers in tab delimited files linked above are also listed below</h2>') - lzsd = round(numpy.log10(zsdmax)) + 1 - scalefactor = 10**lzsd - for relCode, relInfo in REL_LOOKUP.items(): - relName, _, _ = relInfo - outliers = outlierRecords[relCode] - if not outliers: - continue - outliers = [(scalefactor*int(abs(x[3]))+ int(abs(x[2])),x) for x in outliers] # decorate - outliers.sort() - logf.write('### outliers after decorated sort=%s' % outliers) - outliers.reverse() # largest deviation first - logf.write('### outliers after decorated sort=%s' % outliers) - outliers = [x[1] for x in outliers] # undecorate - nrows = len(outliers) - truncated = 0 - if nrows > MAX_SHOW_ROWS: - s = '<h3>%s outlying pairs (top %d of %d) from %s</h3><table border="0" cellpadding="3">' % (relName, - MAX_SHOW_ROWS,nrows,title) - truncated = nrows - MAX_SHOW_ROWS - else: - s = '<h3>%s outlying pairs (n=%d) from %s</h3><table border="0" cellpadding="3">' % (relName,nrows,title) - repOut.append(s) - fhname = '%s_rgGRR_%s_outliers.xls' % (title, relName) - fhpath = os.path.join(outdir,fhname) - fh = open(fhpath, 'w') - newfiles.append(fhname) - explanations.append('%s Outlier Pairs %s, N=%d, Cutoff SD=%f' % (relName,title,len(outliers),Zcutoff)) - fh.write(OUTLIERS_HEADER) - s = ''.join(['<th>%s</th>' % x for x in OUTLIERS_HEADER_list]) - repOut.append('<tr align="center">%s</tr>' % s) - for n,rec in enumerate(outliers): - #(mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd) = rec - fh.write('%f\t%f\t%f\t%f\t%s\t%s\t%s\t%s\t%f\t%f\t%f\t%f\n' % tuple(rec)) - # (mean, sdev, zmean, zsd, fid1, iid1, fid2, iid2, rmm, rmd, rdm, rdd)) - s = '''<td>%f</td><td>%f</td><td>%f</td><td>%f</td><td>%s</td><td>%s</td> - <td>%s</td><td>%s</td><td>%f</td><td>%f</td><td>%f</td><td>%f</td>''' % tuple(rec) - if n < MAX_SHOW_ROWS: - repOut.append('<tr align="center">%s</tr>' % s) - if truncated > 0: - repOut.append('<H2>WARNING: %d rows truncated - see outlier file for all %d rows</H2>' % (truncated, - nrows)) - fh.close() - repOut.append('</table><p>') - - ### Now, draw the plot in jpeg and svg formats, and optionally in the PDF format - ### if requested - logf.write('Plotting ...') - pointColors = [REL_COLORS[rel] for rel in rels] - pointStyles = [REL_POINTS[rel] for rel in rels] - - mainTitle = '%s (%s subjects, %d snp)' % (title, nSubjects, nrsSamples) - svg.write(SVG_HEADER % (SVG_COLORS[0],SVG_COLORS[1],SVG_COLORS[2],SVG_COLORS[3],SVG_COLORS[4], - SVG_COLORS[5],SVG_COLORS[6],SVG_COLORS[0],SVG_COLORS[0],SVG_COLORS[1],SVG_COLORS[1], - SVG_COLORS[2],SVG_COLORS[2],SVG_COLORS[3],SVG_COLORS[3],SVG_COLORS[4],SVG_COLORS[4], - SVG_COLORS[5],SVG_COLORS[5],SVG_COLORS[6],SVG_COLORS[6],mainTitle)) - #rpy.r.jpeg(filename='%s.jpg' % (title), width=1600, height=1200, pointsize=12, quality=100, bg='white') - #rpy.r.par(mai=(1,1,1,0.5)) - #rpy.r('par(xaxs="i",yaxs="i")') - #rpy.r.plot(means, sdevs, main=mainTitle, ylab=Y_AXIS_LABEL, xlab=X_AXIS_LABEL, cex=cexs, col=pointColors, pch=pointStyles, xlim=(0,2), ylim=(0,2)) - #rpy.r.legend(LEGEND_ALIGN, legend=REL_STATES, pch=REL_POINTS, col=REL_COLORS, title=LEGEND_TITLE) - #rpy.r.grid(nx=10, ny=10, col='lightgray', lty='dotted') - #rpy.r.dev_off() - - ### We will now go through each relationship type to partition plot points - ### into "bulk" and "outlier" groups. Bulk points will represent common - ### mean/sdev pairs and will cover the majority of the points in the plot -- - ### they will use generic tooltip informtion about all of the pairs - ### represented by that point. "Outlier" points will be uncommon pairs, - ### with very specific information in their tooltips. It would be nice to - ### keep hte total number of plotted points in the SVG representation to - ### ~10000 (certainly less than 100000?) - pointMap = {} - orderedRels = [y[1] for y in reversed(sorted([(relCounts.get(x, 0),x) for x in REL_LOOKUP.keys()]))] - # do we really want this? I want out of zone points last and big - for relCode in orderedRels: - svgColor = SVG_COLORS[relCode] - relName, relColor, relStyle = REL_LOOKUP[relCode] - svg.write('<g id="%s" style="stroke:%s; fill:%s; fill-opacity:1.0; stroke-width:1;" cursor="pointer">\n' % (relName, svgColor, svgColor)) - pMap = pointMap.setdefault(relCode, {}) - nPoints = 0 - rpairs=[] - rgenos=[] - rmeans=[] - rsdevs=[] - rz = [] - for x,rel in enumerate(rels): # all pairs - if rel == relCode: - s1,s2 = pairs[x] - pid=(s1,s2) - zmean,zsd,r,zrad = pair_data[pid][:4] - rpairs.append(pairs[x]) - rgenos.append(ngenoL[x]) - rmeans.append(means[x]) - rsdevs.append(sdevs[x]) - rz.append(zrad) - ### Now add the svg point group for this relationship to the svg file - for x in range(len(rmeans)): - svgX = '%d' % ((rmeans[x] - 1.0) * PLOT_WIDTH) # changed so mean scale is 1-2 - svgY = '%d' % (PLOT_HEIGHT - (rsdevs[x] * PLOT_HEIGHT)) # changed so sd scale is 0-1 - s1, s2 = rpairs[x] - (fid1,uid1,did1,mid1,sex1,phe1,iid1,d_sid1,m_sid1) = scache[s1] - (fid2,uid2,did2,mid2,sex2,phe2,iid2,d_sid2,m_sid2) = scache[s2] - ngenos = rgenos[x] - nPoints += 1 - point = pMap.setdefault((svgX, svgY), []) - point.append((rmeans[x], rsdevs[x], fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, ngenos,rz[x])) - for (svgX, svgY) in pMap: - points = pMap[(svgX, svgY)] - svgX = int(svgX) - svgY = int(svgY) - if len(points) > 1: - mmean,dmean = calcMeanSD([p[0] for p in points]) - msdev,dsdev = calcMeanSD([p[1] for p in points]) - mgeno,dgeno = calcMeanSD([p[-1] for p in points]) - mingeno = min([p[-1] for p in points]) - maxgeno = max([p[-1] for p in points]) - svg.write("""<circle cx="%d" cy="%d" r="2" - onmouseover="showBTT(evt, %d, %1.2f, %1.2f, %1.2f, %1.2f, %d, %d, %d, %d, %d)" - onmouseout="hideBTT(evt)" />\n""" % (svgX, svgY, relCode, mmean, dmean, msdev, dsdev, len(points), mgeno, dgeno, mingeno, maxgeno)) - else: - mean, sdev, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, ngenos, zrad = points[0][:12] - rmean = float(relstats[relCode]['mean'][0]) - rsdev = float(relstats[relCode]['sd'][0]) - if zrad < 4: - zrad = 2 - elif 4 < zrad < 9: - zrad = 3 # to 9 - else: # > 9 5=15+ - zrad=zrad/3 - zrad = min(zrad,5) # scale limit - if zrad <= 3: - svg.write('<circle cx="%d" cy="%d" r="%s" onmouseover="showOTT(evt, %d, \'%s,%s,%s,%s\', \'%s,%s,%s,%s\', %1.2f, %1.2f, %s, %1.2f, %1.2f)" onmouseout="hideOTT(evt)" />\n' % (svgX, svgY, zrad, relCode, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, mean, sdev, ngenos, rmean, rsdev)) - else: # highlight pairs a long way from expectation by outlining circle in red - svg.write("""<circle cx="%d" cy="%d" r="%s" style="stroke:red; fill:%s; fill-opacity:1.0; stroke-width:1;" - onmouseover="showOTT(evt, %d, \'%s,%s,%s,%s\', \'%s,%s,%s,%s\', %1.2f, %1.2f, %s, %1.2f, %1.2f)" - onmouseout="hideOTT(evt)" />\n""" % \ - (svgX, svgY, zrad, svgColor, relCode, fid1, iid1, did1, mid1, fid2, iid2, did2, mid2, mean, sdev, ngenos, rmean, rsdev)) - svg.write('</g>\n') - - ### Create a pdf as well if indicated on the command line - ### WARNING! for framingham share, with about 50M pairs, this is a 5.5GB pdf! -## if pdftoo: -## pdfname = '%s.pdf' % (title) -## rpy.r.pdf(pdfname, 6, 6) -## rpy.r.par(mai=(1,1,1,0.5)) -## rpy.r('par(xaxs="i",yaxs="i")') -## rpy.r.plot(means, sdevs, main='%s, %d snp' % (title, nSamples), ylab=Y_AXIS_LABEL, xlab=X_AXIS_LABEL, cex=cexs, col=pointColors, pch=pointStyles, xlim=(0,2), ylim=(0,2)) -## rpy.r.legend(LEGEND_ALIGN, legend=REL_STATES, pch=REL_POINTS, col=REL_COLORS, title=LEGEND_TITLE) -## rpy.r.grid(nx=10, ny=10, col='lightgray', lty='dotted') -## rpy.r.dev_off() - - ### Draw polygons - if showPolygons: - svg.write('<g id="polygons" cursor="pointer">\n') - for rel, poly in POLYGONS.items(): - points = ' '.join(['%s,%s' % ((p[0]-1.0)*float(PLOT_WIDTH), (PLOT_HEIGHT - p[1]*PLOT_HEIGHT)) for p in poly]) - svg.write('<polygon points="%s" fill="transparent" style="stroke:%s; stroke-width:1"/>\n' % (points, SVG_COLORS[rel])) - svg.write('</g>\n') - - - svg.write(SVG_FOOTER) - svg.close() - return newfiles,explanations,repOut - -def doIBS(n=100): - """parse parameters from galaxy - expect 'input pbed path' 'basename' 'outpath' 'title' 'logpath' 'n' - <command interpreter="python"> - rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" - '$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' - </command> - - """ - u="""<command interpreter="python"> - rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" - '$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' - </command>""" - - if len(sys.argv) < 8: - print >> sys.stdout, 'Need pbed inpath, basename, out_htmlname, outpath, title, logpath, nSNP, Zcutoff on command line please' - print >> sys.stdout, u - sys.exit(1) - ts = '%s%s' % (string.punctuation,string.whitespace) - ptran = string.maketrans(ts,'_'*len(ts)) - inpath = sys.argv[1] - basename = sys.argv[2] - outhtml = sys.argv[3] - newfilepath = sys.argv[4] - try: - os.makedirs(newfilepath) - except: - pass - title = sys.argv[5].translate(ptran) - logfname = 'Log_%s.txt' % title - logpath = os.path.join(newfilepath,logfname) # log was a child - make part of html extra_files_path zoo - n = int(sys.argv[6]) - try: - Zcutoff = float(sys.argv[7]) - except: - Zcutoff = 2.0 - try: - os.makedirs(newfilepath) - except: - pass - logf = file(logpath,'w') - newfiles,explanations,repOut = doIBSpy(inpath=inpath,basename=basename,outdir=newfilepath, - logf=logf,nrsSamples=n,title=title,pdftoo=0,Zcutoff=Zcutoff) - logf.close() - logfs = file(logpath,'r').readlines() - lf = file(outhtml,'w') - lf.write(galhtmlprefix % PROGNAME) - # this is a mess. todo clean up - should each datatype have it's own directory? Yes - # probably. Then titles are universal - but userId libraries are separate. - s = '<div>Output from %s run at %s<br>\n' % (PROGNAME,timenow()) - lf.write('<h4>%s</h4>\n' % s) - fixed = ["'%s'" % x for x in sys.argv] # add quotes just in case - s = 'If you need to rerun this analysis, the command line was\n<pre>%s</pre>\n</div>' % (' '.join(fixed)) - lf.write(s) - #s = """<object data="%s" type="image/svg+xml" width="%d" height="%d"> - # <embed src="%s" type="image/svg+xml" width="%d" height="%d" /> - # </object>""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT,newfiles[0],PLOT_WIDTH,PLOT_HEIGHT) - s = """ <embed src="%s" type="image/svg+xml" width="%d" height="%d" />""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT) - #s = """ <iframe src="%s" type="image/svg+xml" width="%d" height="%d" />""" % (newfiles[0],PLOT_WIDTH,PLOT_HEIGHT) - lf.write(s) - lf.write('<div><h4>Click the links below to save output files and plots</h4><br><ol>\n') - for i in range(len(newfiles)): - if i == 0: - lf.write('<li><a href="%s" type="image/svg+xml" >%s</a></li>\n' % (newfiles[i],explanations[i])) - else: - lf.write('<li><a href="%s">%s</a></li>\n' % (newfiles[i],explanations[i])) - flist = os.listdir(newfilepath) - for fname in flist: - if not fname in newfiles: - lf.write('<li><a href="%s">%s</a></li>\n' % (fname,fname)) - lf.write('</ol></div>') - lf.write('<div>%s</div>' % ('\n'.join(repOut))) # repOut is a list of tables - lf.write('<div><hr><h3>Log from this job (also stored in %s)</h3><pre>%s</pre><hr></div>' % (logfname,'\n'.join(logfs))) - lf.write('</body></html>\n') - lf.close() - logf.close() - -if __name__ == '__main__': - doIBS() - - +""" +# july 2009: Need to see outliers so need to draw them last? +# could use clustering on the zscores to guess real relationships for unrelateds +# but definitely need to draw last +# added MAX_SHOW_ROWS to limit the length of the main report page +# Changes for Galaxy integration +# added more robust knuth method for one pass mean and sd +# no difference really - let's use scipy.mean() and scipy.std() instead... +# fixed labels and changed to .xls for outlier reports so can open in excel +# interesting - with a few hundred subjects, 5k gives good resolution +# and 100k gives better but not by much +# TODO remove non autosomal markers +# TODO it would be best if label had the zmean and zsd as these are what matter for +# outliers rather than the group mean/sd +# mods to rgGRR.py from channing CVS which John Ziniti has rewritten to produce SVG plots +# to make a Galaxy tool - we need the table of mean and SD for interesting pairs, the SVG and the log +# so the result should be an HTML file + +# rgIBS.py +# use a random subset of markers for a quick ibs +# to identify sample dups and closely related subjects +# try snpMatrix and plink and see which one works best for us? +# abecasis grr plots mean*sd for every subject to show clusters +# mods june 23 rml to avoid non-autosomal markers +# we seem to be distinguishing parent-child by gender - 2 clouds! + + +snpMatrix from David Clayton has: +ibs.stats function to calculate the identity-by-state stats of a group of samples +Description +Given a snp.matrix-class or a X.snp.matrix-class object with N samples, calculates some statistics +about the relatedness of every pair of samples within. + +Usage +ibs.stats(x) +8 ibs.stats +Arguments +x a snp.matrix-class or a X.snp.matrix-class object containing N samples +Details +No-calls are excluded from consideration here. +Value +A data.frame containing N(N - 1)/2 rows, where the row names are the sample name pairs separated +by a comma, and the columns are: +Count count of identical calls, exclusing no-calls +Fraction fraction of identical calls comparied to actual calls being made in both samples +Warning +In some applications, it may be preferable to subset a (random) selection of SNPs first - the +calculation +time increases as N(N - 1)M/2 . Typically for N = 800 samples and M = 3000 SNPs, the +calculation time is about 1 minute. A full GWA scan could take hours, and quite unnecessary for +simple applications such as checking for duplicate or related samples. +Note +This is mostly written to find mislabelled and/or duplicate samples. +Illumina indexes their SNPs in alphabetical order so the mitochondria SNPs comes first - for most +purpose it is undesirable to use these SNPs for IBS purposes. +TODO: Worst-case S4 subsetting seems to make 2 copies of a large object, so one might want to +subset before rbind(), etc; a future version of this routine may contain a built-in subsetting facility +""" +import sys,os,time,random,string,copy,optparse + +try: + set +except NameError: + from Sets import Set as set + +from rgutils import timenow,pruneLD,plinke +import plinkbinJZ + + +opts = None +verbose = False + +showPolygons = False + +class NullDevice: + def write(self, s): + pass + +tempstderr = sys.stderr # save +sys.stderr = NullDevice() +# need to avoid blather about deprecation and other strange stuff from scipy +# the current galaxy job runner assumes that +# the job is in error if anything appears on sys.stderr +# grrrrr. James wants to keep it that way instead of using the +# status flag for some strange reason. Presumably he doesn't use R or (in this case, scipy) +import numpy +import scipy +from scipy import weave + + +sys.stderr=tempstderr + + +PROGNAME = os.path.split(sys.argv[0])[-1] +X_AXIS_LABEL = 'Mean Alleles Shared' +Y_AXIS_LABEL = 'SD Alleles Shared' +LEGEND_ALIGN = 'topleft' +LEGEND_TITLE = 'Relationship' +DEFAULT_SYMBOL_SIZE = 1.0 # default symbol size +DEFAULT_SYMBOL_SIZE = 0.5 # default symbol size + +### Some colors for R/rpy +R_BLACK = 1 +R_RED = 2 +R_GREEN = 3 +R_BLUE = 4 +R_CYAN = 5 +R_PURPLE = 6 +R_YELLOW = 7 +R_GRAY = 8 + +### ... and some point-styles + +### +PLOT_HEIGHT = 600 +PLOT_WIDTH = 1150 + + +#SVG_COLORS = ('black', 'darkblue', 'blue', 'deepskyblue', 'firebrick','maroon','crimson') +#SVG_COLORS = ('cyan','dodgerblue','mediumpurple', 'fuchsia', 'red','gold','gray') +SVG_COLORS = ('cyan','dodgerblue','mediumpurple','forestgreen', 'lightgreen','gold','gray') +# dupe,parentchild,sibpair,halfsib,parents,unrel,unkn +#('orange', 'red', 'green', 'chartreuse', 'blue', 'purple', 'gray') + +OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Rel_Mean)\tSdev(Rel_Mean)\tMean(Rel_Sdev)\tSdev(Rel_Sdev)\n' +OUTLIERS_HEADER_list = ['Mean','Sdev','ZMean','ZSdev','FID1','IID1','FID2','IID2', +'RGMean_M','RGMean_SD','RGSD_M','RGSD_SD'] +TABLE_HEADER='fid1 iid1\tfid2 iid2\tmean\tsdev\tzmean\tzsdev\tgeno\trelcode\n' + + +### Relationship codes, text, and lookups/mappings +N_RELATIONSHIP_TYPES = 7 +REL_DUPE, REL_PARENTCHILD, REL_SIBS, REL_HALFSIBS, REL_RELATED, REL_UNRELATED, REL_UNKNOWN = range(N_RELATIONSHIP_TYPES) +REL_LOOKUP = { + REL_DUPE: ('dupe', R_BLUE, 1), + REL_PARENTCHILD: ('parentchild', R_YELLOW, 1), + REL_SIBS: ('sibpairs', R_RED, 1), + REL_HALFSIBS: ('halfsibs', R_GREEN, 1), + REL_RELATED: ('parents', R_PURPLE, 1), + REL_UNRELATED: ('unrelated', R_CYAN, 1), + REL_UNKNOWN: ('unknown', R_GRAY, 1), + } +OUTLIER_STDEVS = { + REL_DUPE: 2, + REL_PARENTCHILD: 2, + REL_SIBS: 2, + REL_HALFSIBS: 2, + REL_RELATED: 2, + REL_UNRELATED: 3, + REL_UNKNOWN: 2, + } +# note now Z can be passed in + +REL_STATES = [REL_LOOKUP[r][0] for r in range(N_RELATIONSHIP_TYPES)] +REL_COLORS = SVG_COLORS +REL_POINTS = [REL_LOOKUP[r][2] for r in range(N_RELATIONSHIP_TYPES)] + +DEFAULT_MAX_SAMPLE_SIZE = 10000 + +REF_COUNT_HOM1 = 3 +REF_COUNT_HET = 2 +REF_COUNT_HOM2 = 1 +MISSING = 0 +MAX_SHOW_ROWS = 100 # framingham has millions - delays showing output page - so truncate and explain +MARKER_PAIRS_PER_SECOND_SLOW = 15000000.0 +MARKER_PAIRS_PER_SECOND_FAST = 70000000.0 + + +galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> +<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +""" + + +SVG_HEADER = '''<?xml version="1.0" standalone="no"?> +<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.2//EN" "http://www.w3.org/Graphics/SVG/1.2/DTD/svg12.dtd"> + +<svg width="1280" height="800" + xmlns="http://www.w3.org/2000/svg" version="1.2" + xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 1280 800" onload="init()"> + + <script type="text/ecmascript" xlink:href="/static/scripts/checkbox_and_radiobutton.