August 2008 - galaxy-dev - lists.galaxyproject.org

welcome page
by Cathy Riemer 28 Aug '08

28 Aug '08

I had to smile when I saw the "Noodly Appendages". :-) -Cathy

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Main is at rev 1482:c77dea3e745a
by Greg Von Kuster 27 Aug '08

27 Aug '08

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[hg] galaxy 1481: Upgraded twill to 0.9.
by greg＠scofield.bx.psu.edu 27 Aug '08

27 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ed448639d90e changeset: 1481:ed448639d90e user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Aug 26 10:39:47 2008 -0400 description: Upgraded twill to 0.9. 1 file(s) affected in this change: eggs.ini diffs (21 lines): diff -r 6de3006c62b3 -r ed448639d90e eggs.ini --- a/eggs.ini Mon Aug 25 15:28:57 2008 -0400 +++ b/eggs.ini Tue Aug 26 10:39:47 2008 -0400 @@ -41,7 +41,7 @@ simplejson = 1.5 SQLAlchemy = 0.3.11 Tempita = 0.1 -twill = 0.8.3 +twill = 0.9 WebError = 0.8a WebHelpers = 0.2 WebOb = 0.8.5 @@ -86,7 +86,7 @@ simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.3.11.tar.gz Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz -twill = http://darcs.idyll.org/~t/projects/twill-0.8.3.tar.gz +twill = http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz WebHelpers = http://pypi.python.org/packages/source/W/WebHelpers/WebHelpers-0.2.tar.gz WebOb = http://pypi.python.org/packages/source/W/WebOb/WebOb-0.8.5.tar.gz

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[hg] galaxy 1482: Fix for new twill version 0.9.
by greg＠scofield.bx.psu.edu 27 Aug '08

27 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c77dea3e745a changeset: 1482:c77dea3e745a user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 26 17:07:44 2008 -0400 description: Fix for new twill version 0.9. 1 file(s) affected in this change: test/base/twilltestcase.py diffs (36 lines): diff -r ed448639d90e -r c77dea3e745a test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Aug 26 10:39:47 2008 -0400 +++ b/test/base/twilltestcase.py Tue Aug 26 17:07:44 2008 -0400 @@ -7,7 +7,7 @@ import twill import twill.commands as tc -from twill.other_packages import ClientForm +from twill.other_packages._mechanize_dist import ClientForm from elementtree import ElementTree buffer = StringIO.StringIO() @@ -410,7 +410,10 @@ def submit_form( self, form=1, button="runtool_btn", **kwd ): """Populates and submits a form from the keyword arguments""" #Check for onchange attribute, submit a change if required - for i, control in enumerate(tc.showforms()[form-1].controls): + for i, f in enumerate( tc.showforms() ): + if i == form - 1: + break + for i, control in enumerate( f.controls ): try: if 'refresh_on_change' in control.attrs.keys(): changed = False @@ -456,7 +459,10 @@ if not isinstance(value, list): value = [ value ] - for i, control in enumerate(tc.showforms()[form-1].controls): + for i, f in enumerate( tc.showforms() ): + if i == form - 1: + break + for i, control in enumerate( f.controls ): if control.name == key: control.clear() if control.is_of_kind("text"):

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[hg] galaxy 1478: Add excanvas javascript (emulates <canvas> in ...
by greg＠scofield.bx.psu.edu 27 Aug '08

27 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/6eac08f7edcf changeset: 1478:6eac08f7edcf user: James Taylor <james(a)jamestaylor.org> date: Fri Aug 22 17:44:32 2008 -0400 description: Add excanvas javascript (emulates <canvas> in IE using silverlight) 2 file(s) affected in this change: static/scripts/excanvas.js static/scripts/packed/excanvas.js diffs (780 lines): diff -r 99e223f6a132 -r 6eac08f7edcf static/scripts/excanvas.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/excanvas.js Fri Aug 22 17:44:32 2008 -0400 @@ -0,0 +1,770 @@ +// Copyright 2006 Google Inc. +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + + +// Known Issues: (From VML version) +// +// * Patterns are not implemented. +// * Radial gradient are not implemented. The VML version of these look very +// different from the canvas one. +// * Clipping paths are not implemented. +// * Coordsize. The width and height attribute have higher priority than the +// width and height style values which isn't correct. +// * Painting mode isn't implemented. +// * Canvas width/height should is using content-box by default. IE in +// Quirks mode will draw the canvas using border-box. Either change your +// doctype to HTML5 +// (http://www.whatwg.org/specs/web-apps/current-work/#the-doctype) +// or use Box Sizing Behavior from WebFX +// (http://webfx.eae.net/dhtml/boxsizing/boxsizing.html) +// * Optimize. There is always room for speed improvements. + +//Known Issues: Silverlight version +// +// * Doing a transformation during a path (ie lineTo, transform, lineTo) will +// not work corerctly because the transform is done to the whole path (ie +// transform, lineTo, lineTo) +// * Patterns are not yet implemented. + + +// only add this code if we do not already have a canvas implementation +if (!window.CanvasRenderingContext2D) { + +(function () { + + var xamlId; + + var G_vmlCanvasManager_ = { + init: function (opt_doc) { + var doc = opt_doc || document; + // Create a dummy element so that IE will allow canvas elements to be + // recognized. + doc.createElement('canvas'); + if (/MSIE/.test(navigator.userAgent) && !window.opera) { + var self = this; + + createXamlScriptTag(); + + doc.attachEvent('onreadystatechange', function () { + self.init_(doc); + }); + } + }, + + init_: function (doc) { + // setup default css + var ss = doc.createStyleSheet(); + ss.cssText = 'canvas{display:inline-block;overflow:hidden;' + + // default size is 300x150 in Gecko and Opera + 'text-align:left;width:300px;height:150px}' + + 'canvas object{width:100%;height:100%;border:0;' + + 'background:transparen;margin:0}'; + + // find all canvas elements + var els = doc.getElementsByTagName('canvas'); + for (var i = 0; i < els.length; i++) { + if (!els[i].getContext) { + this.initElement(els[i]); + } + } + }, + + + /** + * Public initializes a canvas element so that it can be used as canvas + * element from now on. This is called automatically before the page is + * loaded but if you are creating elements using createElement you need to + * make sure this is called on the element. + * @param {HTMLElement} el The canvas element to initialize. + * @return {HTMLElement} the element that was created. + */ + initElement: function (el) { + el.getContext = function () { + if (this.context_) { + return this.context_; + } + return this.context_ = new CanvasRenderingContext2D_(this); + }; + + var attrs = el.attributes; + if (attrs.width && attrs.width.specified) { + // TODO: use runtimeStyle and coordsize + // el.getContext().setWidth_(attrs.width.nodeValue); + el.style.width = attrs.width.nodeValue + 'px'; + } else { + el.width = el.clientWidth; + } + if (attrs.height && attrs.height.specified) { + // TODO: use runtimeStyle and coordsize + // el.getContext().setHeight_(attrs.height.nodeValue); + el.style.height = attrs.height.nodeValue + 'px'; + } else { + el.height = el.clientHeight; + } + + // insert object tag + el.innerHTML = getObjectHtml(); + + // do not use inline function because that will leak memory + el.attachEvent('onpropertychange', onPropertyChange); + return el; + } + }; + + function onPropertyChange(e) { + var el = e.srcElement; + + switch (e.propertyName) { + case 'width': + el.style.width = el.attributes.width.nodeValue + 'px'; + el.getContext().clearRect(); + break; + case 'height': + el.style.height = el.attributes.height.nodeValue + 'px'; + el.getContext().clearRect(); + break; + } + } + + G_vmlCanvasManager_.init(); + + function createXamlScriptTag() { + // This script tag contains the boilerplate XAML. + document.write('<script type=text/xaml>' + + '<Canvas x:Name="root" ' + + 'xmlns="http://schemas.microsoft.com/client/2007" ' + + 'xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" ' + + 'Width="300" ' + + 'Height="150" ' + + 'Background="Transparent"> ' + + '</Canvas>' + + '</script>'); + // Find the id of the writtenscript file. + var scripts = document.scripts; + var script = scripts[scripts.length - 1]; + xamlId = script.uniqueID; + script.id = xamlId; + } + + function getObjectHtml(fn) { + return '<object type="application/x-silverlight" >' + + '<param name="windowless" value="true">' + + '<param name="background" value="transparent">' + + '<param name="source" value="#' + xamlId + '">' + + '</object>'; + } + + function hasSilverlight() { + try { + new ActiveXObject('AgControl.AgControl'); + return true; + } catch(_) { + return false; + } + } + + // precompute "00" to "FF" + var dec2hex = []; + for (var i = 0; i < 16; i++) { + for (var j = 0; j < 16; j++) { + dec2hex[i * 16 + j] = i.toString(16) + j.toString(16); + } + } + + function createMatrixIdentity() { + return [ + [1, 0, 0], + [0, 1, 0], + [0, 0, 1] + ]; + } + + function matrixMultiply(m1, m2) { + var result = createMatrixIdentity(); + + for (var x = 0; x < 3; x++) { + for (var y = 0; y < 3; y++) { + var sum = 0; + + for (var z = 0; z < 3; z++) { + sum += m1[x][z] * m2[z][y]; + } + + result[x][y] = sum; + } + } + return result; + } + + function doTransform(ctx) { + transformObject(ctx, getRoot(ctx), ctx.m_); + } + + function transformObject(ctx, obj, m) { + var transform = obj.renderTransform; + var matrix; + if (!transform) { + transform = create(ctx, '<MatrixTransform/>'); + matrix = create(ctx, '<Matrix/>'); + transform.matrix = matrix; + obj.renderTransform = transform; + } else { + matrix = transform.matrix; + } + + matrix.m11 = m[0][0]; + matrix.m12 = m[0][1]; + matrix.m21 = m[1][0]; + matrix.m22 = m[1][1]; + matrix.offsetX = m[2][0]; + matrix.offsetY = m[2][1]; + } + + function copyState(o1, o2) { + o2.fillStyle = o1.fillStyle; + o2.lineCap = o1.lineCap; + o2.lineJoin = o1.lineJoin; + o2.lineWidth = o1.lineWidth; + o2.miterLimit = o1.miterLimit; + o2.shadowBlur = o1.shadowBlur; + o2.shadowColor = o1.shadowColor; + o2.shadowOffsetX = o1.shadowOffsetX; + o2.shadowOffsetY = o1.shadowOffsetY; + o2.strokeStyle = o1.strokeStyle; + o2.globalAlpha = o1.globalAlpha; + o2.arcScaleX_ = o1.arcScaleX_; + o2.arcScaleY_ = o1.arcScaleY_; + } + + function translateColor(s) { + var rgbaMatch = /rgba$([^)]+)$/gi.exec(s); + if (rgbaMatch) { + var parts = rgbaMatch[1].split(','); + return '#' + dec2hex[Math.floor(Number(parts[3]) * 255)] + + dec2hex[Number(parts[0])] + + dec2hex[Number(parts[1])] + + dec2hex[Number(parts[2])]; + } + + var rgbMatch = /rgb$([^)]+)$/gi.exec(s); + if (rgbMatch) { + var parts = rgbMatch[1].split(','); + return '#FF' + dec2hex[Number(parts[0])] + + dec2hex[Number(parts[1])] + + dec2hex[Number(parts[2])]; + } + + return s; + } + + function processLineCap(lineCap) { + switch (lineCap) { + case 'butt': + return 'flat'; + case 'round': + return 'round'; + case 'square': + default: + return 'square'; + } + } + + function getRoot(ctx) { + return ctx.canvas.firstChild.content.findName('root'); + } + + function create(ctx, s, opt_args) { + if (opt_args) { + s = s.replace(/\%(\d+)/g, function(match, index) { + return opt_args[Number(index) - 1]; + }); + } + + try { + return ctx.canvas.firstChild.content.createFromXaml(s); + } catch (ex) { + throw Error('Could not create XAML from: ' + s); + } + } + + function drawShape(ctx, s, opt_args) { + var canvas = ctx.lastCanvas_ || create(ctx, '<Canvas/>'); + var shape = create(ctx, s, opt_args); + canvas.children.add(shape); + transformObject(ctx, canvas, ctx.m_); + if (!ctx.lastCanvas_) { + getRoot(ctx).children.add(canvas); + ctx.lastCanvas_ = canvas; + } + return shape; + } + + function createBrushObject(ctx, value) { + if (value instanceof CanvasGradient_) { + return value.createBrush_(ctx); + } else if (value instanceof CanvasPattern_) { + throw Error('Not implemented'); + } else { + return create(ctx, '<SolidColorBrush Color="%1"/>', + [translateColor(value)]); + } + } + + /** + * This class implements CanvasRenderingContext2D interface as described by + * the WHATWG. + * @param {HTMLElement} surfaceElement The element that the 2D context should + * be associated with + */ + function CanvasRenderingContext2D_(surfaceElement) { + this.m_ = createMatrixIdentity(); + this.lastCanvas_ = null; + + this.mStack_ = []; + this.aStack_ = []; + this.currentPath_ = []; + + // Canvas context properties + this.strokeStyle = '#000'; + this.fillStyle = '#000'; + + this.lineWidth = 1; + this.lineJoin = 'miter'; + this.lineCap = 'butt'; + this.miterLimit = 10; + this.globalAlpha = 1; + this.canvas = surfaceElement; + }; + + + var contextPrototype = CanvasRenderingContext2D_.prototype; + + contextPrototype.clearRect = function() { + var root = getRoot(this); + root.children.clear(); + + // TODO: Implement + this.currentPath_ = []; + this.lastCanvas_ = null; + + }; + + contextPrototype.beginPath = function() { + // TODO: Branch current matrix so that save/restore has no effect + // as per safari docs. + + this.currentPath_ = []; + }; + + contextPrototype.moveTo = function(aX, aY) { + this.currentPath_.push('M' + aX + ',' + aY); + }; + + contextPrototype.lineTo = function(aX, aY) { + if (this.currentPath_.length == 0) return; + this.currentPath_.push('L' + aX + ',' + aY); + }; + + contextPrototype.bezierCurveTo = function(aCP1x, aCP1y, + aCP2x, aCP2y, + aX, aY) { + if (this.currentPath_.length == 0) return; + this.currentPath_.push('C' + aCP1x + ',' + aCP1y + ' ' + + aCP2x + ',' + aCP2y + ' ' + + aX + ' ' + aY); + }; + + contextPrototype.quadraticCurveTo = function(aCPx, aCPy, aX, aY) { + if (this.currentPath_.length == 0) return; + this.currentPath_.push('Q' + aCPx + ',' + aCPy + ' ' + + aX + ',' + aY); + }; + + contextPrototype.arcTo = function(x1, y1, x2, y2, radius) { + if (this.currentPath_.length == 0) return; + // TODO: Implement + }; + + contextPrototype.arc = function(aX, aY, aRadius, + aStartAngle, aEndAngle, aClockwise) { + var deltaAngle = Math.abs(aStartAngle - aEndAngle); + // If start and stop are the same WebKit and Moz does nothing + if (aStartAngle == aEndAngle) { + // different browsers behave differently here so we do the easiest thing + return; + } + + var endX = aX + aRadius * Math.cos(aEndAngle); + var endY = aY + aRadius * Math.sin(aEndAngle); + + if (deltaAngle >= 2 * Math.PI) { + // if larger than 2PI + this.arc(aX, aY, aRadius, aStartAngle, aStartAngle + Math.PI, aClockwise); + this.arc(aX, aY, aRadius, aStartAngle + Math.PI, + aStartAngle + 2 * Math.PI, aClockwise); + // now move to end point + this.moveTo(endX, endY); + return; + } + + var startX = aX + aRadius * Math.cos(aStartAngle); + var startY = aY + aRadius * Math.sin(aStartAngle); + var rotationAngle = deltaAngle * 180 / Math.PI; // sign, abs? + var sweepDirection = aClockwise ? 0 : 1; + var isLargeArc = rotationAngle >= 180 == Boolean(aClockwise) ? 0 : 1; + + if (this.currentPath_.length != 0) { + // add line to start point + this.lineTo(startX, startY); + } else { + this.moveTo(startX, startY); + } + + this.currentPath_.push('A' + aRadius + ',' + aRadius + ' ' + + rotationAngle + ' ' + + isLargeArc + ' ' + + sweepDirection + ' ' + + endX + ',' + endY); + }; + + contextPrototype.rect = function(aX, aY, aWidth, aHeight) { + this.moveTo(aX, aY); + this.lineTo(aX + aWidth, aY); + this.lineTo(aX + aWidth, aY + aHeight); + this.lineTo(aX, aY + aHeight); + this.closePath(); + }; + + contextPrototype.strokeRect = function(aX, aY, aWidth, aHeight) { + // Will destroy any existing path (same as FF behaviour) + this.beginPath(); + this.moveTo(aX, aY); + this.lineTo(aX + aWidth, aY); + this.lineTo(aX + aWidth, aY + aHeight); + this.lineTo(aX, aY + aHeight); + this.closePath(); + this.stroke(); + this.currentPath_ = []; + }; + + contextPrototype.fillRect = function(aX, aY, aWidth, aHeight) { + // Will destroy any existing path (same as FF behaviour) + this.beginPath(); + this.moveTo(aX, aY); + this.lineTo(aX + aWidth, aY); + this.lineTo(aX + aWidth, aY + aHeight); + this.lineTo(aX, aY + aHeight); + this.closePath(); + this.fill(); + this.currentPath_ = []; + }; + + contextPrototype.createLinearGradient = function(aX0, aY0, aX1, aY1) { + return new LinearCanvasGradient_(aX0, aY0, aX1, aY1); + }; + + contextPrototype.createRadialGradient = function(x0, y0, + r0, x1, + y1, r1) { + return new RadialCanvasGradient_(x0, y0, r0, x1, y1, r1); + }; + + contextPrototype.drawImage = function (image, var_args) { + var dx, dy, dw, dh, sx, sy, sw, sh; + + // For Silverlight we don't need to get the size of the image since + // Silverlight uses the image original dimension if not provided. + + if (arguments.length == 3) { + dx = arguments[1]; + dy = arguments[2]; + // Keep sx, sy, sw, dw, sh and dh undefined + } else if (arguments.length == 5) { + dx = arguments[1]; + dy = arguments[2]; + dw = arguments[3]; + dh = arguments[4]; + // Keep sx, sy, sw and sh undefined + } else if (arguments.length == 9) { + sx = arguments[1]; + sy = arguments[2]; + sw = arguments[3]; + sh = arguments[4]; + dx = arguments[5]; + dy = arguments[6]; + dw = arguments[7]; + dh = arguments[8]; + } else { + throw Error('Invalid number of arguments'); + } + + var slImage; + + // If we have a source rect we need to clip the image. + if (arguments.length == 9) { + slImage = drawShape(this, '<Image Source="%1"/>', [image.src]); + + var clipRect = create(this, + '<RectangleGeometry Rect="%1,%2,%3,%4"/>', [sx, sy, sw, sh]); + slImage.clip = clipRect; + + var m = createMatrixIdentity(); + + // translate to 0,0 + m[2][0] = -sx; + m[2][1] = -sy; + + // scale + var m2 = createMatrixIdentity(); + m2[0][0] = dw / sw; + m2[1][1] = dh / sh; + + m = matrixMultiply(m, m2); + + // translate to destination + m[2][0] += dx; + m[2][1] += dy; + + transformObject(this, slImage, m); + + } else { + slImage = drawShape(this, + '<Image Source="%1" Canvas.Left="%2" Canvas.Top="%3"/>', + [image.src, dx, dy]); + if (dw != undefined || dh != undefined) { + slImage.width = dw; + slImage.height = dh; + slImage.stretch = 'fill'; + } + } + }; + + contextPrototype.stroke = function() { + if (this.currentPath_.length == 0) return; + var path = drawShape(this, '<Path Data="%1"/>', + [this.currentPath_.join(' ')]); + path.stroke = createBrushObject(this, this.strokeStyle); + path.opacity = this.globalAlpha; + path.strokeThickness = this.lineWidth; + path.strokeMiterLimit = this.miterLimit; + path.strokeLineJoin = this.lineJoin; + // Canvas does not differentiate start from end + path.strokeEndLineCap = path.strokeStartLineCap = + processLineCap(this.lineCap); + }; + + contextPrototype.fill = function() { + if (this.currentPath_.length == 0) return; + var path = drawShape(this, '<Path Data="%1"/>', + [this.currentPath_.join(' ')]); + // The spec says to use non zero but Silverlight uses EvenOdd by defaul + path.data.fillRule = 'NonZero'; + path.fill = createBrushObject(this, this.fillStyle); + // TODO: What about even-odd etc? + }; + + contextPrototype.closePath = function() { + this.currentPath_.push('z'); + }; + + /** + * Sets the transformation matrix and marks things as dirty + */ + function setM(self, m) { + self.m_ = m; + self.lastCanvas_ = null; + }; + + contextPrototype.save = function() { + var o = {}; + copyState(this, o); + this.aStack_.push(o); + this.mStack_.push(this.m_); + setM(this, matrixMultiply(createMatrixIdentity(), this.m_)); + }; + + contextPrototype.restore = function() { + copyState(this.aStack_.pop(), this); + setM(this, this.mStack_.pop()); + }; + + contextPrototype.translate = function(aX, aY) { + var m1 = [ + [1, 0, 0], + [0, 1, 0], + [aX, aY, 1] + ]; + + setM(this, matrixMultiply(m1, this.m_)); + }; + + contextPrototype.rotate = function(aRot) { + var c = Math.cos(aRot); + var s = Math.sin(aRot); + + var m1 = [ + [c, s, 0], + [-s, c, 0], + [0, 0, 1] + ]; + + setM(this, matrixMultiply(m1, this.m_)); + }; + + contextPrototype.scale = function(aX, aY) { + var m1 = [ + [aX, 0, 0], + [0, aY, 0], + [0, 0, 1] + ]; + + setM(this, matrixMultiply(m1, this.m_)); + }; + + contextPrototype.transform = function(m11, m12, m21, m22, dx, dy) { + var m1 = [ + [m11, m12, 0], + [m21, m22, 0], + [ dx, dy, 1] + ]; + + setM(this, matrixMultiply(m1, this.m_)); + }; + + contextPrototype.setTransform = function(m11, m12, m21, m22, dx, dy) { + setM(this, [ + [m11, m12, 0], + [m21, m22, 0], + [ dx, dy, 1], + ]); + }; + + /******** STUBS ********/ + contextPrototype.clip = function() { + // TODO: Implement + }; + + contextPrototype.createPattern = function() { + return new CanvasPattern_; + }; + + // Gradient / Pattern Stubs + function CanvasGradient_() { + this.colors_ = []; + } + + CanvasGradient_.prototype.addColorStop = function(aOffset, aColor) { + aColor = translateColor(aColor); + this.colors_.push({offset: aOffset, color: aColor}); + }; + + CanvasGradient_.prototype.createStops_ = function(ctx, brushObj, colors) { + var gradientStopCollection = brushObj.gradientStops; + for (var i = 0, c; c = colors[i]; i++) { + var color = translateColor(c.color); + gradientStopCollection.add(create(ctx, + '<GradientStop Color="%1" Offset="%2"/>', [color, c.offset])); + } + }; + + function LinearCanvasGradient_(x0, y0, x1, y1) { + CanvasGradient_.call(this); + this.x0_ = x0; + this.y0_ = y0; + this.x1_ = x1; + this.y1_ = y1; + } + LinearCanvasGradient_.prototype = new CanvasGradient_; + + LinearCanvasGradient_.prototype.createBrush_ = function(ctx) { + var brushObj = create(ctx, '<LinearGradientBrush MappingMode="Absolute" ' + + 'StartPoint="%1,%2" EndPoint="%3,%4"/>', + [this.x0_, this.y0_, this.x1_, this.y1_]); + this.createStops_(ctx, brushObj, this.colors_); + return brushObj; + }; + + function isNanOrInfinite(v) { + return isNaN(v) || !isFinite(v); + } + + function RadialCanvasGradient_(x0, y0, r0, x1, y1, r1) { + if (r0 < 0 || r1 < 0 || isNanOrInfinite(x0) || isNanOrInfinite(y0) || + isNanOrInfinite(x1) || isNanOrInfinite(y1)) { + // IE does not support DOMException so this is as close as we get. + var error = Error('DOMException.INDEX_SIZE_ERR'); + error.code = 1; + throw error; + } + + CanvasGradient_.call(this); + this.x0_ = x0; + this.y0_ = y0; + this.r0_ = r0; + this.x1_ = x1; + this.y1_ = y1; + this.r1_ = r1; + } + RadialCanvasGradient_.prototype = new CanvasGradient_; + + CanvasGradient_.prototype.createBrush_ = function(ctx) { + if (this.x0_ == this.x1_ && this.y0_ == this.y1_ && this.r0_ == this.r1_) { + return null; + } + + var radius = Math.max(this.r0_, this.r1_); + var minRadius = Math.min(this.r0_, this.r1_); + var brushObj = create(ctx, '<RadialGradientBrush MappingMode="Absolute" ' + + 'GradientOrigin="%1,%2" Center="%3,%4" ' + + 'RadiusX="%5" RadiusY="%5"/>', + [this.x0_, this.y0_, this.x1_, this.y1_, radius]); + + var colors = this.colors_.concat(); + + if (this.r1_ < this.r0_) { + // reverse color stop array + colors.reverse(); + for (var i = 0, c; c = colors[i]; i++) { + c.offset = 1 - c.offset; + } + } + + // sort the color stops + colors.sort(function(c1, c2) { + return c1.offset - c2.offset; + }); + + if (minRadius > 0) { + // We need to adjust the color stops since SL always have the inner radius + // at (0, 0) so we change the stops in case the min radius is not 0. + for (var i = 0, c; c = colors[i]; i++) { + c.offset = minRadius / radius + (radius - minRadius) / radius * c.offset; + } + } + + this.createStops_(ctx, brushObj, colors); + return brushObj; + }; + + function CanvasPattern_() {} + + // set up externs + G_vmlCanvasManager = G_vmlCanvasManager_; + CanvasRenderingContext2D = CanvasRenderingContext2D_; + CanvasGradient = CanvasGradient_; + CanvasPattern = CanvasPattern_; + +})(); + +} // if diff -r 99e223f6a132 -r 6eac08f7edcf static/scripts/packed/excanvas.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/excanvas.js Fri Aug 22 17:44:32 2008 -0400 @@ -0,0 +1,1 @@ +if(!window.CanvasRenderingContext2D){(function(){var L;var N={init:function(d){var e=d||document;e.createElement("canvas");if(/MSIE/.test(navigator.userAgent)&&!window.opera){var 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1 0

[hg] galaxy 1479: Internet explorer fixes and support -- popup m...
by greg＠scofield.bx.psu.edu 27 Aug '08