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/helper_functions.js"/> + <script type="text/ecmascript" xlink:href="/static/scripts/timer.js"/> + <script type="text/ecmascript"> + <![CDATA[ + var checkBoxes = new Array(); + var radioGroupBandwidth; + var colours = ['%s','%s','%s','%s','%s','%s','%s']; + function init() { + var style = {"font-family":"Arial,Helvetica", "fill":"black", "font-size":12}; + var dist = 12; + var yOffset = 4; + + //A checkBox for each relationship type dupe,parentchild,sibpair,halfsib,parents,unrel,unkn + checkBoxes["dupe"] = new checkBox("dupe","checkboxes",20,40,"cbRect","cbCross",true,"Duplicate",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["parentchild"] = new checkBox("parentchild","checkboxes",20,60,"cbRect","cbCross",true,"Parent-Child",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["sibpairs"] = new checkBox("sibpairs","checkboxes",20,80,"cbRect","cbCross",true,"Sib-pairs",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["halfsibs"] = new checkBox("halfsibs","checkboxes",20,100,"cbRect","cbCross",true,"Half-sibs",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["parents"] = new checkBox("parents","checkboxes",20,120,"cbRect","cbCross",true,"Parents",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["unrelated"] = new checkBox("unrelated","checkboxes",20,140,"cbRect","cbCross",true,"Unrelated",style,dist,yOffset,undefined,hideShowLayer); + checkBoxes["unknown"] = new checkBox("unknown","checkboxes",20,160,"cbRect","cbCross",true,"Unknown",style,dist,yOffset,undefined,hideShowLayer); + + } + + function hideShowLayer(id, status, label) { + var vis = "hidden"; + if (status) { + vis = "visible"; + } + document.getElementById(id).setAttributeNS(null, 'visibility', vis); + } + + function showBTT(evt, rel, mm, dm, md, dd, n, mg, dg, lg, hg) { + var x = parseInt(evt.pageX)-250; + var y = parseInt(evt.pageY)-110; + switch(rel) { + case 0: + fill = colours[rel]; + relt = "dupe"; + break; + case 1: + fill = colours[rel]; + relt = "parentchild"; + break; + case 2: + fill = colours[rel]; + relt = "sibpairs"; + break; + case 3: + fill = colours[rel]; + relt = "halfsibs"; + break; + case 4: + fill = colours[rel]; + relt = "parents"; + break; + case 5: + fill = colours[rel]; + relt = "unrelated"; + break; + case 6: + fill = colours[rel]; + relt = "unknown"; + break; + default: + fill = "cyan"; + relt = "ERROR_CODE: "+rel; + } + + document.getElementById("btRel").textContent = "GROUP: "+relt; + document.getElementById("btMean").textContent = "mean="+mm+" +/- "+dm; + document.getElementById("btSdev").textContent = "sdev="+dm+" +/- "+dd; + document.getElementById("btPair").textContent = "npairs="+n; + document.getElementById("btGeno").textContent = "ngenos="+mg+" +/- "+dg+" (min="+lg+", max="+hg+")"; + document.getElementById("btHead").setAttribute('fill', fill); + + var tt = document.getElementById("btTip"); + tt.setAttribute("transform", "translate("+x+","+y+")"); + tt.setAttribute('visibility', 'visible'); + } + + function showOTT(evt, rel, s1, s2, mean, sdev, ngeno, rmean, rsdev) { + var x = parseInt(evt.pageX)-150; + var y = parseInt(evt.pageY)-180; + + switch(rel) { + case 0: + fill = colours[rel]; + relt = "dupe"; + break; + case 1: + fill = colours[rel]; + relt = "parentchild"; + break; + case 2: + fill = colours[rel]; + relt = "sibpairs"; + break; + case 3: + fill = colours[rel]; + relt = "halfsibs"; + break; + case 4: + fill = colours[rel]; + relt = "parents"; + break; + case 5: + fill = colours[rel]; + relt = "unrelated"; + break; + case 6: + fill = colours[rel]; + relt = "unknown"; + break; + default: + fill = "cyan"; + relt = "ERROR_CODE: "+rel; + } + + document.getElementById("otRel").textContent = "PAIR: "+relt; + document.getElementById("otS1").textContent = "s1="+s1; + document.getElementById("otS2").textContent = "s2="+s2; + document.getElementById("otMean").textContent = "mean="+mean; + document.getElementById("otSdev").textContent = "sdev="+sdev; + document.getElementById("otGeno").textContent = "ngenos="+ngeno; + document.getElementById("otRmean").textContent = "relmean="+rmean; + document.getElementById("otRsdev").textContent = "relsdev="+rsdev; + document.getElementById("otHead").setAttribute('fill', fill); + + var tt = document.getElementById("otTip"); + tt.setAttribute("transform", "translate("+x+","+y+")"); + tt.setAttribute('visibility', 'visible'); + } + + function hideBTT(evt) { + document.getElementById("btTip").setAttributeNS(null, 'visibility', 'hidden'); + } + + function hideOTT(evt) { + document.getElementById("otTip").setAttributeNS(null, 'visibility', 'hidden'); + } + + ]]> + </script> + <defs> +  + <symbol id="cbRect" overflow="visible"> + <rect x="-5" y="-5" width="10" height="10" fill="white" stroke="dimgray" stroke-width="1" cursor="pointer"/> + </symbol> + <symbol id="cbCross" overflow="visible"> + <g pointer-events="none" stroke="black" stroke-width="1"> + <line x1="-3" y1="-3" x2="3" y2="3"/> + <line x1="3" y1="-3" x2="-3" y2="3"/> + </g> + </symbol> + </defs> + +<desc>Developer Works Dynamic Scatter Graph Scaling Example</desc> + + +<g style="stroke-width:1.0; stroke:black; shape-rendering:crispEdges"> +  + <path d="M 100 100 L 1250 100 Z"/> + <path d="M 100 700 L 1250 700 Z"/> + +  + <path d="M 100 100 L 100 700 Z"/> + <path d="M 1250 100 L 1250 700 Z"/> +</g> + +<g transform="translate(100,100)"> + +  + <g style="fill:none; stroke:#dddddd; stroke-width:1; stroke-dasharray:2,2; text-anchor:end; shape-rendering:crispEdges"> + +  + <line x1="125" y1="0" x2="115" y2="600" /> + <line x1="230" y1="0" x2="230" y2="600" /> + <line x1="345" y1="0" x2="345" y2="600" /> + <line x1="460" y1="0" x2="460" y2="600" /> + <line x1="575" y1="0" x2="575" y2="600" style="stroke-dasharray:none;" /> + <line x1="690" y1="0" x2="690" y2="600" /> + <line x1="805" y1="0" x2="805" y2="600" /> + <line x1="920" y1="0" x2="920" y2="600" /> + <line x1="1035" y1="0" x2="1035" y2="600" /> + +  + <line x1="0" y1="60" x2="1150" y2="60" /> + <line x1="0" y1="120" x2="1150" y2="120" /> + <line x1="0" y1="180" x2="1150" y2="180" /> + <line x1="0" y1="240" x2="1150" y2="240" /> + <line x1="0" y1="300" x2="1150" y2="300" style="stroke-dasharray:none;" /> + <line x1="0" y1="360" x2="1150" y2="360" /> + <line x1="0" y1="420" x2="1150" y2="420" /> + <line x1="0" y1="480" x2="1150" y2="480" /> + <line x1="0" y1="540" x2="1150" y2="540" /> + </g> + +  + <g style="fill:black; stroke:none" font-size="12" font-family="Arial" transform="translate(25,25)"> + <rect width="160" height="270" style="fill:none; stroke:black; shape-rendering:crispEdges" /> + <text x="5" y="20" style="fill:black; stroke:none;" font-size="13" font-weight="bold">Given Pair Relationship</text> + <rect x="120" y="35" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="55" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="75" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="95" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="115" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="135" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <rect x="120" y="155" width="10" height="10" fill="%s" stroke="%s" stroke-width="1" cursor="pointer"/> + <text x="15" y="195" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore gt 15</text> + <circle cx="125" cy="192" r="6" style="stroke:red; fill:gold; fill-opacity:1.0; stroke-width:1;"/> + <text x="15" y="215" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore 4 to 15</text> + <circle cx="125" cy="212" r="3" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/> + <text x="15" y="235" style="fill:black; stroke:none" font-size="12" font-family="Arial" >Zscore lt 4</text> + <circle cx="125" cy="232" r="2" style="stroke:gold; fill:gold; fill-opacity:1.0; stroke-width:1;"/> + <g id="checkboxes"> + </g> + </g> + + + <g style='fill:black; stroke:none' font-size="17" font-family="Arial"> +  + <text x="480" y="660">Mean Alleles Shared</text> + <text x="0" y="630" >1.0</text> + <text x="277" y="630" >1.25</text> + <text x="564" y="630" >1.5</text> + <text x="842" y="630" >1.75</text> + <text x="1140" y="630" >2.0</text> + </g> + + <g transform="rotate(270)" style="fill:black; stroke:none" font-size="17" font-family="Arial"> +  + <text x="-350" y="-40">SD Alleles Shared</text> + <text x="-20" y="-10" >1.0</text> + <text x="-165" y="-10" >0.75</text> + <text x="-310" y="-10" >0.5</text> + <text x="-455" y="-10" >0.25</text> + <text x="-600" y="-10" >0.0</text> + </g> + + +<g style="fill:black; stroke:none" font-size="18" font-family="Arial"> + <text x="425" y="-30">%s</text> +</g> + + +''' + +SVG_FOOTER = ''' + +</g> +<g id="btTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial"> + <rect width="250" height="110" style="fill:silver" rx="2" ry="2"/> + <rect id="btHead" width="250" height="20" rx="2" ry="2" /> + <text id="btRel" y="14" x="85">unrelated</text> + <text id="btMean" y="40" x="4">mean=1.5 +/- 0.04</text> + <text id="btSdev" y="60" x="4">sdev=0.7 +/- 0.03</text> + <text id="btPair" y="80" x="4">npairs=1152</text> + <text id="btGeno" y="100" x="4">ngenos=4783 +/- 24 (min=1000, max=5000)</text> +</g> + +<g id="otTip" visibility="hidden" style="stroke-width:1.0; fill:black; stroke:none;" font-size="10" font-family="Arial"> + <rect width="150" height="180" style="fill:silver" rx="2" ry="2"/> + <rect id="otHead" width="150" height="20" rx="2" ry="2" /> + <text id="otRel" y="14" x="40">sibpairs</text> + <text id="otS1" y="40" x="4">s1=fid1,iid1</text> + <text id="otS2" y="60" x="4">s2=fid2,iid2</text> + <text id="otMean" y="80" x="4">mean=1.82</text> + <text id="otSdev" y="100" x="4">sdev=0.7</text> + <text id="otGeno" y="120" x="4">ngeno=4487</text> + <text id="otRmean" y="140" x="4">relmean=1.85</text> + <text id="otRsdev" y="160" x="4">relsdev=0.65</text> +</g> +</svg> +''' + +OUTLIERS_HEADER = 'Mean\tSdev\tZ(mean)\tZ(sdev)\tFID1\tIID1\tFID2\tIID2\tMean(Mean)\tSdev(Mean)\tMean(Sdev)\tSdev(Sdev)\n' + +DEFAULT_MAX_SAMPLE_SIZE = 5000 + +REF_COUNT_HOM1 = 3 +REF_COUNT_HET = 2 +REF_COUNT_HOM2 = 1 +MISSING = 0 + +MARKER_PAIRS_PER_SECOND_SLOW = 15000000 +MARKER_PAIRS_PER_SECOND_FAST = 70000000 + +POLYGONS = { + REL_UNRELATED: ((1.360, 0.655), (1.385, 0.730), (1.620, 0.575), (1.610, 0.505)), + REL_HALFSIBS: ((1.630, 0.500), (1.630, 0.550), (1.648, 0.540), (1.648, 0.490)), + REL_SIBS: ((1.660, 0.510), (1.665, 0.560), (1.820, 0.410), (1.820, 0.390)), + REL_PARENTCHILD: ((1.650, 0.470), (1.650, 0.490), (1.750, 0.440), (1.750, 0.420)), + REL_DUPE: ((1.970, 0.000), (1.970, 0.150), (2.000, 0.150), (2.000, 0.000)), + } + +def distance(point1, point2): + """ Calculate the distance between two points + """ + (x1,y1) = [float(d) for d in point1] + (x2,y2) = [float(d) for d in point2] + dx = abs(x1 - x2) + dy = abs(y1 - y2) + return math.sqrt(dx**2 + dy**2) + +def point_inside_polygon(x, y, poly): + """ Determine if a point (x,y) is inside a given polygon or not + poly is a list of (x,y) pairs. + + Taken from: http://www.ariel.com.au/a/python-point-int-poly.html + """ + + n = len(poly) + inside = False + + p1x,p1y = poly[0] + for i in range(n+1): + p2x,p2y = poly[i % n] + if y > min(p1y,p2y): + if y <= max(p1y,p2y): + if x <= max(p1x,p2x): + if p1y != p2y: + xinters = (y-p1y)*(p2x-p1x)/(p2y-p1y)+p1x + if p1x == p2x or x <= xinters: + inside = not inside + p1x,p1y = p2x,p2y + return inside + +def readMap(pedfile): + """ + """ + mapfile = pedfile.replace('.ped', '.map') + marker_list = [] + if os.path.exists(mapfile): + print 'readMap: %s' % (mapfile) + fh = file(mapfile, 'r') + for line in fh: + marker_list.append(line.strip().split()) + fh.close() + print 'readMap: %s markers' % (len(marker_list)) + return marker_list + +def calcMeanSD(useme): + """ + A numerically stable algorithm is given below. It also computes the mean. + This algorithm is due to Knuth,[1] who cites Welford.[2] + n = 0 + mean = 0 + M2 = 0 + + foreach x in data: + n = n + 1 + delta = x - mean + mean = mean + delta/n + M2 = M2 + delta*(x - mean) // This expression uses the new value of mean + end for + + variance_n = M2/n + variance = M2/(n - 1) + """ + mean = 0.0 + M2 = 0.0 + sd = 0.0 + n = len(useme) + if n > 1: + for i,x in enumerate(useme): + delta = x - mean + mean = mean + delta/(i+1) # knuth uses n+=1 at start + M2 = M2 + delta*(x - mean) # This expression uses the new value of mean + variance = M2/(n-1) # assume is sample so lose 1 DOF + sd = pow(variance,0.5) + return mean,sd + + +def doIBSpy(ped=None,basename='',outdir=None,logf=None, + nrsSamples=10000,title='title',pdftoo=0,Zcutoff=2.0): + #def doIBS(pedName, title, nrsSamples=None, pdftoo=False): + """ started with snpmatrix but GRR uses actual IBS counts and sd's + """ + repOut = [] # text strings to add to the html display + refallele = {} + tblf = '%s_table.xls' % (title) + tbl = file(os.path.join(outdir,tblf), 'w') + tbl.write(TABLE_HEADER) + svgf = '%s.svg' % (title) + svg = file(os.path.join(outdir,svgf), 'w') + + nMarkers = len(ped._markers) + if nMarkers < 5: + print sys.stderr, '### ERROR - %d is too few markers for reliable estimation in %s - terminating' % (nMarkers,PROGNAME) + sys.exit(1) + nSubjects = len(ped._subjects) + nrsSamples = min(nMarkers, nrsSamples) + if opts and opts.use_mito: + markers = range(nMarkers) + nrsSamples = min(len(markers), nrsSamples) + sampleIndexes = sorted(random.sample(markers, nrsSamples)) + else: + autosomals = ped.autosomal_indices() + nrsSamples = min(len(autosomals), nrsSamples) + sampleIndexes = sorted(random.sample(autosomals, nrsSamples)) + + print '' + print 'Getting random.sample of %s from %s total' % (nrsSamples, nMarkers) + npairs = (nSubjects*(nSubjects-1))/2 # total rows in table + newfiles=[svgf,tblf] + explanations = ['rgGRR Plot (requires SVG)','Mean by SD alleles shared - %d rows' % npairs] + # these go with the output file links in the html file + s = 'Reading genotypes for %s subjects and %s markers\n' % (nSubjects, nrsSamples) + logf.write(s) + minUsegenos = nrsSamples/2 # must have half? + nGenotypes = nSubjects*nrsSamples + stime = time.time() + emptyRows = set() + genos = numpy.zeros((nSubjects, nrsSamples), dtype=int) + for s in xrange(nSubjects): + nValid = 0 + #getGenotypesByIndices(self, s, mlist, format) + genos[s] = ped.getGenotypesByIndices(s, sampleIndexes, format='ref') + nValid = sum([1 for g in genos[s] if g]) + if not nValid: + emptyRows.add(s) + sub = ped.getSubject(s) + print 'All missing for row %d (%s)' % (s, sub) + logf.write('All missing for row %d (%s)\n' % (s, sub)) + rtime = time.time() - stime + if verbose: + print '@@Read %s genotypes in %s seconds' % (nGenotypes, rtime) + + + ### Now the expensive part. For each pair of subjects, we get the mean number + ### and standard deviation of shared alleles over all of the markers where both + ### subjects have a known genotype. Identical subjects should have mean shared + ### alleles very close to 2.0 with a standard deviation very close to 0.0. + tot = nSubjects*(nSubjects-1)/2 + nprog = tot/10 + nMarkerpairs = tot * nrsSamples + estimatedTimeSlow = nMarkerpairs/MARKER_PAIRS_PER_SECOND_SLOW + estimatedTimeFast = nMarkerpairs/MARKER_PAIRS_PER_SECOND_FAST + + pairs = [] + pair_data = {} + means = [] ## Mean IBS for each pair + ngenoL = [] ## Count of comparable genotypes for each pair + sdevs = [] ## Standard dev for each pair + rels = [] ## A relationship code for each pair + zmeans = [0.0 for x in xrange(tot)] ## zmean score for each pair for the relgroup + zstds = [0.0 for x in xrange(tot)] ## zstd score for each pair for the relgrp + skip = set() + ndone = 0 ## How many have been done so far + + logf.write('Calculating %d pairs, updating every %d pairs...\n' % (tot, nprog)) + logf.write('Estimated time is %2.2f to %2.2f seconds ...\n' % (estimatedTimeFast, estimatedTimeSlow)) + + t1sum = 0 + t2sum = 0 + t3sum = 0 + now = time.time() + scache = {}

1 0

[hg] galaxy 3632: Enable user to change dbkey from a known key b...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0dc1fc63c945 changeset: 3632:0dc1fc63c945 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Apr 13 10:22:27 2010 -0400 description: Enable user to change dbkey from a known key back to unspecified. This is a hack, but there's no straightforward way to accomplish this without modifying the jquery autocomplete script. diffstat: static/scripts/galaxy.base.js | 11 +++++++++-- 1 files changed, 9 insertions(+), 2 deletions(-) diffs (30 lines): diff -r 968161f35d50 -r 0dc1fc63c945 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Tue Apr 13 10:16:46 2010 -0400 +++ b/static/scripts/galaxy.base.js Tue Apr 13 10:22:27 2010 -0400 @@ -149,10 +149,10 @@ var select_mapping = {}; select_elt.children('option').each( function() { // Get text, value for option. - var text = $(this).text(); + var text = $(this).text(); var value = $(this).attr('value'); - // Ignore values that are '?' + // HACK: dbkey-specific: ignore values that are '?' if (value == '?') { return; } @@ -169,6 +169,13 @@ } }); + // HACK: dbkey-specific: add an unspecified option. We need to add this at the end b/c adding it first mucks + // up the autocomplete sorting for some reason. (I.e. All options that start with the first character of the + // first option are listed before the other, alphabetized options.) + select_options.push( "unspecified (?)" ); + select_mapping[ "unspecified (?)" ] = "?"; + select_mapping[ "?" ] = "?"; + // Set initial text if it's empty. if ( text_input_elt.attr('value') == '' ) { text_input_elt.attr('value', 'Click to Search or Select');

1 0

[hg] galaxy 3631: fixed forms and user_info functional tests
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/968161f35d50 changeset: 3631:968161f35d50 user: rc date: Tue Apr 13 10:16:46 2010 -0400 description: fixed forms and user_info functional tests removed a debugging print stmt diffstat: lib/galaxy/model/__init__.py | 2 +- lib/galaxy/web/controllers/forms.py | 1 - test/functional/test_forms_and_requests.py | 8 ++++---- test/functional/test_user_info.py | 2 +- 4 files changed, 6 insertions(+), 7 deletions(-) diffs (74 lines): diff -r fdf5c92e7fae -r 968161f35d50 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Apr 12 19:11:36 2010 -0400 +++ b/lib/galaxy/model/__init__.py Tue Apr 13 10:16:46 2010 -0400 @@ -1326,7 +1326,7 @@ # the user had already filled out this field and the same form is re-rendered # due to some reason like required fields have been left out. if field[ 'type' ] == 'CheckboxField': - value = CheckboxField.is_checked( util.restore_text( params.get( field_name, False ) ) ) + value = CheckboxField.is_checked( params.get( field_name, False ) ) else: value = util.restore_text( params.get( field_name, '' ) ) elif contents: diff -r fdf5c92e7fae -r 968161f35d50 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Mon Apr 12 19:11:36 2010 -0400 +++ b/lib/galaxy/web/controllers/forms.py Tue Apr 13 10:16:46 2010 -0400 @@ -541,7 +541,6 @@ self.selectbox_options = [] # if the form is for defining samples, then use the sample field types # which does not include TextArea & AddressField - print >> sys.stderr, 'form_type', form_type if form_type == trans.app.model.FormDefinition.types.SAMPLE: for ft in BaseField.sample_field_types(): self.fieldtype.add_option(ft, ft) diff -r fdf5c92e7fae -r 968161f35d50 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Mon Apr 12 19:11:36 2010 -0400 +++ b/test/functional/test_forms_and_requests.py Tue Apr 13 10:16:46 2010 -0400 @@ -106,7 +106,7 @@ """Testing address & library creation""" # first create a regular user self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) self.logout() self.login( email='test(a)bx.psu.edu' ) # first create a library for the request so that it can be submitted later @@ -191,7 +191,7 @@ self.check_page_for_string( name ) # create address self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) self.add_user_address( regular_user1.id, address1 ) global regular_user regular_user = sa_session.query( galaxy.model.User ) \ @@ -206,7 +206,7 @@ """Testing creating, editing and submitting a request as a regular user""" # login as a regular user self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) # set field values fields = ['option1', str(user_address.id), 'field three value'] # create the request @@ -259,7 +259,7 @@ self.home() sa_session.refresh( request_one ) self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email='test1(a)bx.psu.edu', username='regular-user1' ) # check if the request's state is now set to 'complete' self.check_request_grid(state='Complete', request_name=request_one.name) assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" \ diff -r fdf5c92e7fae -r 968161f35d50 test/functional/test_user_info.py --- a/test/functional/test_user_info.py Mon Apr 12 19:11:36 2010 -0400 +++ b/test/functional/test_user_info.py Tue Apr 13 10:16:46 2010 -0400 @@ -162,7 +162,7 @@ # Test changing email and user name - first try an invalid user name self.edit_login_info( new_email='test12_new(a)bx.psu.edu', new_username='test12_new', - check_str1='User name must contain only letters, numbers and' ) + check_str1="User name must contain only lower-case letters, numbers and '-'" ) # Now try a valid user name self.edit_login_info( new_email='test12_new(a)bx.psu.edu', new_username='test12-new',

1 0

[hg] galaxy 3630: Fixed a bug in the new joiner tool
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/fdf5c92e7fae changeset: 3630:fdf5c92e7fae user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Mon Apr 12 19:11:36 2010 -0400 description: Fixed a bug in the new joiner tool diffstat: tools/new_operations/column_join.py | 97 +++++++++++++++++++++++------------ tools/new_operations/column_join.xml | 8 +- 2 files changed, 68 insertions(+), 37 deletions(-) diffs (213 lines): diff -r 6b93e705c8a4 -r fdf5c92e7fae tools/new_operations/column_join.py --- a/tools/new_operations/column_join.py Mon Apr 12 17:24:17 2010 -0400 +++ b/tools/new_operations/column_join.py Mon Apr 12 19:11:36 2010 -0400 @@ -19,6 +19,32 @@ sys.stderr.write( msg ) sys.exit() +def hinge_compare( hinge1, hinge2 ): + """ + Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that + first part handled as text but last part as number + """ + pat = re.compile( '(?P<text>\D*)(?P<number>\d+)?' ) + split_hinge1 = hinge1.split( '\t' ) + split_hinge2 = hinge2.split( '\t' ) + for i in range( len( split_hinge1 ) ): + if split_hinge1[ i ] == split_hinge2[ i ]: + continue + try: + if int( split_hinge1[ i ] ) > int( split_hinge2[ i ] ): + return 1 + else: + return -1 + except ValueError: + try: + if float( split_hinge1[ i ] ) > float( split_hinge2[ i ] ): + return 1 + else: + return -1 + except ValueError: + return ref_compare( split_hinge1[ i ], split_hinge2[ i ]) + return 0 + def ref_compare( ref1, ref2 ): """ Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that @@ -52,35 +78,31 @@ elif text1 < text2: return -1 -def ref_pos_sort( infile, outfile ): +def hinge_sort( infile, outfile, hinge ): """Given input file name, sorts logically (text vs. numeric) into provided output file name.""" - ref_locs = {} + hinge_locs = {} bad_lines = [] fin = open( infile, 'rb' ) line = fin.readline() while line.strip(): - if True: + try: + hinge_parts = line.split( '\t' )[ :hinge ] try: - ref_seq, ref_loc = line.split( '\t' )[:2] - try: - ref_locs[ ref_seq ][ long( ref_loc ) ] = fin.tell() - len( line.strip() ) - 1 - except KeyError: - ref_locs[ ref_seq ] = { long( ref_loc ): fin.tell() - len( line.strip() ) - 1 } - except ValueError: - bad_lines.append( line ) - except ValueError: - bad_line.append( line ) + hinge_locs[ '\t'.join( hinge_parts ) ].append( fin.tell() - len( line.strip() ) - 1 ) + except KeyError: + hinge_locs[ '\t'.join( hinge_parts ) ] = [ fin.tell() - len( line.strip() ) - 1 ] + except ValueError: + bad_line.append( line ) line = fin.readline() fin.close() - refs = ref_locs.keys() - refs.sort( ref_compare ) fin = open( infile, 'rb' ) fout = open( outfile, 'wb' ) - for ref in refs: - locs = ref_locs[ ref ].keys() - locs.sort() + hinge_locs_sorted = hinge_locs.keys() + hinge_locs_sorted.sort( hinge_compare ) + for hinge_loc in hinge_locs_sorted: + locs = hinge_locs[ hinge_loc ] for loc in locs: - fin.seek( ref_locs[ ref ][ loc ] ) + fin.seek( loc ) fout.write( fin.readline() ) fout.close() fin.close() @@ -90,14 +112,17 @@ if len( chr_pos ) == 0 and ''.join( chr_pos ): return '' min_loc = len( chr_pos ) - min_ref_pos = [] + min_hinge = [] loc = 0 for c_pos in chr_pos: if c_pos.strip(): + split_c = c_pos.split( '\t' ) + + ref, pos = c_pos.split( '\t' )[:2] pos = int( pos ) - if not min_ref_pos: - min_ref_pos = [ ref, pos ] + if not min_hinge: + min_hinge = split_c min_loc = loc else: ref_comp = ref_compare( ref, min_ref_pos[0] ) @@ -126,25 +151,33 @@ tmp_file = tempfile.NamedTemporaryFile() tmp_file_name = tmp_file.name tmp_file.close() - ref_pos_sort( in_file, tmp_file_name ) + hinge_sort( in_file, tmp_file_name, hinge ) tmp_file = open( tmp_file_name, 'rb' ) tmp_input_files.append( tmp_file ) # cycle through files, getting smallest line of all files one at a time # also have to keep track of vertical position of extra columns fout = file( output, 'w' ) - old_current_chr_pos = '' + old_current = '' first_line = True current_lines = [ f.readline() for f in tmp_input_files ] last_lines = ''.join( current_lines ).strip() last_loc = -1 + i = 0 while last_lines: # get the "minimum" hinge, which should come first, and the file location in list - current_chr_pos, loc = min_chr_pos( [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] ) + hinges = [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] + hinge_dict = {} + for i in range( len( hinges ) ): + if not hinge_dict.has_key( hinges[ i ] ): + hinge_dict[ hinges[ i ] ] = i + hinges.sort( hinge_compare ) + hinges = [ h for h in hinges if h ] + current, loc = hinges[0], hinge_dict[ hinges[0] ] # first output empty columns for vertical alignment (account for "missing" files) - if current_chr_pos != old_current_chr_pos: + if current != old_current: last_loc = -1 if loc - last_loc > 1: - current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( cols[ hinge: ] ) ) ] + current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( [ col for col in cols if col > hinge ] ) ) ] else: current_data = [] # now output actual data @@ -154,22 +187,20 @@ if col > hinge: current_data.append( split_line[ col - 1 ] ) current_lines[ loc ] = tmp_input_files[ loc ].readline() - if current_chr_pos == old_current_chr_pos: - fout.write( '\t%s' % '\t'.join( current_data ) ) + if current == old_current: + if current_data: + fout.write( '\t%s' % '\t'.join( current_data ) ) else: if not first_line: fout.write( '\n' ) - fout.write( '%s\t%s' % ( current_chr_pos, '\t'.join( current_data ) ) ) + fout.write( '%s\t%s' % ( current, '\t'.join( current_data ) ) ) first_line = False - old_current_chr_pos = current_chr_pos - if last_lines == ''.join( current_lines ).strip(): - break + old_current = current last_lines = ''.join( current_lines ).strip() last_loc = loc fout.write( '\n' ) for f in tmp_input_files: os.unlink( f.name ) fout.close() -# sys.stderr.write('******************\n'+file(fout.name, 'r').read()+'\n******************\n') if __name__ == "__main__" : __main__() diff -r 6b93e705c8a4 -r fdf5c92e7fae tools/new_operations/column_join.xml --- a/tools/new_operations/column_join.xml Mon Apr 12 17:24:17 2010 -0400 +++ b/tools/new_operations/column_join.xml Mon Apr 12 19:11:36 2010 -0400 @@ -21,7 +21,7 @@ </repeat> </inputs> <outputs> - <data name="output" format="pileup" /> + <data name="output" format="tabular" /> </outputs> <tests> <test> @@ -30,7 +30,7 @@ <param name="hinge" value="1,2" /> <param name="input2" value="column_join_in2.pileup" ftype="pileup" /> <param name="input" value="column_join_in3.pileup" ftype="pileup" /> - <output name="output" file="column_join_out1.pileup" ftype="pileup" /> + <output name="output" file="column_join_out1.pileup" ftype="tabular" /> </test> <test> <param name="input1" value="column_join_in4.pileup" ftype="pileup" /> @@ -38,7 +38,7 @@ <param name="hinge" value="1,2" /> <param name="input2" value="column_join_in5.pileup" ftype="pileup" /> <param name="input" value="column_join_in6.pileup" ftype="pileup" /> - <output name="output" file="column_join_out2.pileup" ftype="pileup" /> + <output name="output" file="column_join_out2.pileup" ftype="tabular" /> </test> <test> <param name="input1" value="column_join_in7.pileup" ftype="pileup" /> @@ -46,7 +46,7 @@ <param name="hinge" value="1,2" /> <param name="input2" value="column_join_in8.pileup" ftype="pileup" /> <param name="input" value="column_join_in9.pileup" ftype="pileup" /> - <output name="output" file="column_join_out3.pileup" ftype="pileup" /> + <output name="output" file="column_join_out3.pileup" ftype="tabular" /> </test> </tests> <help>

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[hg] galaxy 3629: If a subdir of the library import dir is a sym...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6b93e705c8a4 changeset: 3629:6b93e705c8a4 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Apr 12 17:24:17 2010 -0400 description: If a subdir of the library import dir is a symlink and we are linking instead of copying data on import, dereference that symlink diffstat: lib/galaxy/web/controllers/library_common.py | 15 +++++++++++++-- 1 files changed, 13 insertions(+), 2 deletions(-) diffs (25 lines): diff -r c19605dca27d -r 6b93e705c8a4 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Apr 12 15:56:13 2010 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Mon Apr 12 17:24:17 2010 -0400 @@ -915,8 +915,19 @@ for entry in os.listdir( full_dir ): # Only import regular files path = os.path.join( full_dir, entry ) - if os.path.islink( path ) and os.path.isfile( path ) and params.get( 'link_data_only', False ): - # If we're linking instead of copying, link the file the link points to, not the link itself. + if os.path.islink( full_dir ) and params.get( 'link_data_only', False ): + # If we're linking instead of copying and the + # sub-"directory" in the import dir is actually a symlink, + # dereference the symlink, but not any of its contents. + link_path = os.readlink( full_dir ) + if os.path.isabs( link_path ): + path = os.path.join( link_path, entry ) + else: + path = os.path.abspath( os.path.join( link_path, entry ) ) + elif os.path.islink( path ) and os.path.isfile( path ) and params.get( 'link_data_only', False ): + # If we're linking instead of copying and the "file" in the + # sub-directory of the import dir is actually a symlink, + # dereference the symlink (one dereference only, Vasili). link_path = os.readlink( path ) if os.path.isabs( link_path ): path = link_path

1 0

[hg] galaxy 3628: Updated NGS tools' stderr handling to use file...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c19605dca27d changeset: 3628:c19605dca27d user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Mon Apr 12 15:56:13 2010 -0400 description: Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output diffstat: tools/metag_tools/megablast_wrapper.py | 13 +++++++++- tools/samtools/sam_merge.py | 15 ++++++++++-- tools/samtools/sam_pileup.py | 18 ++++++++++++--- tools/samtools/sam_to_bam.py | 27 ++++++++++++++++++----- tools/sr_mapping/bowtie_wrapper.py | 26 +++++++++++++++++----- tools/sr_mapping/bowtie_wrapper.xml | 4 +- tools/sr_mapping/bwa_wrapper.py | 38 +++++++++++++++++++++++++-------- 7 files changed, 109 insertions(+), 32 deletions(-) diffs (406 lines): diff -r f32497f2e001 -r c19605dca27d tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/metag_tools/megablast_wrapper.py Mon Apr 12 15:56:13 2010 -0400 @@ -74,24 +74,33 @@ print megablast_command + tmp = tempfile.NamedTemporaryFile().name try: - proc = subprocess.Popen( args=megablast_command, shell=True, stderr=subprocess.PIPE ) + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=megablast_command, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr + if os.path.exists( tmp ): + os.unlink( tmp ) except Exception, e: if os.path.exists( mega_temp_output ): os.unlink( mega_temp_output ) + if os.path.exists( tmp ): + os.unlink( tmp ) stop_err( 'Error indexing reference sequence. ' + str( e ) ) output = open( output_filename, 'w' ) diff -r f32497f2e001 -r c19605dca27d tools/samtools/sam_merge.py --- a/tools/samtools/sam_merge.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/samtools/sam_merge.py Mon Apr 12 15:56:13 2010 -0400 @@ -9,7 +9,7 @@ [input3[,input4[,input5[,...]]]] """ -import os, subprocess, sys +import os, subprocess, sys, tempfile def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) @@ -22,22 +22,31 @@ stop_err( 'There are not enough files to merge' ) filenames = sys.argv[3:] cmd = 'samtools merge %s %s %s' % ( outfile, infile, ' '.join( filenames ) ) + tmp = tempfile.NamedTemporaryFile().name try: - proc = subprocess.Popen( args=cmd, shell=True, stderr=subprocess.PIPE ) + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr + if os.path.exists( tmp ): + os.unlink( tmp ) except Exception, e: + if os.path.exists( tmp ): + os.unlink( tmp ) stop_err( 'Error running SAMtools merge tool\n' + str( e ) ) if os.path.getsize( outfile ) > 0: sys.stdout.write( '%s files merged.' % ( len( sys.argv ) - 2 ) ) diff -r f32497f2e001 -r c19605dca27d tools/samtools/sam_pileup.py --- a/tools/samtools/sam_pileup.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/samtools/sam_pileup.py Mon Apr 12 15:56:13 2010 -0400 @@ -88,36 +88,46 @@ elif options.ref == 'history': os.symlink( options.ownFile, tmpf1_name ) cmdIndex = 'samtools faidx %s' % ( tmpf1_name ) - proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() #did index succeed? if returncode != 0: raise Exception, 'Error creating index file\n' + stderr cmd = cmd % ( opts, tmpf1_name, tmpf0bam_name, options.output1 ) #perform pileup command - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmpDir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() #did it succeed? # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: diff -r f32497f2e001 -r c19605dca27d tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/samtools/sam_to_bam.py Mon Apr 12 15:56:13 2010 -0400 @@ -75,18 +75,23 @@ os.symlink( options.ref_file, fai_index_file_base ) fai_index_file_path = '%s.fai' % fai_index_file_base command = 'samtools faidx %s' % fai_index_file_base - proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr if len( open( fai_index_file_path ).read().strip() ) == 0: @@ -104,18 +109,23 @@ # IMPORTANT NOTE: for some reason the samtools view command gzips the resulting bam file without warning, # and the docs do not currently state that this occurs ( very bad ). command = 'samtools view -bt %s -o %s %s' % ( fai_index_file_path, tmp_aligns_file_name, options.input1 ) - proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr if len( open( tmp_aligns_file_name ).read() ) == 0: @@ -133,18 +143,23 @@ tmp_sorted_aligns_file_name = tmp_sorted_aligns_file.name tmp_sorted_aligns_file.close() command = 'samtools sort %s %s' % ( tmp_aligns_file_name, tmp_sorted_aligns_file_name ) - proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: diff -r f32497f2e001 -r c19605dca27d tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Mon Apr 12 15:56:13 2010 -0400 @@ -186,25 +186,34 @@ ( iautoB, ipacked, ibmax, ibmaxdivn, idcv, inodc, inoref, options.ioffrate, iftab, intoa, iendian, iseed, icutoff, colorspace ) - except ValueError: - indexing_cmds = '%s' % colorspace + except ValueError, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Something is wrong with the indexing parameters and the indexing and alignment could not be run\n' + str( e ) ) ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) ref_file_name = ref_file.name ref_file.close() os.symlink( options.ref, ref_file_name ) cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name ) try: - proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=subprocess.PIPE, stdout=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: @@ -358,18 +367,23 @@ else: cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output ) # align - proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr # check that there are results in the output file diff -r f32497f2e001 -r c19605dca27d tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Mon Apr 12 15:56:13 2010 -0400 @@ -181,8 +181,8 @@ --maxAlignAttempt="None" --forwardAlign="None" --reverseAlign="None" - #end if - #end if + #end if + #end if </command> <inputs> <conditional name="refGenomeSource"> diff -r f32497f2e001 -r c19605dca27d tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py Mon Apr 12 10:30:25 2010 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Mon Apr 12 15:56:13 2010 -0400 @@ -91,18 +91,23 @@ indexing_cmds = '-a %s' % indexingAlg cmd1 = 'bwa index %s %s' % ( indexing_cmds, ref_file_name ) try: - proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' buffsize = 1048576 try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: @@ -166,52 +171,67 @@ try: # align try: - proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: raise Exception, 'Error aligning sequence. ' + str( e ) # and again if paired data try: - if cmd2b: - proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + if cmd2b: + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e: raise Exception, 'Error aligning second sequence. ' + str( e ) # generate align try: - proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) returncode = proc.wait() + tmp_stderr.close() # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) stderr = '' try: while True: - stderr += proc.stderr.read( buffsize ) + stderr += tmp_stderr.read( buffsize ) if not stderr or len( stderr ) % buffsize != 0: break except OverflowError: pass + tmp_stderr.close() if returncode != 0: raise Exception, stderr except Exception, e:

1 0

[hg] galaxy 3627: Allow FASTQ parser to handle extra space padde...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f32497f2e001 changeset: 3627:f32497f2e001 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Apr 12 10:30:25 2010 -0400 description: Allow FASTQ parser to handle extra space padded decimal scores, e.g. '0 ' diffstat: lib/galaxy_utils/sequence/fastq.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 5536d57237a3 -r f32497f2e001 lib/galaxy_utils/sequence/fastq.py --- a/lib/galaxy_utils/sequence/fastq.py Fri Apr 09 18:09:54 2010 -0400 +++ b/lib/galaxy_utils/sequence/fastq.py Mon Apr 12 10:30:25 2010 -0400 @@ -60,7 +60,7 @@ else: quality = self.quality.rstrip() #decimal scores should have a trailing space if quality: - return map( int, quality.split( ' ' ) ) + return [ int( val ) for val in quality.split( ' ' ) if val.strip() ] else: return [] def convert_read_to_format( self, format, force_quality_encoding = None ):

1 0

[hg] galaxy 3626: - Update jQuery.jStore, JSON2
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5536d57237a3 changeset: 3626:5536d57237a3 user: Kanwei Li <kanwei(a)gmail.com> date: Fri Apr 09 18:09:54 2010 -0400 description: - Update jQuery.jStore, JSON2 - Fix issue with all local prefs being deleted on "collapse all" - Refactored history display code into galaxy.base diffstat: static/jStore.Flash.html | 19 - static/jStore.swf | 0 static/scripts/class.js | 80 + static/scripts/galaxy.base.js | 87 + static/scripts/jquery.jstore-all.js | 748 ----------- static/scripts/jquery.jstore.js | 1810 ++++++++++++++++++++++++++++ static/scripts/json2.js | 26 +- static/scripts/packed/class.js | 7 + static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/jquery.jstore-all.js | 1 - static/scripts/packed/jquery.jstore.js | 17 + static/scripts/packed/json2.js | 2 +- templates/display_base.mako | 29 +- templates/history/display.mako | 264 +--- templates/history/view.mako | 259 +--- templates/page/display.mako | 272 +--- templates/root/history.mako | 222 +-- templates/workflow/editor.mako | 42 +- 18 files changed, 2216 insertions(+), 1671 deletions(-) diffs (truncated from 4199 to 3000 lines): diff -r a9402fc7ce1b -r 5536d57237a3 static/jStore.Flash.html --- a/static/jStore.Flash.html Fri Apr 09 13:02:15 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en"> - <head> - <title>Flash External Object</title> - <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <script type="text/javascript"> - /** - * This function captures the flash_ready event. We need to relay this - * back to the parent so it knows flash is ready. - */ - function flash_ready(){ - parent.flash_ready(); - } - </script> - </head> - <body> - <object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#versi…" width="1" height="1" id="jStoreFlash"><param name="allowScriptAccess" value="always" /><param name="movie" value="jStore.swf" /><param name="quality" value="high" /><param name="bgcolor" value="#ffcc00" /><embed src="jStore.swf" quality="high" bgcolor="#ffcc00" width="1" height="1" name="jStoreFlash" align="middle" allowScriptAccess="always" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" /></object> - </body> -</html> \ No newline at end of file diff -r a9402fc7ce1b -r 5536d57237a3 static/jStore.swf Binary file static/jStore.swf has changed diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/class.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/class.js Fri Apr 09 18:09:54 2010 -0400 @@ -0,0 +1,80 @@ +/*! + * Class definition + * + * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) + * Inspired by base2 and Prototype + */ + +"use strict"; + +(function () { + + var initializing = false, + + fnTest = /xyz/.test(function(){xyz;}) ? /\b_super\b/ : /.*/; + + // The base Class implementation (does nothing) + this.Class = function(){}; + + // Create a new Class that inherits from this class + Class.extend = function (prop) + { + var _super = this.prototype; + + // Instantiate a base class (but only create the instance, don't run the init constructor) + initializing = true; + + var prototype = new this(); + + initializing = false; + + // Copy the properties over onto the new prototype + for (var name in prop) + { + + // Check if we're overwriting an existing function + prototype[name] = (typeof prop[name] === "function" && typeof _super[name] === "function" && fnTest.test(prop[name]) ? + + (function(name, fn) + { + return function() + { + var tmp = this._super; + + // Add a new ._super() method that is the same method + // but on the super-class + this._super = _super[name]; + + // The method only need to be bound temporarily, so we + // remove it when we're done executing + var ret = fn.apply(this, arguments); + this._super = tmp; + + return ret; + }; + }(name, prop[name])) : prop[name]); + } + + // The dummy class constructor + function Class() + { + // All construction is actually done in the init method + if (!initializing && this.init) + { + this.init.apply(this, arguments); + } + } + + // Populate our constructed prototype object + Class.prototype = prototype; + + // Enforce the constructor to be what we expect + Class.constructor = Class; + + // And make this class extendable + Class.extend = arguments.callee; + + return Class; + }; + +}()); diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Apr 09 13:02:15 2010 -0400 +++ b/static/scripts/galaxy.base.js Fri Apr 09 18:09:54 2010 -0400 @@ -275,6 +275,93 @@ }); } +function init_history_items(historywrapper, noinit) { + + var action = function() { + // Load saved state and show as necessary + try { + var stored = $.jStore.store("history_expand_state"); + if (stored) { + for (var id in stored) { + $("#" + id + " div.historyItemBody" ).show(); + } + } + } catch(err) { + // Something was wrong with values in storage, so clear storage + $.jStore.remove("history_expand_state"); + } + + // If Mozilla, hide scrollbars in hidden items since they cause animation bugs + if ( $.browser.mozilla ) { + $( "div.historyItemBody" ).each( function() { + if ( ! $(this).is( ":visible" ) ) $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + }) + } + + historywrapper.each( function() { + var id = this.id; + var body = $(this).children( "div.historyItemBody" ); + var peek = body.find( "pre.peek" ) + $(this).children( ".historyItemTitleBar" ).find( ".historyItemTitle" ).wrap( "<a href='#'></a>" ).click( function() { + if ( body.is(":visible") ) { + // Hiding stuff here + if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ) } + body.slideUp( "fast" ); + + if (!noinit) { // Ignore embedded item actions + // Save setting + var prefs = $.jStore.store("history_expand_state"); + if (prefs) { + delete prefs[id]; + $.jStore.store("history_expand_state", prefs); + } + } + } else { + // Showing stuff here + body.slideDown( "fast", function() { + if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } + }); + + if (!noinit) { + // Save setting + var prefs = $.jStore.store("history_expand_state"); + if (prefs === undefined) { prefs = {}; } + prefs[id] = true; + $.jStore.store("history_expand_state", prefs); + } + } + return false; + }); + }); + + // Generate 'collapse all' link + $("#top-links > a.toggle").click( function() { + var prefs = $.jStore.store("history_expand_state"); + if (prefs === undefined) { prefs = {}; } + $( "div.historyItemBody:visible" ).each( function() { + if ( $.browser.mozilla ) { + $(this).find( "pre.peek" ).css( "overflow", "hidden" ); + } + $(this).slideUp( "fast" ); + if (prefs) { + delete prefs[$(this).parent().attr("id")]; + } + }); + $.jStore.store("history_expand_state", prefs); + }).show(); + } + + if (noinit) { + action(); + } else { + // Load jStore for local storage + $.jStore.init("galaxy"); // Auto-select best storage + $.jStore.engineReady(function() { + action(); + }); + } +} + $(document).ready( function() { // Links with confirmation $( "a[confirm]" ).click( function() { diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/jquery.jstore-all.js --- a/static/scripts/jquery.jstore-all.js Fri Apr 09 13:02:15 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,748 +0,0 @@ -/* - * jStore - Persistent Client-Side Storage - * - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - * - * Dual licensed under: - * MIT: http://www.opensource.org/licenses/mit-license.php - * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html - *//** - * Javascript Class Framework - * - * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) - * Inspired by base2 and Prototype - */ -(function(){ - var initializing = false, fnTest = /xyz/.test(function(){xyz;}) ? /\b_super\b/ : /.*/; - - // The base Class implementation (does nothing) - this.Class = function(){}; - - // Create a new Class that inherits from this class - Class.extend = function(prop) { - var _super = this.prototype; - - // Instantiate a base class (but only create the instance, - // don't run the init constructor) - initializing = true; - var prototype = new this(); - initializing = false; - - // Copy the properties over onto the new prototype - for (var name in prop) { - // Check if we're overwriting an existing function - prototype[name] = typeof prop[name] == "function" && - typeof _super[name] == "function" && fnTest.test(prop[name]) ? - (function(name, fn){ - return function() { - var tmp = this._super; - - // Add a new ._super() method that is the same method - // but on the super-class - this._super = _super[name]; - - // The method only need to be bound temporarily, so we - // remove it when we're done executing - var ret = fn.apply(this, arguments); - this._super = tmp; - - return ret; - }; - })(name, prop[name]) : - prop[name]; - } - - // The dummy class constructor - function Class() { - // All construction is actually done in the init method - if ( !initializing && this.init ) - this.init.apply(this, arguments); - } - - // Populate our constructed prototype object - Class.prototype = prototype; - - // Enforce the constructor to be what we expect - Class.constructor = Class; - - // And make this class extendable - Class.extend = arguments.callee; - - return Class; - }; -})(); -/* - * jStore Delegate Framework - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - this.jStoreDelegate = Class.extend({ - init: function(parent){ - // The Object this delgate operates for - this.parent = parent; - // Container for callbacks to dispatch. - // eventType => [ callback, callback, ... ] - this.callbacks = {}; - }, - bind: function(event, callback){ - if ( !$.isFunction(callback) ) return this; - if ( !this.callbacks[ event ] ) this.callbacks[ event ] = []; - - this.callbacks[ event ].push(callback); - - return this; - }, - trigger: function(){ - var parent = this.parent, - args = [].slice.call(arguments), - event = args.shift(), - handlers = this.callbacks[ event ]; - - if ( !handlers ) return false; - - $.each(handlers, function(){ this.apply(parent, args) }); - return this; - } - }); - -})(jQuery);/** - * jStore-jQuery Interface - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Setup the jStore namespace in jQuery for options storage - $.jStore = {}; - - // Seed the options in - $.extend($.jStore, { - EngineOrder: [], - // Engines should put their availability tests within jStore.Availability - Availability: {}, - // Defined engines should enter themselves into the jStore.Engines - Engines: {}, - // Instanciated engines should exist within jStore.Instances - Instances: {}, - // The current engine to use for storage - CurrentEngine: null, - // Provide global settings for overwriting - defaults: { - project: null, - engine: null, - autoload: true, - flash: 'jStore.Flash.html' - }, - // Boolean for ready state handling - isReady: false, - // Boolean for flash ready state handling - isFlashReady: false, - // An event delegate - delegate: new jStoreDelegate($.jStore) - .bind('jStore-ready', function(engine){ - $.jStore.isReady = true; - if ($.jStore.defaults.autoload) engine.connect(); - }) - .bind('flash-ready', function(){ - $.jStore.isFlashReady = true; - }) - }); - - // Enable ready callback for jStore - $.jStore.ready = function(callback){ - if ($.jStore.isReady) callback.apply($.jStore, [$.jStore.CurrentEngine]); - else $.jStore.delegate.bind('jStore-ready', callback); - } - - // Enable failure callback registration for jStore - $.jStore.fail = function(callback){ - $.jStore.delegate.bind('jStore-failure', callback); - } - - // Enable ready callback for Flash - $.jStore.flashReady = function(callback){ - if ($.jStore.isFlashReady) callback.apply($.jStore, [$.jStore.CurrentEngine]); - else $.jStore.delegate.bind('flash-ready', callback); - } - - // Enable and test an engine - $.jStore.use = function(engine, project, identifier){ - project = project || $.jStore.defaults.project || location.hostname.replace(/\./g, '-') || 'unknown'; - - var e = $.jStore.Engines[engine.toLowerCase()] || null, - name = (identifier ? identifier + '.' : '') + project + '.' + engine; - - if ( !e ) throw 'JSTORE_ENGINE_UNDEFINED'; - - // Instanciate the engine - e = new e(project, name); - - // Prevent against naming conflicts - if ($.jStore.Instances[name]) throw 'JSTORE_JRI_CONFLICT'; - - // Test the engine - if (e.isAvailable()){ - $.jStore.Instances[name] = e; // The Easy Way - if (!$.jStore.CurrentEngine){ - $.jStore.CurrentEngine = e; - } - $.jStore.delegate.trigger('jStore-ready', e); - } else { - if (!e.autoload) // Not available - throw 'JSTORE_ENGINE_UNAVILABLE'; - else { // The hard way - e.included(function(){ - if (this.isAvailable()) { // Worked out - $.jStore.Instances[name] = this; - // If there is no current engine, use this one - if (!$.jStore.CurrentEngine){ - $.jStore.CurrentEngine = this; - } - $.jStore.delegate.trigger('jStore-ready', this); - } - else $.jStore.delegate.trigger('jStore-failure', this); - }).include(); - } - } - } - - // Set the current storage engine - $.jStore.setCurrentEngine = function(name){ - if (!$.jStore.Instances.length ) // If no instances exist, attempt to load one - return $.jStore.FindEngine(); - - if (!name && $.jStore.Instances.length >= 1) { // If no name is specified, use the first engine - $.jStore.delegate.trigger('jStore-ready', $.jStore.Instances[0]); - return $.jStore.CurrentEngine = $.jStore.Instances[0]; - } - - if (name && $.jStore.Instances[name]) { // If a name is specified and exists, use it - $.jStore.delegate.trigger('jStore-ready', $.jStore.Instances[name]); - return $.jStore.CurrentEngine = $.jStore.Instances[name]; - } - - throw 'JSTORE_JRI_NO_MATCH'; - } - - // Test all possible engines for straightforward useability - $.jStore.FindEngine = function(){ - $.each($.jStore.EngineOrder, function(k){ - if ($.jStore.Availability[this]()){ // Find the first, easiest option and use it. - $.jStore.use(this, $.jStore.defaults.project, 'default'); - return false; - } - }) - } - - // Provide a simple interface for storing/getting values - $.jStore.store = function(key, value){ - if (!$.jStore.CurrentEngine) return false; - - if ( !value ) // Executing a get command - return $.jStore.CurrentEngine.get(key); - // Executing a set command - return $.jStore.CurrentEngine.set(key, value); - } - // Provide a simple interface for storing/getting values - $.jStore.remove = function(key){ - if (!$.jStore.CurrentEngine) return false; - - return $.jStore.CurrentEngine.rem(key); - } - - // Provide a chainable interface for storing values/getting a value at the end of a chain - $.fn.store = function(key, value){ - if (!