27 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b671c301674a changeset: 1479:b671c301674a user: James Taylor <james(a)jamestaylor.org> date: Fri Aug 22 17:47:43 2008 -0400 description: Internet explorer fixes and support -- popup menus and dialogs work better on IE6+, workflow editor works on IE7 (using excanvas). It actually *nearly* works on IE6 but there are some layout problems that are probably not worth wasting time on. If any IE users can test this that would be great! 13 file(s) affected in this change: static/june_2007_style/base.css.tmpl static/june_2007_style/blue/base.css static/june_2007_style/blue/panel_layout.css static/june_2007_style/panel_layout.css.tmpl static/scripts/galaxy.base.js static/scripts/galaxy.panels.js static/scripts/galaxy.ui.scrollPanel.js static/scripts/galaxy.workflow_editor.canvas.js static/scripts/packed/galaxy.base.js static/scripts/packed/galaxy.panels.js static/scripts/packed/galaxy.workflow_editor.canvas.js templates/workflow/editor.mako templates/workflow/index.mako diffs (648 lines): diff -r 6eac08f7edcf -r b671c301674a static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Aug 22 17:44:32 2008 -0400 +++ b/static/june_2007_style/base.css.tmpl Fri Aug 22 17:47:43 2008 -0400 @@ -358,7 +358,7 @@ font-weight: bold; display: inline-block; cursor: pointer; - margin: -1px; padding: 2px; + padding: 2px; border: solid #aaaaaa 1px; padding-right: 0.5em; padding-left: 0.5em; diff -r 6eac08f7edcf -r b671c301674a static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Aug 22 17:44:32 2008 -0400 +++ b/static/june_2007_style/blue/base.css Fri Aug 22 17:47:43 2008 -0400 @@ -356,7 +356,7 @@ font-weight: bold; display: inline-block; cursor: pointer; - margin: -1px; padding: 2px; + padding: 2px; border: solid #aaaaaa 1px; padding-right: 0.5em; padding-left: 0.5em; diff -r 6eac08f7edcf -r b671c301674a static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Fri Aug 22 17:44:32 2008 -0400 +++ b/static/june_2007_style/blue/panel_layout.css Fri Aug 22 17:47:43 2008 -0400 @@ -244,14 +244,6 @@ top: 0; left: 0; width: 100%; height: 100%; z-index: 20000; } -#overlay-inner { - width: 100%; height: 100%; - background-color:#FFF; - filter:alpha(opacity=75); - -moz-opacity: 0.75; - opacity: 0.75; - z-index: 20000; -} .dialog-box-container { position: relative; @@ -259,15 +251,11 @@ margin-right: auto; margin-left: auto; } -.dialog-box-underlay { - position: absolute; - left: -1em; - right: -1em; - top: -1em; - bottom: -1em; - opacity: 0.5; - background: black; - z-index: -1; + +.dialog-box-wrapper { + position: relative; + padding: 1em; + background-color: rgba(0,0,0,0.5); -moz-border-radius: 1em; -webkit-border-radius: 1em; } diff -r 6eac08f7edcf -r b671c301674a static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Fri Aug 22 17:44:32 2008 -0400 +++ b/static/june_2007_style/panel_layout.css.tmpl Fri Aug 22 17:47:43 2008 -0400 @@ -244,30 +244,17 @@ z-index: 20000; } -#overlay-inner { - width: 100%; height: 100%; - background-color:#FFF; - filter:alpha(opacity=75); - -moz-opacity: 0.75; - opacity: 0.75; - z-index: 20000; -} - .dialog-box-container { position: relative; margin-top: 80px; margin-right: auto; margin-left: auto; } -.dialog-box-underlay { - position: absolute; - left: -1em; - right: -1em; - top: -1em; - bottom: -1em; - opacity: 0.5; - background: black; - z-index: -1; + +.dialog-box-wrapper { + position: relative; + padding: 1em; + background-color: rgba(0,0,0,0.5); -moz-border-radius: 1em; -webkit-border-radius: 1em; } diff -r 6eac08f7edcf -r b671c301674a static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/galaxy.base.js Fri Aug 22 17:47:43 2008 -0400 @@ -29,13 +29,10 @@ function ensure_popup_helper() { // And the helper below the popup menus if ( $( "#popup-helper" ).length == 0 ) { - var e = $("<div id='popup-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 15000;'></div>"); - if ( $.browser.ie ) { - // Element will not capture drags in ie without nonzero opacity, - // but causes flashing in firefox with nonzero opacity - e.css( "opacity", "0.01" ); - } - e.appendTo("body").hide(); + $( "<div id='popup-helper'/>" ).css( { + background: 'white', opacity: 0, zIndex: 15000, + position: 'absolute', top: 0, left: 0, width: '100%', height: '100%' + } ).appendTo( "body" ).hide(); } } diff -r 6eac08f7edcf -r b671c301674a static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/galaxy.panels.js Fri Aug 22 17:47:43 2008 -0400 @@ -6,13 +6,10 @@ function ensure_dd_helper() { // Insert div that covers everything when dragging the borders if ( jq( "#DD-helper" ).length == 0 ) { - var e = jq("<div id='DD-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 9000;'></div>"); - if ( jq.browser.ie ) { - // Element will not capture drags in ie without nonzero opacity, - // but causes flashing in firefox with nonzero opacity - e.css( "opacity", "0.01" ); - } - e.appendTo("body").hide(); + $( "<div id='DD-helper'/>" ).css( { + background: 'white', opacity: 0, zIndex: 9000, + position: 'absolute', top: 0, left: 0, width: '100%', height: '100%' + } ).appendTo( "body" ).hide(); } } @@ -179,6 +176,46 @@ return { handle_minwidth_hint: handle_minwidth_hint }; }; +// Modal dialog boxes + +function hide_modal() { + $(".dialog-box-container" ).fadeOut( function() { $("#overlay").hide(); } ); +}; + +function show_modal( title, body, buttons, extra_buttons ) { + $( ".dialog-box" ).find( ".title" ).html( title ); + var b = $( ".dialog-box" ).find( ".buttons" ).html( "" ); + if ( buttons ) { + $.each( buttons, function( name, value ) { + b.append( $( '<button/>' ).text( name ).click( value ) ); + b.append( " " ); + }); + b.show(); + } else { + b.hide(); + } + var b = $( ".dialog-box" ).find( ".extra_buttons" ).html( "" ); + if ( extra_buttons ) { + $.each( extra_buttons, function( name, value ) { + b.append( $( '<button/>' ).text( name ).click( value ) ); + b.append( " " ); + }); + b.show(); + } else { + b.hide(); + } + if ( body == "progress" ) { + body = $( "<img src='../images/yui/rel_interstitial_loading.gif')' />" ); + } + $( ".dialog-box" ).find( ".body" ).html( body ); + if ( ! $(".dialog-box-container").is( ":visible" ) ) { + $("#overlay").show(); + $(".dialog-box-container").fadeIn() + } +}; + +// Popup -- is this up to date? + function make_popupmenu( button_element, options ) { var menu_element = $( "<div class='popupmenu'><div class='popupmenu-top'><div class='popupmenu-top-inner'/></div></div>" ).appendTo( "body" ); $.each( options, function( k, v ) { diff -r 6eac08f7edcf -r b671c301674a static/scripts/galaxy.ui.scrollPanel.js --- a/static/scripts/galaxy.ui.scrollPanel.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/galaxy.ui.scrollPanel.js Fri Aug 22 17:47:43 2008 -0400 @@ -18,7 +18,7 @@ element_w = element.width(), element_h = element.height(), moved = false, - close = 5, + close_dist = 5, nudge = 23, // Legal panel range p_min_x = - ( panel_w - viewport_w ), @@ -34,21 +34,21 @@ mouse_x = ui.position.left + instance.offset.click.left; mouse_y = ui.position.top + instance.offset.click.top; // Move it - if ( ( panel_pos.left < p_max_x ) && ( mouse_x - close < min_vis_x ) ) { + if ( ( panel_pos.left < p_max_x ) && ( mouse_x - close_dist < min_vis_x ) ) { var t = Math.min( nudge, p_max_x - panel_pos.left ); panel.css( "left", panel_pos.left + t ); moved = true; instance.offset.parent.left += t; ui.position.left -= t } - if ( ( ! moved ) && ( panel_pos.left > p_min_x ) && ( mouse_x + close > max_vis_x ) ) { + if ( ( ! moved ) && ( panel_pos.left > p_min_x ) && ( mouse_x + close_dist > max_vis_x ) ) { var t = Math.min( nudge, panel_pos.left - p_min_x ); panel.css( "left", panel_pos.left - t ); moved = true; instance.offset.parent.left -= t; ui.position.left += t; } - if ( ( ! moved ) && ( panel_pos.top < p_max_y ) && ( mouse_y - close < min_vis_y ) ) { + if ( ( ! moved ) && ( panel_pos.top < p_max_y ) && ( mouse_y - close_dist < min_vis_y ) ) { var t = Math.min( nudge, p_max_y - panel_pos.top ); panel.css( "top", panel_pos.top + t ); // Firefox sometimes moves by less, so we need to check. Yuck. @@ -57,7 +57,7 @@ ui.position.top -= amount_moved; moved = true; } - if ( ( ! moved ) && ( panel_pos.top > p_min_y ) && ( mouse_y + close > max_vis_y ) ) { + if ( ( ! moved ) && ( panel_pos.top > p_min_y ) && ( mouse_y + close_dist > max_vis_y ) ) { var t = Math.min( nudge, panel_pos.top - p_min_x ); panel.css( "top", ( panel_pos.top - t ) + "px" ); // Firefox sometimes moves by less, so we need to check. Yuck. diff -r 6eac08f7edcf -r b671c301674a static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Fri Aug 22 17:47:43 2008 -0400 @@ -32,15 +32,16 @@ this.datatype = datatype; } -OutputTerminal.prototype.__proto__ = Terminal.prototype; +OutputTerminal.prototype = new Terminal; function InputTerminal( element, datatypes ) { Terminal.call( this, element ); this.datatypes = datatypes; } -InputTerminal.prototype = { - __proto__: Terminal.prototype, +InputTerminal.prototype = new Terminal; + +$.extend( InputTerminal.prototype, { can_accept: function ( other ) { if ( this.connectors.length < 1 ) { for ( t in this.datatypes ) { @@ -53,7 +54,7 @@ } return false; } -} +}); function Connector( handle1, handle2 ) { this.canvas = null; @@ -81,6 +82,10 @@ var canvas_container = $("#canvas-container"); if ( ! this.canvas ) { this.canvas = document.createElement( "canvas" ); + // excanvas specific hack + if ( window.G_vmlCanvasManager ) { + G_vmlCanvasManager.initElement( this.canvas ); + } canvas_container.append( $(this.canvas) ); if ( this.dragging ) { this.canvas.style.zIndex = "300" } } @@ -182,14 +187,14 @@ t.remove(); }))) .bind( "mouseleave", function() { - $(this).fadeOut( "fast", function() { $(this).remove() } ) + $(this).remove(); }); // Position it and show t.css( { top: $(this).offset().top - 2, left: $(this).offset().left - t.width(), 'padding-right': $(this).width() } - ).fadeIn( "fast" ); + ).show(); } }, function() {} @@ -272,12 +277,12 @@ var node = this; var b = f.find( ".toolFormBody" ); b.find( "div" ).remove(); - var ibox = $("<div class='inputs'/>").appendTo( b ); + var ibox = $("<div class='inputs'></div>").appendTo( b ); $.each( data.data_inputs, function( i, input ) { - t = $("<div class='terminal input-terminal'></div>") + var t = $("<div class='terminal input-terminal'></div>"); node.enable_input_terminal( t, input.name, input.extensions ); - ibox.append( $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div></div>" ).prepend( t ) ); - }); + ibox.append( $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div>" ).prepend( t ) ); + }); if ( ( data.data_inputs.length > 0 ) && ( data.data_outputs.length > 0 ) ) { b.append( $( "<div class='rule'></div>" ) ); } @@ -305,8 +310,8 @@ } // Update input rows var old_body = el.find( "div.inputs" ); - var new_body = $("<div class='inputs'/>"); - old = old_body.find( "div.input-data-row") + var new_body = $("<div class='inputs'></div>"); + var old = old_body.find( "div.input-data-row") $.each( data.data_inputs, function( i, input ) { var t = $("<div class='terminal input-terminal'></div>"); node.enable_input_terminal( t, input.name, input.extensions ); @@ -322,7 +327,7 @@ $(this).remove(); }); // Append to new body - new_body.append( $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div></div>" ).prepend( t ) ); + new_body.append( $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div>" ).prepend( t ) ); }); old_body.replaceWith( new_body ); // Cleanup any leftover terminals @@ -468,13 +473,21 @@ f.append( b ) // Fix width to computed width // Now add floats - var buttons = $("<div class='buttons' style='float: right'></div>"); - buttons.append( $("<img src='../images/delete_icon.png' />").click( function() { + var buttons = $("<div class='buttons' style='float: right;'></div>"); + buttons.append( $("<img src='../images/delete_icon.png' />").click( function( e ) { node.destroy(); } ).hover( function() { $(this).attr( 'src', "../images/delete_icon_dark.png" ) }, function() { $(this).attr( 'src', "../images/delete_icon.png" ) } ) ); + // zIndex tracking for bring to front + zmax = $("#canvas-container").data( "zmax" ) + if ( ! zmax ) { + zmax = 0; + } + f.css( "zIndex", zmax + 1 ); + $("#canvas-container").data( "zmax", zmax + 1 ); + // Place inside container f.appendTo( "#canvas-container" ); // Position in container var o = $("#canvas-container").position(); @@ -494,13 +507,16 @@ // containment: $("#shim"), // grow: true, click: function( e, ui ) { - var element = $(this).data("draggable").element.get(0); - (function(p) { p.removeChild( element ); p.appendChild( element ) })(element.parentNode) + // Bring to front + zmax = $("#canvas-container").data( "zmax" ) + $(this).css( "zIndex", zmax + 1 ); + $("#canvas-container").data( "zmax", zmax + 1 ); + // Make active workflow.activate_node( node ); }, start: function( e, ui ) { workflow.activate_node( node ); - $(this).css( 'z-index', '1000' ); + $(this).css( 'z-index', $("#canvas-container").data( "zmax" ) + 1000 ); }, drag: function( e, ui ) { $(this).find( ".terminal" ).each( function() { @@ -508,9 +524,11 @@ }) }, stop: function( e, ui ) { - var element = $(this).data("draggable").element.get(0); - (function(p) { p.removeChild( element ); p.appendChild( element ) })(element.parentNode) - $(this).css( 'z-index', '100' ); + // Bring to front + zmax = $("#canvas-container").data( "zmax" ) + $(this).css( "zIndex", zmax + 1 ); + $("#canvas-container").data( "zmax", zmax + 1 ); + // Redraw $(this).find( ".terminal" ).each( function() { this.terminal.redraw(); }); diff -r 6eac08f7edcf -r b671c301674a static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/packed/galaxy.base.js Fri Aug 22 17:47:43 2008 -0400 @@ -1,1 +1,1 @@ -jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[@popupmenu]").each(function(){var B={};$(this).find("a").each(function(){var C=$(this).attr("confirm"),D=$(this).attr("href"),E=$(this).attr("target");B[$(this).text()]=function(){if(!C||confirm(C)){var F=window;if(E=="_parent"){F=window.parent}F.location=D}}});var A=$("#"+$(this).attr("popupmenu"));make_popupmenu(A,B);$(this).remove();A.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){var A=$("<div id='popup-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 15000;'></div>");if($.browser.ie){A.css("opacity","0.01")}A.appendTo("body").hide()}}function make_popupmenu(D,B){ensure_popup_helper();var A=$("<div class='popupmenu'></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=functi on(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(F){var G=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.pageY-2,left:F.pageX-2});return false};$(D).click(E)}; \ No newline at end of file +jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[@popupmenu]").each(function(){var B={};$(this).find("a").each(function(){var C=$(this).attr("confirm"),D=$(this).attr("href"),E=$(this).attr("target");B[$(this).text()]=function(){if(!C||confirm(C)){var F=window;if(E=="_parent"){F=window.parent}F.location=D}}});var A=$("#"+$(this).attr("popupmenu"));make_popupmenu(A,B);$(this).remove();A.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(D,B){ensure_popup_helper();var A=$("<div class='popupmenu'></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E =function(F){var G=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.pageY-2,left:F.pageX-2});return false};$(D).click(E)}; \ No newline at end of file diff -r 6eac08f7edcf -r b671c301674a static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/packed/galaxy.panels.js Fri Aug 22 17:47:43 2008 -0400 @@ -1,1 +1,1 @@ -var hidden_width=7;var border_tweak=9;var jq=jQuery;function ensure_dd_helper(){if(jq("#DD-helper").length==0){var A=jq("<div id='DD-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 9000;'></div>");if(jq.browser.ie){A.css("opacity","0.01")}A.appendTo("body").hide()}}function make_left_panel(E,A,B){var D=false;var C=null;resize=function(F){var G=F;if(F<0){F=0}jq(E).css("width",F);jq(B).css("left",G);jq(A).css("left",F+7);if(document.recalc){document.recalc()}};toggle=function(){if(D){jq(B).removeClass("hover");jq(B).animate({left:C},"fast");jq(E).css("left",-C).show().animate({left:0},"fast",function(){resize(C);jq(B).removeClass("hidden")});D=false}else{C=jq(B).position().left;jq(A).css("left",hidden_width);if(document.recalc){document.recalc()}jq(B).removeClass("hover");jq(E).animate({left:-C},"fast");jq(B).animate({left:-1},"fast",function(){jq(this).addClass("hidden")});D=true}};jq(B).hover(function( ){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(F,G){jq("#DD-helper").show()},stop:function(F,G){jq("#DD-helper").hide();return false},drag:function(F,G){x=G.position.left;x=Math.min(400,Math.max(100,x));if(D){jq(E).css("left",0);jq(B).removeClass("hidden");D=false}resize(x);G.position.left=x;G.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show()}function make_right_panel(A,E,G){var I=false;var F=false;var C=null;var D=function(J){jq(A).css("width",J);jq(E).css("right",J+9);jq(G).css("right",J).css("left","");if(document.recalc){document.recalc()}};var H=function(){if(I){jq(G).removeClass("hover");jq(G).animate({right:C},"fast");jq(A).css("right",-C).show().animate({right:0},"fast",function(){D(C);jq(G).removeClass("hidden")});I=false}else{C=jq(document).width()-jq(G).position().left-border_tweak;jq(E).css("right",hidden_width+1);if(document.recalc){document.recalc()}jq (G).removeClass("hover");jq(A).animate({right:-C},"fast");jq(G).animate({right:-1},"fast",function(){jq(this).addClass("hidden")});I=true}F=false};var B=function(J){var K=jq(E).width()-(I?C:0);if(K<J){if(!I){H();F=true}}else{if(F){H();F=false}}};jq(G).hover(function(){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(J,K){jq("#DD-helper").show()},stop:function(J,K){x=K.position.left;w=jq(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);D(w-x-border_tweak);jq("#DD-helper").hide();return false},click:function(){H()},drag:function(J,K){x=K.position.left;w=jq(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(I){jq(A).css("right",0);jq(G).removeClass("hidden");I=false}D(w-x-border_tweak);K.position.left=x;K.position.top=$(this).data("draggable").originalPosition.top}}).find("div").show();return{handle_minwidth_hint:B}}function make_popupmenu(D,B){var A=$("<div class='popupmenu'><div class='popupmenu-top'><div class='p opupmenu-top-inner'/></div></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(){var F=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.top+$(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)}; \ No newline at end of file +var hidden_width=7;var border_tweak=9;var jq=jQuery;function ensure_dd_helper(){if(jq("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(E,A,B){var D=false;var C=null;resize=function(F){var 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false},drag:function(F,G){x=G.position.left;x=Math.min(400,Math.max(100,x));if(D){jq(E).css("left",0);jq(B).removeClass("hidden");D=false}resize(x);G.position.left=x;G.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show()}function make_right_panel(A,E,G){var I=false;var F=false;var C=null;var D=function(J){jq(A).css("width",J);jq(E).css("right",J+9);jq(G).css("right",J).css("left","");if(document.recalc){document.recalc()}};var H=function(){if(I){jq(G).removeClass("hover");jq(G).animate({right:C},"fast");jq(A).css("right",-C).show().animate({right:0},"fast",function(){D(C);jq(G).removeClass("hidden")});I=false}else{C=jq(document).width()-jq(G).position().left-border_tweak;jq(E).css("right",hidden_width+1);if(document.recalc){document.recalc()}jq(G).removeClass("hover");jq(A).animate({right:-C},"fast");jq(G).anima te({right:-1},"fast",function(){jq(this).addClass("hidden")});I=true}F=false};var B=function(J){var 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dialog-box").find(".buttons").html("");if(D){$.each(D,function(F,G){A.append($("<button/>").text(F).click(G));A.append(" ")});A.show()}else{A.hide()}var A=$(".dialog-box").find(".extra_buttons").html("");if(C){$.each(C,function(F,G){A.append($("<button/>").text(F).click(G));A.append(" ")});A.show()}else{A.hide()}if(B=="progress"){B=$("<img src='../images/yui/rel_interstitial_loading.gif')' />")}$(".dialog-box").find(".body").html(B);if(!$(".dialog-box-container").is(":visible")){$("#overlay").show();$(".dialog-box-container").fadeIn()}}function make_popupmenu(D,B){var A=$("<div class='popupmenu'><div class='popupmenu-top'><div class='popupmenu-top-inner'/></div></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(){var F=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.top+ $(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)}; \ No newline at end of file diff -r 6eac08f7edcf -r b671c301674a static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Fri Aug 22 17:47:43 2008 -0400 @@ -1,1 +1,1 @@ -function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype.__proto__=Terminal.prototype;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype={__proto__:Terminal.prototype,can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}};function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototype ,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.style.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("h eight",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H= E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).fadeOut("fast",function(){$(this).remove()})});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).fadeIn("fast")}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);E.terminal=new OutputTerm inal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors=D.tool_errors;if(this.tool_error s){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'/>").appendTo(A);$.each(D.data_inputs,function(G,F){t=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(t,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(t))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(D){var B=$(this.element),C=this;this.tool_state=D.tool_state;this.form_html=D.form_html;this.tool_errors=D.tool_errors;if(this.tool_errors ){B.addClass("tool-node-error")}else{B.removeClass("tool-node-error")}var E=B.find("div.inputs");var A=$("<div class='inputs'/>");old=E.find("div.input-data-row");$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");C.enable_input_terminal(G,F.name,F.extensions);E.find("div[name="+F.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var I=this.terminal.connectors[0];if(I){G[0].terminal.connectors[0]=I;I.handle2=G[0].terminal}});$(this).remove()});A.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(G))});E.replaceWith(A);E.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; text-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_changed(this)},changed:function(){workflow .node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,function(E,D){var C=prebuild_node("tool",D. name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive()}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A},node_changed:function(A){this.has_changes=true;if(this.active_node==A){this.activate_node(A)}}});function prebuild_node(H,F,K){var E=$("<div class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectable'>"+F+"</div>");E.append(J);E.css( "left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10,scrollSpeed:20,click:function(N,M){var L=$(this).data("draggable").element.get(0);(function(O){O.removeChild(L);O.appendChild(L)})(L.parentNode);workflow.activate _node(C)},start:function(M,L){workflow.activate_node(C);$(this).css("z-index","1000")},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(N,M){var L=$(this).data("draggable").element.get(0);(function(O){O.removeChild(L);O.appendChild(L)})(L.parentNode);$(this).css("z-index","100");$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes}; \ No newline at end of file +function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype=new Terminal;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}});function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototy pe,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.styl e.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("height",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I ,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H=E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).remove()});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).show()}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container"). get(0);E.terminal=new OutputTerminal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors= D.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'></div>").appendTo(A);$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(G,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div>").prepend(G))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(E){var C=$(this.element),D=this;this.tool_state=E.tool_state;this.form_html=E.form_html;this.tool_error s=E.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var F=C.find("div.inputs");var B=$("<div class='inputs'></div>");var A=F.find("div.input-data-row");$.each(E.data_inputs,function(I,G){var H=$("<div class='terminal input-terminal'></div>");D.enable_input_terminal(H,G.name,G.extensions);F.find("div[name="+G.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var J=this.terminal.connectors[0];if(J){H[0].terminal.connectors[0]=J;J.handle2=H[0].terminal}});$(this).remove()});B.append($("<div class='form-row dataRow input-data-row' name='"+G.name+"'>"+G.label+"</div>").prepend(H))});F.replaceWith(B);F.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; text-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_change d(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,functio n(E,D){var C=prebuild_node("tool",D.name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive()}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A},node_changed:function(A){this.has_changes=true;if(this.active_node==A){this.activate_node(A)}}});function prebuild_node(H,F,K){var E=$("<div class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectab le'>"+F+"</div>");E.append(J);E.css("left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right;'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(L){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));zmax=$("#canvas-container").data("zmax");if(!zmax){zmax=0}E.css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10, scrollSpeed:20,click:function(M,L){zmax=$("#canvas-container").data("zmax");$(this).css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);workflow.activate_node(C)},start:function(M,L){workflow.activate_node(C);$(this).css("z-index",$("#canvas-container").data("zmax")+1000)},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(M,L){zmax=$("#canvas-container").data("zmax");$(this).css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes}; \ No newline at end of file diff -r 6eac08f7edcf -r b671c301674a templates/workflow/editor.mako --- a/templates/workflow/editor.mako Fri Aug 22 17:44:32 2008 -0400 +++ b/templates/workflow/editor.mako Fri Aug 22 17:47:43 2008 -0400 @@ -14,8 +14,11 @@ <%def name="javascripts()"> - ## ${parent.javascripts()} - + ${parent.javascripts()} + +  <script type='text/javascript' src="/static/scripts/jquery.js"> </script> <script type='text/javascript' src="/static/scripts/jquery.ui.js"> </script> <script type='text/javascript' src="/static/scripts/galaxy.ui.scrollPanel.js"> </script> @@ -23,46 +26,6 @@ <script type='text/javascript' src="/static/scripts/jquery.form.js"> </script> <script type='text/javascript' src="/static/scripts/jquery.json.js"> </script> - <script type='text/javascript'> - /* Dialog and menu handling tools to be moved to galaxy.layout.js */ - - function hide_modal() { - $(".dialog-box-container" ).fadeOut( function() { $("#overlay").hide(); } ); - }; - - function show_modal( title, body, buttons, extra_buttons ) { - $( ".dialog-box" ).find( ".title" ).html( title ); - var b = $( ".dialog-box" ).find( ".buttons" ).html( "" ); - if ( buttons ) { - $.each( buttons, function( name, value ) { - b.append( $( '<button/>' ).text( name ).click( value ) ); - b.append( " " ); - }); - b.show(); - } else { - b.hide(); - } - var b = $( ".dialog-box" ).find( ".extra_buttons" ).html( "" ); - if ( extra_buttons ) { - $.each( extra_buttons, function( name, value ) { - b.append( $( '<button/>' ).text( name ).click( value ) ); - b.append( " " ); - }); - b.show(); - } else { - b.hide(); - } - if ( body == "progress" ) { - body = $( "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>" ); - } - $( ".dialog-box" ).find( ".body" ).html( body ); - if ( ! $(".dialog-box-container").is( ":visible" ) ) { - $("#overlay").show(); - $(".dialog-box-container").fadeIn() - } - }; - </script> - <script type='text/javascript' src="/static/scripts/galaxy.workflow_editor.canvas.js"> </script> <script type='text/javascript'> @@ -70,38 +33,34 @@ $( function() { // Initialize workflow state reset(); - // Shim (the background of the editor area) causes loss of focus - // $("#shim").click( workflow.clear_active_node ).hoverIntent( { - // over: function () { $("div.toolForm").fadeTo( "fast", 0.7 ) }, - // out: function () { $("div.toolForm").fadeTo( "fast", 1.0 ) }, - // interval: 300 - // }); // Load the datatype info - $.getJSON( "${h.url_for( action='get_datatypes' )}", function( data ) { - populate_datatype_info( data ); - // Load workflow definition - $.ajax( { - url: "${h.url_for( action='load_workflow' )}", - data: { id: "${trans.security.encode_id( workflow_id )}", "_": "true" }, - dataType: 'json', - success: function( data ) { - reset(); - workflow.from_simple( data ); - workflow.has_changes = false; - scroll_to_nodes(); - hide_modal(); - }, - beforeSubmit: function( data ) { - show_modal( "Loading workflow", "progress" ); - } - }); + $.ajax( { + url: "${h.url_for( action='get_datatypes' )}", + dataType: "json", + cache: false, + success: function( data ) { + populate_datatype_info( data ); + // Load workflow definition + $.ajax( { + url: "${h.url_for( action='load_workflow' )}", + data: { id: "${trans.security.encode_id( workflow_id )}", "_": "true" }, + dataType: 'json', + cache: false, + success: function( data ) { + reset(); + workflow.from_simple( data ); + workflow.has_changes = false; + scroll_to_nodes(); + hide_modal(); + }, + beforeSubmit: function( data ) { + show_modal( "Loading workflow", "progress" ); + } + }); + } }); $(document).ajaxError( function ( e, x ) { - // $("#error-display").empty() - // .append( $("<div/>").html( x.responseText ) ) - // .append( $("<div><a>close</a></div>" ).click( function() { $("#error-display").hide(); } ) ) - // .show(); show_modal( "Server error", x.responseText, { "Ignore error" : hide_modal } ); return false; }); @@ -272,7 +231,7 @@ save_current_workflow( do_close ); } }, { - "Don't Save": do_close, + "Don't Save": do_close } ); } else { window.document.location = "${next_url}" @@ -410,20 +369,10 @@ margin: 5px; } - #error-display { - display: none; - position: fixed; - top: 5%; left: 5%; width: 90%; height: 90%; - border: solid red 10px; - background: #FFDDDD; - z-index: 50000; - overflow: auto; - } - canvas { position: absolute; z-index: 10; } canvas.dragging { position: absolute; z-index: 1000; } - .input-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; bottom: 0; left: -16px; z-index: 1500; } - .output-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; bottom: 0; right: -16px; z-index: 1500; } + .input-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; top: 0; left: -16px; z-index: 1500; } + .output-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; top: 0; right: -16px; z-index: 1500; } .drag-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_drag.png')}); position: absolute; z-index: 1500; } .input-terminal-active { background: url(${h.url_for('/static/style/workflow_circle_green.png')}); } ## .input-terminal-hover { background: yellow; border: solid black 1px; } @@ -504,13 +453,11 @@ </style> </%def> - -<div id="error-display"></div> <div id="overlay"> ## Need a table here for centering in IE6 <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0"><tr><td> - <div style="position: relative;"> + <div class="dialog-box-wrapper"> <div class="dialog-box"> <div class="unified-panel-header"> <div class="unified-panel-header-inner"><span class='title'>Loading workflow editor...</span></div> @@ -522,7 +469,6 @@ <div style="clear: both;"></div> </div> </div> - <div class="dialog-box-underlay"></div> </div> </td></tr></table> </div> @@ -558,9 +504,9 @@ %if "[[" in tool.description and "]]" in tool.description: ${tool.description.replace( '[[', '<a id="link-${tool.id}" href="javascript:add_node_for_tool( ${tool.id} )">' % tool.id ).replace( "]]", "</a>" )} %elif tool.name: - <a id="link-${tool.id}" href="javascript:add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description} + <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description} %else: - <a id="link-${tool.id}" href="javascript:add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a> + <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a> %endif </div> %else: @@ -588,7 +534,7 @@ <div id="__workflow__input__" class="toolSectionBody"> <div class="toolSectionBg"> <div class="toolTitle"> - <a href="javascript:add_node_for_module( 'data_input', 'Input Dataset' )">Input dataset</a> + <a href="#" onclick="add_node_for_module( 'data_input', 'Input Dataset' )">Input dataset</a> </div> </div> </div> diff -r 6eac08f7edcf -r b671c301674a templates/workflow/index.mako --- a/templates/workflow/index.mako Fri Aug 22 17:44:32 2008 -0400 +++ b/templates/workflow/index.mako Fri Aug 22 17:47:43 2008 -0400 @@ -21,16 +21,15 @@ </div> %endif -<div> - <div style="float: right;"> - <a class="action-button" href="${h.url_for( action='create' )}"> - <img src="${h.url_for('/static/images/silk/add.png')}" /> - <span>Add a new workflow</span> - </a> - </div> - <h2>Your workflows</h2> +<h2>Your workflows</h2> + +<div style="float: right; margin-top: -2.5em;"> + <a class="action-button" href="${h.url_for( action='create' )}"> + <img src="${h.url_for('/static/images/silk/add.png')}" /> + <span>Add a new workflow</span> + </a> </div> - + %if workflows: <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <tr class="header">

1 0

[hg] galaxy 1480: dbkey must be set after _metadata column is in...
by greg＠scofield.bx.psu.edu 27 Aug '08

27 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/6de3006c62b3 changeset: 1480:6de3006c62b3 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Aug 25 15:28:57 2008 -0400 description: dbkey must be set after _metadata column is initialized in the init of HDA, or else the dbkey is clobered. 1 file(s) affected in this change: lib/galaxy/model/__init__.py diffs (14 lines): diff -r b671c301674a -r 6de3006c62b3 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Aug 22 17:47:43 2008 -0400 +++ b/lib/galaxy/model/__init__.py Mon Aug 25 15:28:57 2008 -0400 @@ -112,9 +112,9 @@ self.blurb = blurb self.peek = peek self.extension = extension - self.dbkey = dbkey self.designation = designation self._metadata = metadata or dict() + self.dbkey = dbkey self.deleted = deleted self.visible = visible # Relationships

1 0

Test is at rev 1533:c77dea3e745a
by Greg Von Kuster 27 Aug '08

27 Aug '08

1 0

Test is at rev 1524:96f8ed6d89cc
by Greg Von Kuster 26 Aug '08

26 Aug '08

1 0

Test is at rev 1523:e68dbb8f6b4c
by Greg Von Kuster 25 Aug '08

25 Aug '08

Thanks, Nate!

1 0

Main is at rev 1476:77f8bf51b2ae
by Greg Von Kuster 22 Aug '08

22 Aug '08

1 0

[hg] galaxy 1477: Fix for dataset_metadata_in_file validator: al...
by greg＠scofield.bx.psu.edu 22 Aug '08

22 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/99e223f6a132 changeset: 1477:99e223f6a132 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Aug 22 11:22:44 2008 -0400 description: Fix for dataset_metadata_in_file validator: all locally cached data files that are columnar must have columns separated by tabs characters, not white space. I've eliminated the 'split' param from the validator as it was causing problems. Extract genomic DNA tool should now finally work correctly. 2 file(s) affected in this change: lib/galaxy/tools/parameters/validation.py tools/extract/extract_genomic_dna.xml diffs (37 lines): diff -r 77f8bf51b2ae -r 99e223f6a132 lib/galaxy/tools/parameters/validation.py --- a/lib/galaxy/tools/parameters/validation.py Fri Aug 22 10:39:58 2008 -0400 +++ b/lib/galaxy/tools/parameters/validation.py Fri Aug 22 11:22:44 2008 -0400 @@ -235,18 +235,17 @@ metadata_name = metadata_name.strip() metadata_column = int( elem.get( "metadata_column", 0 ) ) message = elem.get( "message", "Value for metadata %s was not found in %s." % ( metadata_name, filename ) ) - split = elem.get( "split", None ) line_startswith = elem.get( "line_startswith", None ) if line_startswith: line_startswith = line_startswith.strip() - return cls( filename, metadata_name, metadata_column, message, split, line_startswith ) - def __init__( self, filename, metadata_name, metadata_column, message="Value for metadata not found.", split=None, line_startswith=None ): + return cls( filename, metadata_name, metadata_column, message, line_startswith ) + def __init__( self, filename, metadata_name, metadata_column, message="Value for metadata not found.", line_startswith=None ): self.metadata_name = metadata_name self.message = message self.valid_values = [] for line in open( filename ): if line_startswith is None or line.startswith( line_startswith ): - fields = line.split( split ) + fields = line.split( '\t' ) if metadata_column < len( fields ): self.valid_values.append( fields[metadata_column] ) def validate( self, value, history = None ): diff -r 77f8bf51b2ae -r 99e223f6a132 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Fri Aug 22 10:39:58 2008 -0400 +++ b/tools/extract/extract_genomic_dna.xml Fri Aug 22 11:22:44 2008 -0400 @@ -4,7 +4,7 @@ <inputs> <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"> <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." split="\t" line_startswith="seq" /> + <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="seq" /> </param> <param name="out_format" type="select" label="Output data type"> <option value="fasta">FASTA</option>

1 0

[hg] galaxy 1476: Better fix for interval_maf_to_merged_fasta wh...
by greg＠scofield.bx.psu.edu 22 Aug '08