$.jStore.CurrentEngine) return this; - - var result = $.jStore.store(key, value); - - return !value ? result : this; - } - - // Provide a chainable interface for removing values - $.fn.removeStore = function(key){ - $.jStore.remove(key); - - return this; - } - - // Provide a way for users to call for auto-loading - $.jStore.load = function(){ - if ($.jStore.defaults.engine) - return $.jStore.use($.jStore.defaults.engine, $.jStore.defaults.project, 'default'); - - // Attempt to find a valid engine, and catch any exceptions if we can't - try { - $.jStore.FindEngine(); - } catch (e) {} - } - -})(jQuery); -/** - * jStore Engine Core - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - this.StorageEngine = Class.extend({ - init: function(project, name){ - // Configure the project name - this.project = project; - // The JRI name given by the manager - this.jri = name; - // Cache the data so we can work synchronously - this.data = {}; - // The maximum limit of the storage engine - this.limit = -1; - // Third party script includes - this.includes = []; - // Create an event delegate for users to subscribe to event triggers - this.delegate = new jStoreDelegate(this) - .bind('engine-ready', function(){ - this.isReady = true; - }) - .bind('engine-included', function(){ - this.hasIncluded = true; - }); - // If enabled, the manager will check availability, then run include(), then check again - this.autoload = false; // This should be changed by the engines, if they have required includes - // When set, we're ready to transact data - this.isReady = false; - // When the includer is finished, it will set this to true - this.hasIncluded = false; - }, - // Performs all necessary script includes - include: function(){ - var self = this, - total = this.includes.length, - count = 0; - - $.each(this.includes, function(){ - $.ajax({type: 'get', url: this, dataType: 'script', cache: true, - success: function(){ - count++; - if (count == total) self.delegate.trigger('engine-included'); - } - }) - }); - }, - // This should be overloaded with an actual functionality presence check - isAvailable: function(){ - return false; - }, - /** Event Subscription Shortcuts **/ - ready: function(callback){ - if (this.isReady) callback.apply(this); - else this.delegate.bind('engine-ready', callback); - return this; - }, - included: function(callback){ - if (this.hasIncluded) callback.apply(this); - else this.delegate.bind('engine-included', callback); - return this; - }, - /** Cache Data Access **/ - get: function(key){ - return this.data[key] || null; - }, - set: function(key, value){ - this.data[key] = value; - return value; - }, - rem: function(key){ - var beforeDelete = this.data[key]; - this.data[key] = null; - return beforeDelete; - } - }); - -})(jQuery); -/* - * jStore DOM Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Set up a static test function for this instance - var sessionAvailability = $.jStore.Availability.session = function(){ - return !!window.sessionStorage; - }, - localAvailability = $.jStore.Availability.local = function(){ - return !!(window.localStorage || window.globalStorage); - }; - - this.jStoreDom = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'DOM'; - - // Set the Database limit - this.limit = 5 * 1024 * 1024; - }, - connect: function(){ - // Fire our delegate to indicate we're ready for data transactions - this.delegate.trigger('engine-ready'); - }, - get: function(key){ - var out = this.db.getItem(key); - // Gecko's getItem returns {value: 'the value'}, WebKit returns 'the value' - return out && out.value ? out.value : out - }, - set: function(key, value){ - this.db.setItem(key,value); - return value; - }, - rem: function(key){ - var out = this.get(key); - this.db.removeItem(key); - return out - } - }) - - this.jStoreLocal = jStoreDom.extend({ - connect: function(){ - // Gecko uses a non-standard globalStorage[ www.example.com ] DOM access object for persistant storage. - this.db = !window.globalStorage ? window.localStorage : window.globalStorage[location.hostname]; - this._super(); - }, - isAvailable: localAvailability - }) - - this.jStoreSession = jStoreDom.extend({ - connect: function(){ - this.db = sessionStorage; - this._super(); - }, - isAvailable: sessionAvailability - }) - - $.jStore.Engines.local = jStoreLocal; - $.jStore.Engines.session = jStoreSession; - - // Store the ordering preference - $.jStore.EngineOrder[ 1 ] = 'local'; - -})(jQuery); -/* - * jStore Flash Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - * jStore.swf Copyright (c) 2008 Daniel Bulli (http://www.nuff-respec.com) - */ -(function($){ - - // Set up a static test function for this instance - var avilability = $.jStore.Availability.flash = function(){ - return !!($.jStore.hasFlash('8.0.0')); - } - - this.jStoreFlash = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'Flash'; - - // Bind our flashReady function to the jStore Delegate - var self = this; - $.jStore.flashReady(function(){ self.flashReady() }); - }, - connect: function(){ - var name = 'jstore-flash-embed-' + this.project; - - // To make Flash Storage work on IE, we have to load up an iFrame - // which contains an HTML page that embeds the object using an - // object tag wrapping an embed tag. Of course, this is unnecessary for - // all browsers except for IE, which, to my knowledge, is the only browser - // in existance where you need to complicate your code to fix bugs. Goddamnit. :( - $(document.body) - .append('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" ' + - 'id="jStoreFlashFrame" src="' +$.jStore.defaults.flash + '"></iframe>'); - }, - flashReady: function(e){ - var iFrame = $('#jStoreFlashFrame')[0]; - - // IE - if (iFrame.Document && $.isFunction(iFrame.Document['jStoreFlash'].f_get_cookie)) this.db = iFrame.Document['jStoreFlash']; - // Safari && Firefox - else if (iFrame.contentWindow && iFrame.contentWindow.document){ - var doc = iFrame.contentWindow.document; - // Safari - if ($.isFunction($('object', $(doc))[0].f_get_cookie)) this.db = $('object', $(doc))[0]; - // Firefox - else if ($.isFunction($('embed', $(doc))[0].f_get_cookie)) this.db = $('embed', $(doc))[0]; - } - - // We're ready to process data - if (this.db) this.delegate.trigger('engine-ready'); - }, - isAvailable: avilability, - get: function(key){ - var out = this.db.f_get_cookie(key); - return out == 'null' ? null : out; - }, - set: function(key, value){ - this.db.f_set_cookie(key, value); - return value; - }, - rem: function(key){ - var beforeDelete = this.get(key); - this.db.f_delete_cookie(key); - return beforeDelete; - } - }) - - $.jStore.Engines.flash = jStoreFlash; - - // Store the ordering preference - $.jStore.EngineOrder[ 2 ] = 'flash'; - - /** - * Flash Detection functions copied from the jQuery Flash Plugin - * Copyright (c) 2006 Luke Lutman (http://jquery.lukelutman.com/plugins/flash) - * Dual licensed under the MIT and GPL licenses. - * http://www.opensource.org/licenses/mit-license.php - * http://www.opensource.org/licenses/gpl-license.php - */ - $.jStore.hasFlash = function(version){ - var pv = $.jStore.flashVersion().match(/\d+/g), - rv = version.match(/\d+/g); - - for(var i = 0; i < 3; i++) { - pv[i] = parseInt(pv[i] || 0); - rv[i] = parseInt(rv[i] || 0); - // player is less than required - if(pv[i] < rv[i]) return false; - // player is greater than required - if(pv[i] > rv[i]) return true; - } - // major version, minor version and revision match exactly - return true; - } - - $.jStore.flashVersion = function(){ - // ie - try { - try { - // avoid fp6 minor version lookup issues - // see: http://blog.deconcept.com/2006/01/11/getvariable-setvariable-crash-internet… - var axo = new ActiveXObject('ShockwaveFlash.ShockwaveFlash.6'); - try { axo.AllowScriptAccess = 'always'; } - catch(e) { return '6,0,0'; } - } catch(e) {} - return new ActiveXObject('ShockwaveFlash.ShockwaveFlash').GetVariable('$version').replace(/\D+/g, ',').match(/^,?(.+),?$/)[1]; - // other browsers - } catch(e) { - try { - if(navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin){ - return (navigator.plugins["Shockwave Flash 2.0"] || navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g, ",").match(/^,?(.+),?$/)[1]; - } - } catch(e) {} - } - return '0,0,0'; - } - -})(jQuery); - -// Callback fired when ExternalInterface is established -function flash_ready(){ - $.jStore.delegate.trigger('flash-ready'); -} -/* - * jStore Google Gears Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Set up a static test function for this instance - var avilability = $.jStore.Availability.gears = function(){ - return !!(window.google && window.google.gears) - } - - this.jStoreGears = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'Google Gears'; - - // Add required third-party scripts - this.includes.push('http://code.google.com/apis/gears/gears_init.js'); - - // Allow Autoloading on fail - this.autoload = true; - }, - connect: function(){ - // Create our database connection - var db = this.db = google.gears.factory.create('beta.database'); - db.open( 'jstore-' + this.project ); - db.execute( 'CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)' ); - - // Cache the data from the table - this.updateCache(); - }, - updateCache: function(){ - // Read the database into our cache object - var result = this.db.execute( 'SELECT k,v FROM jstore' ); - while (result.isValidRow()){ - this.data[result.field(0)] = result.field(1); - result.next(); - } result.close(); - - // Fire our delegate to indicate we're ready for data transactions - this.delegate.trigger('engine-ready'); - }, - isAvailable: avilability, - set: function(key, value){ - // Update the database - var db = this.db; - db.execute( 'BEGIN' ); - db.execute( 'INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key,value] ); - db.execute( 'COMMIT' ); - return this._super(key, value); - }, - rem: function(key){ - // Update the database - var db = this.db; - db.execute( 'BEGIN' ); - db.execute( 'DELETE FROM jstore WHERE k = ?', [key] ); - db.execute( 'COMMIT' ); - return this._super(key); - } - }) - - $.jStore.Engines.gears = jStoreGears; - - // Store the ordering preference - $.jStore.EngineOrder[ 3 ] = 'gears'; - -})(jQuery); -/* - * jStore HTML5 Specification Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Set up a static test function for this instance - var avilability = $.jStore.Availability.html5 = function(){ - return !!window.openDatabase - } - - this.jStoreHtml5 = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'HTML5'; - - // Set the Database limit - this.limit = 1024 * 200; - }, - connect: function(){ - // Create our database connection - var db = this.db = openDatabase('jstore-' + this.project, '1.0', this.project, this.limit); - if (!db) throw 'JSTORE_ENGINE_HTML5_NODB'; - db.transaction(function(db){ - db.executeSql( 'CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)' ); - }); - - // Cache the data from the table - this.updateCache(); - }, - updateCache: function(){ - var self = this; - // Read the database into our cache object - this.db.transaction(function(db){ - db.executeSql( 'SELECT k,v FROM jstore', [], function(db, result){ - var rows = result.rows, i = 0, row; - for (; i < rows.length; ++i){ - row = rows.item(i); - self.data[row.k] = row.v; - } - - // Fire our delegate to indicate we're ready for data transactions - self.delegate.trigger('engine-ready'); - }); - }); - }, - isAvailable: avilability, - set: function(key, value){ - // Update the database - this.db.transaction(function(db){ - db.executeSql( 'INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key,value]); - }); - return this._super(key, value); - }, - rem: function(key){ - // Update the database - this.db.transaction(function(db){ - db.executeSql( 'DELETE FROM jstore WHERE k = ?', [key] ) - }) - return this._super(key); - } - }) - - $.jStore.Engines.html5 = jStoreHtml5; - - // Store the ordering preference - $.jStore.EngineOrder[ 0 ] = 'html5'; - -})(jQuery); -/* - * jStore IE Storage Engine - * Copyright (c) 2009 Eric Garside (http://eric.garside.name) - */ -(function($){ - - // Set up a static test function for this instance - var avilability = $.jStore.Availability.ie = function(){ - return !!window.ActiveXObject; - } - - this.jStoreIE = StorageEngine.extend({ - init: function(project, name){ - // Call the parental init object - this._super(project, name); - - // The type of storage engine - this.type = 'IE'; - - // Allow Autoloading on fail - this.limit = 64 * 1024; - }, - connect: function(){ - // Create a hidden div to store attributes in - this.db = $('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-' + this.project + '"></div>') - .appendTo(document.body).get(0); - // Fire our delegate to indicate we're ready for data transactions - this.delegate.trigger('engine-ready'); - }, - isAvailable: avilability, - get: function(key){ - this.db.load(this.project); - return this.db.getAttribute(key); - }, - set: function(key, value){ - this.db.setAttribute(key, value); - this.db.save(this.project); - return value; - }, - rem: function(key){ - var beforeDelete = this.get(key); - this.db.removeAttribute(key); - this.db.save(this.project); - return beforeDelete; - } - }) - - $.jStore.Engines.ie = jStoreIE; - - // Store the ordering preference - $.jStore.EngineOrder[ 4 ] = 'ie'; - -})(jQuery); diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/jquery.jstore.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/jquery.jstore.js Fri Apr 09 18:09:54 2010 -0400 @@ -0,0 +1,1810 @@ +/*! + * jStore 2.0 - Persistent Client Side Storage + * + * Copyright (c) 2010 Eric Garside (http://eric.garside.name/) + * Dual licensed under: + * MIT: http://www.opensource.org/licenses/mit-license.php + * GPLv3: http://www.opensource.org/licenses/gpl-3.0.html + * + * --------------------------- + * + * jStore Flash Storage Component + * + * Copyright (c) 2006 Jeff Lerman (jeff(a)blip.tv) + * Licensed under the Creative Commons Attribution 3.0 United States License: + * http://creativecommons.org/licenses/by/3.0/us + */ + +"use strict"; + +/*global Class, window, jQuery, ActiveXObject, google */ + +/*jslint white: true, browser: true, onevar: true, undef: true, eqeqeq: true, bitwise: true, regexp: false, strict: true, newcap: true, immed: true, maxerr: 50, indent: 4 */ + +(function ($, window) { + + //------------------------------ + // + // Constants + // + //------------------------------ + + //------------------------------ + // Exceptions + //------------------------------ + + /** + * An exception thrown by the StorageEngine class whenever its data accessor methods + * are called before the engine is ready to transact data. + */ + var EX_UNSTABLE = 'JSTORE_ENGINE_UNSTABLE', + + /** + * An exception thrown by jStore whenever an undefined storage engine is referenced for + * some task by an invalid JRI (jStore Resource Identifier). + */ + EX_UNKNOWN = 'JSTORE_UNKNOWN_ENGINE_REQUESTED', + + /** + * An exception thrown by jStore whenever a given flavor of storage is double defined. + */ + EX_COLLISION = 'JSTORE_ENGINE_NAMESPACE_COLLISION', + + /** + * An exception thrown by jStore whenever a jri is double applied to a resource. + */ + EX_DUPLICATE = 'JSTORE_RESOURCE_NAMESPACE_COLLISION', + + /** + * An exception thrown by jStore whenever a given flavor of storage has no defined engine. + */ + EX_UNAVAILABLE = 'JSTORE_ENGINE_UNAVAILABLE', + + /** + * An exception thrown by jStore whenever an invalid flavor type is used. + */ + EX_INVALID = 'JSTORE_INVALID_FLAVOR', + + //------------------------------ + // Regular Expressions + //------------------------------ + + /** + * Regular expression to test property values for being JSON. + */ + RX_JSON = (function () + { + try + { + return new RegExp('^("(\\\\.|[^"\\\\\\n\\r])*?"|[,:{}\\[\\]0-9.\\-+Eaeflnr-u \\n\\r\\t])+?$'); + } + catch (e) + { + return (/^(true|false|null|\[.*\]|\{.*\}|".*"|\d+|\d+\.\d+)$/); + } + }()), + + //------------------------------ + // Storage Flavors + //------------------------------ + + /** + * The storage flavor identifier for HTML5 local storage. + */ + FLAVOR_LOCAL = 'jstore-html5-local', + + /** + * The storage flavor identifier for HTML5 database storage. + */ + FLAVOR_SQL = 'jstore-html5-sql', + + /** + * The storage flavor identifier for Adobe Flash SharedObject storage. + */ + FLAVOR_FLASH = 'jstore-flash', + + /** + * The storage flavor identifier for Google Gears storage. + */ + FLAVOR_GEARS = 'jstore-google-gears', + + /** + * The storage flavor identifier for Internet Explorer storage, available to IE7 and IE6. + */ + FLAVOR_MSIE = 'jstore-msie', + + //------------------------------ + // + // Property Declaration + // + //------------------------------ + + /** + * The base StorageEngine class which each "storage flavor" will extend to meet the + * requirements for its specific implementation. + */ + StorageEngine, + + /** + * The jStore object. Internal to this closure, jStore is referenced by "_". It is + * exposed to jQuery below, and made publicly accessible through jQuery.jStore + */ + _ = {}, + + /** + * The engines available to jStore for use. These are the class definitions for flavored + * storage engines. + * + * Signature: + * { + * <storageFlavor>: <flavoredStorageEngineDefinition>, + * + * ... + * } + */ + definitions = {}, + + /** + * Active engines instantiated by jStore, indexed by their JRI. + * + * Signature: + * { + * <engineJRI>: <engineInstance>, + * + * ... + * } + */ + engines = {}, + + /** + * If we are going to be using the flash storage engine, we want to postpone the jStore ready event until the jStore + * isFlashReady flag is also true. This property is set whenever flash is determined to be the storage engine. + */ + waitForFlash = false, + + /** + * Storage for listeners, indexed by content and event type. + * + * Signature: + * { + * <context>: + * { + * <eventType>: [<listener>, ...], + * + * ... + * }, + * + * ... + * } + */ + events = {}, + + /** + * The configuration for this implementation. + * + * Signature: + * { + * project: <defaultProjectName>, + * + * flash: <pathToFlashBootloader>, + * + * json: <pathToJSONFile>, + * + * errorCallback: <listenerToNotifyOnError> + * } + */ + configurations = + { + project: undefined, + + flash: 'jStore.Flash.html', + + json: 'browser.json.js' + }, + + /** + * The active storage engine, being used to satisfy the get/set/remove functions on the jStore and jQuery + * objects. + */ + active; + + //------------------------------ + // + // Internal Methods + // + //------------------------------ + + /** + * Determine if the given flavor is valid. + * + * @param flavor The flavor to test. + * + * @return True if the flavor is valid, false otherwise. + */ + function validFlavor(flavor) + { + switch (flavor) + { + + case FLAVOR_LOCAL: + case FLAVOR_SQL: + case FLAVOR_FLASH: + case FLAVOR_GEARS: + case FLAVOR_MSIE: + return true; + + default: + return false; + + } + } + + /** + * Performs enhanced type comparison on an object. This is more reliable method + * of type checking a variable than a simple typeof comparison. The reason is that, + * typeof will reduce to the lowest common type. + * + * "typeof []" returns Object, and not Array. + * "typeof {}" returns Object as well. + * + * typecheck( [], 'Array' ) : returns true; + * typecheck( [], 'Object' ) : returns false; + * + * @param type The variable type to check. + * + * @param compare A string representing the literal type to check. + * + * @return True if the variable "type" matches the compare literal. + */ + function typecheck(type, compare) + { + return !type ? false : type.constructor.toString().match(new RegExp(compare + '\$\$', 'i')) !== null; + } + + /** + * If the provided listener is a valid function, it will be triggered with the provided context + * and parameters. + * + * @param listener The listener being triggered. + * + * @param context The context to provide to the listener. + * + * @param parameters The parameters to pass to the listener as arguments. + * + * @return The response of the notified listener. + */ + function notify(listener, context, parameters) + { + if (typecheck(listener, 'Function')) + { + return listener.apply(context || _, typecheck(parameters, 'Array') ? parameters : [parameters]); + } + } + + /** + * Load the given script. + * + * @param path The path to the file to include. + * + * @param listener The listener to notify when the file finishes loading. + */ + function loadScript(path, listener) + { + $.ajax( + { + url: path, + complete: listener || $.noop(), + type: 'GET', + dataType: 'script', + cache: false + }); + } + + /** + * Checks the type of the value, and returns a value safe to persist in any client-side mechanism. + * + * @param value The value which should be prepared for storage. + * + * @return A value safe for storage. + */ + function prepareForStorage(value) + { + if (value === undefined) + { + return ''; + } + + if (typecheck(value, 'Object') || + typecheck(value, 'Array') || + typecheck(value, 'Function')) + { + return JSON.stringify(value); + } + + return value; + } + + /** + * Checks the type of the value, and returns a value safe for access in any client-side mechanism. + * + * @param value The value which should be prepared for use. + * + * @return A value safe for use. + */ + function prepareForRevival(value) + { + return RX_JSON.test(value) ? JSON.parse(value) : value; + } + + /** + * Normalize a key before using it, to ensure it's valid. + * + * @param key The key to normalize. + * + * @return A normalized key, safe for storage. + */ + function normalizeKey(key) + { + return key.replace(/^\s+|\s+$/g, ""); + } + + /** + * Define a flavored storage engine. + * + * @throws EX_COLLISION, EX_INVALID + * + * @param flavor The flavor of engine being defined. + * + * @param definition An object containing the new properties and methods for the engine extension. + * + * @param availability A function to invoke which must return a boolean value indicating the + * availability of the storage flavor on this browser. + */ + function define(flavor, definition, availability) + { + if (!validFlavor(flavor)) + { + throw EX_INVALID; + } + + if (availability[flavor] !== undefined) + { + throw EX_COLLISION; + } + + /** + * The logic here has been reworked so unavailable flavors are discarded, so we don't needlessly + * bloat the runtime size of jStore. + */ + if (notify(availability) === true) + { + _.available[flavor] = true; + + definition.flavor = flavor; + + definitions[flavor] = StorageEngine.extend(definition); + } + else + { + _.available[flavor] = false; + + // Filter the invalid flavor out of the priority list. + _.enginePriority = $.map(_.enginePriority, function (engine) + { + if (engine === flavor) + { + return null; + } + else + { + return engine; + } + }); + } + } + + /** + * Make the jStore library ready. + */ + function makeReady() + { + if (_.isReady) + { + return; + } + + if ((waitForFlash && _.isFlashReady) || !waitForFlash) + { + _.isReady = true; + _.trigger('jstore-ready', [engines[active]]); + } + } + + /** + * Create a best-fit engine. + */ + function createBestFitEngine() + { + _.create(_.enginePriority[0], undefined, 'best-fit'); + } + + /** + * Get the flash version currently supported in this browser. + * + * @return The flash version. + */ + function flashVersion() + { + // MSIE + try + { + // avoid fp6 minor version lookup issues + // see: http://blog.deconcept.com/2006/01/11/getvariable-setvariable-crash-internet… + var axo = new ActiveXObject('ShockwaveFlash.ShockwaveFlash.6'); + + try + { + axo.AllowScriptAccess = 'always'; + } + catch (axo_e) + { + return '6,0,0'; + } + + return new ActiveXObject('ShockwaveFlash.ShockwaveFlash').GetVariable('$version').replace(/\D+/g, ',').match(/^,?(.+),?$/)[1]; + } + + // Real browsers + catch (e) + { + try + { + if (navigator.mimeTypes["application/x-shockwave-flash"].enabledPlugin) + { + return (navigator.plugins["Shockwave Flash 2.0"] || navigator.plugins["Shockwave Flash"]).description.replace(/\D+/g, ",").match(/^,?(.+),?$/)[1]; + } + } + catch (flash_e) + {} + } + + return '0,0,0'; + } + + /** + * Flash Detection functions copied from the jQuery Flash Plugin + * + * Copyright (c) 2006 Luke Lutman (http://jquery.lukelutman.com/plugins/flash) + * + * Dual licensed under the MIT and GPL licenses. + * http://www.opensource.org/licenses/mit-license.php + * http://www.opensource.org/licenses/gpl-license.php + * + * @param version The version to compare to. + * + * @return True if the version is greater than or equal to the required version, false otherwise. + */ + function hasFlashVersion(version) + { + var playerVersion = flashVersion().match(/\d+/g), + requiredVersion = version.match(/\d+/g), + index = 0, + player, + required; + + for (; index < 3; index++) + { + player = parseInt(playerVersion[index], 10); + required = parseInt(requiredVersion[index], 10); + + // Player version is less than what is required. + if (player < required) + { + return false; + } + + // Player version is greater than what is required. + else if (player > required) + { + return true; + } + } + + // Player and required version match exactly. + return true; + } + + //------------------------------ + // + // Plugin Definition + // + //------------------------------ + + //------------------------------ + // Error Declaration + //------------------------------ + + //------------------------------ + // Plugin Creation + //------------------------------ + + /** + * The jStore object. Manages a collection of StorageEngines for particular "storage flavors", or the types + * of storage solutions available to each browser. + * + * 2.0 Version Notes: + * + * - The user is now responsible for third-party script includes, with the exception of flash. + * + * - jStore has been given sole responsibility for testing engine availability. + * + * - For the sake of naming conventions, all property names now start with a lowercase, and are camel-cased. + * + * The following properties have been changed since the 1.2.x release: + * + * - EngineOrder: For the sake of naming conventions, renamed to enginePriority. + * + * The following properties and methods have been removed since the 1.2.x release: + * + * - Availability: jStore's engines would add their availability tests to this object, so jStore could test + * them. With the changes to how availability testing works, this property has been removed. + * A new property, "available" on jStore contains a set of available engines. + * + * - Engines: Formerly contained the definitions of storage engines. This property has been removed, and + * storage of these definitions has been moved internal to the closure. + * + * - Instances: Formerly contained instantiated storage engines. This property has been removed, and storage + * of instantiated engines has been moved internal to the closure. + * + * - CurrentEngine: Formerly contained the active storage engine being used for transacting data through the jStore + * and/or jQuery objects. This property has been removed, and storage of the current engine has + * been moved internal to the closure. A new method, "activeEngine" has been added to jQuery to + * get and set the active engine to use. + * + * - defaults: Formerly used to set the implementation options for jStore. This property has been removed and + * replaced with a new configuration metho on the jStore object. + * + * - delegate: The delegate class has been removed in favor of a much simpler bind/trigger accessor system, which + * is accessible contextually through storage engines, or generically through jStore. + * + * + fail: This registration class bound events on the delegate for jstore-fail events. Instead, use: + * jStore.bind('jstore-failure', listener); + * + * + flashReady: This registration class bound events on the delegate for flash-ready events. The jstore-ready method + * now accounts for waiting for flash readyness, if and only if the flash engine is being used. Simply + * call to jStore.ready(). + * + * + load: Replaced with the init() method, which performs the same basic functions as the old load() method. Also, + * the init function is now domready safe, meaning it wraps itself in a domready listener, so the end user + * doesn't have to. + * + * + FindEngine: Removed entirely. The functionality provided by this method now implicitly occurs with the new define() + * system implemented for engine flavors. + * + * + setCurrentEngine: Replaced by activeEngine(). Set the current active engine by passing in the JRI. + * + * + safeStore: Replaced by a method internal to this closure, "prepareForStorage". + * + * + safeResurrect: Replaced by a method internal to this closure, "prepareForRevival". + * + * + use: Replaced by "create". + */ + $.extend(_, { + + //------------------------------ + // Properties + //------------------------------ + + /** + * The priority order in which engines should be tested for use. The lower their index in the array, the higher + * their priority for use. + * + * Be weary when reconfiguring the priority order of engines! jStore will use the first available engine it finds + * based on its priority when autoloading. + * + * This array is filtered out as engines are defined, with invalid engines being removed. + * + * Signature: + * [FLAVOR_<storageFlavor>, ...] + */ + enginePriority: [FLAVOR_LOCAL, FLAVOR_SQL, FLAVOR_FLASH, FLAVOR_MSIE], + + /** + * A collection of the availability states of engines, indexed by their flavor. + * + * Signature: + * { + * <storageFlavor>: true|false, + * + * ... + * } + */ + available: {}, + + /** + * Flag to determine if the jStore library is ready. jStore becomes ready once the dom is ready and all necessary + * startup procedures required by jStore to function properly are completed. + */ + isReady: false, + + /** + * With the flash storage engine, we have to jump through a couple of hoops before the flash engine is ready to work. + * This flag tracks whether or not the flash storage is available. + */ + isFlashReady: false, + + /** + * The available engine flavors. + */ + flavors: + { + local: FLAVOR_LOCAL, + + sql: FLAVOR_SQL, + + flash: FLAVOR_FLASH, + + gears: FLAVOR_GEARS, + + msie: FLAVOR_MSIE + }, + + //------------------------------ + // Constructor + //------------------------------ + + /** + * Constructor. + * + * @throws EX_INVALID + * + * @param project The name of the jStore project. Used to generate a JRI for the engine we create. + * + * @param configuration Optionally, an object containing configuration options for this implementation. + * + * @param flavor Optionally, the flavor of storage to use. If not provided, jStore will pick the + * best flavor, based on the current browser. + * + * @return jStore + */ + init: function (project, configuration, flavor) + { + // Extend our plugin configurations + $.extend(configurations, {project: project}, configuration); + + $(function () + { + // If JSON parsing isn't defined in this browser, include it. + if (window.JSON === undefined) + { + loadScript(configurations.json); + } + + // If we have an explicit flavor to use, use it. + if (flavor !== undefined) + { + _.create(flavor, project, 'default'); + } + + // Otherwise, attempt to create a best-fit engine. + else + { + createBestFitEngine(); + } + }); + + return _; + }, + + //------------------------------ + // Methods + //------------------------------ + + /** + * Create an instance of a flavored engine. + * + * @throws EX_INVALID, EX_UNAVAILABLE, EX_DUPLICATE + * + * @param flavor The flavor to create the engine with. + * + * @param project The project identifier for this instance. + * + * @param identifier Some arbitrary identifier for this project instance of the engine. + * + * @return The created instance. + */ + create: function (flavor, project, identifier) + { + project = project || configurations.project || location.hostname.replace(/\./g, '-') || 'unknown'; + + if (!validFlavor(flavor)) + { + throw EX_INVALID; + } + + if (definitions[flavor] === undefined) + { + throw EX_UNAVAILABLE; + } + + var jri = (identifier !== undefined ? identifier + '.' : '') + project + '.' + flavor, + engine; + + if (engines[jri] !== undefined) + { + throw EX_DUPLICATE; + } + + // Create our engine instance. + engine = engines[jri] = new definitions[flavor](project, jri); + + // Set up a listener for our jstore-engine-ready event. + engine.ready(function () + { + _.trigger('jstore-engine-ready', [engine]); + }); + + if (flavor === FLAVOR_FLASH && !_.isFlashReady) + { + if (active === undefined) + { + waitForFlash = true; + } + + // Define a window-accessible function for flash to call via ExternalInterface + window.jstore_ready = function () + { + _.isFlashReady = true; + _.trigger('flash-ready'); + + if (active === undefined) + { + makeReady(); + } + + // Remove the callback from the window scope, as it is no longer necessary + window.flash_ready = undefined; + }; + + window.jstore_error = function (message) + { + _.trigger('jstore-error', ['JSTORE_FLASH_EXCEPTION', null, message]); + }; + + $('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" id="jStoreFlashFrame" src="' + + configurations.flash + '"></iframe>').appendTo('body'); + } + else if (active === undefined) + { + active = jri; + makeReady(); + } + + return engine; + }, + + /** + * Fetch an engine by it's JRI. + * + * @param jri The JRI of the engine to retrieve. + * + * @return The requested engine. + */ + engine: function (jri) + { + return engines[jri]; + }, + + /** + * Returns the active storage engine being used. If a value is passed, sets that engine as the active engine. + * + * @throws EX_UNKNOWN + * + * @param jri Optionally, the JRI of the engine to make active, if it should be changed. + * + * @return The active storage engine. + */ + activeEngine: function (jri) + { + if (jri !== undefined) + { + if (engines[jri] === undefined) + { + throw EX_UNKNOWN; + } + else + { + active = jri; + } + } + + return engines[active]; + }, + + /** + * Bind an event listener. + * + * @param event The event to bind a listener on. + * + * @param listener The listener to notify when the event occurs. + * + * @param context The context of the binding. A string representing the engine flavor + * binding the event, or undefined to indicate it's a jStore event. + * + * @return jStore + */ + bind: function (event, listener, context) + { + context = context || 'jstore'; + + if (events[context] === undefined) + { + events[context] = {}; + } + + if (events[context][event] === undefined) + { + events[context][event] = [listener]; + } + else + { + events[context][event].push(listener); + } + + return _; + }, + + /** + * Trigger an event, notifying any bound listeners. + * + * @param event The event to trigger. + * + * @param parameters Any additional parameters to pass to the listeners being notified. + * + * @param context The context of the binding. A string representing the engine flavor + * binding the event, or undefined to indicate it's a jStore event. + * + * @return jStore + */ + trigger: function (event, parameters, context) + { + context = context || 'jstore'; + + if (events[context] !== undefined) + { + if (events[context][event] !