22 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/77f8bf51b2ae changeset: 1476:77f8bf51b2ae user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Aug 22 10:39:58 2008 -0400 description: Better fix for interval_maf_to_merged_fasta when no strand column in input, added functional test. 4 file(s) affected in this change: test-data/13.bed test-data/interval_maf_to_merged_fasta_out3.fasta tools/maf/interval_maf_to_merged_fasta.py tools/maf/interval_maf_to_merged_fasta.xml diffs (716 lines): diff -r 973d6cbeea87 -r 77f8bf51b2ae test-data/13.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/13.bed Fri Aug 22 10:39:58 2008 -0400 @@ -0,0 +1,96 @@ +chr16 20682314 20682813 ENSG00000005187 +chrX 123339504 123340003 ENSG00000009694 +chr3 52503897 52504396 ENSG00000010327 +chr6 112089190 112089689 ENSG00000010810 +chr6 112089249 112089748 ENSG00000010810 +chr6 112089261 112089760 ENSG00000010810 +chr2 31310208 31310707 ENSG00000013016 +chr22 16598265 16598764 ENSG00000015475 +chr22 16598139 16598638 ENSG00000015475 +chr22 16596941 16597440 ENSG00000015475 +chr22 16596908 16597407 ENSG00000015475 +chr12 101335726 101336225 ENSG00000017427 +chr12 101320236 101320735 ENSG00000017427 +chr12 101320163 101320662 ENSG00000017427 +chr12 101313809 101314308 ENSG00000017427 +chr7 99282701 99283200 ENSG00000021461 +chr7 99263073 99263572 ENSG00000021461 +chr19 38013262 38013761 ENSG00000021488 +chr3 52206685 52207184 ENSG00000023330 +chr3 52206657 52207156 ENSG00000023330 +chr10 101532011 101532510 ENSG00000023839 +chr10 101531994 101532493 ENSG00000023839 +chr5 71651457 71651956 ENSG00000049883 +chr3 52796382 52796881 ENSG00000055957 +chr3 52786149 52786648 ENSG00000055957 +chr6 166698400 166698899 ENSG00000060762 +chr6 166698708 166699207 ENSG00000060762 +chr16 2029817 2030316 ENSG00000065057 +chr10 126075862 126076361 ENSG00000065154 +chr10 126075869 126076368 ENSG00000065154 +chr10 123223889 123224388 ENSG00000066468 +chr10 123227846 123228345 ENSG00000066468 +chr10 123229123 123229622 ENSG00000066468 +chr10 123229361 123229860 ENSG00000066468 +chr10 123229555 123230054 ENSG00000066468 +chr10 123231339 123231838 ENSG00000066468 +chr10 123231360 123231859 ENSG00000066468 +chr10 123287470 123287969 ENSG00000066468 +chr1 92746841 92747340 ENSG00000067208 +chr1 92860438 92860937 ENSG00000067208 +chr3 151165384 151165883 ENSG00000070087 +chr16 56546748 56547247 ENSG00000070729 +chr16 56475004 56475503 ENSG00000070729 +chr8 145589254 145589753 ENSG00000071894 +chr1 159899157 159899656 ENSG00000072694 +chr1 159899076 159899575 ENSG00000072694 +chr4 5763326 5763825 ENSG00000072840 +chr2 70753968 70754467 ENSG00000075340 +chr2 70744123 70744622 ENSG00000075340 +chr2 70744138 70744637 ENSG00000075340 +chr2 70742773 70743272 ENSG00000075340 +chr2 70744065 70744564 ENSG00000075340 +chr3 172801314 172801813 ENSG00000075651 +chr3 172812085 172812584 ENSG00000075651 +chr4 74565827 74566326 ENSG00000079557 +chr19 10684644 10685143 ENSG00000079805 +chr19 10689340 10689839 ENSG00000079805 +chr19 10689256 10689755 ENSG00000079805 +chr13 93889844 93890343 ENSG00000080166 +chr2 151974175 151974674 ENSG00000080345 +chr2 151974202 151974701 ENSG00000080345 +chr5 113796627 113797126 ENSG00000080709 +chr5 113725416 113725915 ENSG00000080709 +chr5 113725066 113725565 ENSG00000080709 +chr2 165249579 165250078 ENSG00000082438 +chr2 165249502 165250001 ENSG00000082438 +chr4 187745932 187746431 ENSG00000083857 +chr2 27572711 27573210 ENSG00000084734 +chr1 111758461 111758960 ENSG00000085465 +chr11 49124766 49125265 ENSG00000086205 +chr11 49124879 49125378 ENSG00000086205 +chr7 26298700 26299199 ENSG00000086300 +chr7 26297541 26298040 ENSG00000086300 +chr16 80625865 80626364 ENSG00000086696 +chr19 54159879 54160378 ENSG00000087086 +chr16 55552764 55553263 ENSG00000087237 +chr3 187840344 187840843 ENSG00000090512 +chr3 187840445 187840944 ENSG00000090512 +chr4 25358148 25358647 ENSG00000091490 +chr3 113535219 113535718 ENSG00000091972 +chr3 113534107 113534606 ENSG00000091972 +chr15 40483770 40484269 ENSG00000092529 +chr15 40427094 40427593 ENSG00000092529 +chr15 40481381 40481880 ENSG00000092529 +chr15 40457707 40458206 ENSG00000092529 +chr15 40438491 40438990 ENSG00000092529 +chr1 120055534 120056033 ENSG00000092621 +chr1 120063274 120063773 ENSG00000092621 +chr6 159106769 159107268 ENSG00000092820 +chr6 159106768 159107267 ENSG00000092820 +chr6 159106766 159107265 ENSG00000092820 +chr9 111041832 111042331 ENSG00000095203 +chr9 110974075 110974574 ENSG00000095203 +chr10 94822723 94823222 ENSG00000095596 +chr10 94823138 94823637 ENSG00000095596 +chr10 29005931 29006430 ENSG00000095739 diff -r 973d6cbeea87 -r 77f8bf51b2ae test-data/interval_maf_to_merged_fasta_out3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/interval_maf_to_merged_fasta_out3.fasta Fri Aug 22 10:39:58 2008 -0400 @@ -0,0 +1,480 @@ +>hg18.chr16(+):20682314-20682813 +ctgtggatcagaggaccctgtgccagatcatacaactccttgcagttcatgtaaggactcggattttacctggagtggaaaaagaagcactgaaagatttgagcaggggagtaacctgatagcgtttatgtttAGTCCTGCCACTTCGACAGATAAACGCACCAATGGGCTTGATGAGATTTAGGCCAACCCATAACCGCCCCTCAACTTCTTTCCTTTCAATTTCAAAACTCCTCTATGGCTTCCTCCATCTGTTCTTCCTTCTGAGAAGTGCTCTCTCTGCCCCTTTACAGAACTAACCACTTCGGCAACTCCTTGGACACTTTCCTTCTTGTTAATAATTTGCTTTCTCCGCCCCTCAAAAGCTTGCTGTTTCTGTAAATCATTACCTGTAAGAGGAACCGCTGGGAGTCCTGTAAACTTTAGCCCAGAGCTTGGCTCCTCCTCCAGAATGTCTCCACCAATCAAGGAAAGTGTTTTGGGCCAGTCTTGCTCCTCC +>mm8 +GTCTGGGTCAGAGGACA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTCCCTCCTAGTAACGCACTGCCTTCCCAGCCTACTAAAACTCTGCTGTGTGTACAGATCATTACCTGTAATAAGACAGGCCAGGGTT-ATGTAAACAT----------TCACGCTCCTCCCACCAA-TATATCCACCAATTAAGGAAAGCACTGCCGGCCAGTCTGACTCCTCC + +>hg18.chrX(+):123339504-123340003 +CTACTGATTAGTAGTTTTGTTTTTTTTTTCTTTCCTCCCTCAAGCTTTAGGAGTTGTAAAAAGAATAATAATAGTTCAAGGCAGTATTAAAACCACAGCTGTAAGTAATAAAAAGTGCATTTCCTGAATATAATACAAATGTAACTTTAACAAACTAAAGGCACGAACCAACCAAATACGTATTACAAACTAGAAATGCACAGTTCAAGGTAATCACTATTAAGTAAAAGCTTCAAATATTTGTTTCTAATGGATATTTAAAGCAGTTTGAAAATGATACATCATCAATGAATTGCAAAAACGTATAATTGCTTAAAATATAAGCAAAATAGACTCTAATATTGACATTTTGGATTTGTGATAAAATACATAATCACATTTATGAATGCACTCTCTATATACAGTTCACAAATTATTTTTCCATTAATTTAAAAGAACATCAGAGGTTCTAGGAACTTAAGGTCCATTTTTAGGTTGGTGTGGAGGTATTCAAATTTTC +>mm8 +CAACTTGTTA-TACCTTTTTTTTTTTTTCTTTTCCTCCTCAAAACTTTAGGAGTTGTAAAGAGAACAATAATATTTCAAGGCAGTATTAAAACCACAGTTGTAAGTGATAAAAAGTGCATTTCCTGAATATAATACAAATATAACTTTAGGTAACCAAAGGCACAAACTAACTAAATACATATTACAAACTAGAATTGCACAGTTCAAGGTAATTACTATTAAGGAATAGTTCCAAATATTTCTTCCTAATGAATATTTAAATCGGTTTGAAAATGATACATCACTAGTGAGTTGCAAAAGAGCGCAATCACTTAAAATAGAAGCAAAATAGGCTCCAAGATTGACACATTGGGTTAGTGATAAAATAC---ACCACATTTAAGAATGCACT-TTTATGTACAGTTAACAAATTATTTTCCTATTGACTTCAAAGAATGTCAGAGGTTCTAGGAACTTAAGATCTATTTTTAGGTTGGTGTGGAGGTATTCAAATTTTC + +>hg18.chr3(+):52503897-52504396 +CGGGCAGGACCAGCGGCTCAGGAGTGGCTGGGGCTAGTGAGGGGATGTGGGTCTGGTGGGCTAGCAGGGTGCCTGTAGCGAGTCAGAGCCCCATGAGCGCCCTGGAGTTGGAAAGGTGGAGGCAGGAACAGACAGACCCATTCAGGGGCTGCCCTGCCTTCCGCCGACCAGCACCCCAGGAGCCTCTGAATGAAACACACTGGGCTCGCAGGCGGGGGACTCGTTCACGTGTGCCTTTGGATTTGCTTCAGAACCTCTGATAGAGCCCAGGTCCCGGGGCTCATGGTGGCCTGGACTTCCAGGTTGTGATGCCAGGAGGGTCCCAGCCGGGAAGCCCCGAGCAGGGCTCAGGCCGCCCATGGGGGGTCAGTGGCCAGCACCTTCCCTTCCGCCTGCAGGCTGCTGATATGCAGGAGGAAATCCTGGCGGGTTCCTGTGGGGGTGAGCTGGCGGGGCCTCCGGGCTGCTTTTAAGGCCACTGCCCGCCCCGTCCCGCCTG +>mm8 +--------------GGCTCAGGAAGGCCTGAGGCTGGT-AGGGGAGACCAGTCTGAGGGGCTAGCATGGTGTTTCCACC------------------TCTACTGGTGTCTGAAAGACTGAGGCAGCTGGGGGCCAGCCAGCCCAGGGGCTGTCCAACCTCCTAGGCACCAGAACCCCGA-AGCTTCTGAATG-AAAAAGCCAGCTTGACAGATGGGAAAATTATTTATTGGTGC--TTAAATTTGCTTTAGAATCTCCCCTAGACCCCAGG-CAGGTGGCTAATGGTGGTCTGGACCTCTAGACTATGGTGCCAGGGAGGTCCTGGCCAGGAAGCCCTGAACAGGGCCCAGGTCGTCCATGGGGGGTCACTGGCCAGCGTCTTCCCTTCCGCCTGCAGGCTGCTGATACGCAGGAGGAAATCCTGGTGGGTTCCTGTGGGGGTGAGCTGA---------CGGATAGCTTTTAAAGCGGCTGCCCACCCTGTCCTGCCT- + +>hg18.chr6(+):112089190-112089689 +AAACATGAAAAAAAATTTTATTGTTTTAGACAAAGAGGCCACTTTTGGAAAATAATACTTTTTTTTTTTTAGTTGAATCAGGTGAAGACAGAGTTAAAATCACATAGGATTTGCATTTTTAAAAAAGGAAAGCACTAGGATTGTTGGCACTGGAGTAACTATTTACACTGAACAGAGGTTTGGCCTTTTACATAACATCGATACAATGCATTTTCCAAAGTCTGAGAAATAACAAGGTTCTGTCTCGAATGCTTCACAGAGGAGGTTCGGATTTGGGGACAAGTGTCATTAATGAGGGCCATGGAAGTTCGTCAGCTTCAGAGTCACATGCAATCTGATCCTGGGCGGTTCCGCTGCTGGGGAGCAGCTGGCTACGGAATTGAAAGCTAATGGGGAGGGGTGGGGCAGCCTCTGGGACAAGGCCTCTCTCCGCAGACCCGGGCCTTACAGGTTTTCACCAGGTTGGTACTGGGGCTCTGTCGCGGTAAAGTAGTCTTCC +>mm8 +AAACATGAAAAAAAATTTTATTGTTTTAGACAAAGAGGCCACTTTTGGAAAATAATACTTTTTTTTTTTTAGTTGAATCAGGTGAAGACAGAGTTAAAATCACATAGGATTTGCTTTTTTAAAAAAGGAAAGCACTGGGATTGTTGGCACAGGAGCAGCTATTTACACTGAACAGAGGTTTGGCCTTTGACATAACATCGATACAATGCATTTCC--AAGTCTGAGAAATAACACGCTTCTGTCTCAGATGGTTCACAGAGGAGGTTCGGACTGGGGGACAAGTGTCATTAATGAGGGCCGTGGAAGT---TCAGCTTCAGAGTCACATGCAATCTGATCCTGGACGGTTCCGCTGCTCTGGGGCAGCTGGCTACAGAATTGGAAGCTAATGGGGAGGGGTAGGGAGGCCTC-GGGAAGAGGC----GTCTGAAGCGCAGGCTCTCACAGGTTTTCACCGGGCTGATACTGGGGCTCTGTGGCCGTAAAGTAGTCCTCC + +>hg18.chr6(+):112089249-112089748 +TTTTTTTTTTTAGTTGAATCAGGTGAAGACAGAGTTAAAATCACATAGGATTTGCATTTTTAAAAAAGGAAAGCACTAGGATTGTTGGCACTGGAGTAACTATTTACACTGAACAGAGGTTTGGCCTTTTACATAACATCGATACAATGCATTTTCCAAAGTCTGAGAAATAACAAGGTTCTGTCTCGAATGCTTCACAGAGGAGGTTCGGATTTGGGGACAAGTGTCATTAATGAGGGCCATGGAAGTTCGTCAGCTTCAGAGTCACATGCAATCTGATCCTGGGCGGTTCCGCTGCTGGGGAGCAGCTGGCTACGGAATTGAAAGCTAATGGGGAGGGGTGGGGCAGCCTCTGGGACAAGGCCTCTCTCCGCAGACCCGGGCCTTACAGGTTTTCACCAGGTTGGTACTGGGGCTCTGTCGCGGTAAAGTAGTCTTCCAGGAAGCTCTGCAAGTACTCAAAAGTGGGGCGTTCTTCAGGGTCCTTTTTCCAGCAGTG +>mm8 +TTTTTTTTTTTAGTTGAATCAGGTGAAGACAGAGTTAAAATCACATAGGATTTGCTTTTTTAAAAAAGGAAAGCACTGGGATTGTTGGCACAGGAGCAGCTATTTACACTGAACAGAGGTTTGGCCTTTGACATAACATCGATACAATGCATTTCC--AAGTCTGAGAAATAACACGCTTCTGTCTCAGATGGTTCACAGAGGAGGTTCGGACTGGGGGACAAGTGTCATTAATGAGGGCCGTGGAAGT---TCAGCTTCAGAGTCACATGCAATCTGATCCTGGACGGTTCCGCTGCTCTGGGGCAGCTGGCTACAGAATTGGAAGCTAATGGGGAGGGGTAGGGAGGCCTC-GGGAAGAGGC----GTCTGAAGCGCAGGCTCTCACAGGTTTTCACCGGGCTGATACTGGGGCTCTGTGGCCGTAAAGTAGTCCTCCAGGAAGCCCTGCAAGTACTCGAAGGTCGGGCGCTCTTCCGGATCCTTTTTCCAGCAGTG + +>hg18.chr6(+):112089261-112089760 +GTTGAATCAGGTGAAGACAGAGTTAAAATCACATAGGATTTGCATTTTTAAAAAAGGAAAGCACTAGGATTGTTGGCACTGGAGTAACTATTTACACTGAACAGAGGTTTGGCCTTTTACATAACATCGATACAATGCATTTTCCAAAGTCTGAGAAATAACAAGGTTCTGTCTCGAATGCTTCACAGAGGAGGTTCGGATTTGGGGACAAGTGTCATTAATGAGGGCCATGGAAGTTCGTCAGCTTCAGAGTCACATGCAATCTGATCCTGGGCGGTTCCGCTGCTGGGGAGCAGCTGGCTACGGAATTGAAAGCTAATGGGGAGGGGTGGGGCAGCCTCTGGGACAAGGCCTCTCTCCGCAGACCCGGGCCTTACAGGTTTTCACCAGGTTGGTACTGGGGCTCTGTCGCGGTAAAGTAGTCTTCCAGGAAGCTCTGCAAGTACTCAAAAGTGGGGCGTTCTTCAGGGTCCTTTTTCCAGCAGTGGATCATGAGCTC +>mm8 +GTTGAATCAGGTGAAGACAGAGTTAAAATCACATAGGATTTGCTTTTTTAAAAAAGGAAAGCACTGGGATTGTTGGCACAGGAGCAGCTATTTACACTGAACAGAGGTTTGGCCTTTGACATAACATCGATACAATGCATTTCC--AAGTCTGAGAAATAACACGCTTCTGTCTCAGATGGTTCACAGAGGAGGTTCGGACTGGGGGACAAGTGTCATTAATGAGGGCCGTGGAAGT---TCAGCTTCAGAGTCACATGCAATCTGATCCTGGACGGTTCCGCTGCTCTGGGGCAGCTGGCTACAGAATTGGAAGCTAATGGGGAGGGGTAGGGAGGCCTC-GGGAAGAGGC----GTCTGAAGCGCAGGCTCTCACAGGTTTTCACCGGGCTGATACTGGGGCTCTGTGGCCGTAAAGTAGTCCTCCAGGAAGCCCTGCAAGTACTCGAAGGTCGGGCGCTCTTCCGGATCCTTTTTCCAGCAGTGGATCATGAGCTC + +>hg18.chr2(+):31310208-31310707 +AAGCAGGGAGTGTGATGAATAGGTCAACTCTGTCCTCGCAGCCGTCCCTGAGAGGGCGCTGTTCCCAAATCGAAGCCCCAGAGGCGGAGACTGAGACACCGGCACTCTCCCACTGGACTGGGTCAGCATCCCTCTCCCCGCGCGGCCGCAGGTCTAGAGCTGAGCGCCTGCCCACAAACATGGCGGCGCCCTGCGCGGCTTCCCGTCGCCGCAACCGTGGGGCCGGCCCTGCCTTGCCAGTACTAGGGGACTTCCTCTGCGCGCCGGCTTCCTGCCCAGCTGGCATTTAAACCACCGCCTGGGGCTGCAGGATGCTGCTGCGGATGCAGAGCTGTCCGCGGGCTGGGCAGCGTCGCCGTCTCCCCTGAGCCGCCTCGGTCCGGCAGGAGCGGAGCCGAAGCATCCCTTGCTGCACGCAGGGCAGAGCAGGCGAGGGCTGGGGGCCGATCGGGGACCCCGGCTTGGGACCCCGGCATCTGGCAGTTTCCTTGCAGGTTCA +>mm8 +AAACAGAG-----------TAGGTCAAGGCTGTCTTAGTCTCCGTCCTTGAGAGGGCGCTGCTCCCAAGTCAAATCCCCAG-GGCTGGGAAAGAAATGCCTGCGCTTTCCCACAGGACTCTGGCAGCAGCTTTTTGCCCGCGCGGCCGCA-----------GAGCGCCTGCCCATAGACATGGCGGCGCCCTCCTTGGCTTCGCGTCGCCCTGACCGTGGAGCTGGCCGGGTTTTGCCAGTTCTCGGGGACTTCCTGCACGT-----------------CTGGCATTTAAACGCGCGCCGGGGGCGGCGGGATGCTGCTGCGGATGCGGAGCTGTGTGA------------GCCGCTGCCTACCCGGCGCAGCCTGGGCTCCGCAGTAGCGGAGCTCGAGCATCCTTTAGTC-----------------------------ATCTATCTGGGGA----GACCTGGAACTCAGGCTT----CGGCTTCCCGGCAGGTTTG + +>hg18.chr22(+):16598265-16598764 +GGGCTCCGTCTACACTGGAAGCAGCTATACAGCTGTGACCACATCGAGCTTTAGCCAGTCACACTTCTGGAACTGTCCGTTCAGTCCATCCCCTAGAGCAAGAAAGGAGAAAAAGCCAGAATCAGCTAGGCTCATTCACAAACCAGGCTCCAGAGCTCTGTGCCACAGTAGAGCAAAGCTGGGGTTTATGCAAAAACATGTTCTCCAGACCCCTGAAGTCCTATCCGTGCATCCTACTTTTTGCTACATGGGGGCAACTGCAAAAACAGGCCGTTCAGGCGGTGAGGTGGGTATTCACATCTCCAAGGCACTGACGGTGTCAGGAGGCCCCTGCTGGGTCAGAGGAATCACGATTCTGCCTCAGCCCTCAGTCTCTGGTAAGCTGTCCATACAGACTGCTGCACACGTCTTGCCCACCCTTTCCCCCTTTACATGGGTGTTGGTAAAAGCTGTCCAGGAATGGTCTCAGGCTTACCTCCTTCCAACAATTCAGCTGGGT +>mm8 +TGGTCGCGGTTCCTCTGGAGGCAGTGTCACCA--------------------------TCGGGCTTGTGCGGGC-TCC--TCAGTCCATCTCCTAAGAAAGAGG---------CAGCAGAGTAAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr22(+):16598139-16598638 +GACATTTTCATTCAAGTATATTAATGTAGATATTTTAAAGTGGGTTATAAGTTTAACATTGTCTTTAAAATAGAAGTCACAGCTATCTTCCAGCCTGTCTTCTCTAGGAACGCTGTTGACATGCCAGGGCTCCGTCTACACTGGAAGCAGCTATACAGCTGTGACCACATCGAGCTTTAGCCAGTCACACTTCTGGAACTGTCCGTTCAGTCCATCCCCTAGAGCAAGAAAGGAGAAAAAGCCAGAATCAGCTAGGCTCATTCACAAACCAGGCTCCAGAGCTCTGTGCCACAGTAGAGCAAAGCTGGGGTTTATGCAAAAACATGTTCTCCAGACCCCTGAAGTCCTATCCGTGCATCCTACTTTTTGCTACATGGGGGCAACTGCAAAAACAGGCCGTTCAGGCGGTGAGGTGGGTATTCACATCTCCAAGGCACTGACGGTGTCAGGAGGCCCCTGCTGGGTCAGAGGAATCACGATTCTGCCTCAGCCCTCAGTC +>mm8 +GA---------------------ACGCAGAGA-TGTCCAGTGAATCACCAGCTTGGCCACCACCTGGAAATAGGAGA--CAGCTGTTCTCTGGCCTGTCTTCAGGCCAAGGTCTTTC-------CATGGTCGCGGTTCCTCTGGAGGCAGTGTCACCA--------------------------TCGGGCTTGTGCGGGC-TCC--TCAGTCCATCTCCTAAGAAAGAGG---------CAGCAGAGTAAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr22(+):16596941-16597440 +CCACACTGCGCGGCAGCACTTCTTTTTAGTATTTGTAAGCTTTTGCCCACTTTCAATTGAGCCAGCCCTAGCGTGGTATGTATTGCATGCTGAACAATATAGAGTTTGTTTTTCCTTTCTGATGATTTTAAACTCTTAAAGAACAGGAAAGCATCTGGTAAGAAGAAATCATGAGTCCGTCAGTGCCCTTACTCATATGCGTCTCCAGTGGCCTCATGTTGTGGTCACAGGAGTTTCCTGTTCACAGCAATGTGTGTGATATGGACCCAGCATCCACTGTCGTGCTTTTAAACTGATTCCTGGGACATAGCTTACCACTGGAACAGCAGACCAGTGTTGCACTGTTTCTAAAGCTAAGCTTTTCCTTATTTATTTTGGTACTACCTAAGTGACTTGGTTTTGACTGTCCCTAAGAGAGGGAACCACTTTGCTGAATTTTTAAAAAGTCCAACTGCTCTTTCATCTTTTATGCTTAGAAACCTGTTCTCTCCAGATGCAC +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr22(+):16596908-16597407 +GTGTTAGGAAGATTTATTTCCAAACAGTGGCCTCCACACTGCGCGGCAGCACTTCTTTTTAGTATTTGTAAGCTTTTGCCCACTTTCAATTGAGCCAGCCCTAGCGTGGTATGTATTGCATGCTGAACAATATAGAGTTTGTTTTTCCTTTCTGATGATTTTAAACTCTTAAAGAACAGGAAAGCATCTGGTAAGAAGAAATCATGAGTCCGTCAGTGCCCTTACTCATATGCGTCTCCAGTGGCCTCATGTTGTGGTCACAGGAGTTTCCTGTTCACAGCAATGTGTGTGATATGGACCCAGCATCCACTGTCGTGCTTTTAAACTGATTCCTGGGACATAGCTTACCACTGGAACAGCAGACCAGTGTTGCACTGTTTCTAAAGCTAAGCTTTTCCTTATTTATTTTGGTACTACCTAAGTGACTTGGTTTTGACTGTCCCTAAGAGAGGGAACCACTTTGCTGAATTTTTAAAAAGTCCAACTGCTCTTTCATCTT +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr12(+):101335726-101336225 +CATTTTCCTTTTTTGCCTCTGCATTCAGCATTTCTACTTCCAATCTCCCTCCTCTGCTCTTTCTTCTTTCCTCTGATCTGCAGACTTGCTTCTGTCCCCTCCTTCTGTTCCCctcctggatgtgtctttggccaacctttccttctctgagacttcgtgttcttgttggtagatgggggctgatactgtaaacatcacaaaaataATTGCATTGAGAACAAGTGGTTCCCATGGTGTCCCTTTGAATGAGCTCAGAATGCCCAGGCTCCATATGATGCAGGAGACAGCACTCATGCTGGAGAGGGGTCTAGACCTCAGTCACAAGACCCACCATTCCAGAACTTTGGGACTCATCTCTTGACACCTACCCCCTCCCCAGTTAGAAACCAAGAGGCGCTGGGTCACCTGGGAAGAGAAAGAATGAATCTGCCTTTGCCCCAGCAAGCACGCTTTCCTGCCACATTCACCTAAAAGTCTTTTCTGAGATCCTTGCTTCCTG +>mm8 +--ATGTCCCTCTTTGCCTGCTTGCTCACAGTTCCTAGC-CCAGTCTTTTTTCTCTG----------GGACCTCTGATTTTCCGAGTTGCCTCCGTTACCTCCTCCTGTTCCCCTTCTGGGTGTGTCTTTGGCTCACCTTTCCTTCTCTGCAGCTTCGTTTTCTTGTTTGTCGATAGGGACGGGGACTGCAAACATCACAAAAATAATTGCATTGAGAACGGGTGGCTCCTGTG-----TCTTTGAATCTGCCCAGAATGCCTGGGCTCCATAGGAAACAGAAGCTAGCTTTACTGCTGGAGAGGGTTCTACACCTCAGGCACCAGAGCCGAGGTGCCCGAGCTTTGCGCCTTATCTC-TAATACCCACTTCCTCTTCAGCT---------------------------AGAAGGAACA---------------------------CTCCTTTTCCCTTAATTTGCACAGTGATATCCTTTCTGACTCTTGTGCCCACCG + +>hg18.chr12(+):101320236-101320735 +ATCACTCCTAAAGACAATGTTGGAATGTTTACTTGTGTATTTCATTGGGGGAAACGCCCATCTTTTAAATGTTATCAAACTTATTTTTTGGTAGGTGTTCCAAAGTTTAACAGGTAACTCGTGCAGAGCAAAGGATCCTGCGGTGGCATGTCACTCTTCACTCCTCAGGAGGGTCTTCCTACATCCTGTAGTTCTTGTTTCCTGCACTCCCTCTACTTGCGTTCTTCAAATGTACTTCCTATAAATAAAGGAGAAAAAGTGACATTAACTTGATGAAGTTTTATGTATCCATCTATTTCTAACATTGGGCCTCAACCTTCCATGTCTTACGCCTTACCAGTTGAGCTAATAGAGAGCTTGAACCTTGGTTTTCCTGAGAAGGGCATGTATAGGTGGACAGGCCCTTAGTACTTTTGCCAAACCTCACTCAGGCATCTTCTATGTACCCCTGGTGGCGTGAATACCACAGACAGCTTTATAATCACACAAAGATGAGATT +>mm8 +AGCACTCCTAAAGACGATGTTGGAATGTTTACTTGTATATTTCATTGGGGGAAATGCCCATCTTTGTAATGTTATTGGACTTATTATTTGGTAGGTGTTTCGATGTTTTGCAGGTTGCTCAAGC--AGCAAAGGATCCTGCGGTGATGTGGCATTTTCTGCTCCGTGGGAGGCTCCTCCTACATTCTGTAGGTCTTGTTTCCTGCACTTCCTCTACTTGTGTTCTTCAAATGTACTTCCTGCAAATAAGAAAGATAAGCGGCCATTAAGTTGTTGTGGTTTTCTATATCCAT----TTCTAACACTGGCCCTCAGCCTTTTGTATCTTATGCCTCACCAACCTATCTTAAGGAGGGTTTGAGTCTTGAATTCTTTGAGAA----ACATACAGATGGTCAGGTCTTTAGTTAATTCAACCAAACTTGACCTGGCT--CTAGGAGCACCCA---TAGCATAGGTACC----ATTGCTTCATAATTACACCAAGAGGCTACC + +>hg18.chr12(+):101320163-101320662 +TTTTCTATAGAACATTATTGATAAAAGATCAACAGCAATCTACCAACTCCAGGACCATTTTTGCAAGGTGCAAATCACTCCTAAAGACAATGTTGGAATGTTTACTTGTGTATTTCATTGGGGGAAACGCCCATCTTTTAAATGTTATCAAACTTATTTTTTGGTAGGTGTTCCAAAGTTTAACAGGTAACTCGTGCAGAGCAAAGGATCCTGCGGTGGCATGTCACTCTTCACTCCTCAGGAGGGTCTTCCTACATCCTGTAGTTCTTGTTTCCTGCACTCCCTCTACTTGCGTTCTTCAAATGTACTTCCTATAAATAAAGGAGAAAAAGTGACATTAACTTGATGAAGTTTTATGTATCCATCTATTTCTAACATTGGGCCTCAACCTTCCATGTCTTACGCCTTACCAGTTGAGCTAATAGAGAGCTTGAACCTTGGTTTTCCTGAGAAGGGCATGTATAGGTGGACAGGCCCTTAGTACTTTTGCCAAACCTCA +>mm8 +TTCTCTATAGAATGTTATTGATAAAGGACCAACAGCAATCTACCCACGCCAGGACCACTTTTGCAAGGTGCAAAGCACTCCTAAAGACGATGTTGGAATGTTTACTTGTATATTTCATTGGGGGAAATGCCCATCTTTGTAATGTTATTGGACTTATTATTTGGTAGGTGTTTCGATGTTTTGCAGGTTGCTCAAGC--AGCAAAGGATCCTGCGGTGATGTGGCATTTTCTGCTCCGTGGGAGGCTCCTCCTACATTCTGTAGGTCTTGTTTCCTGCACTTCCTCTACTTGTGTTCTTCAAATGTACTTCCTGCAAATAAGAAAGATAAGCGGCCATTAAGTTGTTGTGGTTTTCTATATCCAT----TTCTAACACTGGCCCTCAGCCTTTTGTATCTTATGCCTCACCAACCTATCTTAAGGAGGGTTTGAGTCTTGAATTCTTTGAGAA----ACATACAGATGGTCAGGTCTTTAGTTAATTCAACCAAACTTG + +>hg18.chr12(+):101313809-101314308 +ATTACTAAAGAAAGATATACCATTTTATTATGACACTCTAGCCATACATTTTCAAAATATGCTTATTAAACAGTAAATGTAAGATAATGATTCAATTAGTTACATTTTTAGAAGTCATTAGGATTGATATTCCTCTGCCATAAGTGAATTGAATAATAATTTCAAATACAATCAGaattaatttaataaaaaatatGCTTTTCAACTAAGACAGATGTAACGAATGGCCAGTCATTATTTTCTGGTTTCAAAGTAGCAGGGGAAATTAATTCAGTGTCTGTAAGTTTATTTATCACACTTGGCCTATAAGTGTGATAAAAATACATGAGGCAAAATACATGATGTAATCCCAATTCTCATAGTTCATTAACTCTTTTACCAAAAAGATCTGACATGGTATTTGGGGCCTTTATGTAAACTGAATATAAGCTGCGTGATATTTGAAAGGTTTTGATATTTTGAATAGACATTTTCATGATACACAGACACAGATAAAAGA +>mm8 +ATTACTAAAGAAAGATATACCATTTTATTATGACACTCTAGCCATACAATTTCAAAATATGCTTACTAAACAGTAAATGTAAGATAATGATTCAGTTAGTTACATTTTTAAGAGTCATTAGGACAGATATTGCTCTGCCATAAATGAATTGAATAACCACTTCAAATACAATCAGGAGTAATTTGATAGAAGATTTTTTTTTGTG-TAAAACACATACAATGAATGACCAAATATTACTTTCAGGTTTC-----AGTAGGG-AAATCAATTCAGTGTCTGTAAGT-TAATCATCACCCTTGGCCTTTAAGTGTGATAAAAATAAATGAAGCAAAATGTGCGTTGTAATCCAGATTCCCATAGCTCCTTAAATCT-TTAACAAAGAGATCTGATATGCTATTTGGAGCTTTCCTGTAAACTTAATATACACTGTATGATGTTTGCAAG----------------------GTTTAAGGATACAGAGACACCGATAGGAGA + +>hg18.chr7(+):99282701-99283200 +TTCTGCTTTGCACAACCCTGGAGGAGTTGCTAGGTCTTGTTCCCATCTATTCTACTGGAAGAACTGGTTCTCTTCCACGTGGAAACCATGCATTTAAAAGGAAACTGGGATATAGTGACTGGAAACCACACCATTTGCCTTGATTCCACCATCCCCCTTCCATATGCTTACAGGAGGCTACACATTCAAGATAAATCTTTATTGagcatctagtatagagcctgccacccagtagatagttactaaatatttgttaaattcatgaTGCCTGTTTAACACATTTTCTACAACTATGGAGATCTCTAAAACTTACGTAGGACAAACTGCTTCTGCTTTGAACTCAAGCCTTTAGGTCCAATGGGATTTCTGAAAAGTGCCTTAAGTTTTGCTGAAGATGAAGAATGGAAGAGAATACGAACATTGCTATCTCCAGCTTTCACCAGTGTAAAATTCAAGGAAGTAAGAAAATAAGGTGATTTATAATTAGAAACTTAAAGGA +>mm8 +TCTTTTTTTGCAAATGCTTGAAAGACACTGCAGGGCTGG--CCTAT----TCTCATGGA-------------TTCTGCAAGGGCGATTTTCATTTAAAGTGAGATGGTCATAGAAAGATGTGAAGCTGTGCCAGATGGATAGATATCACCTTCA----TTTATAGGATTACAGAAATTTTCA--------GTAGAAGATTGTTGAACATCTAGTA-AGATCCAGAAAATT-----ATAGT-----AATGTTTGTTAAATAAATGATGCTTGTTTAATATACTTTCTAAAATTGTGAAGATTATCATAATTTTAATATGATAACCTTCTTTCCATTTGAACCTTAGTTTTTTGGGCCAGTGGGATTCATGAAAAAGGCCATTACCATATCTGAGGATGAAGAATGGAAGAGACTTAGAACACTCCTGTCTCCAACCTTCACCAGTGGCAAACTCAAGGAGGTGATTAGAGAGGGTGTTC-----------ACTTAAGGAA + +>hg18.chr7(+):99263073-99263572 +gctttctaaaaagaattatttttatttgggaataaagcattgcaatgggaatatgcgtgccaaggtaaactatgtgcttattcaggtaggtaaagtaagacaaagtttaaaaaaataatgagaaggattacatatttgttttggaatgattatccttggctataaagatcaataacaagactgacatcagtttgaggttggacaggcagttgctgggcagatgttcttgcagaagtatttttctttaggttCCTGAGAATCTATAACCTTTGGGCTTACCAATAGCAGTGACTGATTTGTTTACTGATTGTTCACAGAATAGGAAATCAAAGGAGGCCAAAATAAGGACAGCCATAATTATTTGCCAATTGTCAATTTGAAAAGGGTACCCAAATCCCTCCATATGAGGAGTAGCATAAGTGGCTTTTCTACTGGCTGCCGCTGTAGACCCACCTCCTTCTCCAGCACATAAATATCGCTGTTAACATTAACTAAATCA +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACAGAATATAAGCTCAAAGG---TCAGAGTAAGAAAATGCATGACCCTTTGACAAATGCCAGGTGAGAAGCCACACCAGACCTACAAGTT--CGAGCATTGTGCAAGTGGCCCTTGTACTGGCTGAATCCCTGTAACCTCCTCCTTTCCCAGCAAATAA-----ATAGACTGGCCTCACTAGATGC + +>hg18.chr19(+):38013262-38013761 +ACATCTGAGTATATTTTATTCGTAAGAAAAAAAGGAAGAAATAACCACAAATATTGCTTAAGAAAATAAATTCAGCTGACTTGGCTACAAGAGACGGAGCTTGTTACTCAGGGTCTTCCTCCGGTGGGACCACTTCCATTAGCATCTGAAGGTGCATGGTAATCGGCTCTGAAATAAGAGTCAAAAATGAGTACAGTTAGTTAGACTGAAATTCGAAAGTTTCACTGGAGTTGTTGTGGGTGAGGGTGACATTGTTTTCAGTCTTTGGTGATGCGTCACCTAGACCCTGTGCTCAGGATGGCCAGCTTTCCTGCCTTCTGGTTGGATTTCACACTTTCCTGGCTTCTGTCTTCTCCCAGAATTGCAGGAATAGAAATAAAAACCTCCTAGGAGTGTCCGGAGGGACGACTGCACTTTCCAGTTCAGATGAGCTGAACAGGAGAAACAGGCAGGCTTTTAATCACATTCACTTAATAAATCTTAACTGGCTGTTACAGGC +>mm8 +ATATCTGAATACATGTTTTCATTAAGAAAAACAGGAAGAAATAACCACAAATATTGCTTACAAAAATAAATTCAGCTG----GGCTACGAGTGATGGA-CCTTTTACTCTGGGTCCTTTTCTGGTGGGACGACTTCCATGAGCATCTGCAGGTGCTTTGTGACCGGCCCTGGAACAGAAGCGAGGCATAGGTGCAGTTAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTAACCACAGTCACTCAGTTAACACTAAGTGGCTGTAGTGCAC + +>hg18.chr3(+):52206685-52207184 +CAGGACCACTCCATTTGTGGGCGATATAGCCAGCTCCACCTCCTCCGGGAAGCCCTTGTTCACAGTTTCCAAAGCAAGCCGCAGGCGGGATGGATCCTGCTTAACACCCCGGCCCAGAACCCCTTGGATCTCCTTCTTCCTCCATGTCCAAGACACCCAGCTTAACAACCCTGTAGCCCCCAACTTGGCCCTAGCGGCACCTCGCCTCGACCTTGCCATTTTATACTCAATTGGGGCGTAGGGTTCTGAAGCCCAGGGTAGTTGGTGGGGAGGCAGCACGAGGGTGCAGGATGAGGTCGGGAAAAGAGACCTCGTCCGCCCACCGCCTAGCGCTTCCTCCTCCCTGCAGGCGAGCCGGGGAATCCCCGGCAGCACCGATATCCGCAGAGCCCAAGAAGTGGGCCTCTCTGCCCCGCCCCCCCGGCTCGCCGAGGGCTACGCGGCGCGCCTGCGCAGAAGAAGGCAGCGCCCAAGGCGCATGCGCAGCGGTCACTCCCGC +>mm8 +CTGGGCCATTATATTCTTGGGCCATCCATCCA-------TGCAGCAAAGAAG--GTCTGTCATCGAAGCAAAGGCAAGCCCTTCGTTGATCGGAT----CTTAAGACCCTGGCCCGAAA-CCC------------CTTCCTATATGCCCAATAAACCCA-TTT-------TTTTAGCCTGTAG-ATTTCCCCGGGTGGGGTTGGTTTCGACCT--------------CAGCGGGGGCGCAGGAGTCTGACGCATAGGGCTGTTCG-TAGAAGGAGACAAGGGACGAAGGGAAGGGATCCAAA-AAGGGACTTGCCCCGTCCACCGCCCTGCGCTCTTGGCTCC------GGCAGCGTAGG-----CCTGAGACATAGTCAGTTGGAGAGGAACAGAGAGGGACCCTGGCACCTTGCCGGGCCGGCTTC-----GG------CGCGCGCGTGCGC-GCGGCAGGCCGCACCCAAGGCGCATGCGCGGCGGTCACTCCGGC + +>hg18.chr3(+):52206657-52207156 +TGAGTGTCCCGCTTCTTCCGCATCCTGCCAGGACCACTCCATTTGTGGGCGATATAGCCAGCTCCACCTCCTCCGGGAAGCCCTTGTTCACAGTTTCCAAAGCAAGCCGCAGGCGGGATGGATCCTGCTTAACACCCCGGCCCAGAACCCCTTGGATCTCCTTCTTCCTCCATGTCCAAGACACCCAGCTTAACAACCCTGTAGCCCCCAACTTGGCCCTAGCGGCACCTCGCCTCGACCTTGCCATTTTATACTCAATTGGGGCGTAGGGTTCTGAAGCCCAGGGTAGTTGGTGGGGAGGCAGCACGAGGGTGCAGGATGAGGTCGGGAAAAGAGACCTCGTCCGCCCACCGCCTAGCGCTTCCTCCTCCCTGCAGGCGAGCCGGGGAATCCCCGGCAGCACCGATATCCGCAGAGCCCAAGAAGTGGGCCTCTCTGCCCCGCCCCCCCGGCTCGCCGAGGGCTACGCGGCGCGCCTGCGCAGAAGAAGGCAGCGCCC +>mm8 +TGGGCTCCCTTCTTCCGCAGCCTCTCTCCTGGGCCATTATATTCTTGGGCCATCCATCCA-------TGCAGCAAAGAAG--GTCTGTCATCGAAGCAAAGGCAAGCCCTTCGTTGATCGGAT----CTTAAGACCCTGGCCCGAAA-CCC------------CTTCCTATATGCCCAATAAACCCA-TTT-------TTTTAGCCTGTAG-ATTTCCCCGGGTGGGGTTGGTTTCGACCT--------------CAGCGGGGGCGCAGGAGTCTGACGCATAGGGCTGTTCG-TAGAAGGAGACAAGGGACGAAGGGAAGGGATCCAAA-AAGGGACTTGCCCCGTCCACCGCCCTGCGCTCTTGGCTCC------GGCAGCGTAGG-----CCTGAGACATAGTCAGTTGGAGAGGAACAGAGAGGGACCCTGGCACCTTGCCGGGCCGGCTTC-----GG------CGCGCGCGTGCGC-GCGGCAGGCCGCACCC + +>hg18.chr10(+):101532011-101532510 +TATATAACATATAGGCTCACACTGGATAAGCTATTTTATAACCTGACTTCTTCAAAGAAAGTTTACATCATGTTTAAACCATGTTTTAGATTCTATATTTTTAATTAAAAATCTAAGGAAGAAGGATATTTCACATTTCTATAAACTCTAAGATCTTGCAGCAGAAGCGAAACTGCACATTTAGGGGTGCCTGCCCCTCTACTGATGCTGCCCTTTGTGGGTCATATGTCCTTAGGAAAATGAAAGACTGTGCACTCTTGATTTGTTGGCCAGCTCTGTTGACATCTTTCAGTGGTTCCTTTTATGTATGGCCACTCCTACAGAGGCCTCTTGTACTTTGGGAACTGGTGAGTCTCCCTGTCCCTAGGGCTTTTTAGTCACATGTCCATCCACTGTTTCAATGTAACATGCATCTAGGCAAGGTTAACGATTAAATGGTTGGGATGAAAGGTCATCCTTTACGGAGAACATCAGAATGGTAGATAATTCCTGTTCCACT +>mm8 +T-------TCATTGATCCACAATGCTTTCGCTCTTTTATAACTTGACTTTTTCAAACAAAGTTTATATTAC-TTTAAACCGTGTTTTATGTTTTAAGTTCTTAATCAAAA----AACTCAGAGGGGTATTTAACATCTCTGTGAACTCTTAGAGTTC-AAACTGAAGTAAAACCCCACATGCAGGGATGCATAGGTTGTGTACTGGACT-TCCGACCT--------------------------------------------------GCCAACTGCATTAATGTCTCTGATTGGTTCTTTCTAGATTTGGTCACA-CTACAGGGGC----AGGGCTTTGAGAAGTGATAAGCCTCCCAGTATCTGGTGATTCCCAGTCACATGTCTGCTCACTGGGATGACATAGCATTCATC-TAGCAAAGTTAACTATTAAGTTGTCAGGATGAAAGGTCAGCCTTTAATCAG----TGAGGATGGAAAGCAATTGCTCATCTGCT + +>hg18.chr10(+):101531994-101532493 +TGAAAGCCTGTATTATGTATATAACATATAGGCTCACACTGGATAAGCTATTTTATAACCTGACTTCTTCAAAGAAAGTTTACATCATGTTTAAACCATGTTTTAGATTCTATATTTTTAATTAAAAATCTAAGGAAGAAGGATATTTCACATTTCTATAAACTCTAAGATCTTGCAGCAGAAGCGAAACTGCACATTTAGGGGTGCCTGCCCCTCTACTGATGCTGCCCTTTGTGGGTCATATGTCCTTAGGAAAATGAAAGACTGTGCACTCTTGATTTGTTGGCCAGCTCTGTTGACATCTTTCAGTGGTTCCTTTTATGTATGGCCACTCCTACAGAGGCCTCTTGTACTTTGGGAACTGGTGAGTCTCCCTGTCCCTAGGGCTTTTTAGTCACATGTCCATCCACTGTTTCAATGTAACATGCATCTAGGCAAGGTTAACGATTAAATGGTTGGGATGAAAGGTCATCCTTTACGGAGAACATCAGAATGGTAG +>mm8 +--------CAAATTATGT-------TCATTGATCCACAATGCTTTCGCTCTTTTATAACTTGACTTTTTCAAACAAAGTTTATATTAC-TTTAAACCGTGTTTTATGTTTTAAGTTCTTAATCAAAA----AACTCAGAGGGGTATTTAACATCTCTGTGAACTCTTAGAGTTC-AAACTGAAGTAAAACCCCACATGCAGGGATGCATAGGTTGTGTACTGGACT-TCCGACCT--------------------------------------------------GCCAACTGCATTAATGTCTCTGATTGGTTCTTTCTAGATTTGGTCACA-CTACAGGGGC----AGGGCTTTGAGAAGTGATAAGCCTCCCAGTATCTGGTGATTCCCAGTCACATGTCTGCTCACTGGGATGACATAGCATTCATC-TAGCAAAGTTAACTATTAAGTTGTCAGGATGAAAGGTCAGCCTTTAATCAG----TGAGGATGGAAA + +>hg18.chr5(+):71651457-71651956 +CCACCCCAACACATAAATCTGGCGAATCATACGCAAATTCCCTCATGCTATATAACCTTCCACTGCTCTTCGTACCTTTGGACAGGAACATACTGTTATTTTAGGGAAGGAAATGGATCAGATACCTTGTCTCCTTCTTCTGCACTACCAAACACCCCAAATGGCGTCCCTAGCAATCAGATTCCAGAAACGTTTCCTCTCCTCTTGAAAGCCCACCGCTCCCTTCACCCAAAAAACAGAATAATCAGGGGCCTAATGAAGCTGTCCGGCCAACCTGCAGGAGAGAGCTGAGGAAGAACCACTTGCCGCGCCAGGAGCATCCCGCGCCGCACTATGGAGGCAGCCATCTTGGAGCGTACCAAAAGGAACAGCCAACGGGTTACGGACAGAGGAAGGGGCGGGGTTACAGCTCGACCTCTCGGGGCGCCCAGAATTGGACGAATCCCTTTTGTCGCTCTCGACGACAGGACCGACGCTCCGCCTCCTCGCCCCGGTTCCA +>mm8 +CTAATTTAATACATTAAACTTGCAAGACATACGCAGA--ACCTCATGC--TACAGCCTTCCCCTACTTTTCAAAAGTTTGGAATGGCGGGTACTAGCCTT-----AAAGAAGAGGGA---------TTATTTTTCCTTTCTGGGTT-ACCAATACCCTAAACGGCTTCTCTAGCAACCGGATCCCAGACGCACTTATGCGCTTCCTGGAAGCCCATCACCCCCTTCCTTCAATAAACAGCGTGCTGGGAGGCCTAATGGAGCTGCACCACCAACCTGCGAGGCAAAGGCGAGACGCGTCTAGTCGCCGAGCCAGGAGCATCCCACACCGCACCATGGGAGCCGCCATCTTGGAGCGCACCAAGTGGA----------AGGCGGGCGTGGG----GGGACAGGCACAGAGCCCGCCTCCGC--------CGGAAGTGGTCCTAC---------CACCTCAGA-G----------------GTCCCCCCTGCCCGGGTCCC + +>hg18.chr3(+):52796382-52796881 +TCCGTCCCCTGAGCCGCCCTTCTCCACATCACCGCGAACTCCCTGCTGCGCTTTGTGAGCTTTTGTGCAGGCTGAACCCCCAGCAGCCTCCACTGGTCCCCTCTTGGTGTGAGTGTATGTCTGTGAGGAGGCAGGACCCCAGGGGAGGGCTGAGACCCCCAGAGGGACGGCTGGGCCCAGGCCTGTTGTGGACAGAGCTGCATGCCTTTCGTGTGGGGCACCGTGGGTGACACTGTCTTCGATAATATGTCCTTGTCTTCTACAGAGATGCTGGGACCCAGAAGGAGTAAGTGGCAGCCATCCTGGCCATTCACATCTCTACCCCTCCTTGATGATCACCCCGTTGGCTTTCTTCCTCCGTTCTAGCTGTCTTCACTGCTTGTCACTGGGAATCTTTAGAACAGACCTCTGAACAGCCTGGCCTCCCCAGCCTGAGGTCCCTGGGGGAGGAGACAGAGAGGGGGCCAGCTAAACATGCCAGGCCAAGCTTCTGTCCCCG +>mm8 +TCTG-------------------------------AATCTCAGGGCTGTGCATCACGAGCCTTT-----GCCTTCCCTCG----GGTCTCCATCAAGCCCCTCTCCCCG---GTGTCTATCTGAG-GAAGTCGAGGGCATTTGAGAGGGCTGAG-CCTACAGTAGTTCATCT----CTCACCCTGTTGAGGAGTGAGCTACATGCCCTGGAGGTGGGGTATC-AGAGTAACAGTGTTT-----------TCCTTGTCTTTTGCAGAGATGGTGGGACCCAGAAGAAGTAAGTGGTAGCCATCTTGGGGACCCCCTTCTTCACCCCTTCCTCCTACTTACCCTGTTGGCTAGCTAGCTCTGCCCTGGCTATCACTAGCTCTGGTTCCTGGGATTCCTTAGGACAAGCCTCCGTACAGCTTGGCTTTCCCAG-----GGTCCCCATTATAAAAGACATA--GGAGGCCAGGTCATCTCCTAGGACCAAACTTTTGTACCCA + +>hg18.chr3(+):52786149-52786648 +atcccagctactcgggaggctgaggcaggagaatcacttgaacccaggaggtggaggttgcactgagccaagatcctgccactgcactctagcactcaagaccaaaactccatctcaaaaaaaaaaaagtaaaGCCTAATGAAGTTTAGAAATCCATTTTTAACTGTTGCTTCTTGCCACATGTCACCGTGTCACTGGTGCTGCCTTGTGCCAGCCCGAGGATGAGATGAGCCATCCGGGGATCCTCACAGTTCACATAGGCTAAGCGCAGTTCTACACAGAGGGACATGGTCTGGAGCCCCATCAGTAGTTTAACCACCCAGAGCTGGGAACCCCCCTGAGGCAAAAAGCTTCCACTGCCAAATTTTGATTCCTCTAAATGTGttaggttgatgcaaaagtcattgcggtttttgtcattaaTATTTGCCTGCACCTTGTCTAATGTTTAATCCATGTTTATCCAGCACTGTATTGATTACTGGTCTGACTGAGGTGA +>mm8 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTTGCCTCCGCTGTGTCTAATGTTTAAACTGTGTTTGTCCAGCACAGTATTAACTAACAGTCTGAGGGAAGTGA + +>hg18.chr6(+):166698400-166698899 +ACAAATATTTAAATCATTTATTGCCATTAAGTTACAGCATCTCAATATATACACTGCATGGAAATACACAGGTAACATTTTTAAACAGTGGGGACAAAATTTTAAGTACGTGGCCAGCTGTTGGTTGTCTTGTGGTCATTAAAGACAATGTTAAGAATCAGGAGTACTTAAGTGCTAGTGGTTACAAATTTTGTTCTCTTCAGTTTTTCATTAAGTAAATTCTAATAGATGATATACATATTACTGCAGATAAAACCATCATCAGAAATTATTAAATTAATTGCATATTTTGAGCTACTCTTTATGGAAAGAAGTAAAATATTTAATACTTGTAAGGCAGCAGAGAGTTGGTTTAGAAACTCTCAGCTATTTCTATAAAAATAGAATGGTTAGTAAAAATAGCATTCAGTGTATTTTCCTTAGGGAGGCTATTTATAATGAAATCTGTGACTCAGCAGCAGCTGGCAATGCTGTCCCTTCAAGACCTTGTTCTTCCTTT +>mm8 +GCAAATATTTAAACCATTTATTGCCATTAAGTTACAG-ATCTGAGT-TACA-----TATGGAAA-ACACCGAT---ACTTGTTATCACTGGAAATTATG-TGTAGACATGTGACCAACTGAGGGTT-TACTATTGTCATTAAAGAAAAAGTCAAGAATTTTGAGTACTTAAGTGCTTGTAGTTATAAATTTTGTTCCCTTAGATTTTTTATTACACAAATCCCAATAGATAATATACATATTACTACAGATAAAACCATCATTCAAAATTATTAAATTAGTTGCATATTTTGAACTACTCTTGATGAAGACAAATAAG--GTTTAGCATTGATAAGGCAGCAGAGAGTGGGTTTAGGGACTCTCGGCTAT-TCAATAATGTTGGCATGGTCATT-AAGATAGCATTCTGTGTTTTCCCTTCAGCACGACTACTCATGCTGAGATCTGTGGCTCAGCAGTGGCTGG-AGCACTGTCTCTTCAAGAGCTGGTCC------T + +>hg18.chr6(+):166698708-166699207 +AAGAAGTAAAATATTTAATACTTGTAAGGCAGCAGAGAGTTGGTTTAGAAACTCTCAGCTATTTCTATAAAAATAGAATGGTTAGTAAAAATAGCATTCAGTGTATTTTCCTTAGGGAGGCTATTTATAATGAAATCTGTGACTCAGCAGCAGCTGGCAATGCTGTCCCTTCAAGACCTTGTTCTTCCTTTTCCATTGTTATGCAGATGCCGTTTTAGTCATCCTGGAAAGAAACAAAAAGAAAAATTCAATGAGAAACAAAATTTCAATGCCAATCGCAAGGGCTTTGGATGGCTTTTAAAAGACACCTTTACATAACATTTATTTCAACTTACAACTTATAAAAACAATAATATaggttgggtatccctcatctgaaatgcttaggcccagacatgtttcagattttttcagatttcggaataactggattataccagttgaacatccctaaactgaaaatccaaaatccaaaatgctccaatgagcacttcctttg +>mm8 +GACAAATAAG--GTTTAGCATTGATAAGGCAGCAGAGAGTGGGTTTAGGGACTCTCGGCTAT-TCAATAATGTTGGCATGGTCATT-AAGATAGCATTCTGTGTTTTCCCTTCAGCACGACTACTCATGCTGAGATCTGTGGCTCAGCAGTGGCTGG-AGCACTGTCTCTTCAAGAGCTGGTCC------TTGTACCGCTATGCAGATGGCCGCTTACTCATCCTGGAAATAATT--GGAGACAATTTCAATGAGACACAAAGTCTA-CCGCCAGTCCCAGAGGCTCTGCATGGCTTTAGAA-GACAAGTTTCTATAACATGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr16(+):2029817-2030316 +CATCTGCAAACACACCAAAGCTTTATTCAACAGGCGTGGCTTCCTGAAGCGTAAAGCCACTTCACAGACGGTGGCCACAGCGGCACCTCGGCCAGAGCCATGCGGCCATCAGAGACCCTGGGCGGCCGGGCAGAGGGCTTGGTTGAGGCAGGCGTGGCAGCGAGGGTGCACAGGCAGACAGGTCTGCTGGCCGAAGCCCACCAAGAGTCCATTGATCTCGTGCCACAGCTCCCTGTGGGGGTGGGGGCTGGGTCAGTGCTGACAGAGGGCGGGCGGGGTGAGCTCTTCTCCCTAGGAAGCCCCCCACATACTCATACCTAGGCAGCCACTCCTCCAGGGCGGCGCGGGTCTCCTCTGGGGACTTGGTTGCCTTCTTGGTCCACCTCAGCCTGTTGGCGATTCTGTGCACATGCGTGTCCACTGCTGCTGGGAGGCCAAGCGGGGTGAACAGGGGCACACTCCACCAGCCTAGCCCGTGCCCCTCCCCGCCCAGAGGCGA +>mm8 +CAGGTGCAAACACCCCCAAAGTTTACCACCCCGCC---------------------------------------CCACAAAGGCACCTCAGAGGAAGCCCTATGGCCCTTAGAGATCCTGGGCAGCAGGGCACAGGGCCTTGTTGAGGCAAGCCTGACATCGAGGATGGACAGGAAGACAGATCTGTTGGCCGAAGCCTACCAGTAGTCCGTTGACCTCACTCCACAGCACCCTGTGAGGGTAAGAGAAAGGTCAGT-------GTGGATGACAGCAGGACACCTCCCTCCCCCAAGCTCACCAAGCTACACTGTACCTGGGTAGCCACTCTTCCAAGTTCTTACGTGTCTCTTCTGGGGTCTTGGTCATCTTCTTGGTCCACCTCAGTCGGTTGGCTATTCTGTGCACATGTGTGTCCACTGCTGCTTGGAGACAAGGCAGGCTGACC--AAGGGCACTCTGCCAG-CTGGGCTGTGTCCCCCCCGGTCCTAAGGTGT + +>hg18.chr10(+):126075862-126076361 +ACATTTGAAATATAAGCTTTATTTTAAATTTAAAGAAGTATTGAAAATAAACATTTTTTACAAATTATAATCAAGCACTCAAAACAATTTAGGAATGTTAAACACTAATTCTTAATTCAAAATAATGACATCCATAGAATACAACCCTGGTGTTGGCCAATATGAAGTTTACTTAATATTAGTATTTTATATACACTTAACCATTAATCCTTCCTAAAATTCAATAACAATGATTTCACTTTATAAGATGAAGCCTTTTATGCAATACCCAGAGATAACTTTTTCAAATATGAAACACTTATACCAGTGAGGAAATTATAAAAACATATATCAATTATACTGAAGGACTTGATTTAGAGGCTGTCTGTATATAGATGCATTTCACCTTAGGAAGTACACATGCACATCAAAACACTTCAACTGAATATAGATGCCATTACATTATTTAGTTACGTTACAAAGCAAACGGCAGGTTCATAAACGTTGTTCTATTATGTAT +>mm8 +-AAAAGAAACATTAAGCTTTATT-------CAAAGAAATACTGAAAATAAA--TGTTTTACAAATTGCAATCAAGC----AAAGTGATTTAGTAATG---------AATTCTCAGA-------------ATCTATATAATAC-ATTCTGGTGTTGGCCAATGAAAAGTTTACTTTAAACTAGTATTTTACATATGCTTAACCTTCAATCA-ACTTAACATTCATTGATAATGATTTAAC------------TGTTC----TGTAGTACTCAGAAATAACTTCT--AAATACAAACCATTCACATCAGCAAGGAAACTGTAAAGACGCACGTAAAT--GACTGCAGGCCTCCATCTGCAGGCTGTACGCAGATGGGTCCGTTTCTCCTTAGAAAGTTCCCA----CACAGTCAAACCTCAACAA---AGAGACGCC-TCTCGCTCTACTTTTCTGTCACGCAGCCACCTGCAGGTTCCTAGGTGTCACTCTATTATGCAT + +>hg18.chr10(+):126075869-126076368 +AAATATAAGCTTTATTTTAAATTTAAAGAAGTATTGAAAATAAACATTTTTTACAAATTATAATCAAGCACTCAAAACAATTTAGGAATGTTAAACACTAATTCTTAATTCAAAATAATGACATCCATAGAATACAACCCTGGTGTTGGCCAATATGAAGTTTACTTAATATTAGTATTTTATATACACTTAACCATTAATCCTTCCTAAAATTCAATAACAATGATTTCACTTTATAAGATGAAGCCTTTTATGCAATACCCAGAGATAACTTTTTCAAATATGAAACACTTATACCAGTGAGGAAATTATAAAAACATATATCAATTATACTGAAGGACTTGATTTAGAGGCTGTCTGTATATAGATGCATTTCACCTTAGGAAGTACACATGCACATCAAAACACTTCAACTGAATATAGATGCCATTACATTATTTAGTTACGTTACAAAGCAAACGGCAGGTTCATAAACGTTGTTCTATTATGTATCAACTGA +>mm8 +AACATTAAGCTTTATT-------CAAAGAAATACTGAAAATAAA--TGTTTTACAAATTGCAATCAAGC----AAAGTGATTTAGTAATG---------AATTCTCAGA-------------ATCTATATAATAC-ATTCTGGTGTTGGCCAATGAAAAGTTTACTTTAAACTAGTATTTTACATATGCTTAACCTTCAATCA-ACTTAACATTCATTGATAATGATTTAAC------------TGTTC----TGTAGTACTCAGAAATAACTTCT--AAATACAAACCATTCACATCAGCAAGGAAACTGTAAAGACGCACGTAAAT--GACTGCAGGCCTCCATCTGCAGGCTGTACGCAGATGGGTCCGTTTCTCCTTAGAAAGTTCCCA----CACAGTCAAACCTCAACAA---AGAGACGCC-TCTCGCTCTACTTTTCTGTCACGCAGCCACCTGCAGGTTCCTAGGTGTCACTCTATTATGCATCAACTGA + +>hg18.chr10(+):123223889-123224388 +AATTTATAAATCTGTAAGTGTCCTCTGTCCCTTTCAAAGAACCTCATGCTATGGATTTTAACTAGTAAGAGACACCAGCAAGCGTCAGTTAAGTGTCCTCTGTCCCTTTCAAAGCACCTCATGCTATGGATTTTAACTAGTAAGAGACACCAGCAAGCATCAGTTAAGTGTCCTCAAAAGAGAATTAgaggctgggagcagtggaatggcttgaacccaggaggcggaagttgcagtgagcctagatcatgccattgcactccagcctAAAAAAGAATTAGAAGAGGAAAAGAAACCTAAAAGGAGTGCAGCCCAAAAGGAGGCAGTGTTCTGAGCTGCAGAAGGAAAAAATCACCTACCCATATGTGCACGGTAAGCTGAATTCAGTCACTGAACAGCTTCATGTGCTGAGGTATCCCTTTGTAAATTGTATTTCAAAGGTCCGGAGCGGATGGTTCCCCAGTGCCGGACATTGAATGCCCTCCCATCCACTGACTTC +>mm8 +-----------------------------------------------------------------------------------------------------------TTCCAAGTCCATCATGCTATAGAGTTTGACTTACAACTGATACAGGCAAAATTCACTCAAGTACTCCCA--------------------------------------------------------------------------------------------ACAAAGGAACTGCAAGAGGACCAAGAACCTGAATAGA---CAACCCAGGAGGACACAGGGTTCTTTG-TGGAGAAG--CAAAGTCACTTGTCCACATATATATTTTAAACTAAACTTTATCTCTGAACTACTCCGTGGCCTAAGGCTCCACTTAGGTAA---TATT----TGGC-----------ACTGTCTGTATG-------TCCACTG----TCTGTACTGTGCCTCT + +>hg18.chr10(+):123227846-123228345 +AGTTGCGTGACATTTATTTTGTCTTGTTAACATTAATATCTGTAGAAACATTTTTATTGTCAGTATAAAAATTAACAGGTTTTATTAAATACTTTCTCCAATTTTGTAACACATAAGATCAGTGTAATCTGCATTCATCTTGCACGGCTATTGCAAAGTGAGTGGGTGTTTCCAAAGCAAAACACAATACTTTAGTACAGAAGGAACAACGGCGATATTTTGTCTGATGTAGGTATGAGGCTGGATCTTTTGGTGAGGTCCTGCCAGAATTAGATGAAAGCAATCCCTTAAAAAGATGGACGTATCCCCAAAACTATCAGCAGAACAACTCTGTGTTTCAATTTTCTATGATGGGACTTGAAGATCCTAACAGGCGTCTCCAACGCCAAAGAGTCTGGAAGCCATTATCAAAATTCACTGAAGAGAATACAGGCTAATCTGATTAATGTGCAACTCAGAAGCAGAAGGCCAGCTGCCAGAGAGAAGCACATTCTGCTAT +>mm8 +AGCTGCGTGACATTTATTTTGTCTTGTTAACATTAATATCTGTAGAAACATTTTTATTGTCAGTATAAAAATTAACAGGTTTTATTAAATACTTTCTCCAATTCCAAAACACATAAAATCAGTGTAATCTGCATACATGTCGCATGACTGTAGCAAAGTGAGTGGGCGTATCCAAAGCAAA--ACAATACTTGAATACGAAATCAACAAAAGCGTTATCTTGTCGGATGTAGCTATTAGGCCAGATCTTTTGGTGAGGTCTTGTCAGAAGTAGCCAGAAGCAAACCCTTAAGAAGATGGAAGGAGGTCCCAGACTCTCAACCGAATGATGCTGTTTTGCCATCCTTCGAGAGGA----TGGAGATTCCCCAAAGGGCTCTTGGTGCTGAAGAATCT-GAAGCTGTTATTAAAACTCACTGAGA---AGCAAGGCAAACGTGATGAATGTGTAACCC--GGGCAGAAGGCCAGCTGCCGGACG-AGA-GGACCCTGCTAT + +>hg18.chr10(+):123229123-123229622 +GTTACATGGTGGCTTGTGGCAGTCCACTGCTCCAGAAACCTTCTTCTCCTCCTGGGGAAGATTACAAGTTTTCAACTGTATAAATCTTTACACATATGCTGATTACTTTTCCAATTATTTACTCCTCTGATCCATATATACAAGTGGAGACAACAAGCTCTGGGAGGCATGGTCTCCCTGCTCAGTGTAGCTAGGTTCCCAGTGCTGTCCTGTTTGGGGACAGGCAGACACAGTCATTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGTTCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACAAGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGCTGAGGTCCAAGTATTCCTGAAAGAAGGGAAGAGAGACGTTTTATTTCATCTTGGGTCAGGATAACAAGGTGAATACGGTTCGAGAGGCTGACTGAGGTCCAAGTATTCCTGAA +>mm8 +GTGGCATGGTGGCTTGCGGCTGTCCACTTATCAGGAAACAGTCTTCCTTTCCTGGTTAGG-TAACATGTTTCCAACTGTATAAATCTTTACACACGTGACAAATATGCTTCCCACTATTTACTCCTCTGATCCATATATACAAGTGGAGGCGACAGGCTCT-GGAGGCACAGCCTCTCTGCTCAGTGTAAGTAGGTTCCTGGTGCTGTCCTGTTTGGGGACAGGAAGACACATTCACTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGCAGACAGGGTTCATAAGGCATGGGGTCTGGAGAAAACACAGAATCGTCCCCTGAAGAACAAGAGCTCCTTGTGTCGGGGTAACTAGGAGAATACTGTTCGAGAGGCTGGGTGAGATCCAAGTATTCCTGCAAGAAGGGAAGAGAGACGTTTTATTTCACCTTGGGTCAGGATAACAAGGTGAATACGGTTCGAGAGGCTGACTGAGGTCCAAGTATTCCTGCA + +>hg18.chr10(+):123229361-123229860 +CATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGTTCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACAAGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGCTGAGGTCCAAGTATTCCTGAAAGAAGGGAAGAGAGACGTTTTATTTCATCTTGGGTCAGGATAACAAGGTGAATACGGTTCGAGAGGCTGACTGAGGTCCAAGTATTCCTGAAAGAAGGGAAGAGAAGAGTTTTATTTCAAACACAAACTCTTGAGATGTGGGTATTGGACGTGGGACAGGACAGGAGACCCCTAGAAGGTGAACAGAGACCCAGCCCACCTGACTTCCACGAAGACCTCCCTGAGACCACGTCTGATGTACCCCAGGCTGTCCTTAGCTTTTCTCTTGGAATCCATCATAAATCAACTATTGACAGGTAGAGAACAATAAAACCTAGTTGAGCTATAGGT +>mm8 +CATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGCAGACAGGGTTCATAAGGCATGGGGTCTGGAGAAAACACAGAATCGTCCCCTGAAGAACAAGAGCTCCTTGTGTCGGGGTAACTAGGAGAATACTGTTCGAGAGGCTGGGTGAGATCCAAGTATTCCTGCAAGAAGGGAAGAGAGACGTTTTATTTCACCTTGGGTCAGGATAACAAGGTGAATACGGTTCGAGAGGCTGACTGAGGTCCAAGTATTCCTGCAAGAAGGGAAGAGAAGAATCTCATTTTAAACAGAAGCTCCTGAAAAATCTCTATCAGATTTGGGAAGGGACGGGGAACCCCCGGAAGCTTTCCAGAGGCCTAGCTCACCCCAGTG-TACAAAGACCTCCCTGATACCCCACTCCATTCACTCCAGGCTACCCTGAACTTTTCTCTTACGACACAGCATCTATAAACCACCAGCAGGCAGCAGACCATAAAACATAG-TGAACTGCTGGT + +>hg18.chr10(+):123229555-123230054 +CATCTTGGGTCAGGATAACAAGGTGAATACGGTTCGAGAGGCTGACTGAGGTCCAAGTATTCCTGAAAGAAGGGAAGAGAAGAGTTTTATTTCAAACACAAACTCTTGAGATGTGGGTATTGGACGTGGGACAGGACAGGAGACCCCTAGAAGGTGAACAGAGACCCAGCCCACCTGACTTCCACGAAGACCTCCCTGAGACCACGTCTGATGTACCCCAGGCTGTCCTTAGCTTTTCTCTTGGAATCCATCATAAATCAACTATTGACAGGTAGAGAACAATAAAACCTAGTTGAGCTATAGGTGCTGGGCAGGCAACTCGGCTTCACACGGACCTAAATAACCCGCTGAGTCTACACCACCTCCTCACTAGAGCCCTTGCTTCAAATGCGAGCCCCAGCAAAATGAAAACCGGTAACATGTTGTGGGTCCCCAGACCCCCTTTAAGTAGTTGAGACTATGAATATTTATTTTCTGAATTACATTTTACTATTGTAGT +>mm8 +CACCTTGGGTCAGGATAACAAGGTGAATACGGTTCGAGAGGCTGACTGAGGTCCAAGTATTCCTGCAAGAAGGGAAGAGAAGAATCTCATTTTAAACAGAAGCTCCTGAAAAATCTCTATCAGATTTGGGAAGGGACGGGGAACCCCCGGAAGCTTTCCAGAGGCCTAGCTCACCCCAGTG-TACAAAGACCTCCCTGATACCCCACTCCATTCACTCCAGGCTACCCTGAACTTTTCTCTTACGACACAGCATCTATAAACCACCAGCAGGCAGCAGACCATAAAACATAG-TGAACTGCTGGTAGCAGGTTGCCCACTCTGCTACA---GGACCTCGGTGACCCACTATAT--ACAGC-CCTCTTCACTACGGCTCACAATCGGAGTTTAAGACCCAGTGAAGT--AAACCCAG-----------------CAGGA-CCCTTTACAAAGCCAGGAC-ATGAATATGTATTTTCGGAATCACATTCTACAGTTGTCAT + +>hg18.chr10(+):123231339-123231838 +ttttattttttttttttttgagacggagtctcgctctgtcgccaaggctggaatgcaatggcatgatctcggctcactgcaacctccgcctccccggttcaagtgactctcctgcctcagcctcccggagtagctgggattacaggtgcacaccaacacgcccggctaattttttgtatctttagtagagacagggtttcaccatgttggccaggctggtctggaactcctgacctcatgatccgcctgcctcggcctcccaaagtgctgggattacaggcatgagccactgcgcctgaccAACTTTTCCCAGTTTCTCAATGAAGCCATAAACTTTCAGATCTGATAGGAAAAAAACAGGGATATCAGTAGATTCCAAGTCTACAGTTAAAGGAACTTATACTAGAAACAACAATTTTGGCAGAAGAAGAAAGTTGGTTTCTTCCCCCCCTTGAACCGTTCCTTTCCTTTCAACTTCTGAAGGTCAGCTGTATTCATT +>mm8 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGTTTCTAAATGAAGCTGT-AACCTTCAGATCTGACTGGGGGT--GGGGGGCTATCACTGGATTCCAAGCCTAGGGTTAAAGGAACTTAGGCTAGAAACAACAGTTTTGGCAGGAGAAGAAAGTTGGCTTTTTTTCCCCCTTGAACTATTCCTTTCCTTTCAACTTCTGAAGGTCAGCTGTGTTCATT + +>hg18.chr10(+):123231360-123231859 +gacggagtctcgctctgtcgccaaggctggaatgcaatggcatgatctcggctcactgcaacctccgcctccccggttcaagtgactctcctgcctcagcctcccggagtagctgggattacaggtgcacaccaacacgcccggctaattttttgtatctttagtagagacagggtttcaccatgttggccaggctggtctggaactcctgacctcatgatccgcctgcctcggcctcccaaagtgctgggattacaggcatgagccactgcgcctgaccAACTTTTCCCAGTTTCTCAATGAAGCCATAAACTTTCAGATCTGATAGGAAAAAAACAGGGATATCAGTAGATTCCAAGTCTACAGTTAAAGGAACTTATACTAGAAACAACAATTTTGGCAGAAGAAGAAAGTTGGTTTCTTCCCCCCCTTGAACCGTTCCTTTCCTTTCAACTTCTGAAGGTCAGCTGTATTCATTTAAGTGCAATCTCTTCCTTTA +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGTTTCTAAATGAAGCTGT-AACCTTCAGATCTGACTGGGGGT--GGGGGGCTATCACTGGATTCCAAGCCTAGGGTTAAAGGAACTTAGGCTAGAAACAACAGTTTTGGCAGGAGAAGAAAGTTGGCTTTTTTTCCCCCTTGAACTATTCCTTTCCTTTCAACTTCTGAAGGTCAGCTGTGTTCATTTAAATGCAAGCTCTCCCTTTA + +>hg18.chr10(+):123287470-123287969 +GTCTTCAATGTTTAATTAAAATGGCCTACTTATCTGTGCACTCTGACAAAAATGTATTTATAAGCTCATATACATGGTTCCCTTTGCACAGAGGAAATAGATGCCAGGAACAGACACTGAATTGGTACCGTCTAATGACTTTCTTGTGATGGAAGTGAAGGGCCCTCAACATTCACCTTTTTCCAGCCAGCCACAGGCTCAGTCCTCAGACCTTTTCCTTTACTCTTCAGCTGGCCTTCTACAGTTGCCCTGTTGGGGAAATGATGCTTCTCTTTTAAAACCAAAGGTCTGCTACAGCACATCTGTACCCTTTTCACCTGCCCAATTAACATTTTCAGAGTAATCTCAGCTTCCAAAATGTCAGACATTTCATACCACGTCCACTTTACACAGATGACGCTTGGGAACCATGAGGATCATGCAAAGCTCATAAACCCTGGCTGCCTGGAAAACAGAATATTGTCAGATGACAGAAGCAGCCTTGTAAAATGATAGTAGA +>mm8 +ACCTTAAATGGGAAATGAAAATGATCCGCTTATGGGTGCACTGTGACAAAAACCTATTTGTGAGCTCAAACATGTGGTTCCTTTGGCTCAGA-GAAATGTCTTCCAGGAATAAGCATTGAGCTAATTTCTGACATTGACTTTTTTC----------------------------------TTCCAGCCAGACAGGGACTCAGTCATTAAAT-----CTGTTTCTTTACTCTTTGTATGATA-AGTTGCCCTTCTTTAACCTTGTTGCCTCTCTTTTAAAAACAA-----------------------------CCCTTGCACGTACCAAGAATTTCAACATAATCTTAACTTCCAAAA--TGAAATGTTTTATACCACATCTACCTGATAAAAATAATGCTTAGGGGCCAAGAAGACTCCCCCAAGCCCATAAAACCTGGCTACCCAGGAAACAGAACACAGTCATACGACAGACGAGACCTTCTCAGATGACATTGGA + +>hg18.chr1(+):92746841-92747340 +TCTTATAAAATGGAAAACTTTAATTGTTTAAAGAAAAGGCACAAGTAAACATTTCAGGTTATCATACAATGTTACAATAAAAAATTCCAATAGCAAAATGAAACACATTATAACTTTGCTTCTTGGTAGTATACTGAATGTATTATTCTATCATCTCCTCTTTGGAGTAAAAAGAAGGGATAGGCAGATCAATGGATGTGATGTAAAAACTTGGATCATAAATAGCATCCACTATACCTTTAACCAGAAATTAAACTTCAGTAGaattaaaattaatttttaaaaCTTAGTTTTGTTAATAATAGAGCAGCAGTAACTTTCAAGCTAAAACTCATTGTTTTGGTAAGTAAATAACTGATTTCATGAAATGTTCGCTGTCAATGTCTGGTATGTTAATATACATTAATCAAGCTGGTCATGAAACAGTTTTACCAAAATATAATTCATATACTTATTTTACTTTAAACCTGAATATTACAGTACATTATATAAAAGATAA +>mm8 +TCTTGTAAAATGAGAAACTTTAATTATTTAAAGCAAAGGCACAAGTAGACATTTTAGGTT---ATACAGTGTTACAATAAGAAAACCCCGCAGGACAATGAAATACGTTGTAACTTTGCATGTCC-----------AATGGATTACCATGTCAGCTCTTCTCTGGAGGGAAGGGG-----TATGTAGACCCACAGATGT------AAAAGTTGGATGTTAAATAGCATCTACCCTATTGCCAATAAGaaatttaatt--aatagaattaataagaaattttaaaaattGTT--TGCTAAT-CTAGAGCAGCAATAACTTTCAAGCTAAAACTCATTACTTTAGTAAGTAAGTTACGGATTCTAC-AAATGTTGGCCATCGATGTCT----TGGTATTGTGCAATATCCATGCTGGCCATGAA--AAGCTTACCAAAACATAATTGATATCCTTAACT---TTTAAAACTGAATATTACAGTGCATTATGCAA------A + +>hg18.chr1(+):92860438-92860937 +tacgcattaaaaaatattattttaagaaggggtccacaggttccagactgccaacagtgttgatagcagacacaaacacaaaaacggtaagaacctttgTACTTAagaaactcttgaagatatacacaaggaaacataagcaagaatgttcagagtagcactgtttgcaagagcaaaaaggagagtggatcaataaattgaggtatagtcactgacagacttttctaaaagtccttaaaatgacagaactggagttacatgtataaacatggacaaatttcTTAATCTAAATACATGGGTGTTTGATACAATAATCTTTAGATTACTACACACCACCACCATTACCCTATACtatttttatttatttatttttCATTTATCAATGTAAAAATTTCATGGATTACCACCAGTCCAAATACTGGCATTTAGGAACCAGTGCCTATTACCATCCTGCTTCCAGCAAAATCCATCCAAAATCACACTTATTAGTCAGCAATGG +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr3(+):151165384-151165883 +GTTGGAATAAATTTATTTCATCTGTCTGTAAACAAGGTGTTTAATAGTTATGGCATTTTTTTAAATGCATATTAAATCAGATGAGTTAGACTGTATCCCAGATGTAACAAAGTGCAGGGAAAGAAATGGACAAATCAGCAACAAGATTTGTTTTTAAATCTGTACATTATCCACAAGGCCCAAACAATAGAAGCAAATACTAGAATGTCCCTAAAGTAGTGCCATTCGAAAGAAACCCTTAATAGGTCAGTTAAAATCCATCTCACAATAGCAACAGTTCATTTTAACAATAGTATGGCACAGAATACATATGAAAAAAATTCATCACAAGACAGCCAAGTCCACAATAATGCAACTTCATATAAAAACTCAAGCTGCAAATAAAAATTGGTCCTATGAAGAACAAACTGGACACACTCCAGATGGTTATGTTGGGATACCTAATGTCCATAATGGCAGCCTTTTACAATTTTACTAAAGAGTAGAGCTGGTGTGCAAA +>mm8 +GTTGGAATAAATTTATTTCATCTGTCTGTAAACAAGGTGTTTAATAGTTATGGCATTTTTTTAAATGCATATTAAGTCAGATGAGTTAGACTGTATCCCAGATGTAACAAAGTGCAGGGAAAGAAATGGACAAATCAGCAACAAGATTTGTTTTTAAATCTGTACATTATCCACAATGCCCAAACAATAGAAGC-AATACTAGAATGTCCCTAAGGTAGTGCCATTCGAAAG--------------------GAAATCCATCTCACAATAGCAACAGTTCATTTTAACAATAGTATGGCACAGGATACATATGAAAAAAATACATCACAAGACAGCCAAGTCCACAATAATGCAACTTCATATAAAAACCTAAGCTGCAAATAAAAATTGGTCCTATGAAAAATAAACTGGACACACTCCAGATGGTTATGTTGGGATACCTAATATCCATAATGGCAGCC-TTTACA--TTTTCTCAAGAGCACAGCTGGTGTGC-AA + +>hg18.chr16(+):56546748-56547247 +CAGAGACCTCCAGCTCCCATCACCCCTGAAACAAAGGAGAAGACAGGGTGGGTGGCTGGGTGGACAGGCGgagggaatgagtgagtgagtgagtgagtggatgagtgaatgaatgGGGAAGGTAAGGGACACATATCCCCCAGCCTCTCAGAGTCTCCCCATGACATGGGACGtgagtggaatggtgtctcccaaaaagataattgcaagtcctaaccccattacttgtgaatgtgaccttatttggaaatagcttctttgcaggtgtgattaagttaaggatctcaaagtgagatcatcccggattgagggtgggccctaaatccagtgactgatgtcctttttaaagaacggagagggaggcttgacacacacagacacagaggtaaaggctgtgtagagacggaggcgggcactggaggacagccagaagccaaggtttgccaaggaccgcaagtggccaccaggagcaaggagagcagcatgggcatgtctcgct +>mm8 +CAGAGGCCTCCAGCTGCTGTCGCCCCTGAAACAAAGGAGGTGACAGAGTAGGAGGATGGATGGATAGACAGATGGAAtggatggatgagtggatgagtggatgagtggatggatgggAGAGGAAGTGAACATGTAT-CCCCAGACCCTC--AGTCACCCCAT-------GTAGCGGATTAAAAAGTGTC-CCTGAAAAGACATGCCTAGGTCCT-ATTCTATCCTATATAAATGTGACTTTATTTGAAAATACAGTCTTTGAGAATATTATTGTCCTCAGAATCTCAAAGCAAAAGACTTCTGAATTTAGGGCAGGCCTTCCCCC-AGTGACAGTCA----------------------------------AG---GACACAGGGAGTAA------------------------ATAGAAGGACAGCTGGAAGCCAAGGAGGCTCAAG------------------GGAATCAGGAGAGCGGCAAGGACATTCCACACC + +>hg18.chr16(+):56475004-56475503 +tttgagatgaggtctcgctatgttgcccagtctgctctccaactcttggcctccagtgatcctcctgcttcggcttcccaaagcactgggattataggcatgagccaccatgcccggcAGTGAAGTATTTTCTATCCTTGAAATGTGTTAGACAAATTCCTGAGGGGAAACCCCACACATTCAATAACACTTTACTTTTTCAGCAAAGCTTCCCATGTATTGGAGCCTCATTTTATCCCTCACCCATGAACTTTAAAAGTGGAAAATCATTTTGTTCTTAAAAAGAGGAACAGTCAGGAAAAGGTAGGGCTCTCAAATGATAGTGAGAGCTCAGGGACTCGAACACTTGATGCAACTTGTCGAGCTCAGGCCCAGCCCCGCGAGGAGCTGAGTCGGGGCTGGCGTGCTGGCGGGACGGTCAGAGCTGCAGCCACTGAGGTCACGACTACGGAAAAGCATCTTCTCTTGAGCCGTGGGGGAAGGTGGGGCGCTGGGGCGC +>mm8 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGGACCCTACCAAGTCATCAACCCTTGATTTGTCTAGTAGAGTTCTCCTTGTGTTGGAGCCCTCTTCTAGTCTCTCCTCAAATCTTTGAGAAGTACAAGGCGGTTTTCTTCTTGAAAATAGCAACCTCAGGAAGGGAGCAGGGTGCTCAGGGAATGGCAGGAGCTCGAGGGCACTACCACCTGGTGAAATTTG---AGCGTTTCTACAAGCCTGTGAGAAGGCGCCCTTAGGCTGGGACGCT-----------------------------------------------------------------TGGCGAG---------GCGGGGGTTC + +>hg18.chr8(+):145589254-145589753 +CAAGCAAAAAATGTTTTTCCTTGTGTTTTGTACAAAAAGGGGGTGGGAGGTAGTTCCGTGTGCTGGTGGTGACGGCATCCACGGGGCTAGAAGTGGGCGGTGACGCGGTCCGTCTCCAGCAAGTCGTCCAGGATCTGCAGGGGATGGAAgggtgggtgggtgggtgggtgggGATGCACACGGAggggcggggcgcgcggggggcggggcgcgcACTCACTATGTCTGGTGTGGTGCCGATCTTCTTGGCTAGCTCGCTGCGCTCCATGGTGCTCAGGTACAGGTAGCGGTTGAGCAGCTCCCCATCCAGCACGTTGCGCACGGCATTCTGGAGGGTGCGGCGGTCCACGTGCAGCATCCTGGGGCGTACAGGCACAGGTGTCAGGGCAGGCTGGGGTGGAGGGGGTGCTGCACGCGGGCGGGGCCGGGGCTCACCGGAAGGCGCGGGGGTTGAGGCCGGCGTGGTGTGGCAGCATGGTGGTCAGCGCGTTCTGCAGCA +>mm8 +GAA---AGAAATCGTTTTCTTTGTGTTTTATACAAAATGGTAGAGGGAAGT------GTACAACACCAGA-GCAGCATCC-TAGAGTTAGAAGTGAGCCGTGACCCGGTCTGTCTCCAGCAAGTCATCCAGGATCTGTGGGTGATGGA----GAGGTAAAGGTGTAGACAGGAA---GGGTGGTGAGGGCGA--GGCCGAGGGCGAGGGCGT-TACTCACAATGTCAGGCGTGGTACCTATCTTCTTGGCCAGCTCACTGCGCTCCATGGTGCTGAGGTATAGGTAGCGGTTTAGCAGTTCCCCATCAAGGACGTTGCGCACAGCATTCTGCAAGATGCGCCGGTCTACGTGCAACATTCTGGGGTG-GTAGACATAAAGGTCAGGGCAATGTGGAGTACAGGGTGAGAC---CGGGGAAGGGGC--GCACTCACCGGAAGGCGCGGGGGTTGAGGCCAGCGTGGTGGGGTAGCATGGTCGTCAGTGCATTCTGCAGCA + +>hg18.chr1(+):159899157-159899656 +TGGTAGGTGGCCTGGAGTCCCCATGCTCAATTTCAAGAAGCATCCAGATTCCAGGGCCTGGGTCTCCAAATGGAAGTAGAAGTACTAGAAGATTGCTGGTGCACGCTGTCCTGCATCACCCTTTCTCAGGAGGATAGAGACTGAAACAGGAGGTTCTGAGCTGAGTTTTGGTGACCATTTCCCTCTTTCTCCCAGAGGCCCAGGCCAGCTGTGGCCTCAGAGGAAGAAGAAGGGAGTTGTTTCCCTAGTTTCTAAAATTTCTGTGAATTTGAACATGGGCTACACCAGATTTATTCTGGGAAGCTCTGAATCTTCTAGGAGGGAAAGACTGAGAGGAAAGAGGGTGGAAAGGGAGGAGCCTGTGATAAAACAGAACATTTCTTTTTCACTTCCCCTTTCAGACTCCAGAATTTGTTTGCCCTCTAGGGTAGAATCCGCCAAGCTTTGAGAGAAGGCTGTGACTGCTGTGCTCTGGGCGCCAGCTCGCTCCAGGGAGTGA +>mm8 +TGGTAAGTGGTTGTGGGTACCTTTATTCAGTTTCTGGAGGAGTCCAGATCCCACAGACTGGACCTTC---------------------AAGACTCTTG-------CCATCCTCCAT------------------CACAGACTGAGGCAAATGACTCTGAGCTGCGTTGGGGTGAAGTTTTCCCTCTCTGTACCAGACGTCCAGGTCAGCTACGGCTCCAGCAGAACATGAAGGGAGTTGTTTCTC-AGTGTCTAAA--------AAATTGTGATTTGAGCTGAATCCAGTTTATTCTGGTAAGTCCTGAGTCTTCTAATAGAGAACGGATGAAAGGAAAGAGGGTGGAAGGGGAGGAGCCCAGGATTAAACAGACCGTTTC-TTTTCACTTCCCCATTTGGACTTCACAATTTGTCTGTTCTC-TGGGTACTATCTGCCAAGCCGGGAGGGAAGCCTGTGCCTGCAG-----------CTGACTCGCTCCAG-AGCTGA + +>hg18.chr1(+):159899076-159899575 +GCCATCCTGACATACCTCCTTGTCCTTGTTCCACAACTCAGCAGTGAGTCTGGGATTATGACAATAGAGAAAATTAAATGATGGTAGGTGGCCTGGAGTCCCCATGCTCAATTTCAAGAAGCATCCAGATTCCAGGGCCTGGGTCTCCAAATGGAAGTAGAAGTACTAGAAGATTGCTGGTGCACGCTGTCCTGCATCACCCTTTCTCAGGAGGATAGAGACTGAAACAGGAGGTTCTGAGCTGAGTTTTGGTGACCATTTCCCTCTTTCTCCCAGAGGCCCAGGCCAGCTGTGGCCTCAGAGGAAGAAGAAGGGAGTTGTTTCCCTAGTTTCTAAAATTTCTGTGAATTTGAACATGGGCTACACCAGATTTATTCTGGGAAGCTCTGAATCTTCTAGGAGGGAAAGACTGAGAGGAAAGAGGGTGGAAAGGGAGGAGCCTGTGATAAAACAGAACATTTCTTTTTCACTTCCCCTTTCAGACTCCAGAATTTGTTTG +>mm8 +GCTGTTCTCACATATGGCCTAGCTTTTGGTCTACAATCCAACAGTGAGCTGGGGATTGTGATAACAGAGAAACCCAGATGGTGGTAAGTGGTTGTGGGTACCTTTATTCAGTTTCTGGAGGAGTCCAGATCCCACAGACTGGACCTTC---------------------AAGACTCTTG-------CCATCCTCCAT------------------CACAGACTGAGGCAAATGACTCTGAGCTGCGTTGGGGTGAAGTTTTCCCTCTCTGTACCAGACGTCCAGGTCAGCTACGGCTCCAGCAGAACATGAAGGGAGTTGTTTCTC-AGTGTCTAAA--------AAATTGTGATTTGAGCTGAATCCAGTTTATTCTGGTAAGTCCTGAGTCTTCTAATAGAGAACGGATGAAAGGAAAGAGGGTGGAAGGGGAGGAGCCCAGGATTAAACAGACCGTTTC-TTTTCACTTCCCCATTTGGACTTCACAATTTGTCTG + +>hg18.chr4(+):5763326-5763825 +CGTCTCAGTGGGGTCTGGGTGTAAGGATCCCTTTACCCATCCTCCTAGTGGAGACTGAGTGTAACGGTGTCTCCACCCATTGTCTCGACCTTCCCTGGGACAAAATAAGATTAAAACAGGAGTCTTCGCGTGAGCAAGTTCAGAGGCGTGGAGGGCGGTGTGTTCCCGGGAAGGTTGATGGGTAGAGGTTAGGGGCAAGGGCAGGGGGTTGGAATTGCATtgatcccagcgtcttcatcaggaggatgggcggagcacccaccgcagagggttattgagaaagttaatgagatcattaagctaaatgcgtagcatattctaagcctcaaaaaaCTTAAAGGAGCCTTCTAAGCCTCAGTAAAGTTAAAGGGGTGGAAACCGGGCCCCCCTCCGGAAGGGTCCGGGGCTGGGAGGCGCGTCTGTCTCTGGGCATGCTCAGTGCAGGGGCAGGGCTGGGGCGGGGGTGGCTGAAAGTTTTGAGCGGTGATCCAGGCTCCTC +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGCCTCGGGCTGAAAGGCGCGCCCCG-GCTGCGCATGCTCAGTGCA-CTGTAGGGATGGCCCGGAAA-GGCTGAAAGTTTGGGGCGGCGGTCCAAGCTCCTC + +>hg18.chr2(+):70753968-70754467 +GAAGAGAACCAGCCAGGAGCTTTGTGTCGTGAGCACAGAGCACATCAACGGGTAAGAGGTGGACCCACAACCACCAACTCCCCTTATTTTATTTTTTGCTGACTCCCCTTAAAAACACCCATGATTTCTTTGCATGTAACTATTGTTTAATTCATCAAATTTACATTTTCTGTCCAAACAATCCCTAGGGATAAAAAGTGCCATGTTCCTCTATTTGCTTTTCAATTGGCACATTAGAGCTCCAAGCAAGCCAGCAAGGGttttttggtttttgctgttgttgtttgagatgaagtctccctctgtcacccaggctggagtgcagtggtgtgacctcagctcactgtaacctccgccttctgggttcaagcaattctcctgccacagcctcctgagtatctgagatttttggcgtgtaccaccatgcctggctaatttttgtatttttagtagagacggggtttcaccatgttggccagactggtctcgaactgctgac +>mm8 +---------TGGACAAGAC-CTGGTGCTGCAA--------CACAAGCACAGAT-GGAGGCAGAGTCCCCACC-------------------------GCTGGCTCTCCAGAGGGTCACCTGGGGCTTGTTCTCAGGGGATTACCAGTTAACTCAGCTAGCTTACAACTTCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr2(+):70744123-70744622 +TCTTTTTCTTCTTTGAGGGAGACTTGGAAGGTGAGCCCTCTGGGGACATGGGGCCGCTGGTGACCGACTCGGTTTTGTCCTTAGAGGTATCAACATCCGTGTCAGCACTGGTGGTCATCTGGCTCAGGCCTTTGCTGAGGATTTCCTCTGCCGTCTGCTCCTCCTCCCTCCCGTTGACCACCACCCCTTCCGGCTGGGTTGTTTCGGGCTCTGTGGTGGCGGCTTTGCTTGTTTCTGTCTTCTTAGTACCTTCTAGAAAAAGATCAAAAGATATGACCTGTAAGATTTCATTCAGGTGACAGCTTCCACCTGGGGCTAACAGAACCATTTCTAGGGAATTCTATAAAATCAATCCAGAGCGAGGGGAGGGCCAGCCTGATGTTGAGGGATGGCTACCAGAGACAGATGGAAGGACTGGGTTCTGATCTGCACCTTCCATGTGGCCTGTCCTGGGAACACCCCCTTGCAGGCTGGCAGCTCTGGGCTCTTGTCTATGAAT +>mm8 +TCTTTTTCTTTTTGGAGGGTGACTTAGAGGGCGAGCCCTCTGGGGACAAGGGGCCACTGGTAACTGACTCGGTTTTGTCCTTGTAGCTGTCGCCATCAGTGTCAGCGTTGGTGGTCATCTGGCCCAGTCCTTTGCTGAGGGCCTCTTCTACGCTCGGCTCCTCCTCCTTCCCATTCACCACCAGCCCTTCTGGTTTCACTGGCTCAGGCTCTGTGTT---GGCTTCGCTGACTTCTGTCTTCTTGGTA---TCTAGGAAAAGACCAGAAGACCCAACCTGTAAGATTTCATGAAGGCG--AGTGT----------TCAACAGAACCACTTCTAGGGAGGTCTGGAG-------CCAGG--GAAGTGCAGGCTGGCATGGGGTGGGAGAAGGATCCTGGAACAGAGGAGGGGTGGCGT---------TCTCACCTCTCACTA--CCTGCCTGGGGAACACCCATTGCGCAGGTGGTAACTCTGGGTCCTTGTCTACATTT + +>hg18.chr2(+):70744138-70744637 +AGGGAGACTTGGAAGGTGAGCCCTCTGGGGACATGGGGCCGCTGGTGACCGACTCGGTTTTGTCCTTAGAGGTATCAACATCCGTGTCAGCACTGGTGGTCATCTGGCTCAGGCCTTTGCTGAGGATTTCCTCTGCCGTCTGCTCCTCCTCCCTCCCGTTGACCACCACCCCTTCCGGCTGGGTTGTTTCGGGCTCTGTGGTGGCGGCTTTGCTTGTTTCTGTCTTCTTAGTACCTTCTAGAAAAAGATCAAAAGATATGACCTGTAAGATTTCATTCAGGTGACAGCTTCCACCTGGGGCTAACAGAACCATTTCTAGGGAATTCTATAAAATCAATCCAGAGCGAGGGGAGGGCCAGCCTGATGTTGAGGGATGGCTACCAGAGACAGATGGAAGGACTGGGTTCTGATCTGCACCTTCCATGTGGCCTGTCCTGGGAACACCCCCTTGCAGGCTGGCAGCTCTGGGCTCTTGTCTATGAATTTAGATGGATATTAA +>mm8 +AGGGTGACTTAGAGGGCGAGCCCTCTGGGGACAAGGGGCCACTGGTAACTGACTCGGTTTTGTCCTTGTAGCTGTCGCCATCAGTGTCAGCGTTGGTGGTCATCTGGCCCAGTCCTTTGCTGAGGGCCTCTTCTACGCTCGGCTCCTCCTCCTTCCCATTCACCACCAGCCCTTCTGGTTTCACTGGCTCAGGCTCTGTGTT---GGCTTCGCTGACTTCTGTCTTCTTGGTA---TCTAGGAAAAGACCAGAAGACCCAACCTGTAAGATTTCATGAAGGCG--AGTGT----------TCAACAGAACCACTTCTAGGGAGGTCTGGAG-------CCAGG--GAAGTGCAGGCTGGCATGGGGTGGGAGAAGGATCCTGGAACAGAGGAGGGGTGGCGT---------TCTCACCTCTCACTA--CCTGCCTGGGGAACACCCATTGCGCAGGTGGTAACTCTGGGTCCTTGTCTACATTTTGAAATATATGTTGG + +>hg18.chr2(+):70742773-70743272 +AAGAGAATGGATTGTCTAATTTTTAGGAGCCAACAAATGCTCATTAATCAATGCCCCACGGAAGAACATGAGAAGACAGTGTTGGCATTTAAAACAATAACTGTGGCCATTACCAGGCCCCAGGATGGACAGATAGGGACAAGGACAGGGATACCCAGCATTTCTCTGAGAGCTGGTGCAAGAGGATTAATCCTGAAGGGCTCATTTCTGATTCTCCTCTGCTGGACAAAGAATGACTGAGTTGGAACCTCAGAGGGTGCAAGTCAAGGTGCCAAGAGTAAGATGCCAGTTTCGGTCTGTAAGCAAGTGTTTCTGGGGGTGAGGGAAGGTCAGGGGAAACCTGACCACTGGACAGGAGTGAGGCAGGTACAGTGCATTGCTCCAGGTGTCATGCAAAGCTAGAAAGTCAGCATTTCCTCTGTTGTTTTGATCCTCCTTATACAACCCAAAGCCAACAGAGGATTTCAACTTCCCCAAATTTCTGCCCTGAGCATTAAAC +>mm8 +AGGAAGATGGATTGTC-------TTGGAGCCAGA-AGTGTTCACTAACCAATCCTCCTTAGGAGGATATGGGAAACCAGTGTTGGCGTTTAAAATAACAGCTCTGCCTATTGCCAAGCTTCAGGATGCA-AGAGAGTGATGGGCTTGGGAATGCCAGCCGTGTCTTTAAGAGTTGGTGAGAGAGAATTAACCCCAAAGGACTCATTTCTGACCATCCTCTCCTGTACCC--TCTGACTGAGTTGGGACC-CAAAAAGCCAAGGTCAAGATGCCAAGAGCAAGAT----TTTCTGGTCTGTGGGCAAGAGCCCTTGGGGATGTGGGAAGGCCAAGGGACACCTGGCTGCCAGGCAAGAGTGAGGCAGATACA-------GCCCTGCATAGCATGCAAAGCCAAAGGGGTA----------------TCTGA-CCTCCTCACACAACTCAATGCCAGCAACAGATTTGGATGTCCCAGAATTTCTTCCCTGAGCATGAGAC + +>hg18.chr2(+):70744065-70744564 +CAGGACTCCACTTTCTCCTTCTTTTTGCTCTTTTTCAGGAAGGAGGGGGTTCGGAATTTCTTTTTCTTCTTTGAGGGAGACTTGGAAGGTGAGCCCTCTGGGGACATGGGGCCGCTGGTGACCGACTCGGTTTTGTCCTTAGAGGTATCAACATCCGTGTCAGCACTGGTGGTCATCTGGCTCAGGCCTTTGCTGAGGATTTCCTCTGCCGTCTGCTCCTCCTCCCTCCCGTTGACCACCACCCCTTCCGGCTGGGTTGTTTCGGGCTCTGTGGTGGCGGCTTTGCTTGTTTCTGTCTTCTTAGTACCTTCTAGAAAAAGATCAAAAGATATGACCTGTAAGATTTCATTCAGGTGACAGCTTCCACCTGGGGCTAACAGAACCATTTCTAGGGAATTCTATAAAATCAATCCAGAGCGAGGGGAGGGCCAGCCTGATGTTGAGGGATGGCTACCAGAGACAGATGGAAGGACTGGGTTCTGATCTGCACCTTCCATGT +>mm8 +CAGGATTCCACCTTCTCCTTCTTCTTGCTTTTCTTCAGGAACGAGGGGGTTCGGAATTTCTTTTTCTTTTTGGAGGGTGACTTAGAGGGCGAGCCCTCTGGGGACAAGGGGCCACTGGTAACTGACTCGGTTTTGTCCTTGTAGCTGTCGCCATCAGTGTCAGCGTTGGTGGTCATCTGGCCCAGTCCTTTGCTGAGGGCCTCTTCTACGCTCGGCTCCTCCTCCTTCCCATTCACCACCAGCCCTTCTGGTTTCACTGGCTCAGGCTCTGTGTT---GGCTTCGCTGACTTCTGTCTTCTTGGTA---TCTAGGAAAAGACCAGAAGACCCAACCTGTAAGATTTCATGAAGGCG--AGTGT----------TCAACAGAACCACTTCTAGGGAGGTCTGGAG-------CCAGG--GAAGTGCAGGCTGGCATGGGGTGGGAGAAGGATCCTGGAACAGAGGAGGGGTGGCGT---------TCTCACCTCTCACTA + +>hg18.chr3(+):172801314-172801813 +ATTTCATTAGCTCTCTCCTTCACCTTGtttattaattctacaagcatttattgccatctcctatgtgccaagcactggtccaggctctggggatacactatgaacaaaatacagtgaagtccctgccccatggagcttacattctagtagggggagacagacaaacacataaatacaaaatatcagagggtTCAAAACAGCTTAGAGGTATCTTGCCTGAATTCTGTTTACTGCATATCCTCATTCTTGGGCAATGATAAAGTGAAGAGAGAGGCCAACAATGGGCTGCAGCAATGTTGctagtcccagctctaccatctacacattgagtggatttaagtgagttctcatctgatctgagcctcagtttcctcatctataaaatggggagaaattggattaaattacttataagggaaagggtcctttcaggctttTTTCATGAGAGTAGGGTGCTGAAAATCAAGAGCCAGTTTGTTGACTCCTCTAAGGtttaaaa +>mm8 +AGCTCATCAGCTCCCTCTCCTGTATAATATTttcactccacaaacatttacccacatgtcctttgtactaggcactgtttcagagtctgaagacaaac-----taaacaacctatgaagtctctgccgtgtccaggtaccattctagtagtgg-----agacaaagaaacaCAG-------ATTACAGGATTCGAAAGAGC--AGAAGACGCCCT------GTCTGAAACCTCCATGTCCTTCGTCTGGGGTAATAATGAAGTGAGGAGAGA---CTAACACTGGGTGCAGGAGT-CTGTT---------------GTACATCTGATGGGCAGGTCTACATCATTACTCCTCCAATGTAACCCTCT---------GCTGTACCATGGGGAGGG-TTAAAGTAAATGATTTATTATAGGTC----TGTGCCAGACCTTTCTAATGAGAACATTTTGTACAAAATCAAGAACCATTTTTTTTACTGCTTTAAGGtt----- + +>hg18.chr3(+):172812085-172812584 +CAGGGATCTTCGACACCTGGAGTCATTTTAGACCTGAAAACAGAAGTTTCCACATTTAAATTTTACACCAGCAGTCACTGGCATACCCCTTCAATAATTTTTATTATATCCTTGTATTACTGGAATTAATTTGATTTTAAAAACTTAAATGGAAGCTGGAGGGTTTGACCTGGTCTAGTCCTAATTCAGTTAAGGACTAGTATTTAATtggctcacgtctgtaatcccagtgctttgagaggccaaggcaggaggatcacttaaagccaggagtttgagaccagcctgggcagcacagcgagacacggtatctacaaaaaatttttaaaaattagctgggtgtggtgacacgggcctgtagtcccagctactcggaatgctgagccaggaggattgcttgagcctaggaattcaaggatgcaatgagctgtaactgcaccactgcaGTTTTTTCTACTGCACGTGACAGTAATAAAAAGCTATTAAAATAAAAAATAtt +>mm8 +CAGAGA--------------AGTCCTTTTAAACCATGGAAGTGTGATACTCACACTTAAATCTGAGACCAGCAACTACGGGA--GTTCTTTGGGTCATATCCCTGTAAT-------AAAGTGAAATTAC-----TTTTAAAATCTTACACAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATGAT---AGACTATTAAAATACtatgtatg + +>hg18.chr4(+):74565827-74566326 +ttttttatatgttgactgacaggttgttttcatattttggctattgtgaataatgaggtaataaacaccgaagtgcaggtatatcttcTTAATTTTTTAtttttaatttttgtgagtacatagtaggcgtacatatttatatatctttgagatactgatttcacttcctttggatatatatgcataagagagattgcttgattatatCTGTTCTGGCCCTTTGTTCCTTTAACATTTGCAGTATTTTAAGTTTTTTTTTGGTTGTCTATTTGATTAAGTATTGTGCATACTTAGCCTGTGGACTTTTGTTCCAACTCAGTAGATTTTTTCCAGCGAAACACAAAGGTAATTTTTTTTTCTGGTTAATATTTAGCAAGAATTCTGCAGAGTGATCAAAAAAATCAAATACTCAGTATTTCAGAAATAGATTAAATAGGTTACTTTTTTACTGATAATGTGAAAGAATGATATAAAAACTTGATTTTCCTCAACAACATTA +>mm8 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGTCTTTTC-TTCTTTAACATTTGGAGTATGTTA--------------CAACTTTTGGAAGGAGGATTATTCTTAC----CCTGTGGGCTTTTATTCCAATTCAGCAGATTTTTTTCAGTGAAACACAGCATAAT--TTTTCCCCTAGTTAATAATTACCTAGAATT-TGCACCAGGACCAAAAAA---AAAGCCTATGTATTTCAGAAATAGATTAACTAAGTTACTTTTTAACAAGTTAGGTCAAAGAATACTATAAAAAGTTGTTTTTCCCCAGTCACATTG + +>hg18.chr19(+):10684644-10685143 +CTGCACGCACTGCTGCACAGTGACAACACGGCCGCGCTGCACCACCTCACGGTCCACAACATCGCCTACCAGGTGAGCCAGTGCCCGGGGCAAGGTGGGCGGGGGTGTCCTAGGTGCGTATGCCCCACGCTGACCTCCCCTCCCCGCAGCTGCAGCTCATGAGCGCCGTCCGCACCAGCATCGTGGAGAAGCGCTTCCCGGACTTCGTGCGGGACTTCATGGGCGCCATGTACGGGGATCCCACCCTCTGTCCCACCTGGGCCACTGACGCTCTGGCCTCTGTGGGAATCACACTGGGCTGACCTGGCATTGGGAgagggagggaggaaggaagggagggagggGCTGGAAGATACTGAAGGATTCCTTTTTGAAAGGTTTTTTTTATTGTAACTTACAGAGTGTGTCTGTGTCTTCTTGAGGAAGTGGCCTGTCTGGGTCCCCCTCCCAGTCTGAGCGTCATTGCAGTGGAATATCTCCCCTTCTCACCAATCATAAC +>mm8 +CTGCATGCCCTGCTACACAGTGACAACACTACAGCACTACACCACCTAACCGTGCACAACATTGCCTATCAGGTGACCTGGAGGGCAGGGCGGGTGGGGCGGGGACACTCTTGGTGCTGGTGGCTCACACTGATGCTTCTGCCCTGCAGCTGCAGCTCCTGAGTGCCGTGCGCAGCAGTATCTTGGAACAGCGCTTTCCTGACTTTGTACGAAACTTCATGCGCACTATGTATGGTGACCACAGCCTCTGTCCTGCCTGGGCCGTTGAAGCACTGGCCTCTGTGGGAATCATGCTCACATGACCTGGTTGCT-GGGAAGGACACTGGGGTATGGGGA---------------ATTCTGAAGGATTCTTTTTTAAAAAGATTTTGTTACTATTGTTTTCATCTTGTGTCTGTC--TTCTT-------------------------------------------------------------------------------- + +>hg18.chr19(+):10689340-10689839 +GCAACGAAGTGATATTTATATGAACCAATGGGAAATTCTTAGGGAACGAGGTAGTAGCTCAATCCCCAACACCATTGGTCCACATTGTCTACTGGCACGTCTGCCTGCCAATAAGATGGTGGAACTTCGCCAATGGGCAGAGCCAACGTGCCTTTTTCGGAAACACCCCCTTCCTCTCTTGACAACTTGCTTTCTGCCGCTATTGGCTGTTGCACAACAGTGACGGTTCTTTTGTCCAATAAGTCAGCAAGACGGTCCCCAGGGGGAAGGTTTACTCAACCATAGGCCCGTGCCTAGTTTTTATTGGCTAGTGTATCCGAGTGGCGGTGCAGCAGGCCAGTCGCGTGCGGCGCGAGTGCTTTGGGCGCAGCCCCCGGGGCCGGGGCGGGAGGTCGCTCGGGTCGGGTGTCGCCTGAGAACCGGATGAGGCGGCGACCGTGAGGCCGAGCCGGGAGCGGGCGTCTTGCCGAGGCCCGGGCGGGCGGGGAGCAACGGCTAC +>mm8 +GTAGAGAAGTGATATTTATATCAGCCAATGAGAAATTTTTACGGAATTAACTAGTGTCTGGATCCCTTACACCCTTGG--CAGGTT-------GACGTTTC-TGCGACCAATAAGCCAACCCGAATCACCTAGTGAGCGAGGCCTCAGTGTCTTTTCCAGAGACCCCGCCTTCCCGGTCTGACAACCCG-GTTTGACTTCTATTGGCTTTCACTTAAGAGTGACAGTTTTATTACCCAGTGAATTTGTGAGAT--------------TAGCCCTTC----------CTCGTGCCTT--TTTTATTGGCTCACGTTCTTGAGTGGCAGTGCTTTGAACCAATTGGATATAGCAGTAGGGTTGCGGACTCCGCCCCGGAGGCCGGGAGGGTTGTTCGCTCGGGTCGGGTGTCGCCTGAGAACCGGATGAGGCGGCGACTCTGAGGCCGAGCCGGGAGCGGGCGTCGCGGCGGAGACCGGGCGGGCAGGAAGCAACGGCCAC + +>hg18.chr19(+):10689256-10689755 +GTTTTTCTGATTGACAGATATGGTTCTCAATGATAGTCAAGATTCGGATGTTAAAGCCCGCCCTCTTTTGCCTGGTTGGCTGGAGCAACGAAGTGATATTTATATGAACCAATGGGAAATTCTTAGGGAACGAGGTAGTAGCTCAATCCCCAACACCATTGGTCCACATTGTCTACTGGCACGTCTGCCTGCCAATAAGATGGTGGAACTTCGCCAATGGGCAGAGCCAACGTGCCTTTTTCGGAAACACCCCCTTCCTCTCTTGACAACTTGCTTTCTGCCGCTATTGGCTGTTGCACAACAGTGACGGTTCTTTTGTCCAATAAGTCAGCAAGACGGTCCCCAGGGGGAAGGTTTACTCAACCATAGGCCCGTGCCTAGTTTTTATTGGCTAGTGTATCCGAGTGGCGGTGCAGCAGGCCAGTCGCGTGCGGCGCGAGTGCTTTGGGCGCAGCCCCCGGGGCCGGGGCGGGAGGTCGCTCGGGTCGGGTGTCGCCTG +>mm8 +-----------------------------------------------------------GCTCTCTTTCCTCTTACTGGTTGGAGTAGAGAAGTGATATTTATATCAGCCAATGAGAAATTTTTACGGAATTAACTAGTGTCTGGATCCCTTACACCCTTGG--CAGGTT-------GACGTTTC-TGCGACCAATAAGCCAACCCGAATCACCTAGTGAGCGAGGCCTCAGTGTCTTTTCCAGAGACCCCGCCTTCCCGGTCTGACAACCCG-GTTTGACTTCTATTGGCTTTCACTTAAGAGTGACAGTTTTATTACCCAGTGAATTTGTGAGAT--------------TAGCCCTTC----------CTCGTGCCTT--TTTTATTGGCTCACGTTCTTGAGTGGCAGTGCTTTGAACCAATTGGATATAGCAGTAGGGTTGCGGACTCCGCCCCGGAGGCCGGGAGGGTTGTTCGCTCGGGTCGGGTGTCGCCTG + +>hg18.chr13(+):93889844-93890343 +AATGCTTTCAGAAAAGGAGGAGGCTTAATCAATATTGGGGGGGGGGTTATTATTAGATATCACAAATTGTCAGGTCTATCTTTATTTGAAGGTAGAGGTAGCCTCAAGCACTTTAGTTGGGTTTGTTAAACAAGCAAGCAAAGCGGAAACTACAGCTAAGCATCTTCTGAATGAGATCATCATCACTATAGAAGAACCTATGTCAAAGATCTTCAACTCAAGAAGGAACAGTGAGGATTAGTTCCTTTATTGTCAGCGTCAGAACTGTGGCTTGGCCAGCCTCTTCTCTTAGGTAAGGCATGAGCA--CTAGGCTTCTTCTGTGTATCTCTTGCTGCTTAAATGTGTCTCCATTAGGGGTGTATATCCTTTTCGAAGTCTTCTATATTGAAGAAAAGCCAACAGCACAAAAAGACCAACCAAAGCCACCAGTGTTCCCATGACTACTAAGAGAGTTGTGGGCCAACCTGGAGTTTCTTCAACTGAAACTAAAGCAGAAG +>mm8 +--TGCTTATAGAATAGAAAGAGGCTTATTCAATAT-----AAGGACTTTTAATCAAAGGTCACATATAACTAGCCACACCTTACTTTGACCGTGGTGAATGACCCAAGCATTTTGTCTGTGT-------ACAA-TAAGCAAAGCAGCAACTAGAGATAATTGTCTGCTAAGGCATATCATCATCACTACTAAAGAGCACACGCTGAAGAGTTCCACCTCAAGAAGCGACGGTG-TAATTAGTTACT-----------------ACCCAGGTCAGGCC------------------AGGTAGGAGCA--CTAGGCTTCCTCCGTGTATCTCTTGCTGCTGAGACCTGTCTCCATTAAGGGCGCATAGCCTTTGCGAAGCCTTCTGTATTGAAGAAAAGCCAGCAACCCCAAGAGCAAGACGAAAGCTCCCAGGATTCCAATGACCACTGAGAGAGTTGTGGACCAAACTGGAGCTTCTTCCTCTGCAATGAGAGCAGACA + +>hg18.chr2(+):151974175-151974674 +tttgtatttttgttttttttaagtagagacggggtttcaccatgtgttggccaggctggtctcgaactcctgacctcagactcggcctcccaaagtgcttggattacaaggtgtgagtcaccgcgcccggccAGCTCTTAGTCTTAAACCCAACAGTACGTTATCTCCTTTTGCTAACTGATTTGTTGCTAAAACTTCAACAAGCACTGGACTTGGAGTTTGAACACTTAGTCTGAGGGCCCACTATGTTCAGTCTAGTGAGTCTGAGCAATTAACTCACATTTTGAATTTCAAGTCTCTCGCCTTAGGCAAAACACCACCACCTGATGCTCACCAGAGGGGCGTGACGCGGCAGCTgggcagggaagggatgggaagggatgggaagggaGGCGATCGATAACTCCGGTGTGCCGCTGACTGTTGGATTGGCTCGAACTTCTCCCGCCAGGCCTAACCTACTCCCGCGCACTCCTGGGCCCGCCCAGCCGCCATCTTG +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------CAAGCCCAACAGCCTGCCATTCACTCTCAATAAATGGTTTTGTG-GGCTCCTTTGGGAAGCACTGGAGT-----TTTGCAAACTTGGTCGGCTGAGCAAGTAGCTGGAGTCAGGTGGAGTGGGGC-ACTAATTTACATCACCCATCTCTAGCCCCGGGCTGGAGGCGATACACACCCCCC--GAGGTGCTCcgggggcgggg--gcgggggcgggggcgggCAGCA---------------------GGCCATCGAGCAGCCCGGCGCGCCACCGCCCGTTGGATTGGCTCGAGCCTCTCCCGCCAGGCCTgcccggctcccgcgcgccgctgggcccgccccgccgccATCTTG + +>hg18.chr2(+):151974202-151974701 +gacggggtttcaccatgtgttggccaggctggtctcgaactcctgacctcagactcggcctcccaaagtgcttggattacaaggtgtgagtcaccgcgcccggccAGCTCTTAGTCTTAAACCCAACAGTACGTTATCTCCTTTTGCTAACTGATTTGTTGCTAAAACTTCAACAAGCACTGGACTTGGAGTTTGAACACTTAGTCTGAGGGCCCACTATGTTCAGTCTAGTGAGTCTGAGCAATTAACTCACATTTTGAATTTCAAGTCTCTCGCCTTAGGCAAAACACCACCACCTGATGCTCACCAGAGGGGCGTGACGCGGCAGCTgggcagggaagggatgggaagggatgggaagggaGGCGATCGATAACTCCGGTGTGCCGCTGACTGTTGGATTGGCTCGAACTTCTCCCGCCAGGCCTAACCTACTCCCGCGCACTCCTGGGCCCGCCCAGCCGCCATCTTGGTCTAGGAGGGAGCGCGCCGCACGCGT +>mm8 +---------------------------------------------------------------------------------------------------------------------CAAGCCCAACAGCCTGCCATTCACTCTCAATAAATGGTTTTGTG-GGCTCCTTTGGGAAGCACTGGAGT-----TTTGCAAACTTGGTCGGCTGAGCAAGTAGCTGGAGTCAGGTGGAGTGGGGC-ACTAATTTACATCACCCATCTCTAGCCCCGGGCTGGAGGCGATACACACCCCCC--GAGGTGCTCcgggggcgggg--gcgggggcgggggcgggCAGCA---------------------GGCCATCGAGCAGCCCGGCGCGCCACCGCCCGTTGGATTGGCTCGAGCCTCTCCCGCCAGGCCTgcccggctcccgcgcgccgctgggcccgccccgccgccATCTTGGTCGTGGAG-GAGCGGGCTGCACGCGT + +>hg18.chr5(+):113796627-113797126 +agtcccatcgaccacccaagggctgagtagtgcgggcgcacagcacgggactggcaggcagctccacctgcagcccctgtgcaggatccactgggtgaagccagctgggctcctgagtctggtggggccttggagaacctttatgtctagcccagggattgtaaatacaccaattggcattctgtatctagctcaaggtttgtaaatacaccaatcagcaccctgtgtctagctcagggtttgtgaatgcaccaatcgacactgtatctagctactctggtggggccttggagaacctttgtgtggacactctgtatctgtctaatctggtggggacgtggagaacctttgtgtctagctcagggattgtaaacacaccaatcagtgccctgtcaaaacagaccactcggctctaccaatcagcaggatgtgggtggggccagataagagaataaaagcaggctactggagccagcagtggcaacccgctcgggtcctc +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr5(+):113725416-113725915 +AGGCGGAATCCCTGCCCTGGAGCGCCCTGGCTCTGGACTGCACCCCCCTAGGGTTTGTCCTGCAGATTCCCCTCCCCATCTTTCTCTGCCACACACGCTTCCCTAAGCCGCGCGCGCCGCAAACTCAGTCTCGGTCCCCGCAGGTGATGTCATGCCCATTGTTTTGGTGCGCCCAACCAATCGGACTCGCCGCCTGGATTCTACCGGAGCCGGCATGGGCCCTTCCTCGCACCAGCAGCAGGAGTCCCCGCTCCCGACCATAACGCATTGCGCAGGGTGCACCACCGCTTGGTCTCCCTGCAGCTTTAACAGCCCTGACATGGAAACCCCATTGCAGTTCCAGCGCGGCTTCTTCCCAGAGCAGCCGCCGCCGCCGCCGCGCTCCTCACACCTGCATTGCCAGCAGCAGCAACAGAGCCAGGACAAGCCGTGCCCGCCCTTCGCGCCCCTCCCGCACCCTCACCACCACCCGCACCTCGCGCACCAGCAGCCGGCCAGC +>mm8 +AGATGGAATTCCTGCCTTGGAGTGCCCTGACCCCGGCCTAAGCCCCCAGGGGTTTCATTCTGCAGGTTCCCCTCCCAACCTCTCTC--ACACACATGCTCCCCTAAGCCGCGCGCGCCGCAAACTCAGTCTTGGTCCCTGCAGGTGATGTCATGCCCATTGTTTTGGTGCGCCCAACCAATCGGACTCGCCGCCTGGATTCTACCGGAGCCGGCATGGGCCCTTCCTCGCACCAGCAGCAGGAGTCCCCGCTCCCGACCATAACGCATTGCGCAGGGTGCACCACCGCCTGGTCTCCCTGCAGCTTTAACAGCTCTGACATGGAAACCCCATTGCAGTTCCAGCGCGGCTTCTTCCCAGAGCAGCCGCCGCCACCGCCGCGCTCCTCACACCTGCATTGCCAGCAGCAGCAACAGAGCCAGGACAAGCCGTGCGCGCCCTTCGCGCCCCTCCCGCACCCTCACCACCACCCGCACCTCGCGCACCAGCAGCCGGGCAGC + +>hg18.chr5(+):113725066-113725565 +AAACTTTTTCTCCCCAAAGCCAGTGCCCCCGCAGTTACTTGGCGGGCAGCCGGCAGCCCACTCTCGGCGGGATGATCTGGGAGAAGCGGGCGTGGGACGAGGGGGCTGCTGTTTTGCAGCCCTGCGAGGCGTGCAGTCGGAGAAGTGGTCGGGGTTCCACACCGTCCCTGAGCCTGCCCCCGGCCAAGGTGGCCCGACGTGCTGCAGTGGCTGGCGCAGGTGATCCGGGCAGCGCGTCCGGCACTAGTCAAGGGGGCAGCGGCACGGGAGGGAGGGGCGCCTTTCTCTTTTCTCCTCCCCCTGCAGCCCAGCTGCACTGCGTGGGGGCTCTCCATCTCCACGCAATCAGCAGGCGGAATCCCTGCCCTGGAGCGCCCTGGCTCTGGACTGCACCCCCCTAGGGTTTGTCCTGCAGATTCCCCTCCCCATCTTTCTCTGCCACACACGCTTCCCTAAGCCGCGCGCGCCGCAAACTCAGTCTCGGTCCCCGCAGGTGATG +>mm8 +AAACTTCTTCTCCCCAAAGCCGGTGCCCCCGCAGTTACTTGGCTAGCAGCCTGCAGCCCACTCTCGGCAGGACGATGCGGGAGAGAGA---GTGGGGCGAGCAGG-TGCTGCCTTGCAGCCCTACAAGGCTAGAGGGCGGGAGAGTAGCTCGGGTTTCTCCCTGCCTTGGCGCCTGCCCCAGACCAGGGTGGCCAGACATGCTGCAGTGTCCCAGGCAGGTCATTCGGGCAGCATGTTCCGCACCAGTCA-GGGGGCCGCGGCAGTAGAGCAAGAGCAATCGCTCTC---TCTCCCACCTCTGCAGCCCGCCTGCATGGGGTGGGGGCTCAGTCTTCCCACGCGATCCGCAGATGGAATTCCTGCCTTGGAGTGCCCTGACCCCGGCCTAAGCCCCCAGGGGTTTCATTCTGCAGGTTCCCCTCCCAACCTCTCTC--ACACACATGCTCCCCTAAGCCGCGCGCGCCGCAAACTCAGTCTTGGTCCCTGCAGGTGATG + +>hg18.chr2(+):165249579-165250078 +GTTTTAGTGAAAACAAATTTAATATCATCTTGTTTGAACAAAGCTTTCAGAATAAGTGAGCAATTAAATTCTTAAAGTAGGGACAGAACACCAACAGGCTCTAGACTCCGGAAGAGCTGTAAGCCGACAAATGGGCATTGTTTTGCTTAACAGTTTTAGCTTCAATGTAAATATATATTATTACTTAGAATATTAGCATCTGAACTATATAATGACTATTTTATCATTTTACTTGAATTAAAACCAGAATTTCTGGAACTTCCAAATAGTCTTTAAAGTTTTTCAATATAAACATAAACTAACCCCTATTCCTCTCTACATATCAAATGTGAAATAACTGTCACAATATATCAGCATTTTCACAGAAAGATGTTTAAGGCTTCTGGCACATAAAATGTGTAATTTCTGTGTGACAATGTCATAATTATATACAGAAAATATTTAAAATTCTTGTAGAATTTAAGTTCTAAAGATTAAAAAAACAAGAGTTCCATGTTAA +>mm8 +GCTTTA--GGAAA-AAGTTCAGTGTCAGG-TGTCTGAGC--AGTCTTTTGAATAAAAGAGGAATAAAATTAT-TAAGGAAGTCCAGGACACTAACACGTTCTAAACTTCTGGGCCACTGGAAGCCGACAATCAAGTACTGTTTCTCTCAACGATTTTGGCTTTCAGGAAAATATATATTATTATTTAGATGGCTAGCATCTGAGATACATAATGACTAACTTAGCATTTTCTTTAAAAAAAAATCAGGATTTTGCAAATGTCTGA------CTTCAAAGTTTTGAATGTGGACATAAACTAACC-CTATTCCTCCTTATAG--CAAAAGTGAAATAACTGCCACAATGTATCAACATTTTCACAGGGATA-TTTTAAGGCCTCTGGCATAGAAAATATGCAATATCTGTGTAACAACATCATAATTATATACAGAAAATATCTTAAATTCTTGTGCAATTTTACTTCTAAAGGTTAAA---------GTGTTCTATTTA + +>hg18.chr2(+):165249502-165250001 +TTTAAAAAGCACCCCAAATATACAACTTGCTTTTATTAAATTGAAAAAAAAATCCCCAAGAGGCAGATATCCCAGTAGTTTTAGTGAAAACAAATTTAATATCATCTTGTTTGAACAAAGCTTTCAGAATAAGTGAGCAATTAAATTCTTAAAGTAGGGACAGAACACCAACAGGCTCTAGACTCCGGAAGAGCTGTAAGCCGACAAATGGGCATTGTTTTGCTTAACAGTTTTAGCTTCAATGTAAATATATATTATTACTTAGAATATTAGCATCTGAACTATATAATGACTATTTTATCATTTTACTTGAATTAAAACCAGAATTTCTGGAACTTCCAAATAGTCTTTAAAGTTTTTCAATATAAACATAAACTAACCCCTATTCCTCTCTACATATCAAATGTGAAATAACTGTCACAATATATCAGCATTTTCACAGAAAGATGTTTAAGGCTTCTGGCACATAAAATGTGTAATTTCTGTGTGACAATGTCAT +>mm8 +GAAACAACAGACTGTAAATATATAACTTGCTTTTATTAAACGGAAAAAGGTTTGTCAGGATGACAGATACTCCAGTAGCTTTA--GGAAA-AAGTTCAGTGTCAGG-TGTCTGAGC--AGTCTTTTGAATAAAAGAGGAATAAAATTAT-TAAGGAAGTCCAGGACACTAACACGTTCTAAACTTCTGGGCCACTGGAAGCCGACAATCAAGTACTGTTTCTCTCAACGATTTTGGCTTTCAGGAAAATATATATTATTATTTAGATGGCTAGCATCTGAGATACATAATGACTAACTTAGCATTTTCTTTAAAAAAAAATCAGGATTTTGCAAATGTCTGA------CTTCAAAGTTTTGAATGTGGACATAAACTAACC-CTATTCCTCCTTATAG--CAAAAGTGAAATAACTGCCACAATGTATCAACATTTTCACAGGGATA-TTTTAAGGCCTCTGGCATAGAAAATATGCAATATCTGTGTAACAACATCAT + +>hg18.chr4(+):187745932-187746431 +AAGCTCAAGTATTTTATTAATAATTTATTGTCAGTAAGAAAGACTGGCTAATGGTAGTTTTCATTAAAAACCTTTACAAGACCATTGCATCACAAATATACAGACACTATAAAAACTGTGTCATGGTGGTTTTGGTTCTAAACAGGTATGCAGAAGGTCCCCGTTACACTTTCCAATAATGAAAAATGTTTATAATTCTAAATACAGCAACCCATGTAAGACATGTTCATGTATCTGATCTCTCCTTCATCCTATGTACAGCTAGAAATGAATGACTACACTGAAATGTACTAACAAAATGTCACACTTCAGTGGAAAAAGACAGAATGAAACCCTGGTTATAGTAAAAAAAAAAAAATCAGGGTGCTAGATAATGGCACTGACACCACCAAAATTCAGTTGAAACAAATGCACAAAATATCTTGGAAATCTAGTTAAAACTATGAAAAATCAAATCTGTACATAAAATTTACAAAAAAAAGAGACAGGAAAATTAAAA +>mm8 +AAGCTAAAGTATTTTATTAATAATTTATTGTCAGTAAGAAAGGCTGGCTAATGATAGTTTTCAGTAAAAACCTTTACAAGACCATTGCATCACAAATATACAGACACTATAAAAACCGTGTCGTGGTGGTTTTGGTTCTAAACAGGTATGCAGAAGGTCCCCTTCACACTTTCCAATAATGAAAAATGTTTATAATCCT-AATACAGCAACCCATTTAAGACATGTCCA-GTAACAGGTC--GTCCACACCCTATGTACAGCTA---------CACTGGACCGAAATGTGTCAATGAAATGTCATACTTCAGAGGAAAAGAACAGCGTGAAACCCTGGTTACATCAGAAAA-------TCA-GATGCTAGGCAACGACGCTAACACCACACAGATCCAGCAGAAACAAAAACACGAGGCGTCCTGAAAACCTAGGTAAAACTAGGAaaaatcaaaTCTGTACATAAAATTTACACAAAGAAGC-----AAAAATTAAAA + +>hg18.chr2(+):27572711-27573210 +TTTTTCCCGCTGTAATATCCAGTACAGTGTGTGCACACTTGGGGCTCAGAAGCTTCTACTGCCTTCCTTTCTGAGAGGAGAGGATAAAATGGGACCAGTGGGACTGACTGTGTGTGCTGAGCATGTGATCAAGCCATGGGCCAGGTCCTCTGACTTGTGCTGACTTGGTGACCCTGATCTCTGGCCTCGGAGGACACTTGCCCAGGGATTCTCACTGCCGTGGGTGTTGTCCTGCACTCCCAGGCTCCAGGTCCTCTGTAGAAGAGGGCATTGTCCCGGTAGGGCAAGAGTCCCGAGCCTCAGGTCTTCCTCTTCAGGGGCCAAAGCAGAGGCTGGCGAGTCAGGGTGCTTGCAAAGAGGAAGCCCAGGAGTTTCCCTGGGGTTACCAGAGGGCTGGGGGCCTAGTGACCAGGAAAGGGTGGTGCTCTGAGAGCCCAGGGTGCTTGGGTTAATCATCACTGGGGCTCAGATAAGGCCCTGCCAACTGGAAGCAGAGTCA +>mm8 +-CATCTCCTCTGTGATATCCAGTTCAGTGTTCGCACACCTGGGGTCCAGAAGCGTCTATTGCTTTTCTTTCAGAGAGGAGCAGATAAAATGAG-CCAGTGGGGC------TGCATGCTGA-CATGTGATCAAGCCATGACCTGAGTCCTCTGACTTCTACT--------GACCCTGATCTCTGGCCTTTGGAGGCATTTGTTCAGGGATTCTTTCTGACCTGGG---TGTTCTGCAAGGGCAAAA----------GCAAAGAACGT----CTGGTCCTCTTCTCCAAGGGCAG------------------------------------AGGCTGGCAAGCCAGAGTATACGCAAAGAGGACCCTCAGGAGCTCCTGTGGGCTGGCCGGCGACAGGAACGGGTGTTGA--AGAGAGGGGTGGTGTTTTGAGAGGC-AGGGTTCTTAGGTTAATCATCTCCATGGCTCAGATAAGACCCTGCCAACTGGAAGCA-AATTA + +>hg18.chr1(+):111758461-111758960 +GGTTCTTGTGTTTACAGTTTATTTAATGGAAAAGAGATTGGCCTATTCTGGTTTTGATGCCTGCTTTGCCCCGGGATGAGAAGGCTTCCAACATGTCACTTAGAAGAAAAGACAAGGGTTTTCCCTGGTTTCTGACACCAGAGGGGCTTAGGCTTCTTCATCCACAGCAGAGTTTTCTGGGATTTCTTTTTTTAGAGAAAGAGGACTTGTTTGAGGGGTTACTGAGTTGACAGAGGAATGGTTTCCATAGATGGGAACAAAGCGGTTGTCAAAAGCTAGAGGAGTTTGTTCCGGGAGCTGGATGACGGGGCTGGAGGACAGCATCATCCTGTTTTCAGCTTCCATCTGAAGACCCAAGTTACCCATCCTGGGGTGAGTGCCCACCTCAGAAGTCAAATTCTCCCCTCTTAAAGGCATAGTCTGCCCTTCAGGGGTGACTGATATGTTTCTGGAGGGGACAGTCACCTTTTCACGGGCCACAGCCTTCCTTCTAGGGGCC +>mm8 +GATTCTCATGCTTCCAGTTTATTCAATAGAAAGGAGATTAGCCCATGGTGACTTTGGTGCCAGCTTTGCCCCAACATGAGGTAACGTCTGTTGTATCACATAGAAGAAAGGACAAGTGTTTTCCCTCGGATTTGCCACCAATGGAGCTCATGATCTTTGATTCATAACAGAGTTTTCTAGGTTTTCTTTTTTTTAAGAGAAAGA-TTTGTTAGAAGGGCAATTGAATTGACA----AATGGTTCCTATCAGTAAGAGTGAAGCATTTTTCAAAAATGAAAGAAGTATATCATAGGAACAAGACAATAGAGCTGGAAGA----------------------------------CCAATTTCACCCATCTTGGAGTACGTTTCTACCTCAGTAATCAAACTTGCCCATTTTAGAGTTTTACTCTGTCCATTAGGGGTAGCTGACATCTCTCTAGGGGAAACAGTGGCCTTTTCAAGTACCATAGTCTTCTTCCTGGGAGTC + +>hg18.chr11(+):49124766-49125265 +TATAATATTCAACTTTATTTCAAATATACCAATTTTAAAATTTATCAATATACCCATTACGATTCTTTCTGAGTGACATACCACACAAATTCAATACGGATTCTCTAAAGAATCCTCTTAGGCTACTTCACTCAAAGTCTCTGCAGCTGCCTGCACTGTGAAGGCTGCAACATAAATCTGTCTCTTCACTTCTCCCCAGGCCTTGGAAGGGTCCACTTTGCTTTCAATATCAAACAGAGCATCATAAATTCCTGGGAATGACTCCCCTGCATACTTGTTGTGGCTGCTTGGAGCATAGATGACATGCCTGTTGATAAAATCGTTTGCTGTTTATTAGGTGCCCAAATGATATACAAGAGAAACACAAGAGCACTCTGCAATTCCTGGATTGCATATTCCTATAACAATTTGAACAAGCCACTTGTCAACTGAACTTCCAAGTTCAATCATCTCTGAAGACTATTATATGAAATCTATAGtaattaattatatttttatt +>mm8 +---attatCCACTTTTGTTTTGAatgtatgcatgtgtatatatatatatataAGCTCCATAGTTCCATAGGGAT--------------------TTTGTG-ATTCTGTAGAATGTGTTTAAGCTACTTCCCTCAGAGTCTCTGCTGCAGCTTGCACTGTAAAGGTTGCAATAGAAATCTGTCTCTTCACTTCGTTCCAGGCCTTAGAAGCATTGACTTTGCTACTTATATCAAAAAGGGCATCATAAATCCCAGGGAATGATTCTCCTGCATACTTGTTGTGGCTGCTTGGAGCATAGATGATATGCCTGTTGATGAAACATATCTTTGTCCATTAATTGCACAAGCAACATACAAGAGAATAAAGGCA-----CTATA---CACACATGTCATACTCCTGTCCTGGCTTGAATAAGTCACTTGTTACCTGAGTTT-AAAATGCAATAATATCCAGGCAC------------------ATAAATACATATAATTTTTGC + +>hg18.chr11(+):49124879-49125378 +CCTCTTAGGCTACTTCACTCAAAGTCTCTGCAGCTGCCTGCACTGTGAAGGCTGCAACATAAATCTGTCTCTTCACTTCTCCCCAGGCCTTGGAAGGGTCCACTTTGCTTTCAATATCAAACAGAGCATCATAAATTCCTGGGAATGACTCCCCTGCATACTTGTTGTGGCTGCTTGGAGCATAGATGACATGCCTGTTGATAAAATCGTTTGCTGTTTATTAGGTGCCCAAATGATATACAAGAGAAACACAAGAGCACTCTGCAATTCCTGGATTGCATATTCCTATAACAATTTGAACAAGCCACTTGTCAACTGAACTTCCAAGTTCAATCATCTCTGAAGACTATTATATGAAATCTATAGtaattaattatatttttatttcaaacaaataaattaaaGTGGTTCAGTGCTACAAAACTAACAATGATGATAGTAACCACAGCAATCATTCTTGGTATTTAATGtttacttgcaatttttctgatgtttagaa +>mm8 +GTGTTTAAGCTACTTCCCTCAGAGTCTCTGCTGCAGCTTGCACTGTAAAGGTTGCAATAGAAATCTGTCTCTTCACTTCGTTCCAGGCCTTAGAAGCATTGACTTTGCTACTTATATCAAAAAGGGCATCATAAATCCCAGGGAATGATTCTCCTGCATACTTGTTGTGGCTGCTTGGAGCATAGATGATATGCCTGTTGATGAAACATATCTTTGTCCATTAATTGCACAAGCAACATACAAGAGAATAAAGGCA-----CTATA---CACACATGTCATACTCCTGTCCTGGCTTGAATAAGTCACTTGTTACCTGAGTTT-AAAATGCAATAATATCCAGGCAC------------------ATAAATACATATAATTTTTGCTTTAATGAATAACTCAAAGTGGTTCAGATAAATAAAAATAACAGTAAGGACAGT--TGATGTTAATTGTGCTTAATACTTAAAAACAACTTATA-TTTTTATAGTTACTAAAA + +>hg18.chr7(+):26298700-26299199 +GAGAAGGCCCAGGGGAAAATCCATATAATTGACTGATTATCAGATTTGGTGACCAGGAAAGCAACAGCCTGTTTTTCAGTTCCGATGCATCATACTTTTCTCAAATTACACGGATTATTGAGGGGGATCGTCACGGAATGGGGAGCAACATGTCCTGCTGAAAGGAAGGGCTTCTATCTCTACAAGACACGTTAAAaatgatggtatcagaaaattagaacggggaggaggcttgcacatgatctccatcaaacctttcattttacagacagggaggctaaggccgagggacgctgagtgttgggaccaggatcattcagccagatgggagcagaaccaggcctacaacctggcaggcttctgacttccaccccgGAGTTATGTCCACCTCTGGGGCCTGGGAACTGGGTTTGGATTGCATAAGCTCCCCCTCCTCTCCCAGGAGGGGGCTGGGCTGGAGGCTGAGGCCTTCGCCAGGAAGAAGCAGGGACTGCTTGGA +>mm8 +GAAAAGGCCGCGGAGGAAACCCACGCTGTGAGCTGATGATCGGGTTTGCTGAGTTGGGAAGCAACAGCCTGTTTATCGGTTCTGACACATCACACTTTGCTAAAATTACAAGTATTGTTAA-GGGGATGGTCACGGGATG-------------TCTGCT-------------------TCCGCAAAGCACATGGAGAGCGATGG-ATCAGAAATTGAGAACACTGA------TCTTTCGTGATCTCCATCAACCCTTTTAGTTTGCGACAGGGGAAACCAAGGTCTGCAAGGGTGGAGC------------AGCATGCA-CCCGGTGGGAG-------------------------------------------GGGTGTGTGAAAATCCCTCTCGTCCGGGGAGTGGGCTTGT---------------------------GGGAGTGGCCGGAAGTG-GGCTGGGGGTATT------------ATGGAACTCCTTCAA + +>hg18.chr7(+):26297541-26298040 +CAGTTTAAGTGATGATTGTGGTTTCCCATGCAAACAGGTGTGGGGACCCAGCCTCAGGTGCCATTTGGGAAATGCTTTCCTCAGTCAGGTCCCTTGGCAGATCTCATTAGCTTTCCCCCCAAATGTTTTATTGAGACATTTCAAACATAGACAAAAACTGAAATAATTTTATATAAACACCATAGCCCACCACCTAGATGCTATGAACATTCTGCCATTCTTGTTTATCACGTTATTTATCCGTCCTCCTCCCCATCGGCAATCCTCCCCATAACTGTGGGGTCAGGGTTAGGAAGCTTAAGGTGACTCAGGTGGCGAATTCCGAAGGGTGCCGCTGGAGCACCTCCAGCCTCAACGTCCGGACTAATGGGGGCATTTCCTCCCTAACTCAATTTCAGGAAGCAGGAGGCTAGCTCTGCAGGGTGGGGGCGCACCTGGGCTGGGCTGCGCGGAGGCGGCGGAAGCACTAGGCGCGGCGCCCACAGGCGGACGGCTGGCG +>mm8 +-----------------------------GCACACAGGTGGTGAGAGCCAGCTCAGATGATC-TATAGGAA---------CCGGACATAT-CTTTGGCAGATCTCA-TAGCTTTCTCCTCATCTTTTTTAAAGGGAGATATTAAA--------AATATTG--------TTATACAAAAGTAAT-GCCCTCCATCGAGATCCTGCTAACATCTAGTCATGCTTGTTTGTTATTGGCTTCTCTCATCTTGATTCC------------------TCACTGCTGGGT--------------------------AGGGAGAAAGACCCGCTAGCTA-------------------------------------GGTGGCCTTTCCTACGTT-------------------AAGGCTGGCA----------------------------GTggcg-------ggtgggggtggggggc----------------ggcggcgggcg + +>hg18.chr16(+):80625865-80626364 +AATATCTTCCTCTACTTTCATATCCCTCTCCATCCAACCCTTCAGCCTGCCTCAGTTGGGATTTGTAGGAGTCCTGAAGCTATGGACCAGATCAGAGGTGCCTTCCCTTCCAGAATCTATTTTCCAAACTTCATCGATTGCCTATATTTATATGCATGCATGcacacacacgcacacacacacacacacTCTCACTCACTCCCGAGTCAGAAAAAGGACTCAGCACCCAGACATACTGCAGGCTCTTGAAGAAGACAGTATTTTCCTGTGAGCTAGAGGATCTTCCTGTTATTCTCCATGCAGTTCAAATTCTGTCAATTATTATCCAGTTAGTCATCGCTCCAGAGGTGGACTGTCATTAAAAAAAAATAGAAGGTGTGTGTTTGTGGGTGAGTATGTGCATGTGTTGTGTATGCAGGGGGTGGGGAGGGGCGAGAGCGGTCAAATAGGAAGTGCCTTGGTATTTATGTTGAAGTGCACACTGGTTTAAATTACCCAC +>mm8 +AGAGCCTTTTTTTGGCT-------------CATTGAGCCCTTAA-CCTGTCTCAG------TTGGCAGTAGTCCTCCAGATACAGGCCAGATCGGGGATGCTCTCTCTT--AGAATCCACTTTCCAAGCTTCACTGATTACCTGGAT-------------AacacacacacacacacacacacacacactcacacatacagatcacTCGGAAAAAGAACTCAAC------CAACACAGGAGGCATCCAAAGGAGA---------------------------------TTGTCTTCTT-----TTCCAAGTCTGTCAATCATTATCTGAGTAAACATCTGTC---AGGTGGGA------------------gtaggtgtgtgtgtgtatgtgtgtgtgtacgtgtgttgtgtgtgtATGTGTAAGTGTTGAG-------TGCCTTAGGGGAATGAGC-AGGTATTTATATCACAGTGCACA---GTTTAAATTACATCC + +>hg18.chr19(+):54159879-54160378 +AAGGATCCGGAGACTCCTTATCTCGCAGCGCAAACCTCAGGCAACTACAGGTCCTCCCTGCACCTTTGAGGTGCCCCTCCCCCCACTCAAGGTTCCAGAAAAATCCATGCCCTCGGAAACCCCAGAATCTTACTTTCCCGAGGCACCCCAGGACCCCAGGGTCATCAGTTCACAGGGCTGTTAGTGCTCCCATAAAACTCTAGCCTCCCAGAGGGACCCCAGCCCCCACCCTCCCGCCCACGAACCCCTGCATTTCCAGAATCAGCCCCAGGGCCCCAACCCCCCCAAGCCCCCATTTCACAACACGCTGGCGCTACAGGCGCGTGACTTCCCCTTGCTTTGGGGCGGGGGGCTGAGACTCCTATGTGCTCCGGATTGGTCAGGCACGGCCTTCGGCCCCGCCTCCTGCCACCGCAGATTGGCCGCTAGCCCTCCCCGAGCGCCCTGCCTCCGAGGGCCGGCGCACCATAAAAGAAGCCGCCCTAGCCACGTCCCCTCG +>mm8 +ATGACGTGACATATCCCTT------CATTGTGTGCATTGGACATATGGAGGTTCCCTTTGCATTACAGAATTACCCCACACTCAGCCCA--TCCCCAG----ATCCATGTTCTC--AGGCCCCAAAA-TTCTCTTTTGTGAGACACCAAAGGACCTCGAAGTCATCCCCTCCCCAGGGTCTCAGTGACCCGGAG-----------------------CCCAG----AACCCT-------GCGACCCC-------TCCAGGTTGCGCCTCCGGATCCGGACCCCCCCAAGCCTCCATTTCACAA-GGCCTCGCGCTCCAGTCCCGTGACTTCATCTCACTGGGTGGGTGGGGAGCGAGGTTCCCCTCAGCTCCGGATTGGTCAAGTATACTTTTCGTCTCCGCCTCACGCCACCGCCGATTGGTTAGTCTCGGGCCTGGGGCACCCCTCCTCCGGAGGTCAACATGCTATAAAAGGAGCGCTCCTTGCCGGGACTTAGAG + +>hg18.chr16(+):55552764-55553263 +AAAGTCTACATAGAGGACTGTTTCTGGggtacccagatgcagcgtcaaatgccatggaatactacagtgaggacattatcctttcaagctttcaaatcagagcaagggaaaggtcgatgctagagtttctctagcacccatgaagccctctccctttttctactgagttttactttacaggcaacagcaggcttcaagcttggggtcattgtcgggcaacagtatctggcaagaattcaatgtctttttctcatagtcattgtattttggcctctttctatttatggcaactgagagagaaagcttattcctagatatatgtatttaagtaaaaaataaatgaattcatggaaacatattaagcaattatccagataacataagggatggcaaaaatggtgcagatggtGGAGGGGAGACAAGTAGAAGTTGGGGTGCTCTTGTTGAATGTCTGGCTCTGAACTCTAGAGGAGGCCGCAGGGGCTGGGCAGGAAGGAGG +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr3(+):187840344-187840843 +CATTGTTTAAAAATAACTTAAATGATGATAAGTAGAACATTTTCCACCCAGATGGCCAAAGTGCTTAAGGAATCTCAACTGTGCTTCTGGCAGATGACTGTGGGGTTCAACTACCTCCCTGATCTAACAAGGGCTTTGCACACAGAGTGTCAGCCAGGAAGTCTGAATTCACCAAGCACCACTGGGACATAAGATAACTATTAGAGTGGCCAAGGAGACCTCCACAGCAAAGGTGTTAGGGGAGAGGGGGAGAATGGGACAGTCCTCCATATTCCTATTCAGGAGGGGACCTGCAAATCAGAATCTAATCATAAGAGCCTTGAACAAATGTTATGATTTCTCAGGAAACAGTTGGGAAACTTAAATTCATTTGTATGTACAGGTGGATATGAGGTTGCTCAAGGGTCTAAGGTTAGAATCATTGGGAAATGCTATCCAAAGTACTGACTTAGGAAAATCCAAGTTCAGAATTCAAGGTGAACTTGGTTAGCCCTTCCAG +>mm8 +T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCTTGATCAAACATTATAATTCCT-GGGAAAGGGTTAGGAAACTTGGATTTATTTACA--------CGAAA---GGCATGCTC-CGGATCCAAGGTTAGAA-CACTGACAAATCCAATCCAAAATATTGACTCA-AAAACTGCTTGTTTGGACCTCAGGGCAAGTCCTAGTAGGCTATTCTG + +>hg18.chr3(+):187840445-187840944 +GGGGTTCAACTACCTCCCTGATCTAACAAGGGCTTTGCACACAGAGTGTCAGCCAGGAAGTCTGAATTCACCAAGCACCACTGGGACATAAGATAACTATTAGAGTGGCCAAGGAGACCTCCACAGCAAAGGTGTTAGGGGAGAGGGGGAGAATGGGACAGTCCTCCATATTCCTATTCAGGAGGGGACCTGCAAATCAGAATCTAATCATAAGAGCCTTGAACAAATGTTATGATTTCTCAGGAAACAGTTGGGAAACTTAAATTCATTTGTATGTACAGGTGGATATGAGGTTGCTCAAGGGTCTAAGGTTAGAATCATTGGGAAATGCTATCCAAAGTACTGACTTAGGAAAATCCAAGTTCAGAATTCAAGGTGAACTTGGTTAGCCCTTCCAGTTGTAACAAAACCGCTCAAGTCTGCCTTAAAGAGCCTTACAAGCCAGCCAGTCCCTGCAGCTCCACAAACTGACCCATCCTGGGCCTTGTTCTCCACAGAA +>mm8 +-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCTTGATCAAACATTATAATTCCT-GGGAAAGGGTTAGGAAACTTGGATTTATTTACA--------CGAAA---GGCATGCTC-CGGATCCAAGGTTAGAA-CACTGACAAATCCAATCCAAAATATTGACTCA-AAAACTGCTTGTTTGGACCTCAGGGCAAGTCCTAGTAGGCTATTCTGTTGCAGTAAAGCTGCTCAAGTGAACCTTGAG--GCCCCACGGCAGGGCTCGTCCTGGCAGCTCTAT--ACTGACACATCCTGGATCTTGTTCCCCACAGAA + +>hg18.chr4(+):25358148-25358647 +GTAGTCAATTGTATAAAAATAATTTTATTTACTACTGTAAATAAAGTAGTGCAAAGAGTAGTTTGGACCCACAATATTGCATTACTGATTTATTCACTACCTTAGCAGCATGTAGTATACAGACATTCTGCTCTTCCTCTTCCTCTCTAacacacacacacacacacacacacacaTATCCCTGTACAGACTCACGCAGGCATGAGGGGTAGGGATGAAACTATAAGCTAGAGGCTTACTTGCTGCATATTCCGTTGCTGCCAGTCTATTCTAACGTGTAATTCATGGAGAAGACTACAGTTAAGTACTAAGAATCTTCTAAATGTAATTTCATGGATTGCAATTGAAATGTAAAAGATATCCGACAATGCCATTAAATGATTCGGAAGCACTAGGACCCTAGAAAAATTCAAGGAGAAAAATGTAAACCAATTTACAAAGCTATTGCCCTCCCTGCATTTCCAGGCACAAACAATTTATTTCAAGGTGCCTTATAACT +>mm8 +GTAGTCAACTGTAGAAAAATAATTTTATTTACTACTGTAAATAAAGTAGTGCAAAGA-TAGTTTGAACCCACAGTATTGCGTTACTGATTTATTTACTACTGTAGCAGCATACAGTGCACAGACACTCTGTTCTTTTTTTGTCC-TCTTACACAC----ACTCTCTCTCACACACACACACCTATACAGACACAGGCAGGCATAAGGGGTGGTGATGAACCTATGAACTAACAGCTTGTTTTCTGCGTATTCCATTGCTGCCAGTCTATTCTAAT-GGTGACTCATGAAGCAGACTACACTTAAACGGTAAAGATTTCCTAGATGTTATTGCATGTGTTATGATGGAAACATAAACGATACCCAATAATGTCATCAAATGATTTGGAAGCACTATGACCCTAGAAAAATCCAGGGGAAAAAATGTAAACCAATGTACAATGTTATCGCCTTCCCTGTGTGTGGAGT--------GTTTGTCTCAAGGCTCCTTCTAGCT + +>hg18.chr3(+):113535219-113535718 +TTCCAGGCTCGCTTTCTCCGGGAGAGCTCCTGCGTCTCCTCTTTGTTATGCAGCCCCTTTCTCCCTCCTAGCCCTTGCCTGGGGGAAGCCATGAAGGATCAGTTAAAGCTGAAGCTACACTTGAGAGAGCTGAAATGCTCTGTGATCATAATGCTTTGAAGGGTTAACCCCGGGTATCTAGAGAAACAGACATTTTGTTTATTCGGAACCAGCTTACAAGACAAAAAACGGAGAAGGTTTTCATATATCCCATTGGTATATGAAATCCAAATACAATGGTATTGGTATAAGAATCCAAATACAGTGAATGCCTCAAGATAATTTTTTCATGTATGGTTTGTTGGCAAGACCACATAGCCAATGATTTCACTGTCTTTCTTAACAAAGGAGAATGGTGGTCTGTGAGCTACGGTCTACTGCAAGCTAGATGCTGTTAATCTTCTTTGTAACTATCCTTCTAAAAATGAATTATTACCTCGTTTTACACATAAACAGGCGG +>mm8 +TCTCG--CTTGCTC-------------------------TCTTTCTCA----CCCCCTCTCTTGCTGCTGCTCCTTGCCT--AGGAAACCATGAAGCATCTAGCAGTACTGCAGC-------GAGCAAGCC--ACAGCTTAGTGGTCTT-------------GTTATGCCAAGGTATTTAGAGAGGCCGACATTTTGAGTCTTTGGTACT-GTTTACAAGGCAGAAAAAAGGAAGGGTGGTCATACGCCTTATT----------CTTTATACACACGGA-ATTGGTATGCGAATCTAAACGCAATTAAACCC--CAGGTACCCTTTTCATCAG------GCTGACAAGACC----GAC------TTGTGTTACCTTTCTTAACAAAGAGGAATGTGG-----------------ATCTGTCAGCTAGATGCTCTTAATGTTC-AAACA---------------AGGAATTGCTTTC-TGTTTTACAAAGAATCGGAGAG + +>hg18.chr3(+):113534107-113534606 +-----------------------agaagaagaagaaggagaagaaggagaaggagaaggGAAAAAAGAATCCTCATCATTAATGCAAGTGGAAGGAAACTCTTCACCAAAGAATTGATCACATCATGAAAGGTGAAATCATTACGGAATTGCTTAAATATATAATTTGAATCTGGatttaaaaataataaatgtaagttttttctttaaaaaaaaaaaaaaGTCCATTGGTTAAATTCAGCTTGAATCCTTTGCCACTACATCAAGAGCTAACAGGTCAACAACTGATCTCCACAACCTCCCACCTCATTTCCTTTCTCAGTCCAGGTAGCAGGAAAATGGAAAAAAAAAAATGATTTTTTTTTTCCAAACACTTTGTCAGTTTCCCCAGCGGTCACCTTTGAAAAGGGAAAAATGTCTGAAAATAGACAAAGCTGAATATAAACATCATTTAATTCCCCCCACACAGACAGCCTCCGCTCCTGTGAGGGCGTGGGGAA +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr15(+):40483770-40484269 +gcttcatcaatgaggtgatgtatgtgaagtgtctggcacagcatgggcactcaaACAGAGGTGCTTTTTCACACTTTAcaccttacaaggtacttttcacatgtgtcatcgcgatacttgcaaggttgctgagaggtagatggggttataatccctggtgttcaagaaaggaagcagaggctcaatggggttgaatgacttctctgagttcacagagctcagtaagtggcagggttggaactcacattcagactctctgactccagacttaggtttttccgcacctccacgctgAGGCCAGCCCCAGGCAGTGAGAAGCCCAAAGTCCGAAGCACAGAGTGCTGTGTGTTGGGCTCTGTGTGTTGAGGAGTCTTGTGACTGCCTTGGGGCTTTGGGCTGTAGTCAGCTGACAGTCCTTTGTGCTCTGTGGGGATGACGTAGGCCAATGGGAGGACAAATGCCCCTCTGAACTGTCTTCTGGGCAGTGACAGTCATGGTC +>mm8 +gtttaatctataagctcacacatgtgaaatgTCAGGTGTAGCATGTGCAT-CACAAGGG-----------------TA----TTTCTAGATATCCTTCATGACTGTTACATCATTTCTT-CAAACATTTGGAGAAGtggataaggttgtcatcccagcttttcactcgagaaggtggtggctcagtggggttaaatggcttccttgcactcctggag-gcaggaagtggcagGTAGGG-----AAGTTTAGAGTCTC--------------------------------------------------------------------------------------------TCGGTGTAATG----GAGGAGACTCAGGTCTGCCATGGACCTTGTGGCTGTAGTGACTTGACCC-------------------------------------AGGACAAACGCCCCACTGAGTGTCTTTC-AGGTAGTGACTCC-ATGATC + +>hg18.chr15(+):40427094-40427593 +CTGCAGTGAGTGAGGACAAAAGTCATCTGTCCAAACCAAGAAACCACCATCAGTTATACATACACACATACACAGACTTCTGGGCCCACTCACACAGACAGAAAACTTCACTCTTCAGCAGGGTTCTGGAAATAAGCATGTATATACTACACTGATAGGAAAATTTAAAATACAAAATAGGAAAAGCCACTTATAGGATGGGCAGAAAGGAATTCATCACTTAAGAGGAAAAAACAGCAAAGACAGGTATAGATAACAAACCAATGAAGGGTGGGAAGTTTCCCTAATAATTAAAAAGTGGACCATTCTTCAGCGTTAGAGCTCTTTTCCTTTTAATGCCAGGACCCCCATATTTGCCATCTCTGTGCCCCAAAATTTATTTTGCCTACAAATCCGTACTTGTAGACTGTGaattttataaaatgaaatatttttaaattCTACCTTGAAATTTTCTTATATGAATACTGCTTCCCTGAGCGTGCTGCTCTGTTACAGA +>mm8 +--------------GGCAGAAGTCATCTCCACAGACAGACAAACC---CTTTGTTCCACAAGT-CCCAT-----------TGCACCTACTTACATAAACAGAAAAATCCACTCTGTAGCAAGTCTCTAGAGTAACATGCTTGC-TATTTTATTGAC----AAGTTGAAAATAAGTCTTTAGAGGGGCCTCTAACAAGATGAGTAGAATAAAATTCATTGTGTCAGTGAAAAA-GTGGCAAAGACAGGTAGAGATAATAAG----TGGGGGGTAGGTAATTGCCCAAAT-ACCAAGAGATGGACTATTTTTAATTTTTTCAGTTCATTTTCTTTTCATCTCACAGTCCCCATGCTTGCCACTGCTCTTGCCACAGATATTCTTTGCTT--GAGTTTATATCTGTAAAGAGTGGATCTCATATCGTGAAATAC-----------ACTTGAAAAGTTGTCCATAT-AGCATGTCATTCCTGAGAGTGCTGCTGTGTTACAGA + +>hg18.chr15(+):40481381-40481880 +TGGCTTCCTCAATACCCAGTGACCCACAGAGCTCCTGGTATCAGGACCACTTGTGTTTGTAACAAGCAAAAAATACCAGGGGGGGCATTAGAGAGGCAGTGGAGCGGGCCTGGCAGAACAGGTGCCTGGGGGTCAGGCTTCCGCATGCGGGCTGCAGTTGCTGGCATTGCCTTCCGCAGGCTCCTCATCCTCATTCACATCTGAAGCATCTTCCTTTCTGTTTCTTCTCAAGGTTCCCAAAGAGGTATAGCAGCAGCAGCGGCCAGCAGTTGTGTGCAGCACTACCCAGGGGGCCCCGAGTCTGTCTGTGGCTCGTCGAGAAGCTTCCTGGTGGGGTTTGTGGGCAGGACTGTGATAGGAGAGGGCCTTGCCTGTGTTATTTCCACTGCAGAGCAGGTGCCTCAGGGCATTGCATGACCCATGACTACCACCCCCAGGATGTGCACTTTCTCCCTCGCACCAGACACTGCACGTCACACACATGCCTTTGCACACTCAC +>mm8 +TGGTTTTTCGTGTCCCCAGTGACCAACAGGGCTCCTGCTCTCAGGCTCACACATGTCTGTCACCAGT-GTAAATACCA-CAGTTGCA-------GAAGGCAGGACGGAGCTGGCCGGGTGGTAG-CAGGAGTTAGAGCCTACTCATGTGTCT----------GGCATTCCCTTCTGCAGACTCTGTACCCTCATTTACATCAGAGATG-TTCTTTTTCTATTTCGCTTCCAGGTTCCCAAAGAGGTATAGCAGTGGCAGCGGGCAGCCGTGGTGTGCAGCA-TTCCTTGGGGGTCCTAAGTCTGTCTGTGGCCCCCTAAGAAGATTCCTGGTAGGGTTGGTGATCGAGGC--TGATAGGA--------------------------------------------------------------GGGTACCACGCCCAGAATGCACGTTTTCTCCCTCCCACCAGACACCGCACATCAAACACACACCTTCCCACACTTAT + +>hg18.chr15(+):40457707-40458206 +cctgtgggtaattaatctggttgcccccaccccggggggagctatcctgccgtgagtgatcaaaagttagttttaggaccacatgagtaaacaagctctttagataaactcctctacattcctatgtatctgtgccctaagctattaagtggattcggctgccttcagccaaacactttatgcaaacctctaggccttccaagagggtttgtgtttatatcctataaattcatcttaaaatttttgccaccagcctgactgaactcccaaaagtgataacctctccttcatttttaatattagtaatttgtgttttcatttttcttgtttagcatggctaaaggtttatcaattctattgatctttccaaagaaccatttttgttttcattgactttctattgttttcttgttttttatttcattcatttctgctctgattttttattgtttcttttcttctgcttgctttaggcttaagtatctcttctatagtgtac +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr15(+):40438491-40438990 +ATTTTCTCAAATGAGGACTCTGCTGAGTAGCATTTTCCATGCAGACATTTCCAATGAGCGCTGACCCAAGAACATTCTAAAAAAGATACCAAATCTAACATTGAATAATGTTCTGATATCCTAAAATTTTAGGACTAAAAATCATGTTCTCTAAAATTCACAGAATATTTTTGTAGAATTCAGTACCTCCCGTTCACCCTAACTAGCTTTTTTGCAATATTGTTTTCCATTCATTTGATGGCCAGTAGTTGGGTGGTCTGTATAACTGCCTACTCAATAACATGTCAGCAGTTCTCAGCTTCTTTCCAGTGTTCACCTTACTCAGATACTCCCTTTTCATTTTCTGGCAACACCAGCACTTCATGGCAACAGAAATGTCCCTAGCCAGGTTCTCTCTCTACCATGCAGTCTCTCTTGCTCTCATACTCACAGTGTTTCTTCACATCTATTTTTAGTTTTCCTGGCTCAAGCATCTTCAGGCCACTGAAACACAACCCTC +>mm8 +ATTTCCTTGACTGGAAATTCTGCTGAGTGGCATTTTCTACCCA----GTTGGACTGAAAGCCGACTCCAGAACATTCTAGAAAAGATACTGGCTCTAA---------------------------------------------------------------------------------------------------------------------AATACTGTTTTCCATGTATCCAGCGGCTGCTGCTTCAGTAGCCTGCATGACTGCCTAGTCCTTTACACA---------CTTTGCTGATTTCTGGTGTTCAGCTGTCTCAGACA-----CTCTCACTTCTTGACAAGCCGAGTTCTTAATGTCAACAGAAATACCTCCAGCTAGGTCCTTC-GCGACCACTCAGTCTCTGTGGCTTTCATGATCACAACCTCACTTCATGTCTATTTTTAGTTTTCCTGGCTTAAGCTTCTACAGGCCACTGAAACACAACCCTC + +>hg18.chr1(+):120055534-120056033 +tttactgagaatgatgatttccaatttcatccatgtccctacaaaggacatgaactcatcattttttatggctgcatagtattccatggtgtatatgtgccatattttcttaatccagtctatcattgttggacattttctttttgatagtcgaattcccttcaacgtctagcacagtgccttgcacatttacccactcaaaaaaaatttcgtaaggaattaataaatGAATCCTTAGGAGGAAAAGTGAAAATGAAGTTTTTCTCTCAGGATGAGGTGTATTTCTCCGTTCATTTCAGATATGCATCAGCTAGTCAGCGTAAATTGTGCTTTTTATATGCTCACCAGGTGTAGGTAAGAGCTTTGGCTGAGATGGAGAAATTCATCGCGGGAGGATAATAAAGCGGGCAGGGATTTGGCAACCTCAGAGCCGCGAGGAGGAGGCGGAGTCGCGGAGAGTTTGAGTATTTCCGTCCAATCAAAAGGAGACTGTAAGAGG +>mm8 +-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATAAATG-GTCTTTAAGAGGAAAAGTTACTATGAGATTTAATTCCCTCGTGGCAGCGTATTTC--TGTTTATTTCCAATATAAATCAGCCTGCTGGCATAAATCGTGCGTGTTA-AAGCTCACCCGGGGCAGGTAAGGGCTTCA---CTGCTGGA-AGTGTAGTCTGTGTAGGataaaaaaaaaaaaaaaaaTGTGGGAGGCTCTGCCC------GGGGAGGCGGAGT--CAGAGAGTTTAAGCATTTCTGACCAATCAAAAGGAGACTGTTGGCGC + +>hg18.chr1(+):120063274-120063773 +AAATCAGAATACCTCCAGGTGCTCACCTGGTGTTGGCCTCAGCACTGGGGCAGTCAGCACTGAGGTGGCTTCTGTTTGATTCCTCTAAGCCCTGGGTGCCCATGTGACTTGTATACACCCAGGTCATAATCAGTTTAGCATAATGCCAGATACGTACATAGCGGGCATCCGATAAAATGAAGGAAGAAAAGTACAGGGGAGGGGAAGGGAAAGtaggcaggcttaactttgttgggcttcagtttttcctctgtaaaatggagttggaccagatgctggtgaacatttcttcaaatctcccactctgacgttctGCTTCagaacctcagacataaaaggatttggagtgtcttccaggccgcctgcatgtttctctctgctggtaggcacagcccccaagcagtgaggatgtgtgatgcataaacacctccagaggaatcgttctactattgctcttgaacaattcttccagtgtttagaagctcttaaggcttaaata +>mm8 +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>hg18.chr6(+):159106769-159107268 +CCTTTGCAAAGCTTTTATTTCATGTCTGCGGCATGGAATCCACCTGCACATGGCATCTTAGCTGTGAAGGAGAAAGCAGTGCACGAGAAGGAATGAGTGGGCGGAACCAACGGCCTCCACAAGCTGCCTTCCAGCAGCCTGCCAAGGCCATGGCAGAGAGAGACTGCAAACAAACAAACACAAGCAAACAGAGTCTCTTCACAGCTGGAGTCTGAAAGCTCATAGTGGCATGTGTGAATCTGACAAAATTAAAAGTGTGCATAGTCCATTACATGCATAAAACACTAATAATAATCCTGTTTACACGTGACTGCAGCAGGCAGGTCCAGCTCCACCACTGCCCTCCTGCCACATCACATCAAGTGCCATGGTTTAGAGGGTTTTTCATATGTAATTCTTTTATTCTGTAAAAGGTAACAAAATATACAGAACAAAACTTTCCCTTTTTAAAACTAATGTTACAAATCTGTATTATCACTTGTATATAAATAGTATATAG +>mm8 +GCCTTGGAGAGCTTTTATTGTGTGTATCTGGTGCGGAGT-CACCCGCACAGGACATCACAACCAAGGAGGC-----TAGTCCGCGAAAGGAAGGAAG---------------------ACAAACTG-----------------AAAAC--GGGA----ACAAGTTGCTCACAA-----------TAAAGAGCGTCCCTTCAGGGCTGGAGTCTGGATGCTCTCGGTGTCAAATAAGAAACTGACAGAAATGGAAGTGTGCAT-----TTTACGTGCACAAAAC-CCACTAACATTTTTGTACAGTGGTGATTACTGCAGTCA---TCGGTTTCCCGACTGCCCCTGTG-----TCAGATCAAGTGTCTCGG-TTACATGGTTCTTAATGTTGAATTCTTTTATTCTGTAAAAGGTAACAAAATATACAGAACAAAACTTTCCCTTTTTAAAACTAATGTTACAAACCCATATTATCGCTTATATATAAATACTATATAG + +>hg18.chr6(+):159106768-159107267 +GCCTTTGCAAAGCTTTTATTTCATGTCTGCGGCATGGAATCCACCTGCACATGGCATCTTAGCTGTGAAGGAGAAAGCAGTGCACGAGAAGGAATGAGTGGGCGGAACCAACGGCCTCCACAAGCTGCCTTCCAGCAGCCTGCCAAGGCCATGGCAGAGAGAGACTGCAAACAAACAAACACAAGCAAACAGAGTCTCTTCACAGCTGGAGTCTGAAAGCTCATAGTGGCATGTGTGAATCTGACAAAATTAAAAGTGTGCATAGTCCATTACATGCATAAAACACTAATAATAATCCTGTTTACACGTGACTGCAGCAGGCAGGTCCAGCTCCACCACTGCCCTCCTGCCACATCACATCAAGTGCCATGGTTTAGAGGGTTTTTCATATGTAATTCTTTTATTCTGTAAAAGGTAACAAAATATACAGAACAAAACTTTCCCTTTTTAAAACTAATGTTACAAATCTGTATTATCACTTGTATATAAATAGTATATA +>mm8 +GGCCTTGGAGAGCTTTTATTGTGTGTATCTGGTGCGGAGT-CACCCGCACAGGACATCACAACCAAGGAGGC-----TAGTCCGCGAAAGGAAGGAAG---------------------ACAAACTG-----------------AAAAC--GGGA----ACAAGTTGCTCACAA-----------TAAAGAGCGTCCCTTCAGGGCTGGAGTCTGGATGCTCTCGGTGTCAAATAAGAAACTGACAGAAATGGAAGTGTGCAT-----TTTACGTGCACAAAAC-CCACTAACATTTTTGTACAGTGGTGATTACTGCAGTCA---TCGGTTTCCCGACTGCCCCTGTG-----TCAGATCAAGTGTCTCGG-TTACATGGTTCTTAATGTTGAATTCTTTTATTCTGTAAAAGGTAACAAAATATACAGAACAAAACTTTCCCTTTTTAAAACTAATGTTACAAACCCATATTATCGCTTATATATAAATACTATATA + +>hg18.chr6(+):159106766-159107265 +GTGCCTTTGCAAAGCTTTTATTTCATGTCTGCGGCATGGAATCCACCTGCACATGGCATCTTAGCTGTGAAGGAGAAAGCAGTGCACGAGAAGGAATGAGTGGGCGGAACCAACGGCCTCCACAAGCTGCCTTCCAGCAGCCTGCCAAGGCCATGGCAGAGAGAGACTGCAAACAAACAAACACAAGCAAACAGAGTCTCTTCACAGCTGGAGTCTGAAAGCTCATAGTGGCATGTGTGAATCTGACAAAATTAAAAGTGTGCATAGTCCATTACATGCATAAAACACTAATAATAATCCTGTTTACACGTGACTGCAGCAGGCAGGTCCAGCTCCACCACTGCCCTCCTGCCACATCACATCAAGTGCCATGGTTTAGAGGGTTTTTCATATGTAATTCTTTTATTCTGTAAAAGGTAACAAAATATACAGAACAAAACTTTCCCTTTTTAAAACTAATGTTACAAATCTGTATTATCACTTGTATATAAATAGTATA +>mm8 +AAGGCCTTGGAGAGCTTTTATTGTGTGTATCTGGTGCGGAGT-CACCCGCACAGGACATCACAACCAAGGAGGC-----TAGTCCGCGAAAGGAAGGAAG---------------------ACAAACTG-----------------AAAAC--GGGA----ACAAGTTGCTCACAA-----------TAAAGAGCGTCCCTTCAGGGCTGGAGTCTGGATGCTCTCGGTGTCAAATAAGAAACTGACAGAAATGGAAGTGTGCAT-----TTTACGTGCACAAAAC-CCACTAACATTTTTGTACAGTGGTGATTACTGCAGTCA---TCGGTTTCCCGACTGCCCCTGTG-----TCAGATCAAGTGTCTCGG-TTACATGGTTCTTAATGTTGAATTCTTTTATTCTGTAAAAGGTAACAAAATATACAGAACAAAACTTTCCCTTTTTAAAACTAATGTTACAAACCCATATTATCGCTTATATATAAATACTATA + +>hg18.chr9(+):111041832-111042331 +ttaagcagagaggtatttattagagggtattatatggcatacacaatttccaggagcccacagataagggtttggatgccttcctgccaggaagagcacaagtagccaggacaaacacgtacctttacaggactattactgaggaaatcccactgccaccactTCTCTCTACTCAGCACCTGTGACAGGCAGGACAACCTTCACCAGAGTTGCCCCAGATGAAGAAAGGCATCAGCTGCTGTGCCTATAAGATCCACTCTTGCCAAGAGCAGCCTCATTCTAGGATGATCTTGCTCCACCCACCTAACTGAATGCTCACCTTCAGACTTCCAAAAGCCAACTGTTCTGTTACCAAGGTCATTCACAAATGAGACTTCTGCATAGCAACAAGAATCAATTTAAAAAAAATGAAGATGGAGTCAAAAAAAAAGCAAGAATAATCTTTATTCCTTGGAAACACATTTGTAAAAATGCTATCAATAAGATGAAAAGATTCAGA +>mm8 +TTAAGCAGAAGG--CTTTGATCGA----------------GGATCATCTTTAAGAAGCCACAGACAGA-----------------GCCAAGAAGAG-GTAAGCAACCACGAGAAGGTGTACCCGTCACAGGACTGTTATCAGGGAACACCCA-------GGTGTCTCTCTGCTCTGCACATGGAACAGGTACTGCAGCCTCTTCCAGAAGCGCATCGG---GAGAATCACCCCAGTCACTGTACCTATA-------------------GGAGCCTCAGTGAAGGATGGTTTTGTCCCAACCACATAACTGAAGGTTCACCTTCGGA-CACCCTGAGTCAACTGTACCATGAGTGAGATCA-----AAGGGAGGCTTCTGTGCAG----AAGAATCAAC------GCAATGAAGATGGAGTCCAAAAAAAAACAAGAATAATCTTTATTACTTGGAGACACA-TTGTAAAAATGTTAGCAGTAAGATGAAGAGACCCAGA + +>hg18.chr9(+):110974075-110974574 +GAAACCATGGAATCCTCTTATTTTACTGGTTAGAGGTGAGCTGCCAAAGGTACTGGGTTTCAAATACAGTAACAGCCAACTTGTTTGTGGTCAGACTTCCAGTGACGTCAACCTTCAGAAACTTCAACATCTGTGAACTCTGGGGGAAGCGGGGAAGAAGCAGGAAGCCCAGAGCCTCCTGGAAACACTGGCCAAAAAGCCCATGCATCCCTTCTTGGAAGCCAAGCAGATCTGACACATAGGAAATACTGGCTTTCCTGGCTTCCCCAAGAAACCTTCAGCTTTGCCCTGGAGGTTTCCATCAGCGAGCAGGAGGTGAAGAGCAGAAGCCTCAGAAAGCAGGTTAGAAGAGGAAGAGGGTGCTGGGTTGGCAAGAAGTGACAGCCCCATATTGTACGGGAACATATTTTGTATCATGTGCACAAGATAAAGAACAGCTAAAGCTGTTTTAAAAGTATAGCCGGGGGACATAGGGGTAAAAGGACCCAAACGCTACAAT +>mm8 +GC---CAC----TCCT---------CTCCTTGGGA-TGAACTGCCTGCGGTTCTGGGTTGCACATACAAGAGCAACCAGCATGTTTGTGCTCAGGTTTGCAGGGATGTCCACCCACTGAGACT------CTTGTGAGCCCAGGGAGAGGTGGGGACAAGGTAGGAGCTTGCAAGCCTCCTGAACGCAGCGGCTAGAACCTCCATGCACACCTACCTAGGAACAAATCAAGTCAGACTCGTGGGATACACAT-GTGGCCCGAAAG-CTCCGGAAACCTTCTGCTGTGTTCTGGAGGCTTCCATCTGAGAGCAAGG-GGGAGGAGTGCACACTGCAGAGAGCAGCTCAGAAGAGGAAGCAGCTGCTGGGTTGGCAGGAGGTGACAACCCTGTGTTCTATAGGAACATGGTTTGTGTCACGTGCACATGATAGAGGACAGCCAAAGCCATTTTGCTAGTA-ATCTAGGGGCTTCGTGAGTAAAAAGACCCAAAAACTCCACT + +>hg18.chr10(+):94822723-94823222 +ccttcctcttataccgtctctttatcctgccaGGGCTAAGGACCCCCTTCCCTGCTGTCCAGCTGGGGCGCCAAGCAGCAGGGCCCTCCGAATAGGCGAGCTGTGCTTGGATCTCAGAGACGGGCACCGACTGCCGAGCCCCAGACGAAGTGCCCCAGGGTCGGGGATCAGGCTTGTGCAGGGTAGCACCTGGGGACCTGAGGGACCTGGAGGCCTTCTTGTATCCTGAAGTAGGACCTTCTAAGACTTCATGAGTCCTGGCCCCCTTGCAGGGGTTGGGGAGCTGGGGATCCCAGATCTGCCTATTGCGCCCGATGCCCCGAGGCTCTCTCTTGGACTCTGGCCCTGAGTTCTTCTGCGCGATCCTTCGGAGACGTCTGGAGGCCTGCTTTATGcatctctcttggacctcagtttccccacacgtgggaggaggcagctggacgattcctgaaaggactttccCTTGCTTCCTCATCACGTGGAAGAGAGCCCACCC +>mm8 +CTCCCTGTATTC-----CTCCCCATTCTGCCTGGACTGGGGGCCCTCTTCCCGGCCGCTTGGCTGAGGTTGCAAGCCCCAGGGCTATAGGAATGGGCCGGCTTGGCGGTATTACTACAGTGGAG-GTTGACTTTGGAGCCTCTGGTACCAGGGCTTAGAGAAGGGAGTCAGGCATGTGCAAGGCTGCACCTGGGGGCCC-AGAGACCTGGAGGCTTCTTTGAACTCGAAAGCAGGATTTTCCAAGTCTTCATGCGC-TGGCTCGCCTGTGGGGCCCTGGAAAGCTAGCG-TCCACGATCCGCCAGTCATACTTGACCTCCGAGACCG---GCTAGGACCCTCGCCCTGGGATCTTCTT-GGGATCCTCCAGA----TCAGGAAGCGT---------------TTGGAATCTCATTTACTCAACCGGTGGGTCAAGTCCATTGGATGATTCTTGAACGC----------GCTTTCCAAGCCAATGGAAAAGAGCCCACGA + +>hg18.chr10(+):94823138-94823637 +ttccccacacgtgggaggaggcagctggacgattcctgaaaggactttccCTTGCTTCCTCATCACGTGGAAGAGAGCCCACCCGGCACCTGGAAATGGAAAGCCAGTGAAGGCTGCTTTGGGCCGGGGCAGCGGGTGGGACCGGGCGGGAGGGATTCCAAAGAGACCGCCGGGAAGGCTAGAGCTTGGAATTCCGGCTCCTCGGAGTCCTGGCCCTCCCCCACCGCCGCCTCGGAGCTCAGCACACCTTGGATGGGGGAGGCGGGCAGCTCCTAGCCCCGCACCCCAGGAGGCGCGCTCGGAGGGAAGCCGCCACCGCGCCGCCTCTGCCTCGGCGCGGAACAAACGGTTAAAGATTTTGGGCAGCGCCTCGCGGGGGGAGGAGCCAGGGGCCCAATCCGCAATTAAAGATGAACTTTGGGTGAACTAATTGTCTGACCAAGGTAACGTGGGCAGCAACCTGGGCCGCCTATAAAGCGGCAGCGCCGTGGGGTTTGAA +>mm8 +TACTCAACCGGTGGGTCAAGTCCATTGGATGATTCTTGAACGC----------GCTTTCCAAGCCAATGGAAAAGAGCCCACGAGGCGCCTGTGAATGGTGAGCTGG----GAAGGCTTCGGGCTCGGGCAGCTGGTTCGACCCGGCTCGAGGGACAGCAGAGAGACAGCTAGGAAACCCAGGACTCCAAATTCCCACTTCTTGGAACCCCGACTCCCCCCCCCCGCCGCCTCGGAGCTCTGCACACCTAGGACAAGGAAAGAGGTG--TTCCTAGTCCCGCACCCCAGGAGGCGCGCTCAGAGGGAAGCCGCCAGTGCGCCGCCTCTGCCTCGGCGCGGAACAAACGGTTAAAGATTTTGGGCAGCGCCTCGAGGGGGGAGGAGCCAGGGGCCCGATCCGCAATTAAAGATGAACTTTGGGTGAACTAATTGTCTGACCAAGGTAACGTGGGCAGTAACCTGGGCGGCCTATAAAGAGGGCGCGCGGCGGGGTTCGGA + +>hg18.chr10(+):29005931-29006430 +CCGCCTCCCCCGGGCTCCCACCCGAACCCTCCTCCGCCACCTGCACAGGCCGGGGCATTGTCACTCGCCCCTGGGGGTTCCAGAAAACGCAGTGCGGCCGGGGAGGACGACCACACGGACCCCCTGCGTGTTTCGGGGGGCACCCAAAAGAAGCCCCGCGCTGGGGAACGCTGACCACCCGAGGCTGAGCCGTCAGGGTCTCGGAGGCGGGTTCCCGAGCCGGTCCCGGGGCTGGGCTCCCCCGGCGCCTCGCGAAGGTCACTGACGCGCAGGCCTCCGCAAGGGGGAGCGCGGGAGACGGCAGCGCACCAGCCGGGCGCCCCAGCCGGGCGCCCCAGACGCCGGCGCCGCTCGGAGCCGCCGGGCAGGTCCCCCAGCGCTCGCGTCTGGGCCCGCCCCCCGCTGCGGGGCGGATTGACAGGAGCCCGGCGGCCAATCGGACGCCGTggggcggggcgaggcggggcggtgcaggccggCTCCCGGCGCGGGGCGCTAT +>mm8 +CTGCCCCTTCTTGACTATCACCCTACTCCTCCTCGGCCA--CGCGCGGGCGGGCGTATTGTTACATGGCCCTGGTGGTTTCGGCAACCGAAGTATGGCCGAGGATGATGACTACTGAGATCCCTTGCAGGTTTCAGGTGGGACAAAAGCGAAGCCACGTGCTGGAGGCCGCTGACCA---GAGACTGAGCAGTGAGGGTCTCGTAGCAAA--CTCCGAACCTATCTAGAAGAGGGGCT-CTGCGACGCATAT--GAGGCTGT--TCGCGCAGGCGTTCGCTAGGGGGAGTGCT-----------------------GCGGCCGTGTCCACAGTGCTACTTGCCAGCGCCAGCGGGAGCCCGGCGGCTTGTCTGCCTTAGCCCGCGTCTGGCCCCGCCCCCTGCGGCTGGGCCCTGGGGCTAGAG-GCGTCCGCCAATCGGAGAGTG-GAGGCGGGGCAGGGCGGGGCCGCGCTGGCCCACTCTGGGCGCCGGGCGCTAT + diff -r 973d6cbeea87 -r 77f8bf51b2ae tools/maf/interval_maf_to_merged_fasta.py --- a/tools/maf/interval_maf_to_merged_fasta.py Thu Aug 21 16:49:16 2008 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.py Fri Aug 22 10:39:58 2008 -0400 @@ -33,17 +33,23 @@ assert sys.version_info[:2] >= ( 2, 4 ) +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + def __main__(): #Parse Command Line options, args = doc_optparse.parse( __doc__ ) mincols = 0 - - if options.dbkey: primary_species = options.dbkey - else: primary_species = None + strand_col = -1 + + if options.dbkey: + primary_species = options.dbkey + else: + primary_species = None if primary_species in [None, "?", "None"]: - print >>sys.stderr, "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file." - sys.exit() + stop_err( "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file." ) include_primary = True if options.species: @@ -52,43 +58,40 @@ secondary_species = None species = None else: - try: secondary_species.remove( primary_species ) - except: include_primary = False + try: + secondary_species.remove( primary_species ) + except: + include_primary = False species = [primary_species] + secondary_species - if options.interval_file: interval_file = options.interval_file + if options.interval_file: + interval_file = options.interval_file else: - print >>sys.stderr, "Input interval file has not been specified." - sys.exit() + stop_err( "Input interval file has not been specified." ) - if options.output_file: output_file = options.output_file + if options.output_file: + output_file = options.output_file else: - print >>sys.stderr, "Output file has not been specified." - sys.exit() + stop_err( "Output file has not been specified." ) if not options.geneBED: if options.chromCol: chr_col = int( options.chromCol ) - 1 else: - print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." - sys.exit() + stop_err( "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." ) if options.startCol: start_col = int( options.startCol ) - 1 else: - print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes." - sys.exit() + stop_err( "Start column not set, click the pencil icon in the history item to set the metadata attributes." ) if options.endCol: end_col = int( options.endCol ) - 1 else: - print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes." - sys.exit() - + stop_err( "End column not set, click the pencil icon in the history item to set the metadata attributes." ) + if options.strandCol: strand_col = int( options.strandCol ) - 1 - else: - strandCol = -1 mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir #Finish parsing command line @@ -99,21 +102,17 @@ if options.mafSourceType.lower() in ["cached"]: index = maf_utilities.maf_index_by_uid( options.mafSource, mafIndexFile ) if index is None: - print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( options.mafSource ) - sys.exit() + stop_err( "The MAF source specified (%s) appears to be invalid." % ( options.mafSource ) ) elif options.mafSourceType.lower() in ["user"]: #index maf for use here, need to remove index_file when finished index, index_filename = maf_utilities.build_maf_index( options.mafSource, species = [primary_species] ) if index is None: - print >> sys.stderr, "Your MAF file appears to be malformed." - sys.exit() + stop_err( "Your MAF file appears to be malformed." ) else: - print >> sys.stderr, "Invalid MAF source type specified." - sys.exit() + stop_err( "Invalid MAF source type specified." ) #open output file output = open( output_file, "w" ) - if options.geneBED: region_enumerator = maf_utilities.line_enumerator( open( interval_file, "r" ).readlines() ) diff -r 973d6cbeea87 -r 77f8bf51b2ae tools/maf/interval_maf_to_merged_fasta.xml --- a/tools/maf/interval_maf_to_merged_fasta.xml Thu Aug 21 16:49:16 2008 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.xml Fri Aug 22 10:39:58 2008 -0400 @@ -56,6 +56,13 @@ </outputs> <tests> <test> + <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/> + <param name="species" value="hg18,mm8"/> + <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" /> + </test> + <test> <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> <param name="maf_source" value="cached"/> <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/>