== undefined) + { + $.each(events[context][event], function () + { + notify(this, _, parameters); + }); + } + } + + return _; + }, + + /** + * Bind a listener to be notified when jStore causes a non-fatal exception. + * + * @param listener The listener to notify when a failure occurs. + */ + error: function (listener) + { + _.bind('jstore-error', listener); + }, + + /** + * Bind a listener to be notified when jStore is ready. + * + * @param listener The listener to notify when jStore is ready. + * + * @return jStore + */ + ready: function (listener) + { + if (_.isReady) + { + notify(listener); + } + else + { + _.bind('jstore-ready', listener); + } + + return _; + }, + + /** + * Bind a listener to be notified when jStore and the default engine are ready. + * + * @param listener The listener to notify when jStore and it's default engine are ready. + * + * @return jStore + */ + engineReady: function (listener) + { + if (_.isReady) + { + notify(listener); + } + else + { + _.bind('jstore-engine-ready', listener); + } + + return _; + }, + + /** + * A combined getter/setter for the active engine. + * + * @param key The key of the property to get, or set. + * + * @param value If a valid value is provided, sets the engine. + * + * @return The requested property value. + */ + store: function (key, value) + { + return value === undefined ? _.get(key) : _.set(key, value); + }, + + /** + * Remove a property from the active engine. + * + * @param key The key of the property to remove. + * + * @return The value of the property before removal. + */ + remove: function (key) + { + return _.activeEngine().remove(key); + }, + + /** + * Get a property from the active engine. + * + * @param key The key of the property to get. + * + * @return The value of the property. + */ + get: function (key) + { + return _.activeEngine().get(key); + }, + + /** + * Set a property on the active engine. + * + * @param key The key of the property to set. + * + * @param value The value to set the property to. + * + * @return The new value of the property. + */ + set: function (key, value) + { + return _.activeEngine().set(key, value); + } + + }); + + //------------------------------ + // Core Extension + //------------------------------ + + //------------------------------ + // + // Class Definition + // + //------------------------------ + + /** + * The StorageEngine class is the unified API through which jStore accesses and manipulates + * the various storage flavors available. + * + * 2.0 Version Notes: + * + * - All third-party loading is now the responsibility of the developer. + * + * - The delegate class has been removed entirely. Engines have been given "bind" and "trigger" methods + * to interact directly with the delegate like-replacement that has been added to jStore. + * + * - Engine availability has been moved out of the engines themselves, and elevated to a jStore + * responsibility. + * + * The following methods have changed since the 1.2.x release: + * + * - get: When "get"ting a non-stored property, the get function will now return "undefined" + * instead of "null". "null" can now be used as a valid property value. + * + * - rem: Renamed to "remove". I always felt dirty about "rem" being vaguely explicit. + * + * The following properties have been removed since the 1.2.x release: + * + * - autoload: Part of the third-party loading logic. + * + * - hasIncluded: Part of the third-party loading logic. + * + * - includes: Part of the third-party loading logic. + * + * - isAvailable: Part of the availability logic elevated to jStore. + * + * @throws EX_UNSTABLE + */ + StorageEngine = Class.extend({ + + //------------------------------ + // Properties + //------------------------------ + + /** + * The project which owns this storage engine. + */ + project: undefined, + + /** + * The JRI (jStore Resource Identifier) acts as a uuid for this specific instance + * of the storage engine. + */ + jri: undefined, + + /** + * The flavor of this engine. + */ + flavor: undefined, + + /** + * The actual database object which data is transacted through. + */ + database: undefined, + + /** + * A StorageEngine should always respond to fetch requests synchronously. However, some + * of the storage flavors require callback-based asynchronous access. To get around this, + * we simlpy require all engines to function off a primary data cache, to allow for + * synchronous access across all implementations. + * + * Signature: + * { + * <propertyKey>: <propertyValue>, + * + * ... + * } + */ + data: undefined, + + /** + * A number of storage engines enforce a size limit as to what they will persist for a given site. + * This limit is not monitored or computed by jStore currently, and this property will merely give + * a static indication of the total size alloted to the engine, as defined by the storage flavor. + */ + limit: undefined, + + /** + * Each storage flavor has a different process to go through before it's "ready" to transact data. This + * property stores the state of the engine's readyness, and uses it to notify listeners whenever jStore + * is ready to function. + */ + isReady: undefined, + + //------------------------------ + // Constructor + //------------------------------ + + /** + * Constructor. + * + * @param project The project which instantiated this engine. + * + * @param jri The uuid assigned to this instance by jStore. + */ + init: function (project, jri) + { + this.project = project; + this.jri = jri; + this.data = {}; + this.isReady = false; + this.updateCache(); + }, + + //------------------------------ + // Methods + //------------------------------ + + /** + * Update the cache. + */ + updateCache: function () + { + this.isReady = true; + this.trigger('engine-ready', [this]); + }, + + /** + * Bind a listener to an event dispatched by this engine. + * + * @param event The event to bind on. + * + * @param listener The listener to notify when the event occurs. + */ + bind: function (event, listener) + { + _.bind(event, listener, this.jri); + }, + + /** + * Trigger an event, notifying all bound listeners. + * + * @param event The event to trigger. + * + * @param parameters An optional Array of parameters to pass to the listeners. + */ + trigger: function (event, parameters) + { + _.trigger(event, parameters, this.jri); + }, + + /** + * Bind a listener to the StorageEngine's ready event. + * + * @param listener The listener to notify whenever this engine is ready to transact data. + */ + ready: function (listener) + { + if (this.isReady) + { + notify(listener, this); + } + else + { + this.bind('engine-ready', listener); + } + }, + + /** + * Get a property from the StorageEngine. + * + * @param key The property key of the data to retrieve. + * + * @return The property value, or "undefined" if the property isn't stored. + */ + get: function (key) + { + this.__interruptAccess(); + + return this.data[key]; + }, + + /** + * Sets a property in the StorageEngine. + * + * @param key The key of the property. + * + * @param value The value of the property. + * + * @return The new value of the property. + */ + set: function (key, value) + { + this.__interruptAccess(); + + key = normalizeKey(key); + + try + { + this.__set(key, value); + } + catch (e) + { + _.trigger('jstore-error', ['JSTORE_STORAGE_FAILURE', this.jri, e]); + } + + this.data[key] = value; + + return value; + }, + + /** + * Removes a property from the StorageEngine. + * + * @param key The property key of the data to remove. + * + * @return The value of the property, before it was removed. + */ + remove: function (key) + { + this.__interruptAccess(); + + key = normalizeKey(key); + + try + { + this.__remove(key); + } + catch (e) + { + _.trigger('jstore-error', ['JSTORE_REMOVE_FAILURE', this.jri, e]); + } + + var buffer = this.data[key]; + + this.data[key] = undefined; + + return buffer; + }, + + //------------------------------ + // Internal Methods + //------------------------------ + + /** + * Ensures the engine is in a stable state for transacting data. + * + * @throws EX_UNSTABLE + */ + __interruptAccess: function () + { + if (!this.isReady) + { + throw EX_UNSTABLE; + } + }, + + /** + * Sets a property in the StorageEngine. This method should be overloaded to provide actual + * storage flavor integration. + * + * @param key The key of the property. + * + * @param value The value of the property. + * + * @return The new value of the property. + */ + __set: function (key, value) + { + return; + }, + + /** + * Removes a property from the StorageEngine. This method should be overloaded to provide actual + * storage flavor integration. + * + * @param key The property key of the data to remove. + * + * @return The value of the property, before it was removed. + */ + __remove: function (key) + { + return; + } + + }); + + //------------------------------ + // + // jQuery Hooks + // + //------------------------------ + + $.extend($.fn, { + + //------------------------------ + // Methods + //------------------------------ + + /** + * A combined getter/setter for the active engine. + * + * @param key The key of the property to get, or set. + * + * @param value If a valid value is provided, sets the engine. + * + * @return jQuery + */ + store: function (key, value) + { + if (value === undefined) + { + _.get(key); + } + else + { + _.set(key, value); + } + + return this; + }, + + /** + * Remove a property from the active engine. + * + * @param key The key of the property to remove. + * + * @return jQuery + */ + removeStore: function (key) + { + _.activeEngine().remove(key); + + return this; + }, + + /** + * Get a property from the active engine. + * + * @param key The key of the property to get. + * + * @return The value of the property. + */ + getStore: function (key) + { + return _.activeEngine().get(key); + }, + + /** + * Set a property on the active engine. + * + * @param key The key of the property to set. + * + * @param value The value to set the property to. + * + * @return jQuery + */ + setStore: function (key, value) + { + _.activeEngine().set(key, value); + + return this; + } + + }); + + //------------------------------ + // + // Event Bindings + // + //------------------------------ + + //------------------------------ + // + // Startup Code + // + //------------------------------ + + //------------------------------ + // Expose jStore through jQuery + //------------------------------ + + window.jStore = $.jStore = _; + + //------------------------------ + // + // Engine Definitions + // + //------------------------------ + + //------------------------------ + // Local + //------------------------------ + + define(FLAVOR_LOCAL, + { + //------------------------------ + // Properties + //------------------------------ + + limit: parseInt(5e5, 16), + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + this.database = window.globalStorage === undefined ? window.localStorage : window.globalStorage[location.hostname]; + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function () + { + var key, value; + + for (key in this.database) + { + var has_key = false; + if (this.database.hasOwnProperty) { + if (this.database.hasOwnProperty(key)) { + has_key = true; + } + } else { // IE 8 + if (this.database.getItem(key) !== null) { + has_key = true; + } + } + + if (has_key) { + value = this.database.getItem(key); + + // Gecko's getItem returns {value: 'the value'}, WebKit returns 'the value' + this.data[key] = prepareForRevival(value && value.value ? value.value : value); + } + } + + this._super(); + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + this.database.setItem(key, prepareForStorage(value)); + }, + + __remove: function (key) + { + this.database.removeItem(key); + } + }, + + function () + { + return window.localStorage !== undefined || window.globalStorage !== undefined; + }); + + //------------------------------ + // SQL + //------------------------------ + + define(FLAVOR_SQL, + { + //------------------------------ + // Properties + //------------------------------ + + limit: parseInt(32e3, 16), + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + this.database = window.openDatabase('jstore-' + project, '1.0', project, this.limit); + + if (!this.database) + { + throw 'JSTORE_SQL_NO_DB'; + } + + this.database.transaction(function (database) + { + database.executeSql('CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)'); + }); + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function () + { + var self = this, + _super = this._super; + + this.database.transaction(function (database) + { + database.executeSql('SELECT k,v FROM jstore', [], function (database, result) + { + var rows = result.rows, + index = 0, + row; + + for (; index < rows.length; ++index) + { + row = rows.item(index); + self.data[row.k] = prepareForRevival(row.v); + } + + _super.apply(self); + }); + }); + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + this.database.transaction(function (database) + { + database.executeSql('INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key, prepareForStorage(value)]); + }); + }, + + __remove: function (key) + { + this.database.transaction(function (database) + { + database.executeSql('DELETE FROM jstore WHERE k = ?', [key]); + }); + } + }, + + function () + { + return window.openDatabase !== undefined; + }); + + //------------------------------ + // Flash + //------------------------------ + + define(FLAVOR_FLASH, + { + //------------------------------ + // Properties + //------------------------------ + + limit: -1, + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + var self = this; + + _.bind('flash-ready', function () + { + self.__flashReadyListener(); + }); + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function (enable) + { + /** + * The default call to updateCache passes no variable, so we can short circuit the + * ready state until we explictly call this after flash ready. + */ + if (enable === true) + { + var key, + dataset = this.database.jstore_get_all(); + + for (key in dataset) + { + if (dataset.hasOwnProperty(key)) + { + this.data[key] = prepareForRevival(this.database.jstore_get(key)); + } + } + + this._super(); + } + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + if (!this.database.jstore_set(key, prepareForStorage(value))) + { + _.trigger('jstore-error', ['JSTORE_STORAGE_FAILURE', this.jri, 'Flash Exception']); + } + }, + + __remove: function (key) + { + this.database.jstore_remove(key); + }, + + /** + * Triggered whenever flash is ready. + */ + __flashReadyListener: function () + { + var iFrame = $('#jStoreFlashFrame')[0], + frameDocument; + + // MSIE + if (iFrame.Document !== undefined && typecheck(iFrame.Document.jStoreFlash.jstore_get, 'Function')) + { + this.database = iFrame.Document.jStoreFlash; + } + + // Real Browsers + else if (iFrame.contentWindow && iFrame.contentWindow.document) + { + frameDocument = $(iFrame.contentWindow.document); + + // Webkit + if (typecheck($('object', frameDocument)[0].jstore_get, 'Function')) + { + this.database = $('object', frameDocument)[0]; + } + + // Gecko + else if (typecheck($('embed', frameDocument)[0].jstore_get, 'Function')) + { + this.database = $('embed', frameDocument)[0]; + } + } + + if (this.database === undefined) + { + throw 'JSTORE_FLASH_REFERENCE_ISSUE'; + } + else + { + this.updateCache(true); + } + } + }, + + function () + { + return hasFlashVersion('9.0.0'); + }); + + //------------------------------ + // Gears + //------------------------------ + + define(FLAVOR_GEARS, + { + //------------------------------ + // Properties + //------------------------------ + + limit: -1, + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + this.database = google.gears.factory.create('beta.database'); + this.database.open('jstore-' + project); + this.database.execute('CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)'); + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function () + { + var result = this.database.execute('SELECT k,v FROM jstore'); + + while (result.isValidRow()) + { + this.data[result.field(0)] = prepareForRevival(result.field(1)); + result.next(); + } + + result.close(); + + this._super(); + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + this.database.execute('BEGIN'); + this.database.execute('INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)', [key, prepareForStorage(value)]); + this.database.execute('COMMIT'); + }, + + __remove: function (key) + { + this.database.execute('BEGIN'); + this.database.execute('DELETE FROM jstore WHERE k = ?', [key]); + this.database.execute('COMMIT'); + } + }, + + function () + { + return window.google !== undefined && window.google.gears !== undefined; + }); + + //------------------------------ + // MSIE + //------------------------------ + + define(FLAVOR_MSIE, + { + //------------------------------ + // Properties + //------------------------------ + + limit: parseInt(1e4, 16), + + //------------------------------ + // Constructor + //------------------------------ + + init: function (project, name) + { + this.database = $('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-' + project + '"></div>') + .appendTo(document.body).get(0); + + this._super(project, name); + }, + + //------------------------------ + // Methods + //------------------------------ + + updateCache: function () + { + this.database.load(this.project); + + var node = document.getElementById('jstore-' + this.project), + xmlDoc = node.XMLDocument, + root, + index = 0; + + if (xmlDoc && xmlDoc.documentElement && xmlDoc.documentElement.attributes) + { + root = xmlDoc.documentElement; + + for (; index < root.attributes.length; ++index) + { + this.data[root.attributes.item(index).nodeName] = prepareForRevival(root.attributes.item(index).nodeValue); + } + } + + this._super(); + }, + + //------------------------------ + // Internal methods + //------------------------------ + + __set: function (key, value) + { + this.database.setAttribute(key, prepareForStorage(value)); + this.database.save(this.project); + }, + + __remove: function (key) + { + this.database.removeAttribute(key); + this.database.save(this.project); + } + }, + + function () + { + return window.ActiveXObject !== undefined; + }); + +}(jQuery, window)); diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/json2.js --- a/static/scripts/json2.js Fri Apr 09 13:02:15 2010 -0400 +++ b/static/scripts/json2.js Fri Apr 09 18:09:54 2010 -0400 @@ -1,6 +1,6 @@ /* http://www.JSON.org/json2.js - 2009-06-29 + 2010-03-20 Public Domain. @@ -8,6 +8,14 @@ See http://www.JSON.org/js.html + + This code should be minified before deployment. + See http://javascript.crockford.com/jsmin.html + + USE YOUR OWN COPY. IT IS EXTREMELY UNWISE TO LOAD CODE FROM SERVERS YOU DO + NOT CONTROL. + + This file creates a global JSON object containing two methods: stringify and parse. @@ -33,7 +41,7 @@ value represented by the name/value pair that should be serialized, or undefined if nothing should be serialized. The toJSON method will be passed the key associated with the value, and this will be - bound to the object holding the key. + bound to the value For example, this would serialize Dates as ISO strings. @@ -136,15 +144,9 @@ This is a reference implementation. You are free to copy, modify, or redistribute. - - This code should be minified before deployment. - See http://javascript.crockford.com/jsmin.html - - USE YOUR OWN COPY. IT IS EXTREMELY UNWISE TO LOAD CODE FROM SERVERS YOU DO - NOT CONTROL. */ -/*jslint evil: true */ +/*jslint evil: true, strict: false */ /*members "", "\b", "\t", "\n", "\f", "\r", "\"", JSON, "\\", apply, call, charCodeAt, getUTCDate, getUTCFullYear, getUTCHours, @@ -153,10 +155,13 @@ test, toJSON, toString, valueOf */ + // Create a JSON object only if one does not already exist. We create the // methods in a closure to avoid creating global variables. -var JSON = JSON || {}; +if (!this.JSON) { + this.JSON = {}; +} (function () { @@ -428,6 +433,7 @@ // Unicode characters with escape sequences. JavaScript handles many characters // incorrectly, either silently deleting them, or treating them as line endings. + text = String(text); cx.lastIndex = 0; if (cx.test(text)) { text = text.replace(cx, function (a) { diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/packed/class.