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[hg] galaxy 1475: (no commit message)
by greg＠scofield.bx.psu.edu 21 Aug '08

21 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/973d6cbeea87 changeset: 1475:973d6cbeea87 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Aug 21 16:49:16 2008 -0400 description: (no commit message) 1 file(s) affected in this change: tools/extract/extract_genomic_dna.xml diffs (12 lines): diff -r cea8c4d68ad0 -r 973d6cbeea87 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Thu Aug 21 08:54:51 2008 -0400 +++ b/tools/extract/extract_genomic_dna.xml Thu Aug 21 16:49:16 2008 -0400 @@ -4,7 +4,7 @@ <inputs> <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"> <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." split=" " line_startswith="seq" /> + <validator type="dataset_metadata_in_file" filename="alignseq.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." split="\t" line_startswith="seq" /> </param> <param name="out_format" type="select" label="Output data type"> <option value="fasta">FASTA</option>

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Main is at rev 1474:cea8c4d68ad0
by Greg Von Kuster 21 Aug '08

21 Aug '08

1 0

[hg] galaxy 1474: Reverting extract_genomic_dna and blat_wrapper...
by greg＠scofield.bx.psu.edu 21 Aug '08

21 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/cea8c4d68ad0 changeset: 1474:cea8c4d68ad0 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Aug 21 08:54:51 2008 -0400 description: Reverting extract_genomic_dna and blat_wrapper tools to rev 1472. 2 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/metag_tools/blat_wrapper.py diffs (42 lines): diff -r 8cda62b46162 -r cea8c4d68ad0 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Tue Aug 19 13:35:44 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Thu Aug 21 08:54:51 2008 -0400 @@ -35,7 +35,7 @@ for line in open( nib_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[1] == dbkey: @@ -49,7 +49,7 @@ for line in open( twobit_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue if fields[0] == dbkey: diff -r 8cda62b46162 -r cea8c4d68ad0 tools/metag_tools/blat_wrapper.py --- a/tools/metag_tools/blat_wrapper.py Tue Aug 19 13:35:44 2008 -0400 +++ b/tools/metag_tools/blat_wrapper.py Thu Aug 21 08:54:51 2008 -0400 @@ -15,7 +15,7 @@ for i, line in enumerate( file( nib_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[0] == 'seq': @@ -31,7 +31,7 @@ for i, line in enumerate( file( twobit_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue twobits[( fields[0] )] = fields[1]

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[hg] galaxy 1473: Unbreaking 2 tools that I just broke.
by greg＠scofield.bx.psu.edu 19 Aug '08

19 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/8cda62b46162 changeset: 1473:8cda62b46162 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 19 13:35:44 2008 -0400 description: Unbreaking 2 tools that I just broke. 2 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/metag_tools/blat_wrapper.py diffs (42 lines): diff -r c81fa25c67e5 -r 8cda62b46162 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Tue Aug 19 10:44:08 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Tue Aug 19 13:35:44 2008 -0400 @@ -35,7 +35,7 @@ for line in open( nib_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): - fields = line.split( '\t' ) + fields = line.split() if len( fields ) < 3: continue if fields[1] == dbkey: @@ -49,7 +49,7 @@ for line in open( twobit_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split( '\t' ) + fields = line.split() if len( fields ) < 2: continue if fields[0] == dbkey: diff -r c81fa25c67e5 -r 8cda62b46162 tools/metag_tools/blat_wrapper.py --- a/tools/metag_tools/blat_wrapper.py Tue Aug 19 10:44:08 2008 -0400 +++ b/tools/metag_tools/blat_wrapper.py Tue Aug 19 13:35:44 2008 -0400 @@ -15,7 +15,7 @@ for i, line in enumerate( file( nib_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split( '\t' ) + fields = line.split() if len( fields ) < 3: continue if fields[0] == 'seq': @@ -31,7 +31,7 @@ for i, line in enumerate( file( twobit_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split( '\t' ) + fields = line.split() if len( fields ) < 2: continue twobits[( fields[0] )] = fields[1]

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Main is at rev 1472:c81fa25c67e5
by Greg Von Kuster 19 Aug '08

19 Aug '08

1 0

[hg] galaxy 1472: Some tool fixes:
by Nate Coraor 19 Aug '08

19 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c81fa25c67e5 changeset: 1472:c81fa25c67e5 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 19 10:44:08 2008 -0400 description: Some tool fixes: 1) fix for interval_maf_to_merged_fasta when strand column not included in input metadata 2) Tools using alignseq.loc now split on TAB rather than wihite space 3 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/maf/interval_maf_to_merged_fasta.py tools/metag_tools/blat_wrapper.py diffs (84 lines): diff -r 1958657d8f8d -r c81fa25c67e5 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Tue Aug 19 10:44:08 2008 -0400 @@ -35,7 +35,7 @@ for line in open( nib_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[1] == dbkey: @@ -49,7 +49,7 @@ for line in open( twobit_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue if fields[0] == dbkey: diff -r 1958657d8f8d -r c81fa25c67e5 tools/maf/interval_maf_to_merged_fasta.py --- a/tools/maf/interval_maf_to_merged_fasta.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.py Tue Aug 19 10:44:08 2008 -0400 @@ -67,25 +67,29 @@ sys.exit() if not options.geneBED: - if options.chromCol: chr_col = int( options.chromCol ) - 1 + if options.chromCol: + chr_col = int( options.chromCol ) - 1 else: - print >>sys.stderr, "Chromosome column has not been specified." + print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.startCol: start_col = int( options.startCol ) - 1 + if options.startCol: + start_col = int( options.startCol ) - 1 else: - print >>sys.stderr, "Start column has not been specified." + print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.endCol: end_col = int( options.endCol ) - 1 + if options.endCol: + end_col = int( options.endCol ) - 1 else: - print >>sys.stderr, "End column has not been specified." + print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.strandCol: strand_col = int( options.strandCol ) - 1 + if options.strandCol: + strand_col = int( options.strandCol ) - 1 else: - print >>sys.stderr, "Strand column has not been specified." - sys.exit() + strandCol = -1 + mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir #Finish parsing command line diff -r 1958657d8f8d -r c81fa25c67e5 tools/metag_tools/blat_wrapper.py --- a/tools/metag_tools/blat_wrapper.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/metag_tools/blat_wrapper.py Tue Aug 19 10:44:08 2008 -0400 @@ -15,7 +15,7 @@ for i, line in enumerate( file( nib_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[0] == 'seq': @@ -31,7 +31,7 @@ for i, line in enumerate( file( twobit_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue twobits[( fields[0] )] = fields[1]

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New (reckless) tools
by Assaf Gordon 18 Aug '08

18 Aug '08

Hello, I'd like to share three tools that I've recently made. One is semi-useful, the other too are completely reckless. The first one is an improved "sort" tool, which allows sorting according to multiple keys. it uses the GNU sort utility, and therefor doesn't need a script file (except for the XML itself). BEGIN SORT TOOL --------------- <tool id="cshl_sort_tool" name="Sort"> <command>sort #for $key in $sortkeys '-k ${key.column},${key.column}${key.order}${key.style}' #end for $input > $out_file1</command> <inputs> <param format="txt" name="input" type="data" label="Sort Query" /> <repeat name="sortkeys" title="sort key"> <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" /> <param name="order" type="select" display="radio" label="in"> <option value="r">Descending order</option> <option value="">Ascending order</option> </param> <param name="style" type="select" display="radio" label="Flavor"> <option value="n">Numerical sort</option> <option value="">Alphabetical sort</option> </param> </repeat> </inputs> <outputs> <data format="input" name="out_file1" metadata_source="input"/> </outputs> </tool> -------------- END SORT TOOL The two other tools allow running AWK and SED directly from galaxy. These should NEVER EVER be installed on a publicly accessible system (as a matter of fact, these shouldn't be install on any system... ) The reason I wrote these tools, is that sometimes the galaxy tools just can't do something which would be very simple to do, if I just had access to sed or awk. This usually happens when biologists here work on galaxy, and get 'stuck' trying to do something which just can't be done with the current galaxy tools. Then they ask me to do it. One way (for me) to do it is to SSH into the galaxy server, get the dataset file, run sed/awk, create a new file, and manually upload it back to galaxy. Another way is to run awk and sed from within galaxy... I won't say this is the most elegant solution ever - but it gets the job done. Note about security: With these tools - there is NONE. An AWK script can execute shell commands (the 'system' function) and can read any local file (the 'getline' command). A SED script can read files (the 'r' command) and write files (the 'w' command). The 'password' field is completely useless. The password is not hidden, and the web browser will probably cache it and display it the next time you access the tool's page. BEGIN AWK TOOL -------------- <tool id="cshl_awk_tool" name="awk"> <command>awk '$url_paste' OFS="\t" $input > $output </command> <inputs> <param format="txt" name="input" type="data" label="File to process" />  <param name="url_paste" type="text" area="true" size="5x35" label="AWK Program" help=""> <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> </param>  <param name="passwd" type="text" area="false" label="Secret password"> <validator type="regex" message="Oops! wrong password.">^awk$</validator> </param> </inputs> <outputs> <data format="txt" name="output" metadata_source="input" /> </outputs> </tool> -------------- END AWK TOOL BEGIN SED TOOL -------------- <tool id="cshl_sed_tool" name="sed"> <command>sed '$url_paste' $input > $output </command> <inputs> <param format="txt" name="input" type="data" label="File to process" />  <param name="url_paste" type="text" area="true" size="5x35" label="SED Program" help=""> <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> </param>  <param name="passwd" type="text" area="false" label="Secret password"> <validator type="regex" message="Oops! wrong password.">^sed$</validator> </param> </inputs> <outputs> <data format="txt" name="output" metadata_source="input" /> </outputs> </tool> -------------- END SED TOOL The above XML snippets are free for use under the same license as galaxy (the LICENSE.txt file). -Gordon.

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Main is at rev 1471:1958657d8f8d
by Greg Von Kuster 12 Aug '08

12 Aug '08

1 0

[hg] galaxy 1471: Fix for interval2maf.py when metadata missing ...
by greg＠scofield.bx.psu.edu 12 Aug '08

12 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/1958657d8f8d changeset: 1471:1958657d8f8d user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 12 10:04:28 2008 -0400 description: Fix for interval2maf.py when metadata missing strand column value. 1 file(s) affected in this change: tools/maf/interval2maf.py diffs (31 lines): diff -r 78e84936b7a3 -r 1958657d8f8d tools/maf/interval2maf.py --- a/tools/maf/interval2maf.py Tue Aug 12 09:18:47 2008 -0400 +++ b/tools/maf/interval2maf.py Tue Aug 12 10:04:28 2008 -0400 @@ -54,23 +54,22 @@ if options.chromCol: chromCol = int( options.chromCol ) - 1 else: - print >>sys.stderr, "Chromosome column has not been specified." + print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() if options.startCol: startCol = int( options.startCol ) - 1 else: - print >>sys.stderr, "Start column has not been specified." + print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() if options.endCol: endCol = int( options.endCol ) - 1 else: - print >>sys.stderr, "End column has not been specified." + print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() if options.strandCol: strandCol = int( options.strandCol ) - 1 else: - print >>sys.stderr, "Strand column has not been specified." - sys.exit() + strandCol = -1 if options.interval_file: interval_file = options.interval_file else:

1 0

Main is at rev 1470:78e84936b7a3
by Nate Coraor 12 Aug '08

12 Aug '08

1 0

[hg] galaxy 1469: Reports: Wrap the stderr and traceback in pre ...
by Nate Coraor 12 Aug '08

12 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b9142bbae4ad changeset: 1469:b9142bbae4ad user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Aug 08 13:42:32 2008 -0400 description: Reports: Wrap the stderr and traceback in pre tags so they display nicely. 6 file(s) affected in this change: lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako diffs (105 lines): diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css --- a/lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css Thu Aug 07 19:28:42 2008 -0400 +++ b/lib/galaxy/webapps/reports/static/january_2008_style/blue/base.css Fri Aug 08 13:42:32 2008 -0400 @@ -322,3 +322,6 @@ display: none; } +pre { + font-size: 80%; +} diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako --- a/lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako Thu Aug 07 19:28:42 2008 -0400 +++ b/lib/galaxy/webapps/reports/templates/jobs_all_unfinished.mako Fri Aug 08 13:42:32 2008 -0400 @@ -60,13 +60,13 @@ <td colspan="5">Stderr</td> </tr> <tr> - <td colspan="5">${job[9]}</td> + <td colspan="5"><pre>${job[9]}</pre></td> </tr> <tr class="header"> <td colspan="5">Stack Trace</td> </tr> <tr> - <td colspan="5">${job[10]}</td> + <td colspan="5"><pre>${job[10]}</pre></td> </tr> <tr class="header"> <td colspan="5">Info</td> diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako --- a/lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako Thu Aug 07 19:28:42 2008 -0400 +++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_all.mako Fri Aug 08 13:42:32 2008 -0400 @@ -64,13 +64,13 @@ <td colspan="5">Stderr</td> </tr> <tr> - <td colspan="5">${job[9]}</td> + <td colspan="5"><pre>${job[9]}</pre></td> </tr> <tr class="header"> <td colspan="5">Stack Trace</td> </tr> <tr> - <td colspan="5">${job[10]}</td> + <td colspan="5"><pre>${job[10]}</pre></td> </tr> <tr class="header"> <td colspan="5">Info</td> diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako --- a/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Thu Aug 07 19:28:42 2008 -0400 +++ b/lib/galaxy/webapps/reports/templates/jobs_specified_date_in_error.mako Fri Aug 08 13:42:32 2008 -0400 @@ -51,13 +51,13 @@ <td colspan="5">Stderr</td> </tr> <tr> - <td colspan="5">${job[9]}</td> + <td colspan="5"><pre>${job[9]}</pre></td> </tr> <tr class="header"> <td colspan="5">Stack Trace</td> </tr> <tr> - <td colspan="5">${job[10]}</td> + <td colspan="5"><pre>${job[10]}</pre></td> </tr> <tr class="header"> <td colspan="5">Info</td> diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako --- a/lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako Thu Aug 07 19:28:42 2008 -0400 +++ b/lib/galaxy/webapps/reports/templates/jobs_tool_for_month.mako Fri Aug 08 13:42:32 2008 -0400 @@ -64,13 +64,13 @@ <td colspan="5">Stderr</td> </tr> <tr> - <td colspan="5">${job[9]}</td> + <td colspan="5"><pre>${job[9]}</pre></td> </tr> <tr class="header"> <td colspan="5">Stack Trace</td> </tr> <tr> - <td colspan="5">${job[10]}</td> + <td colspan="5"><pre>${job[10]}</pre></td> </tr> <tr class="header"> <td colspan="5">Info</td> diff -r c17db2e5f334 -r b9142bbae4ad lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako --- a/lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako Thu Aug 07 19:28:42 2008 -0400 +++ b/lib/galaxy/webapps/reports/templates/jobs_user_for_month.mako Fri Aug 08 13:42:32 2008 -0400 @@ -64,13 +64,13 @@ <td colspan="5">Stderr</td> </tr> <tr> - <td colspan="5">${job[9]}</td> + <td colspan="5"><pre>${job[9]}</pre></td> </tr> <tr class="header"> <td colspan="5">Stack Trace</td> </tr> <tr> - <td colspan="5">${job[10]}</td> + <td colspan="5"><pre>${job[10]}</pre></td> </tr> <tr class="header"> <td colspan="5">Info</td>

1 0

[hg] galaxy 1470: Fix for Extract Genomic DNA when input file me...
by Nate Coraor 12 Aug '08

12 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/78e84936b7a3 changeset: 1470:78e84936b7a3 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 12 09:18:47 2008 -0400 description: Fix for Extract Genomic DNA when input file metadata missing strand column value. 2 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/extract/extract_genomic_dna.xml diffs (79 lines): diff -r b9142bbae4ad -r 78e84936b7a3 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Fri Aug 08 13:42:32 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Tue Aug 12 09:18:47 2008 -0400 @@ -1,7 +1,10 @@ #!/usr/bin/env python """ -usage: extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format GALAXY_DATA_INDEX_DIR -by Wen-Yu Chung +usage: %prog $input $out_file1 + -1, --cols=N,N,N,N: Columns for start, end, strand in input file + -d, --dbkey=N: Genome build of input file + -o, --output_format=N: the data type of the output file + -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc and twobit.loc """ from galaxy import eggs import pkg_resources @@ -10,6 +13,7 @@ from bx.cookbook import doc_optparse import bx.seq.nib import bx.seq.twobit +from galaxy.tools.util.galaxyops import * assert sys.version_info[:2] >= ( 2, 4 ) @@ -54,32 +58,18 @@ return twobit_path def __main__(): - input_filename = sys.argv[1] - output_filename = sys.argv[2] - includes_strand_col = False + options, args = doc_optparse.parse( __doc__ ) + try: + chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols ) + dbkey = options.dbkey + output_format = options.output_format + GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR + input_filename, output_filename = args + except: + doc_optparse.exception() + + includes_strand_col = strand_col >= 0 strand = None - # If any of the following exceptions are thrown, we need to improve the metadata validator. - try: - chrom_col = int( sys.argv[3] ) - 1 - except: - stop_err( "Chrom column not properly set, click the pencil icon in your history item to set it." ) - try: - start_col = int( sys.argv[4] ) - 1 - except: - stop_err( "Start column not properly set, click the pencil icon in your history item to set it." ) - try: - end_col = int( sys.argv[5] ) - 1 - except: - stop_err( "End column not properly set, click the pencil icon in your history item to set it." ) - try: - strand_col = int( sys.argv[6] ) - 1 - if strand_col >= 0: - includes_strand_col = True - except: - pass - dbkey = sys.argv[7] - output_format = sys.argv[8] - GALAXY_DATA_INDEX_DIR = sys.argv[9] nibs = {} twobits = {} nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ) diff -r b9142bbae4ad -r 78e84936b7a3 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Fri Aug 08 13:42:32 2008 -0400 +++ b/tools/extract/extract_genomic_dna.xml Tue Aug 12 09:18:47 2008 -0400 @@ -1,6 +1,6 @@ <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.1.0"> <description>using coordinates from assembled/unassembled genomes</description> - <command interpreter="python">extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format ${GALAXY_DATA_INDEX_DIR}</command> + <command interpreter="python">extract_genomic_dna.py $input $out_file1 -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}</command> <inputs> <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"> <validator type="unspecified_build" />

1 0

[hg] galaxy 1468: Updating packed versions of javascripts.
by James Taylor 08 Aug '08