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/class.js Fri Apr 09 18:09:54 2010 -0400 @@ -0,0 +1,7 @@ +/* + * Class definition + * + * Copyright (c) 2008 John Resig (http://ejohn.org/blog/simple-javascript-inheritance/) + * Inspired by base2 and Prototype + */ +"use strict";(function(){var a=false,b=/xyz/.test(function(){xyz})?/\b_super\b/:/.*/;this.Class=function(){};Class.extend=function(g){var f=this.prototype;a=true;var e=new this();a=false;for(var d in g){e[d]=(typeof g[d]==="function"&&typeof f[d]==="function"&&b.test(g[d])?(function(h,i){return function(){var k=this._super;this._super=f[h];var j=i.apply(this,arguments);this._super=k;return j}}(d,g[d])):g[d])}function c(){if(!a&&this.init){this.init.apply(this,arguments)}}c.prototype=e;c.constructor=c;c.extend=arguments.callee;return c}}()); \ No newline at end of file diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Apr 09 13:02:15 2010 -0400 +++ b/static/scripts/packed/galaxy.base.js Fri Apr 09 18:09:54 2010 -0400 @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen! 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function(d,e){this.db.setItem(d,e);return e},rem:function(e){var d=this.get(e);this.db.removeItem(e);return d}});this.jStoreLocal=jStoreDom.extend({connect:function(){this.db=!window.globalStorage?window.localStorage:window.globalStorage[location.hostname];this._super()},isAvailable:a});this.jStoreSession=jStoreDom.extend({connect:function(){this.db=sessionStorage;this._super()},isAvailable:b});c.jStore.Engines.local=jStoreLocal;c.jStore.Engines.session=jStoreSession;c.jStore.EngineOrder[1]="local"})(jQuery);(function(b){var a=b.jStore.Availability.flash=function(){return !!(b.jStore.hasFlash("8.0.0"))};this.jStoreFlash=StorageEngine.extend({init:function(e,d){this._super(e,d);this.type="Flash";var c=this;b.jStore.flashReady(function(){c.flashReady()})},connect:function(){var c="jstore-flash-embed-"+this.project;b(document.body).append('<iframe style="height:1px;width:1px;position:absolute;left:0;top:0;margin-left:-100px;" id="jStoreFlashFrame" src="'+b.jStore.defaults.flas! h+'"></iframe>')},flashReady:function(f){var c=b("#jStoreFlashFrame")[ 0];if(c.Document&&b.isFunction(c.Document.jStoreFlash.f_get_cookie)){this.db=c.Document.jStoreFlash}else{if(c.contentWindow&&c.contentWindow.document){var d=c.contentWindow.document;if(b.isFunction(b("object",b(d))[0].f_get_cookie)){this.db=b("object",b(d))[0]}else{if(b.isFunction(b("embed",b(d))[0].f_get_cookie)){this.db=b("embed",b(d))[0]}}}}if(this.db){this.delegate.trigger("engine-ready")}},isAvailable:a,get:function(d){var c=this.db.f_get_cookie(d);return c=="null"?null:c},set:function(c,d){this.db.f_set_cookie(c,d);return d},rem:function(c){var d=this.get(c);this.db.f_delete_cookie(c);return d}});b.jStore.Engines.flash=jStoreFlash;b.jStore.EngineOrder[2]="flash";b.jStore.hasFlash=function(c){var e=b.jStore.flashVersion().match(/\d+/g),f=c.match(/\d+/g);for(var d=0;d<3;d++){e[d]=parseInt(e[d]||0);f[d]=parseInt(f[d]||0);if(e[d]<f[d]){return false}if(e[d]>f[d]){return true}}return true};b.jStore.flashVersion=function(){try{try{var c=new ActiveXObject("ShockwaveFlash.Shock! 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(I){return E.activeEngine().remove(I)},get:function(I){return E.active Engine().get(I)},set:function(I,J){return E.activeEngine().set(I,J)}});u=Class.extend({project:undefined,jri:undefined,flavor:undefined,database:undefined,data:undefined,limit:undefined,isReady:undefined,init:function(J,I){this.project=J;this.jri=I;this.data={};this.isReady=false;this.updateCache()},updateCache:function(){this.isReady=true;this.trigger("engine-ready",[this])},bind:function(I,J){E.bind(I,J,this.jri)},trigger:function(J,I){E.trigger(J,I,this.jri)},ready:function(I){if(this.isReady){s(I,this)}else{this.bind("engine-ready",I)}},get:function(I){this.__interruptAccess();return this.data[I]},set:function(I,J){this.__interruptAccess();I=w(I);try{this.__set(I,J)}catch(K){E.trigger("jstore-error",["JSTORE_STORAGE_FAILURE",this.jri,K])}this.data[I]=J;return J},remove:function(J){this.__interruptAccess();J=w(J);try{this.__remove(J)}catch(K){E.trigger("jstore-error",["JSTORE_REMOVE_FAILURE",this.jri,K])}var I=this.data[J];this.data[J]=undefined;return I},__interruptAcces! s:function(){if(!this.isReady){throw h}},__set:function(I,J){return},__remove:function(I){return}});i.extend(i.fn,{store:function(I,J){if(J===undefined){E.get(I)}else{E.set(I,J)}return this},removeStore:function(I){E.activeEngine().remove(I);return this},getStore:function(I){return E.activeEngine().get(I)},setStore:function(I,J){E.activeEngine().set(I,J);return this}});n.jStore=i.jStore=E;e(b,{limit:parseInt(500000,16),init:function(J,I){this.database=n.globalStorage===undefined?n.localStorage:n.globalStorage[location.hostname];this._super(J,I)},updateCache:function(){var J,K;for(J in this.database){var I=false;if(this.database.hasOwnProperty){if(this.database.hasOwnProperty(J)){I=true}}else{if(this.database.getItem(J)!==null){I=true}}if(I){K=this.database.getItem(J);this.data[J]=k(K&&K.value?K.value:K)}}this._super()},__set:function(I,J){this.database.setItem(I,x(J))},__remove:function(I){this.database.removeItem(I)}},function(){return n.localStorage!==undefined||n.globalS! torage!==undefined});e(y,{limit:parseInt(32000,16),init:function(J,I){ this.database=n.openDatabase("jstore-"+J,"1.0",J,this.limit);if(!this.database){throw"JSTORE_SQL_NO_DB"}this.database.transaction(function(K){K.executeSql("CREATE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v TEXT NOT NULL)")});this._super(J,I)},updateCache:function(){var I=this,J=this._super;this.database.transaction(function(K){K.executeSql("SELECT k,v FROM jstore",[],function(O,L){var N=L.rows,M=0,P;for(;M<N.length;++M){P=N.item(M);I.data[P.k]=k(P.v)}J.apply(I)})})},__set:function(I,J){this.database.transaction(function(K){K.executeSql("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[I,x(J)])})},__remove:function(I){this.database.transaction(function(J){J.executeSql("DELETE FROM jstore WHERE k = ?",[I])})}},function(){return n.openDatabase!==undefined});e(F,{limit:-1,init:function(K,J){var I=this;E.bind("flash-ready",function(){I.__flashReadyListener()});this._super(K,J)},updateCache:function(I){if(I===true){var J,K=this.database.jstore_get_all();f! or(J in K){if(K.hasOwnProperty(J)){this.data[J]=k(this.database.jstore_get(J))}}this._super()}},__set:function(I,J){if(!this.database.jstore_set(I,x(J))){E.trigger("jstore-error",["JSTORE_STORAGE_FAILURE",this.jri,"Flash Exception"])}},__remove:function(I){this.database.jstore_remove(I)},__flashReadyListener:function(){var I=i("#jStoreFlashFrame")[0],J;if(I.Document!==undefined&&g(I.Document.jStoreFlash.jstore_get,"Function")){this.database=I.Document.jStoreFlash}else{if(I.contentWindow&&I.contentWindow.document){J=i(I.contentWindow.document);if(g(i("object",J)[0].jstore_get,"Function")){this.database=i("object",J)[0]}else{if(g(i("embed",J)[0].jstore_get,"Function")){this.database=i("embed",J)[0]}}}}if(this.database===undefined){throw"JSTORE_FLASH_REFERENCE_ISSUE"}else{this.updateCache(true)}}},function(){return B("9.0.0")});e(G,{limit:-1,init:function(J,I){this.database=google.gears.factory.create("beta.database");this.database.open("jstore-"+J);this.database.execute("CREA! TE TABLE IF NOT EXISTS jstore (k TEXT UNIQUE NOT NULL PRIMARY KEY, v T EXT NOT NULL)");this._super(J,I)},updateCache:function(){var I=this.database.execute("SELECT k,v FROM jstore");while(I.isValidRow()){this.data[I.field(0)]=k(I.field(1));I.next()}I.close();this._super()},__set:function(I,J){this.database.execute("BEGIN");this.database.execute("INSERT OR REPLACE INTO jstore(k, v) VALUES (?, ?)",[I,x(J)]);this.database.execute("COMMIT")},__remove:function(I){this.database.execute("BEGIN");this.database.execute("DELETE FROM jstore WHERE k = ?",[I]);this.database.execute("COMMIT")}},function(){return n.google!==undefined&&n.google.gears!==undefined});e(A,{limit:parseInt(10000,16),init:function(J,I){this.database=i('<div style="display:none;behavior:url(\'#default#userData\')" id="jstore-'+J+'"></div>').appendTo(document.body).get(0);this._super(J,I)},updateCache:function(){this.database.load(this.project);var K=document.getElementById("jstore-"+this.project),L=K.XMLDocument,I,J=0;if(L&&L.documentElement&&L.documentElement.attributes){I=L.document! Element;for(;J<I.attributes.length;++J){this.data[I.attributes.item(J).nodeName]=k(I.attributes.item(J).nodeValue)}}this._super()},__set:function(I,J){this.database.setAttribute(I,x(J));this.database.save(this.project)},__remove:function(I){this.database.removeAttribute(I);this.database.save(this.project)}},function(){return n.ActiveXObject!==undefined})}(jQuery,window)); \ No newline at end of file diff -r a9402fc7ce1b -r 5536d57237a3 static/scripts/packed/json2.js --- a/static/scripts/packed/json2.js Fri Apr 09 13:02:15 2010 -0400 +++ b/static/scripts/packed/json2.js Fri Apr 09 18:09:54 2010 -0400 @@ -1,1 +1,1 @@ -var JSON=JSON||{};(function(){function f(n){return n<10?"0"+n:n}if(typeof Date.prototype.toJSON!=="function"){Date.prototype.toJSON=function(key){return isFinite(this.valueOf())?this.getUTCFullYear()+"-"+f(this.getUTCMonth()+1)+"-"+f(this.getUTCDate())+"T"+f(this.getUTCHours())+":"+f(this.getUTCMinutes())+":"+f(this.getUTCSeconds())+"Z":null};String.prototype.toJSON=Number.prototype.toJSON=Boolean.prototype.toJSON=function(key){return this.valueOf()}}var cx=/[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,escapable=/[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,gap,indent,meta={"\b":"\\b","\t":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},rep;function quote(string){escapable.lastIndex=0;return escapable.test(string)?'"'+string.replace(escapable,function(a){var c=meta[a];return typeof c==="string"?c:"\\u"+("0000"+a.charCodeAt(0! ).toString(16)).slice(-4)})+'"':'"'+string+'"'}function str(key,holder){var i,k,v,length,mind=gap,partial,value=holder[key];if(value&&typeof value==="object"&&typeof value.toJSON==="function"){value=value.toJSON(key)}if(typeof rep==="function"){value=rep.call(holder,key,value)}switch(typeof value){case"string":return quote(value);case"number":return isFinite(value)?String(value):"null";case"boolean":case"null":return String(value);case"object":if(!value){return"null"}gap+=indent;partial=[];if(Object.prototype.toString.apply(value)==="[object Array]"){length=value.length;for(i=0;i<length;i+=1){partial[i]=str(i,value)||"null"}v=partial.length===0?"[]":gap?"[\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"]":"["+partial.join(",")+"]";gap=mind;return v}if(rep&&typeof rep==="object"){length=rep.length;for(i=0;i<length;i+=1){k=rep[i];if(typeof k==="string"){v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}else{for(k in value){if(Object.hasOwnProperty.call(value,k)){v=st! r(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}v=partial. length===0?"{}":gap?"{\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"}":"{"+partial.join(",")+"}";gap=mind;return v}}if(typeof JSON.stringify!=="function"){JSON.stringify=function(value,replacer,space){var i;gap="";indent="";if(typeof space==="number"){for(i=0;i<space;i+=1){indent+=" "}}else{if(typeof space==="string"){indent=space}}rep=replacer;if(replacer&&typeof replacer!=="function"&&(typeof replacer!=="object"||typeof replacer.length!=="number")){throw new Error("JSON.stringify")}return str("",{"":value})}}if(typeof JSON.parse!=="function"){JSON.parse=function(text,reviver){var j;function walk(holder,key){var k,v,value=holder[key];if(value&&typeof value==="object"){for(k in value){if(Object.hasOwnProperty.call(value,k)){v=walk(value,k);if(v!==undefined){value[k]=v}else{delete value[k]}}}}return reviver.call(holder,key,value)}cx.lastIndex=0;if(cx.test(text)){text=text.replace(cx,function(a){return"\\u"+("0000"+a.charCodeAt(0).toString(16)).slice(-4)})}if(/^[\],:{}\s]*$/.test! (text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))){j=eval("("+text+")");return typeof reviver==="function"?walk({"":j},""):j}throw new SyntaxError("JSON.parse")}}}()); \ No newline at end of file +if(!this.JSON){this.JSON={}}(function(){function f(n){return n<10?"0"+n:n}if(typeof Date.prototype.toJSON!=="function"){Date.prototype.toJSON=function(key){return isFinite(this.valueOf())?this.getUTCFullYear()+"-"+f(this.getUTCMonth()+1)+"-"+f(this.getUTCDate())+"T"+f(this.getUTCHours())+":"+f(this.getUTCMinutes())+":"+f(this.getUTCSeconds())+"Z":null};String.prototype.toJSON=Number.prototype.toJSON=Boolean.prototype.toJSON=function(key){return this.valueOf()}}var cx=/[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,escapable=/[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,gap,indent,meta={"\b":"\\b","\t":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},rep;function quote(string){escapable.lastIndex=0;return escapable.test(string)?'"'+string.replace(escapable,function(a){var c=meta[a];return typeof c==="string"?c:"\\u"+("0000"+a.ch! arCodeAt(0).toString(16)).slice(-4)})+'"':'"'+string+'"'}function str(key,holder){var i,k,v,length,mind=gap,partial,value=holder[key];if(value&&typeof value==="object"&&typeof value.toJSON==="function"){value=value.toJSON(key)}if(typeof rep==="function"){value=rep.call(holder,key,value)}switch(typeof value){case"string":return quote(value);case"number":return isFinite(value)?String(value):"null";case"boolean":case"null":return String(value);case"object":if(!value){return"null"}gap+=indent;partial=[];if(Object.prototype.toString.apply(value)==="[object Array]"){length=value.length;for(i=0;i<length;i+=1){partial[i]=str(i,value)||"null"}v=partial.length===0?"[]":gap?"[\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"]":"["+partial.join(",")+"]";gap=mind;return v}if(rep&&typeof rep==="object"){length=rep.length;for(i=0;i<length;i+=1){k=rep[i];if(typeof k==="string"){v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}else{for(k in value){if(Object.hasOwnProperty.call(valu! e,k)){v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}} v=partial.length===0?"{}":gap?"{\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"}":"{"+partial.join(",")+"}";gap=mind;return v}}if(typeof JSON.stringify!=="function"){JSON.stringify=function(value,replacer,space){var i;gap="";indent="";if(typeof space==="number"){for(i=0;i<space;i+=1){indent+=" "}}else{if(typeof space==="string"){indent=space}}rep=replacer;if(replacer&&typeof replacer!=="function"&&(typeof replacer!=="object"||typeof replacer.length!=="number")){throw new Error("JSON.stringify")}return str("",{"":value})}}if(typeof JSON.parse!=="function"){JSON.parse=function(text,reviver){var j;function walk(holder,key){var k,v,value=holder[key];if(value&&typeof value==="object"){for(k in value){if(Object.hasOwnProperty.call(value,k)){v=walk(value,k);if(v!==undefined){value[k]=v}else{delete value[k]}}}}return reviver.call(holder,key,value)}text=String(text);cx.lastIndex=0;if(cx.test(text)){text=text.replace(cx,function(a){return"\\u"+("0000"+a.charCodeAt(0).toString(16)).slice(-! 4)})}if(/^[\],:{}\s]*$/.test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))){j=eval("("+text+")");return typeof reviver==="function"?walk({"":j},""):j}throw new SyntaxError("JSON.parse")}}}()); \ No newline at end of file diff -r a9402fc7ce1b -r 5536d57237a3 templates/display_base.mako --- a/templates/display_base.mako Fri Apr 09 13:02:15 2010 -0400 +++ b/templates/display_base.mako Fri Apr 09 18:09:54 2010 -0400 @@ -32,29 +32,25 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "jquery.autocomplete", "jquery.jstore-all", "autocomplete_tagging" )} + ${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "class", "jquery.jstore", "jquery.autocomplete", "autocomplete_tagging" )} <script type="text/javascript"> - // + // Handle click on community tag. - // - function community_tag_click(tag_name, tag_value) - { + function community_tag_click(tag_name, tag_value) { <% controller_name = get_controller_name( item ) %> var href = '${h.url_for ( controller='/' + controller_name , action='list_published')}'; href = href + "?f-tags=" + tag_name; - if (tag_value != undefined && tag_value != "") + if (tag_value != undefined && tag_value != "") { href = href + ":" + tag_value; + } self.location = href; } - $(document).ready( function() - { + $(function() { // Set links to Galaxy screencasts to open in overlay. - $(this).find("a[href^='http://screencast.g2.bx.psu.edu/']").each( function() - { - $(this).click( function() - { + $(this).find("a[href^='http://screencast.g2.bx.psu.edu/']").each( function() { + $(this).click( function() { var href = $(this).attr('href'); show_in_overlay( { @@ -67,7 +63,8 @@ return false; }); }); - + // Init history boxes + init_history_items( $("div.historyItemWrapper") ); }); </script> </%def> @@ -76,14 +73,12 @@ ${parent.stylesheets()} ${h.css( "autocomplete_tagging", "embed_item" )} <style type="text/css"> - .page-body - { + .page-body { padding: 10px; ## float: left; ## width: 65%; } - .page-meta - { + .page-meta { float: right; width: 27%; padding: 0.5em; diff -r a9402fc7ce1b -r 5536d57237a3 templates/history/display.mako --- a/templates/history/display.mako Fri Apr 09 13:02:15 2010 -0400 +++ b/templates/history/display.mako Fri Apr 09 18:09:54 2010 -0400 @@ -1,207 +1,14 @@ <%inherit file="/display_base.mako"/> <%namespace file="/root/history_common.mako" import="render_dataset" /> +## Set vars so that there's no need to change the code below. +<% + history = published_item + datasets = published_item_data +%> + <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery.jstore-all" )} - - ## Set vars so that there's no need to change the code below. - <% - history = published_item - datasets = published_item_data - %> - - <script type="text/javascript"> - $(function() { - // Load jStore for local storage - $.extend(jQuery.jStore.defaults, { project: 'galaxy', flash: '/static/jStore.Flash.html' }) - $.jStore.load(); // Auto-select best storage

1 0