08 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c17db2e5f334 changeset: 1468:c17db2e5f334 user: James Taylor <james(a)jamestaylor.org> date: Thu Aug 07 19:28:42 2008 -0400 description: Updating packed versions of javascripts. 12 file(s) affected in this change: static/scripts/packed/IE7.js static/scripts/packed/IE8.js static/scripts/packed/cookie_set.js static/scripts/packed/galaxy.base.js static/scripts/packed/galaxy.panels.js static/scripts/packed/galaxy.ui.scrollPanel.js static/scripts/packed/galaxy.workflow_editor.canvas.js static/scripts/packed/ie7-recalc.js static/scripts/packed/jquery.cookie.js static/scripts/packed/jquery.form.js static/scripts/packed/jquery.hoverIntent.js static/scripts/packed/jquery.json.js diffs (99 lines): diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/IE7.js --- a/static/scripts/packed/IE7.js Thu Aug 07 11:41:59 2008 -0400 +++ b/static/scripts/packed/IE7.js Thu Aug 07 19:28:42 2008 -0400 @@ -1,2 +1,1 @@ -/* IE7/IE8.js - copyright 2004-2008, Dean 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iousElementSibling=function(node){while(node&&(node=node.previousSibling)&&(node.nodeType!=1||node.nodeName=="!")){continue}return node};var IMPLIED_ASTERISK=/([\s>+~,]|[^(]\+|^)([#.:\[])/g,IMPLIED_SPACE=/(^|,)([^\s>+~])/g,WHITESPACE=/\s*([\s>+~(),]|^|$)\s*/g,WILD_CARD=/\s\*\s/g;var CSSParser=RegGrp.extend({constructor:function(items){this.base(items);this.sorter=new RegGrp;this.sorter.add(/:not$[^)]*$/,RegGrp.IGNORE);this.sorter.add(/([ >](\*|[\w-]+))([^: >+~]*)(:\w+-child($[^)]+$)?)([^: >+~]*)/,"$1$3$6$4")},ignoreCase:true,escape:function(selector){return this.optimise(this.format(selector))},format:function(selector){return selector.replace(WHITESPACE,"$1").replace(IMPLIED_SPACE,"$1 $2").replace(IMPLIED_ASTERISK,"$1*$2")},optimise:function(selector){return this.sorter.exec(selector.replace(WILD_CARD,">* "))},unescape:function(selector){return decode(selector)}});var _OPERATORS={"":"%1!=null","=":"%1=='%2'","~=":/(^| )%1( |$)/,"|=":/^%1(-|$)/,"^=":/^%1/,"$=":/%1$/,"*=" :/%1/};var _PSEUDO_CLASSES={"first-child":"!IE7._getPreviousElementSibling(e%1)",link:"e%1.currentStyle['ie7-link']=='link'",visited:"e%1.currentStyle['ie7-link']=='visited'"};var _VAR="var p%2=0,i%2,e%2,n%2=e%1.";var _ID="e%1.sourceIndex";var _TEST="var g="+_ID+";if(!p[g]){p[g]=1;";var _STORE="r[r.length]=e%1;if(s)return e%1;";var _FN="var _selectorFunction=function(e0,s){IE7._indexed++;var r=[],p={},reg=[%1],d=document;";var reg;var _index;var _wild;var _list;var _duplicate;var _cache={};var cssParser=new CSSParser({" (\\*|[\\w-]+)#([\\w-]+)":function(match,tagName,id){_wild=false;var replacement="var e%2=IE7._byId(d,'%4');if(e%2&&";if(tagName!="*"){replacement+="e%2.nodeName=='%3'&&"}replacement+="(e%1==d||e%1.contains(e%2))){";if(_list){replacement+=format("i%1=n%1.length;",_list)}return format(replacement,_index++,_index,tagName.toUpperCase(),id)}," (\\*|[\\w-]+)":function(match,tagName){_duplicate++;_wild=tagName=="*";var replacement=_VAR;replacement+=(_wild&&_MSIE5)?" all":"getElementsByTagName('%3')";replacement+=";for(i%2=0;(e%2=n%2[i%2]);i%2++){";return format(replacement,_index++,_list=_index,tagName.toUpperCase())},">(\\*|[\\w-]+)":function(match,tagName){var children=_list;_wild=tagName=="*";var replacement=_VAR;replacement+=children?"children":"childNodes";if(!_wild&&children){replacement+=".tags('%3')"}replacement+=";for(i%2=0;(e%2=n%2[i%2]);i%2++){";if(_wild){replacement+="if(e%2.nodeType==1){";_wild=_MSIE5}else{if(!children){replacement+="if(e%2.nodeName=='%3'){"}}return format(replacement,_index++,_list=_index,tagName.toUpperCase())},"\\+(\\*|[\\w-]+)":function(match,tagName){var replacement="";if(_wild){replacement+="if(e%1.nodeName!='!'){"}_wild=false;replacement+="e%1=IE7._getNextElementSibling(e%1);if(e%1";if(tagName!="*"){replacement+="&&e%1.nodeName=='%2'"}replacement+="){";return format(replacement,_index,tagName.toUpperCase())},"~(\\*|[\\w-]+)":function(match,tagName){var replacement="";if(_wild){replacement+="if(e%1.no deName!='!'){"}_wild=false;_duplicate=2;replacement+="while(e%1=e%1.nextSibling){if(e%1.ie7_adjacent==IE7._indexed)break;if(";if(tagName=="*"){replacement+="e%1.nodeType==1";if(_MSIE5){replacement+="&&e%1.nodeName!='!'"}}else{replacement+="e%1.nodeName=='%2'"}replacement+="){e%1.ie7_adjacent=IE7._indexed;";return format(replacement,_index,tagName.toUpperCase())},"#([\\w-]+)":function(match,id){_wild=false;var replacement="if(e%1.id=='%2'){";if(_list){replacement+=format("i%1=n%1.length;",_list)}return format(replacement,_index,id)},"\\.([\\w-]+)":function(match,className){_wild=false;reg.push(new RegExp("(^|\\s)"+rescape(className)+"(\\s|$)"));return format("if(e%1.className&&reg[%2].test(e%1.className)){",_index,reg.length-1)},"\\[([\\w-]+)\\s*([^=]?=)?\\s*([^\\]]*)\\]":function(match,attr,operator,value){var alias=_ATTRIBUTES[attr]||attr;if(operator){var getAttribute="e%1.getAttribute('%2',2)";if(!_EVALUATED.test(attr)){getAttribute="e%1.%3||"+getAttribute}attr=format("("+ getAttribute+")",_index,attr,alias)}else{attr=format("IE7._getAttribute(e%1,'%2')",_index,attr)}var replacement=_OPERATORS[operator||""]||"0";if(replacement&&replacement.source){reg.push(new RegExp(format(replacement.source,rescape(cssParser.unescape(value)))));replacement="reg[%2].test(%1)";value=reg.length-1}return"if("+format(replacement,attr,value)+"){"},":+([\\w-]+)(\$([^)]+)\$)?":function(match,pseudoClass,$2,args){pseudoClass=_PSEUDO_CLASSES[pseudoClass];return"if("+(pseudoClass?format(pseudoClass,_index,args||""):"0")+"){"}});var HYPERLINK=/a(#[\w-]+)?(\.[\w-]+)?:(hover|active)/i;var BRACE1=/\s*\{\s*/,BRACE2=/\s*\}\s*/,COMMA=/\s*\,\s*/;var FIRST_LINE_LETTER=/(.*)(:first-(line|letter))/;var styleSheets=document.styleSheets;IE7.CSS=new (Fix.extend({parser:new Parser,screen:"",print:"",styles:[],rules:[],pseudoClasses:appVersion<7?"first\\-child":"",dynamicPseudoClasses:{toString:function(){var strings=[];for(var pseudoClass in this){strings.push(pseudoClass)}return s trings.join("|")}},init:function(){var NONE="^\x01$";var CLASS="\\[class=?[^\\]]*\\]";var pseudoClasses=[];if(this.pseudoClasses){pseudoClasses.push(this.pseudoClasses)}var dynamicPseudoClasses=this.dynamicPseudoClasses.toString();if(dynamicPseudoClasses){pseudoClasses.push(dynamicPseudoClasses)}pseudoClasses=pseudoClasses.join("|");var unknown=appVersion<7?["[>+~[(]|([:.])\\w+\\1"]:[CLASS];if(pseudoClasses){unknown.push(":("+pseudoClasses+")")}this.UNKNOWN=new RegExp(unknown.join("|")||NONE,"i");var complex=appVersion<7?["\\[[^\\]]+\\]|[^\\s(\\[]+\\s*[+~]"]:[CLASS];var complexRule=complex.concat();if(pseudoClasses){complexRule.push(":("+pseudoClasses+")")}Rule.COMPLEX=new RegExp(complexRule.join("|")||NONE,"ig");if(this.pseudoClasses){complex.push(":("+this.pseudoClasses+")")}DynamicRule.COMPLEX=new RegExp(complex.join("|")||NONE,"i");DynamicRule.MATCH=new RegExp(dynamicPseudoClasses?"(.*):("+dynamicPseudoClasses+")(.*)":NONE,"i");this.createStyleSheet();this.refresh()},add EventHandler:function(){addEventHandler.apply(null,arguments)},addFix:function(expression,replacement){this.parser.add(expression,replacement)},addRecalc:function(propertyName,test,handler,replacement){test=new RegExp("([{;\\s])"+propertyName+"\\s*:\\s*"+test+"[^;}]*");var id=this.recalcs.length;if(replacement){replacement=propertyName+":"+replacement}this.addFix(test,function(match,$1){return(replacement?$1+replacement:match)+";ie7-"+match.slice(1)+";ie7_recalc"+id+":1"});this.recalcs.push(arguments);return id},apply:function(){this.getInlineStyles();new StyleSheet("screen");this.trash()},createStyleSheet:function(){this.styleSheet=document.createStyleSheet();this.styleSheet.ie7=true;this.styleSheet.owningElement.ie7=true;this.styleSheet.cssText=HEADER},getInlineStyles:function(){var styleSheets=document.getElementsByTagName("style"),styleSheet;for(var i=styleSheets.length-1;(styleSheet=styleSheets[i]);i--){if(!styleSheet.disabled&&!styleSheet.ie7){this.styles.push(styleShe et.innerHTML)}}},getText:function(styleSheet,path){try{var cssText=styleSheet.cssText}catch(e){cssText=""}if(httpRequest){cssText=loadFile(styleSheet.href,path)||cssText}return cssText},recalc:function(){this.screen.recalc();var RECALCS=/ie7_recalc\d+/g;var start=HEADER.match(/[{,]/g).length;var stop=start+(this.screen.cssText.match(/\{/g)||"").length;var rules=this.styleSheet.rules,rule;var calcs,calc,elements,element,i,j,k,id;for(i=start;i<stop;i++){rule=rules[i];var cssText=rule.style.cssText;if(rule&&(calcs=cssText.match(RECALCS))){elements=cssQuery(rule.selectorText);if(elements.length){for(j=0;j<calcs.length;j++){id=calcs[j];calc=IE7.CSS.recalcs[id.slice(10)][2];for(k=0;(element=elements[k]);k++){if(element.currentStyle[id]){calc(element,cssText)}}}}}}},refresh:function(){this.styleSheet.cssText=HEADER+this.screen+this.print},trash:function(){for(var i=0;i<styleSheets.length;i++){if(!styleSheets[i].ie7){try{var cssText=styleSheets[i].cssText}catch(e){cssText=""}if(cssT ext){styleSheets[i].cssText=""}}}}}));var StyleSheet=Base.extend({constructor:function(media){this.media=media;this.load();IE7.CSS[media]=this;IE7.CSS.refresh()},createRule:function(selector,cssText){if(IE7.CSS.UNKNOWN.test(selector)){var match;if(PseudoElement&&(match=selector.match(PseudoElement.MATCH))){return new PseudoElement(match[1],match[2],cssText)}else{if(match=selector.match(DynamicRule.MATCH)){if(!HYPERLINK.test(match[0])||DynamicRule.COMPLEX.test(match[0])){return new DynamicRule(selector,match[1],match[2],match[3],cssText)}}else{return new Rule(selector,cssText)}}}return selector+" {"+cssText+"}"},getText:function(){var _inlineStyles=[].concat(IE7.CSS.styles);var MEDIA=/@media\s+([^{]*)\{([^@]+\})\s*\}/gi;var ALL=/\ball\b|^$/i,SCREEN=/\bscreen\b/i,PRINT=/\bprint\b/i;function _parseMedia(cssText,media){_filterMedia.value=media;return cssText.replace(MEDIA,_filterMedia)}function _filterMedia(match,media,cssText){media=_simpleMedia(media);switch(media){case"screen ":case"print":if(media!=_filterMedia.value){return""}case"all":return cssText}return""}function _simpleMedia(media){if(ALL.test(media)){return"all"}else{if(SCREEN.test(media)){return(PRINT.test(media))?"all":"screen"}else{if(PRINT.test(media)){return"print"}}}}var self=this;function _getCSSText(styleSheet,path,media,level){var cssText="";if(!level){media=_simpleMedia(styleSheet.media);level=0}if(media=="all"||media==self.media){if(level<3){for(var i=0;i<styleSheet.imports.length;i++){cssText+=_getCSSText(styleSheet.imports[i],getPath(styleSheet.href,path),media,level+1)}}cssText+=encode(styleSheet.href?_loadStyleSheet(styleSheet,path):_inlineStyles.pop()||"");cssText=_parseMedia(cssText,self.media)}return cssText}var fileCache={};function _loadStyleSheet(styleSheet,path){var url=makePath(styleSheet.href,path);if(fileCache[url]){return""}fileCache[url]=(styleSheet.disabled)?"":_fixUrls(IE7.CSS.getText(styleSheet,path),getPath(styleSheet.href,path));return fileCache[url]}var U RL=/(url\s*$\s*['"]?)([\w\.]+[^:$]*['"]?\))/gi;function _fixUrls(cssText,pathname){return cssText.replace(URL,"$1"+pathname.slice(0,pathname.lastIndexOf("/")+1)+"$2")}for(var i=0;i<styleSheets.length;i++){if(!styleSheets[i].disabled&&!styleSheets[i].ie7){this.cssText+=_getCSSText(styleSheets[i])}}},load:function(){this.cssText="";this.getText();this.parse();this.cssText=decode(this.cssText);fileCache={}},parse:function(){this.cssText=IE7.CSS.parser.exec(this.cssText);var offset=IE7.CSS.rules.length;var rules=this.cssText.split(BRACE2),rule;var selectors,cssText,i,j;for(i=0;i<rules.length;i++){rule=rules[i].split(BRACE1);selectors=rule[0].split(COMMA);cssText=rule[1];for(j=0;j<selectors.length;j++){selectors[j]=cssText?this.createRule(selectors[j],cssText):""}rules[i]=selectors.join("\n")}this.cssText=rules.join("\n");this.rules=IE7.CSS.rules.slice(offset)},recalc:function(){var rule,i;for(i=0;(rule=this.rules[i]);i++){rule.recalc()}},toString:function(){return"@media "+thi s.media+"{"+this.cssText+"}"}});var PseudoElement;var Rule=IE7.Rule=Base.extend({constructor:function(selector,cssText){this.id=IE7.CSS.rules.length;this.className=Rule.PREFIX+this.id;selector=selector.match(FIRST_LINE_LETTER)||selector||"*";this.selector=selector[1]||selector;this.selectorText=this.parse(this.selector)+(selector[2]||"");this.cssText=cssText;this.MATCH=new RegExp("\\s"+this.className+"(\\s|$)","g");IE7.CSS.rules.push(this);this.init()},init:Undefined,add:function(element){element.className+=" "+this.className},recalc:function(){var match=cssQuery(this.selector);for(var i=0;i<match.length;i++){this.add(match[i])}},parse:function(selector){var simple=selector.replace(Rule.CHILD," ").replace(Rule.COMPLEX,"");if(appVersion<7){simple=simple.replace(Rule.MULTI,"")}var tags=match(simple,Rule.TAGS).length-match(selector,Rule.TAGS).length;var classes=match(simple,Rule.CLASSES).length-match(selector,Rule.CLASSES).length+1;while(classes>0&&Rule.CLASS.test(simple)){simp le=simple.replace(Rule.CLASS,"");classes--}while(tags>0&&Rule.TAG.test(simple)){simple=simple.replace(Rule.TAG,"$1*");tags--}simple+="."+this.className;classes=Math.min(classes,2);tags=Math.min(tags,2);var score=-10*classes-tags;if(score>0){simple=simple+","+Rule.MAP[score]+" "+simple}return simple},remove:function(element){element.className=element.className.replace(this.MATCH,"$1")},toString:function(){return format("%1 {%2}",this.selectorText,this.cssText)}},{CHILD:/>/g,CLASS:/\.[\w-]+/,CLASSES:/[.:\[]/g,MULTI:/(\.[\w-]+)+/g,PREFIX:"ie7_class",TAG:/^\w+|([\s>+~])\w+/,TAGS:/^\w|[\s>+~]\w/g,MAP:{1:"html",2:"html body",10:".ie7_html",11:"html.ie7_html",12:"html.ie7_html body",20:".ie7_html .ie7_body",21:"html.ie7_html .ie7_body",22:"html.ie7_html body.ie7_body"}});var DynamicRule=Rule.extend({constructor:function(selector,attach,dynamicPseudoClass,target,cssText){this.attach=attach||"*";this.dynamicPseudoClass=IE7.CSS.dynamicPseudoClasses[dynamicPseudoClass];this.target=targ et;this.base(selector,cssText)},recalc:function(){var attaches=cssQuery(this.attach),attach;for(var i=0;attach=attaches[i];i++){var target=this.target?cssQuery(this.target,attach):[attach];if(target.length){this.dynamicPseudoClass.apply(attach,target,this)}}}});var DynamicPseudoClass=Base.extend({constructor:function(name,apply){this.name=name;this.apply=apply;this.instances={};IE7.CSS.dynamicPseudoClasses[name]=this},register:function(instance){var _class=instance[2];instance.id=_class.id+instance[0].uniqueID;if(!this.instances[instance.id]){var target=instance[1],j;for(j=0;j<target.length;j++){_class.add(target[j])}this.instances[instance.id]=instance}},unregister:function(instance){if(this.instances[instance.id]){var _class=instance[2];var target=instance[1],j;for(j=0;j<target.length;j++){_class.remove(target[j])}delete this.instances[instance.id]}}});if(appVersion<7){var Hover=new DynamicPseudoClass("hover",function(element){var instance=arguments;IE7.CSS.addEventHandler (element,appVersion<5.5?"onmouseover":"onmouseenter",function(){Hover.register(instance)});IE7.CSS.addEventHandler(element,appVersion<5.5?"onmouseout":"onmouseleave",function(){Hover.unregister(instance)})});addEventHandler(document,"onmouseup",function(){var instances=Hover.instances;for(var i in instances){if(!instances[i][0].contains(event.srcElement)){Hover.unregister(instances[i])}}})}IE7.CSS.addRecalc("[\\w-]+","inherit",function(element,cssText){var inherited=cssText.match(/[\w-]+\s*:\s*inherit/g);for(var i=0;i<inherited.length;i++){var propertyName=inherited[i].replace(/ie7\-|\s*:\s*inherit/g,"").replace(/\-([a-z])/g,function(match,chr){return chr.toUpperCase()});element.runtimeStyle[propertyName]=element.parentElement.currentStyle[propertyName]}});IE7.HTML=new (Fix.extend({fixed:{},init:Undefined,addFix:function(){this.fixes.push(arguments)},apply:function(){for(var i=0;i<this.fixes.length;i++){var match=cssQuery(this.fixes[i][0]);var fix=this.fixes[i][1];for(var j= 0;j<match.length;j++){fix(match[j])}}},addRecalc:function(){this.recalcs.push(arguments)},recalc:function(){for(var i=0;i<this.recalcs.length;i++){var match=cssQuery(this.recalcs[i][0]);var recalc=this.recalcs[i][1],element;var key=Math.pow(2,i);for(var j=0;(element=match[j]);j++){var uniqueID=element.uniqueID;if((this.fixed[uniqueID]&key)==0){element=recalc(element)||element;this.fixed[uniqueID]|=key}}}}}));if(appVersion<7){document.createElement("abbr");IE7.HTML.addRecalc("label",function(label){if(!label.htmlFor){var firstChildControl=cssQuery("input,textarea",label,true);if(firstChildControl){addEventHandler(label,"onclick",function(){firstChildControl.click()})}}})}var NUMERIC="[.\\d]";new function(_){var layout=IE7.Layout=this;HEADER+="*{boxSizing:content-box}";IE7.hasLayout=appVersion<5.5?function(element){return element.clientWidth}:function(element){return element.currentStyle.hasLayout};layout.boxSizing=function(element){if(!IE7.hasLayout(element)){element.style.he ight="0cm";if(element.currentStyle.verticalAlign=="auto"){element.runtimeStyle.verticalAlign="top"}collapseMargins(element)}};function collapseMargins(element){if(element!=viewport&&element.currentStyle.position!="absolute"){collapseMargin(element,"marginTop");collapseMargin(element,"marginBottom")}}function collapseMargin(element,type){if(!element.runtimeStyle[type]){var parentElement=element.parentElement;if(parentElement&&IE7.hasLayout(parentElement)&&!IE7[type=="marginTop"?"_getPreviousElementSibling":"_getNextElementSibling"](element)){return }var child=cssQuery(">*:"+(type=="marginTop"?"first":"last")+"-child",element,true);if(child&&child.currentStyle.styleFloat=="none"&&IE7.hasLayout(child)){collapseMargin(child,type);margin=_getMargin(element,element.currentStyle[type]);childMargin=_getMargin(child,child.currentStyle[type]);if(margin<0||childMargin<0){element.runtimeStyle[type]=margin+childMargin}else{element.runtimeStyle[type]=Math.max(childMargin,margin)}child.run timeStyle[type]="0px"}}}function _getMargin(element,value){return value=="auto"?0:getPixelValue(element,value)}var UNIT=/^[.\d][\w%]*$/,AUTO=/^(auto|0cm)$/;var applyWidth,applyHeight;IE7.Layout.borderBox=function(element){applyWidth(element);applyHeight(element)};var fixWidth=function(HEIGHT){applyWidth=function(element){if(!PERCENT.test(element.currentStyle.width)){fixWidth(element)}collapseMargins(element)};function fixWidth(element,value){if(!element.runtimeStyle.fixedWidth){if(!value){value=element.currentStyle.width}element.runtimeStyle.fixedWidth=(UNIT.test(value))?Math.max(0,getFixedWidth(element,value)):value;setOverrideStyle(element,"width",element.runtimeStyle.fixedWidth)}}function layoutWidth(element){if(!isFixed(element)){var layoutParent=element.offsetParent;while(layoutParent&&!IE7.hasLayout(layoutParent)){layoutParent=layoutParent.offsetParent}}return(layoutParent||viewport).clientWidth}function getPixelWidth(element,value){if(PERCENT.test(value)){return parse Int(parseFloat(value)/100*layoutWidth(element))}return getPixelValue(element,value)}var getFixedWidth=function(element,value){var borderBox=element.currentStyle["box-sizing"]=="border-box";var adjustment=0;if(quirksMode&&!borderBox){adjustment+=getBorderWidth(element)+getWidth(element,"padding")}else{if(!quirksMode&&borderBox){adjustment-=getBorderWidth(element)+getWidth(element,"padding")}}return getPixelWidth(element,value)+adjustment};function getBorderWidth(element){return element.offsetWidth-element.clientWidth}function getWidth(element,type){return getPixelWidth(element,element.currentStyle[type+"Left"])+getPixelWidth(element,element.currentStyle[type+"Right"])}HEADER+="*{minWidth:none;maxWidth:none;min-width:none;max-width:none}";layout.minWidth=function(element){if(element.currentStyle["min-width"]!=null){element.style.minWidth=element.currentStyle["min-width"]}if(register(arguments.callee,element,element.currentStyle.minWidth!="none")){layout.boxSizing(element);fixW idth(element);resizeWidth(element)}};eval("IE7.Layout.maxWidth="+String(layout.minWidth).replace(/min/g,"max"));function resizeWidth(element){var rect=element.getBoundingClientRect();var width=rect.right-rect.left;if(element.currentStyle.minWidth!="none"&&width<=getFixedWidth(element,element.currentStyle.minWidth)){element.runtimeStyle.width=element.currentStyle.minWidth}else{if(element.currentStyle.maxWidth!="none"&&width>=getFixedWidth(element,element.currentStyle.maxWidth)){element.runtimeStyle.width=element.currentStyle.maxWidth}else{element.runtimeStyle.width=element.runtimeStyle.fixedWidth}}}function fixRight(element){if(register(fixRight,element,/^(fixed|absolute)$/.test(element.currentStyle.position)&&getDefinedStyle(element,"left")!="auto"&&getDefinedStyle(element,"right")!="auto"&&AUTO.test(getDefinedStyle(element,"width")))){resizeRight(element);IE7.Layout.boxSizing(element)}}IE7.Layout.fixRight=fixRight;function resizeRight(element){var left=getPixelWidth(element ,element.runtimeStyle._left||element.currentStyle.left);var width=layoutWidth(element)-getPixelWidth(element,element.currentStyle.right)-left-getWidth(element,"margin");if(parseInt(element.runtimeStyle.width)==width){return }element.runtimeStyle.width="";if(isFixed(element)||HEIGHT||element.offsetWidth<width){if(!quirksMode){width-=getBorderWidth(element)+getWidth(element,"padding")}if(width<0){width=0}element.runtimeStyle.fixedWidth=width;setOverrideStyle(element,"width",width)}}var clientWidth=0;addResize(function(){if(!viewport){return }var i,wider=(clientWidth<viewport.clientWidth);clientWidth=viewport.clientWidth;var elements=layout.minWidth.elements;for(i in elements){var element=elements[i];var fixedWidth=(parseInt(element.runtimeStyle.width)==getFixedWidth(element,element.currentStyle.minWidth));if(wider&&fixedWidth){element.runtimeStyle.width=""}if(wider==fixedWidth){resizeWidth(element)}}var elements=layout.maxWidth.elements;for(i in elements){var element=elements[ i];var 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Q=/'/.test(replacement.replace(/\\./g,""))?'"':"'";replacement=replacement.replace(/\n/g,"\\n").replace(/\r/g,"\\r").replace(/\$(\d+)/g,Q+"+(arguments[$1]||"+Q+Q+")+"+Q);replacement=new Function("return "+Q+replacement.replace(/(['"])\1\+(.*)\+\1\1$/,"$1")+Q)}}this.length=RegGrp.count(expression);this.replacement=replacement;this.toString=K(expression)}}),count:function(expression){expression=String(expression).replace(_RG_ESCAPE_CHARS,"").replace(_RG_ESCAPE_BRACKETS,"");return match(expression,_RG_BRACKETS).length}});function extend(object,source){if(object&&source){var proto=(typeof source=="function"?Function:Object).prototype;var i=_HIDDEN.length,key;if(prototyping){while(key=_HIDDEN[--i]){var value=source[key];if(value!=proto[key] ){if(_BASE.test(value)){_override(object,key,value)}else{object[key]=value}}}}for(key in source){if(proto[key]===undefined){var value=source[key];if(object[key]&&typeof 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all":"getElementsByTagName('%3')";replacement+=";for(i%2=0;(e%2=n%2[i%2]);i%2++){";return format(replacement,_index++,_list=_index,tagName.toUpperCase())},">(\\*|[\\w-]+)":function(match,tagName){var children=_list;_wild=tagName=="*";var replacement=_VAR;replacement+=children?"children":"childNodes";if(!_wild&&children){replacement+=".tags('%3')"}replacement+=";for(i%2=0;(e%2=n%2[i%2]);i%2++){";if(_wild){replacement+="if(e%2.nodeType==1){";_wild=_MSIE5}else{if(!children){replacement+="if(e%2.nodeName=='%3'){"}}return format(replacement,_index++,_list=_index,tagName.toUpperCase())},"\\+(\\*|[\\w-]+)":function(match,tagName){var replacement="";if(_wild){replacement+="if(e%1.nodeName!='!'){"}_wild=false;replacement+="e%1=IE7._getNextElementSibling(e%1);if(e%1";if(tagName!="*"){replacement+="&&e%1.nodeName=='%2'"}replacement+="){";return format(replacement,_index,tagName.toUpperCase())},"~(\\*|[\\w-]+)":function(match,tagName){var replacement="";if(_wild){replacement+="if(e%1.no deName!='!'){"}_wild=false;_duplicate=2;replacement+="while(e%1=e%1.nextSibling){if(e%1.ie7_adjacent==IE7._indexed)break;if(";if(tagName=="*"){replacement+="e%1.nodeType==1";if(_MSIE5){replacement+="&&e%1.nodeName!='!'"}}else{replacement+="e%1.nodeName=='%2'"}replacement+="){e%1.ie7_adjacent=IE7._indexed;";return format(replacement,_index,tagName.toUpperCase())},"#([\\w-]+)":function(match,id){_wild=false;var replacement="if(e%1.id=='%2'){";if(_list){replacement+=format("i%1=n%1.length;",_list)}return format(replacement,_index,id)},"\\.([\\w-]+)":function(match,className){_wild=false;reg.push(new RegExp("(^|\\s)"+rescape(className)+"(\\s|$)"));return format("if(e%1.className&&reg[%2].test(e%1.className)){",_index,reg.length-1)},"\\[([\\w-]+)\\s*([^=]?=)?\\s*([^\\]]*)\\]":function(match,attr,operator,value){var alias=_ATTRIBUTES[attr]||attr;if(operator){var getAttribute="e%1.getAttribute('%2',2)";if(!_EVALUATED.test(attr)){getAttribute="e%1.%3||"+getAttribute}attr=format("("+ getAttribute+")",_index,attr,alias)}else{attr=format("IE7._getAttribute(e%1,'%2')",_index,attr)}var replacement=_OPERATORS[operator||""]||"0";if(replacement&&replacement.source){reg.push(new RegExp(format(replacement.source,rescape(cssParser.unescape(value)))));replacement="reg[%2].test(%1)";value=reg.length-1}return"if("+format(replacement,attr,value)+"){"},":+([\\w-]+)(\$([^)]+)\$)?":function(match,pseudoClass,$2,args){pseudoClass=_PSEUDO_CLASSES[pseudoClass];return"if("+(pseudoClass?format(pseudoClass,_index,args||""):"0")+"){"}});var HYPERLINK=/a(#[\w-]+)?(\.[\w-]+)?:(hover|active)/i;var BRACE1=/\s*\{\s*/,BRACE2=/\s*\}\s*/,COMMA=/\s*\,\s*/;var FIRST_LINE_LETTER=/(.*)(:first-(line|letter))/;var styleSheets=document.styleSheets;IE7.CSS=new (Fix.extend({parser:new Parser,screen:"",print:"",styles:[],rules:[],pseudoClasses:appVersion<7?"first\\-child":"",dynamicPseudoClasses:{toString:function(){var strings=[];for(var pseudoClass in this){strings.push(pseudoClass)}return s trings.join("|")}},init:function(){var NONE="^\x01$";var CLASS="\\[class=?[^\\]]*\\]";var pseudoClasses=[];if(this.pseudoClasses){pseudoClasses.push(this.pseudoClasses)}var dynamicPseudoClasses=this.dynamicPseudoClasses.toString();if(dynamicPseudoClasses){pseudoClasses.push(dynamicPseudoClasses)}pseudoClasses=pseudoClasses.join("|");var unknown=appVersion<7?["[>+~[(]|([:.])\\w+\\1"]:[CLASS];if(pseudoClasses){unknown.push(":("+pseudoClasses+")")}this.UNKNOWN=new RegExp(unknown.join("|")||NONE,"i");var complex=appVersion<7?["\\[[^\\]]+\\]|[^\\s(\\[]+\\s*[+~]"]:[CLASS];var complexRule=complex.concat();if(pseudoClasses){complexRule.push(":("+pseudoClasses+")")}Rule.COMPLEX=new RegExp(complexRule.join("|")||NONE,"ig");if(this.pseudoClasses){complex.push(":("+this.pseudoClasses+")")}DynamicRule.COMPLEX=new RegExp(complex.join("|")||NONE,"i");DynamicRule.MATCH=new RegExp(dynamicPseudoClasses?"(.*):("+dynamicPseudoClasses+")(.*)":NONE,"i");this.createStyleSheet();this.refresh()},add EventHandler:function(){addEventHandler.apply(null,arguments)},addFix:function(expression,replacement){this.parser.add(expression,replacement)},addRecalc:function(propertyName,test,handler,replacement){test=new RegExp("([{;\\s])"+propertyName+"\\s*:\\s*"+test+"[^;}]*");var id=this.recalcs.length;if(replacement){replacement=propertyName+":"+replacement}this.addFix(test,function(match,$1){return(replacement?$1+replacement:match)+";ie7-"+match.slice(1)+";ie7_recalc"+id+":1"});this.recalcs.push(arguments);return id},apply:function(){this.getInlineStyles();new StyleSheet("screen");this.trash()},createStyleSheet:function(){this.styleSheet=document.createStyleSheet();this.styleSheet.ie7=true;this.styleSheet.owningElement.ie7=true;this.styleSheet.cssText=HEADER},getInlineStyles:function(){var styleSheets=document.getElementsByTagName("style"),styleSheet;for(var i=styleSheets.length-1;(styleSheet=styleSheets[i]);i--){if(!styleSheet.disabled&&!styleSheet.ie7){this.styles.push(styleShe et.innerHTML)}}},getText:function(styleSheet,path){try{var cssText=styleSheet.cssText}catch(e){cssText=""}if(httpRequest){cssText=loadFile(styleSheet.href,path)||cssText}return cssText},recalc:function(){this.screen.recalc();var RECALCS=/ie7_recalc\d+/g;var start=HEADER.match(/[{,]/g).length;var stop=start+(this.screen.cssText.match(/\{/g)||"").length;var rules=this.styleSheet.rules,rule;var calcs,calc,elements,element,i,j,k,id;for(i=start;i<stop;i++){rule=rules[i];var cssText=rule.style.cssText;if(rule&&(calcs=cssText.match(RECALCS))){elements=cssQuery(rule.selectorText);if(elements.length){for(j=0;j<calcs.length;j++){id=calcs[j];calc=IE7.CSS.recalcs[id.slice(10)][2];for(k=0;(element=elements[k]);k++){if(element.currentStyle[id]){calc(element,cssText)}}}}}}},refresh:function(){this.styleSheet.cssText=HEADER+this.screen+this.print},trash:function(){for(var i=0;i<styleSheets.length;i++){if(!styleSheets[i].ie7){try{var cssText=styleSheets[i].cssText}catch(e){cssText=""}if(cssT ext){styleSheets[i].cssText=""}}}}}));var StyleSheet=Base.extend({constructor:function(media){this.media=media;this.load();IE7.CSS[media]=this;IE7.CSS.refresh()},createRule:function(selector,cssText){if(IE7.CSS.UNKNOWN.test(selector)){var match;if(PseudoElement&&(match=selector.match(PseudoElement.MATCH))){return new PseudoElement(match[1],match[2],cssText)}else{if(match=selector.match(DynamicRule.MATCH)){if(!HYPERLINK.test(match[0])||DynamicRule.COMPLEX.test(match[0])){return new DynamicRule(selector,match[1],match[2],match[3],cssText)}}else{return new Rule(selector,cssText)}}}return selector+" {"+cssText+"}"},getText:function(){var _inlineStyles=[].concat(IE7.CSS.styles);var MEDIA=/@media\s+([^{]*)\{([^@]+\})\s*\}/gi;var ALL=/\ball\b|^$/i,SCREEN=/\bscreen\b/i,PRINT=/\bprint\b/i;function _parseMedia(cssText,media){_filterMedia.value=media;return cssText.replace(MEDIA,_filterMedia)}function _filterMedia(match,media,cssText){media=_simpleMedia(media);switch(media){case"screen ":case"print":if(media!=_filterMedia.value){return""}case"all":return cssText}return""}function _simpleMedia(media){if(ALL.test(media)){return"all"}else{if(SCREEN.test(media)){return(PRINT.test(media))?"all":"screen"}else{if(PRINT.test(media)){return"print"}}}}var self=this;function _getCSSText(styleSheet,path,media,level){var cssText="";if(!level){media=_simpleMedia(styleSheet.media);level=0}if(media=="all"||media==self.media){if(level<3){for(var i=0;i<styleSheet.imports.length;i++){cssText+=_getCSSText(styleSheet.imports[i],getPath(styleSheet.href,path),media,level+1)}}cssText+=encode(styleSheet.href?_loadStyleSheet(styleSheet,path):_inlineStyles.pop()||"");cssText=_parseMedia(cssText,self.media)}return cssText}var fileCache={};function _loadStyleSheet(styleSheet,path){var url=makePath(styleSheet.href,path);if(fileCache[url]){return""}fileCache[url]=(styleSheet.disabled)?"":_fixUrls(IE7.CSS.getText(styleSheet,path),getPath(styleSheet.href,path));return fileCache[url]}var U RL=/(url\s*$\s*['"]?)([\w\.]+[^:$]*['"]?\))/gi;function _fixUrls(cssText,pathname){return cssText.replace(URL,"$1"+pathname.slice(0,pathname.lastIndexOf("/")+1)+"$2")}for(var i=0;i<styleSheets.length;i++){if(!styleSheets[i].disabled&&!styleSheets[i].ie7){this.cssText+=_getCSSText(styleSheets[i])}}},load:function(){this.cssText="";this.getText();this.parse();this.cssText=decode(this.cssText);fileCache={}},parse:function(){this.cssText=IE7.CSS.parser.exec(this.cssText);var offset=IE7.CSS.rules.length;var rules=this.cssText.split(BRACE2),rule;var selectors,cssText,i,j;for(i=0;i<rules.length;i++){rule=rules[i].split(BRACE1);selectors=rule[0].split(COMMA);cssText=rule[1];for(j=0;j<selectors.length;j++){selectors[j]=cssText?this.createRule(selectors[j],cssText):""}rules[i]=selectors.join("\n")}this.cssText=rules.join("\n");this.rules=IE7.CSS.rules.slice(offset)},recalc:function(){var rule,i;for(i=0;(rule=this.rules[i]);i++){rule.recalc()}},toString:function(){return"@media "+thi s.media+"{"+this.cssText+"}"}});var PseudoElement;var Rule=IE7.Rule=Base.extend({constructor:function(selector,cssText){this.id=IE7.CSS.rules.length;this.className=Rule.PREFIX+this.id;selector=selector.match(FIRST_LINE_LETTER)||selector||"*";this.selector=selector[1]||selector;this.selectorText=this.parse(this.selector)+(selector[2]||"");this.cssText=cssText;this.MATCH=new RegExp("\\s"+this.className+"(\\s|$)","g");IE7.CSS.rules.push(this);this.init()},init:Undefined,add:function(element){element.className+=" "+this.className},recalc:function(){var match=cssQuery(this.selector);for(var i=0;i<match.length;i++){this.add(match[i])}},parse:function(selector){var simple=selector.replace(Rule.CHILD," ").replace(Rule.COMPLEX,"");if(appVersion<7){simple=simple.replace(Rule.MULTI,"")}var tags=match(simple,Rule.TAGS).length-match(selector,Rule.TAGS).length;var classes=match(simple,Rule.CLASSES).length-match(selector,Rule.CLASSES).length+1;while(classes>0&&Rule.CLASS.test(simple)){simp le=simple.replace(Rule.CLASS,"");classes--}while(tags>0&&Rule.TAG.test(simple)){simple=simple.replace(Rule.TAG,"$1*");tags--}simple+="."+this.className;classes=Math.min(classes,2);tags=Math.min(tags,2);var score=-10*classes-tags;if(score>0){simple=simple+","+Rule.MAP[score]+" "+simple}return simple},remove:function(element){element.className=element.className.replace(this.MATCH,"$1")},toString:function(){return format("%1 {%2}",this.selectorText,this.cssText)}},{CHILD:/>/g,CLASS:/\.[\w-]+/,CLASSES:/[.:\[]/g,MULTI:/(\.[\w-]+)+/g,PREFIX:"ie7_class",TAG:/^\w+|([\s>+~])\w+/,TAGS:/^\w|[\s>+~]\w/g,MAP:{1:"html",2:"html body",10:".ie7_html",11:"html.ie7_html",12:"html.ie7_html body",20:".ie7_html .ie7_body",21:"html.ie7_html .ie7_body",22:"html.ie7_html body.ie7_body"}});var DynamicRule=Rule.extend({constructor:function(selector,attach,dynamicPseudoClass,target,cssText){this.attach=attach||"*";this.dynamicPseudoClass=IE7.CSS.dynamicPseudoClasses[dynamicPseudoClass];this.target=targ et;this.base(selector,cssText)},recalc:function(){var attaches=cssQuery(this.attach),attach;for(var i=0;attach=attaches[i];i++){var target=this.target?cssQuery(this.target,attach):[attach];if(target.length){this.dynamicPseudoClass.apply(attach,target,this)}}}});var DynamicPseudoClass=Base.extend({constructor:function(name,apply){this.name=name;this.apply=apply;this.instances={};IE7.CSS.dynamicPseudoClasses[name]=this},register:function(instance){var _class=instance[2];instance.id=_class.id+instance[0].uniqueID;if(!this.instances[instance.id]){var target=instance[1],j;for(j=0;j<target.length;j++){_class.add(target[j])}this.instances[instance.id]=instance}},unregister:function(instance){if(this.instances[instance.id]){var _class=instance[2];var target=instance[1],j;for(j=0;j<target.length;j++){_class.remove(target[j])}delete this.instances[instance.id]}}});if(appVersion<7){var Hover=new DynamicPseudoClass("hover",function(element){var instance=arguments;IE7.CSS.addEventHandler (element,appVersion<5.5?"onmouseover":"onmouseenter",function(){Hover.register(instance)});IE7.CSS.addEventHandler(element,appVersion<5.5?"onmouseout":"onmouseleave",function(){Hover.unregister(instance)})});addEventHandler(document,"onmouseup",function(){var instances=Hover.instances;for(var i in instances){if(!instances[i][0].contains(event.srcElement)){Hover.unregister(instances[i])}}})}IE7.CSS.addRecalc("[\\w-]+","inherit",function(element,cssText){var inherited=cssText.match(/[\w-]+\s*:\s*inherit/g);for(var i=0;i<inherited.length;i++){var propertyName=inherited[i].replace(/ie7\-|\s*:\s*inherit/g,"").replace(/\-([a-z])/g,function(match,chr){return chr.toUpperCase()});element.runtimeStyle[propertyName]=element.parentElement.currentStyle[propertyName]}});IE7.HTML=new (Fix.extend({fixed:{},init:Undefined,addFix:function(){this.fixes.push(arguments)},apply:function(){for(var i=0;i<this.fixes.length;i++){var match=cssQuery(this.fixes[i][0]);var fix=this.fixes[i][1];for(var j= 0;j<match.length;j++){fix(match[j])}}},addRecalc:function(){this.recalcs.push(arguments)},recalc:function(){for(var i=0;i<this.recalcs.length;i++){var match=cssQuery(this.recalcs[i][0]);var recalc=this.recalcs[i][1],element;var key=Math.pow(2,i);for(var j=0;(element=match[j]);j++){var uniqueID=element.uniqueID;if((this.fixed[uniqueID]&key)==0){element=recalc(element)||element;this.fixed[uniqueID]|=key}}}}}));if(appVersion<7){document.createElement("abbr");IE7.HTML.addRecalc("label",function(label){if(!label.htmlFor){var firstChildControl=cssQuery("input,textarea",label,true);if(firstChildControl){addEventHandler(label,"onclick",function(){firstChildControl.click()})}}})}var NUMERIC="[.\\d]";new function(_){var layout=IE7.Layout=this;HEADER+="*{boxSizing:content-box}";IE7.hasLayout=appVersion<5.5?function(element){return element.clientWidth}:function(element){return element.currentStyle.hasLayout};layout.boxSizing=function(element){if(!IE7.hasLayout(element)){element.style.he ight="0cm";if(element.currentStyle.verticalAlign=="auto"){element.runtimeStyle.verticalAlign="top"}collapseMargins(element)}};function collapseMargins(element){if(element!=viewport&&element.currentStyle.position!="absolute"){collapseMargin(element,"marginTop");collapseMargin(element,"marginBottom")}}function collapseMargin(element,type){if(!element.runtimeStyle[type]){var parentElement=element.parentElement;if(parentElement&&IE7.hasLayout(parentElement)&&!IE7[type=="marginTop"?"_getPreviousElementSibling":"_getNextElementSibling"](element)){return }var child=cssQuery(">*:"+(type=="marginTop"?"first":"last")+"-child",element,true);if(child&&child.currentStyle.styleFloat=="none"&&IE7.hasLayout(child)){collapseMargin(child,type);margin=_getMargin(element,element.currentStyle[type]);childMargin=_getMargin(child,child.currentStyle[type]);if(margin<0||childMargin<0){element.runtimeStyle[type]=margin+childMargin}else{element.runtimeStyle[type]=Math.max(childMargin,margin)}child.run timeStyle[type]="0px"}}}function _getMargin(element,value){return value=="auto"?0:getPixelValue(element,value)}var UNIT=/^[.\d][\w%]*$/,AUTO=/^(auto|0cm)$/;var applyWidth,applyHeight;IE7.Layout.borderBox=function(element){applyWidth(element);applyHeight(element)};var fixWidth=function(HEIGHT){applyWidth=function(element){if(!PERCENT.test(element.currentStyle.width)){fixWidth(element)}collapseMargins(element)};function fixWidth(element,value){if(!element.runtimeStyle.fixedWidth){if(!value){value=element.currentStyle.width}element.runtimeStyle.fixedWidth=(UNIT.test(value))?Math.max(0,getFixedWidth(element,value)):value;setOverrideStyle(element,"width",element.runtimeStyle.fixedWidth)}}function layoutWidth(element){if(!isFixed(element)){var layoutParent=element.offsetParent;while(layoutParent&&!IE7.hasLayout(layoutParent)){layoutParent=layoutParent.offsetParent}}return(layoutParent||viewport).clientWidth}function getPixelWidth(element,value){if(PERCENT.test(value)){return parse Int(parseFloat(value)/100*layoutWidth(element))}return getPixelValue(element,value)}var getFixedWidth=function(element,value){var borderBox=element.currentStyle["box-sizing"]=="border-box";var adjustment=0;if(quirksMode&&!borderBox){adjustment+=getBorderWidth(element)+getWidth(element,"padding")}else{if(!quirksMode&&borderBox){adjustment-=getBorderWidth(element)+getWidth(element,"padding")}}return getPixelWidth(element,value)+adjustment};function getBorderWidth(element){return element.offsetWidth-element.clientWidth}function getWidth(element,type){return getPixelWidth(element,element.currentStyle[type+"Left"])+getPixelWidth(element,element.currentStyle[type+"Right"])}HEADER+="*{minWidth:none;maxWidth:none;min-width:none;max-width:none}";layout.minWidth=function(element){if(element.currentStyle["min-width"]!=null){element.style.minWidth=element.currentStyle["min-width"]}if(register(arguments.callee,element,element.currentStyle.minWidth!="none")){layout.boxSizing(element);fixW idth(element);resizeWidth(element)}};eval("IE7.Layout.maxWidth="+String(layout.minWidth).replace(/min/g,"max"));function resizeWidth(element){var rect=element.getBoundingClientRect();var width=rect.right-rect.left;if(element.currentStyle.minWidth!="none"&&width<=getFixedWidth(element,element.currentStyle.minWidth)){element.runtimeStyle.width=element.currentStyle.minWidth}else{if(element.currentStyle.maxWidth!="none"&&width>=getFixedWidth(element,element.currentStyle.maxWidth)){element.runtimeStyle.width=element.currentStyle.maxWidth}else{element.runtimeStyle.width=element.runtimeStyle.fixedWidth}}}function fixRight(element){if(register(fixRight,element,/^(fixed|absolute)$/.test(element.currentStyle.position)&&getDefinedStyle(element,"left")!="auto"&&getDefinedStyle(element,"right")!="auto"&&AUTO.test(getDefinedStyle(element,"width")))){resizeRight(element);IE7.Layout.boxSizing(element)}}IE7.Layout.fixRight=fixRight;function resizeRight(element){var left=getPixelWidth(element ,element.runtimeStyle._left||element.currentStyle.left);var width=layoutWidth(element)-getPixelWidth(element,element.currentStyle.right)-left-getWidth(element,"margin");if(parseInt(element.runtimeStyle.width)==width){return }element.runtimeStyle.width="";if(isFixed(element)||HEIGHT||element.offsetWidth<width){if(!quirksMode){width-=getBorderWidth(element)+getWidth(element,"padding")}if(width<0){width=0}element.runtimeStyle.fixedWidth=width;setOverrideStyle(element,"width",width)}}var clientWidth=0;addResize(function(){if(!viewport){return }var i,wider=(clientWidth<viewport.clientWidth);clientWidth=viewport.clientWidth;var elements=layout.minWidth.elements;for(i in elements){var element=elements[i];var fixedWidth=(parseInt(element.runtimeStyle.width)==getFixedWidth(element,element.currentStyle.minWidth));if(wider&&fixedWidth){element.runtimeStyle.width=""}if(wider==fixedWidth){resizeWidth(element)}}var elements=layout.maxWidth.elements;for(i in elements){var element=elements[ i];var fixedWidth=(parseInt(element.runtimeStyle.width)==getFixedWidth(element,element.currentStyle.maxWidth));if(!wider&&fixedWidth){element.runtimeStyle.width=""}if(wider!=fixedWidth){resizeWidth(element)}}for(i in fixRight.elements){resizeRight(fixRight.elements[i])}});if(quirksMode){IE7.CSS.addRecalc("width",NUMERIC,applyWidth)}if(appVersion<7){IE7.CSS.addRecalc("min-width",NUMERIC,layout.minWidth);IE7.CSS.addRecalc("max-width",NUMERIC,layout.maxWidth);IE7.CSS.addRecalc("right",NUMERIC,fixRight)}};eval("var fixHeight="+rotate(fixWidth));fixWidth();fixHeight(true)};var BLANK_GIF=makePath("blank.gif",path);var ALPHA_IMAGE_LOADER="DXImageTransform.Microsoft.AlphaImageLoader";var PNG_FILTER="progid:"+ALPHA_IMAGE_LOADER+"(src='%1',sizingMethod='%2')";var PNG;var filtered=[];function fixImage(element){if(PNG.test(element.src)){var image=new Image(element.width,element.height);image.onload=function(){element.width=image.width;element.height=image.height;image=null};image.src=el ement.src;element.pngSrc=element.src;addFilter(element)}}if(appVersion>=5.5&&appVersion<7){IE7.CSS.addFix(/background(-image)?\s*:\s*([^};]*)?url$([^$]+)\)([^;}]*)?/,function(match,$1,$2,url,$4){url=getString(url);return PNG.test(url)?"filter:"+format(PNG_FILTER,url,"crop")+";zoom:1;background"+($1||"")+":"+($2||"")+"none"+($4||""):match});IE7.HTML.addRecalc("img,input",function(element){if(element.tagName=="INPUT"&&element.type!="image"){return }fixImage(element);addEventHandler(element,"onpropertychange",function(){if(!printing&&event.propertyName=="src"&&element.src.indexOf(BLANK_GIF)==-1){fixImage(element)}})});var printing=false;addEventHandler(window,"onbeforeprint",function(){printing=true;for(var i=0;i<filtered.length;i++){removeFilter(filtered[i])}});addEventHandler(window,"onafterprint",function(){for(var i=0;i<filtered.length;i++){addFilter(filtered[i])}printing=false})}function addFilter(element,sizingMethod){var filter=element.filters[ALPHA_IMAGE_LOADER];if(fi lter){filter.src=element.src;filter.enabled=true}else{element.runtimeStyle.filter=format(PNG_FILTER,element.src,sizingMethod||"scale");filtered.push(element)}element.src=BLANK_GIF}function removeFilter(element){element.src=element.pngSrc;element.filters[ALPHA_IMAGE_LOADER].enabled=false}new function(_){if(appVersion>=7){return }IE7.CSS.addRecalc("position","fixed",_positionFixed,"absolute");IE7.CSS.addRecalc("background(-attachment)?","[^};]*fixed",_backgroundFixed);var $viewport=quirksMode?"body":"documentElement";function _fixBackground(){if(body.currentStyle.backgroundAttachment!="fixed"){if(body.currentStyle.backgroundImage=="none"){body.runtimeStyle.backgroundRepeat="no-repeat";body.runtimeStyle.backgroundImage="url("+BLANK_GIF+")"}body.runtimeStyle.backgroundAttachment="fixed"}_fixBackground=Undefined}var _tmp=createTempElement("img");function _isFixed(element){return element?isFixed(element)||_isFixed(element.parentElement):false}function _setExpression(element,proper tyName,expression){setTimeout("document.all."+element.uniqueID+".runtimeStyle.setExpression('"+propertyName+"','"+expression+"')",0)}function _backgroundFixed(element){if(register(_backgroundFixed,element,element.currentStyle.backgroundAttachment=="fixed"&&!element.contains(body))){_fixBackground();bgLeft(element);bgTop(element);_backgroundPosition(element)}}function _backgroundPosition(element){_tmp.src=element.currentStyle.backgroundImage.slice(5,-2);var parentElement=element.canHaveChildren?element:element.parentElement;parentElement.appendChild(_tmp);setOffsetLeft(element);setOffsetTop(element);parentElement.removeChild(_tmp)}function bgLeft(element){element.style.backgroundPositionX=element.currentStyle.backgroundPositionX;if(!_isFixed(element)){_setExpression(element,"backgroundPositionX","(parseInt(runtimeStyle.offsetLeft)+document."+$viewport+".scrollLeft)||0")}}eval(rotate(bgLeft));function setOffsetLeft(element){var propertyName=_isFixed(element)?"backgroundPositio nX":"offsetLeft";element.runtimeStyle[propertyName]=getOffsetLeft(element,element.style.backgroundPositionX)-element.getBoundingClientRect().left-element.clientLeft+2}eval(rotate(setOffsetLeft));function getOffsetLeft(element,position){switch(position){case"left":case"top":return 0;case"right":case"bottom":return viewport.clientWidth-_tmp.offsetWidth;case"center":return(viewport.clientWidth-_tmp.offsetWidth)/2;default:if(PERCENT.test(position)){return parseInt((viewport.clientWidth-_tmp.offsetWidth)*parseFloat(position)/100)}_tmp.style.left=position;return _tmp.offsetLeft}}eval(rotate(getOffsetLeft));function _positionFixed(element){if(register(_positionFixed,element,isFixed(element))){setOverrideStyle(element,"position","absolute");setOverrideStyle(element,"left",element.currentStyle.left);setOverrideStyle(element,"top",element.currentStyle.top);_fixBackground();IE7.Layout.fixRight(element);_foregroundPosition(element)}}function _foregroundPosition(element,recalc){positionT op(element,recalc);positionLeft(element,recalc,true);if(!element.runtimeStyle.autoLeft&&element.currentStyle.marginLeft=="auto"&&element.currentStyle.right!="auto"){var left=viewport.clientWidth-getPixelWidth(element,element.currentStyle.right)-getPixelWidth(element,element.runtimeStyle._left)-element.clientWidth;if(element.currentStyle.marginRight=="auto"){left=parseInt(left/2)}if(_isFixed(element.offsetParent)){element.runtimeStyle.pixelLeft+=left}else{element.runtimeStyle.shiftLeft=left}}clipWidth(element);clipHeight(element)}function clipWidth(element){var fixWidth=element.runtimeStyle.fixWidth;element.runtimeStyle.borderRightWidth="";element.runtimeStyle.width=fixWidth?getPixelWidth(element,fixWidth):"";if(element.currentStyle.width!="auto"){var rect=element.getBoundingClientRect();var width=element.offsetWidth-viewport.clientWidth+rect.left-2;if(width>=0){element.runtimeStyle.borderRightWidth="0px";width=Math.max(getPixelValue(element,element.currentStyle.width)-width, 0);setOverrideStyle(element,"width",width);return width}}}eval(rotate(clipWidth));function positionLeft(element,recalc){if(!recalc&&PERCENT.test(element.currentStyle.width)){element.runtimeStyle.fixWidth=element.currentStyle.width}if(element.runtimeStyle.fixWidth){element.runtimeStyle.width=getPixelWidth(element,element.runtimeStyle.fixWidth)}element.runtimeStyle.shiftLeft=0;element.runtimeStyle._left=element.currentStyle.left;element.runtimeStyle.autoLeft=element.currentStyle.right!="auto"&&element.currentStyle.left=="auto";element.runtimeStyle.left="";element.runtimeStyle.screenLeft=getScreenLeft(element);element.runtimeStyle.pixelLeft=element.runtimeStyle.screenLeft;if(!recalc&&!_isFixed(element.offsetParent)){_setExpression(element,"pixelLeft","runtimeStyle.screenLeft+runtimeStyle.shiftLeft+document."+$viewport+".scrollLeft")}}eval(rotate(positionLeft));function getScreenLeft(element){var screenLeft=element.offsetLeft,nested=1;if(element.runtimeStyle.autoLeft){screenLeft =viewport.clientWidth-element.offsetWidth-getPixelWidth(element,element.currentStyle.right)}if(element.currentStyle.marginLeft!="auto"){screenLeft-=getPixelWidth(element,element.currentStyle.marginLeft)}while(element=element.offsetParent){if(element.currentStyle.position!="static"){nested=-1}screenLeft+=element.offsetLeft*nested}return screenLeft}eval(rotate(getScreenLeft));function getPixelWidth(element,value){return PERCENT.test(value)?parseInt(parseFloat(value)/100*viewport.clientWidth):getPixelValue(element,value)}eval(rotate(getPixelWidth));function _resize(){var elements=_backgroundFixed.elements;for(var i in elements){_backgroundPosition(elements[i])}elements=_positionFixed.elements;for(i in elements){_foregroundPosition(elements[i],true);_foregroundPosition(elements[i],true)}_timer=0}var _timer;addResize(function(){if(!_timer){_timer=setTimeout(_resize,0)}})};var WRAPPER_STYLE={backgroundColor:"transparent",backgroundImage:"none",backgroundPositionX:null,backgroundPo sitionY:null,backgroundRepeat:null,borderTopWidth:0,borderRightWidth:0,borderBottomWidth:0,borderLeftStyle:"none",borderTopStyle:"none",borderRightStyle:"none",borderBottomStyle:"none",borderLeftWidth:0,height:null,marginTop:0,marginBottom:0,marginRight:0,marginLeft:0,width:"100%"};IE7.CSS.addRecalc("overflow","visible",function(element){if(element.parentNode.ie7_wrapped){return }if(IE7.Layout&&element.currentStyle["max-height"]!="auto"){IE7.Layout.maxHeight(element)}if(element.currentStyle.marginLeft=="auto"){element.style.marginLeft=0}if(element.currentStyle.marginRight=="auto"){element.style.marginRight=0}var wrapper=document.createElement(ANON);wrapper.ie7_wrapped=element;for(var propertyName in WRAPPER_STYLE){wrapper.style[propertyName]=element.currentStyle[propertyName];if(WRAPPER_STYLE[propertyName]!=null){element.runtimeStyle[propertyName]=WRAPPER_STYLE[propertyName]}}wrapper.style.display="block";wrapper.style.position="relative";element.runtimeStyle.position="absol ute";element.parentNode.insertBefore(wrapper,element);wrapper.appendChild(element)});function ie7Quirks(){var FONT_SIZES="xx-small,x-small,small,medium,large,x-large,xx-large".split(",");for(var i=0;i<FONT_SIZES.length;i++){FONT_SIZES[FONT_SIZES[i]]=FONT_SIZES[i-1]||"0.67em"}IE7.CSS.addFix(/(font(-size)?\s*:\s*)([\w.-]+)/,function(match,label,size,value){return label+(FONT_SIZES[value]||value)});if(appVersion<6){var NEGATIVE=/^\-/,LENGTH=/(em|ex)$/i;var EM=/em$/i,EX=/ex$/i;getPixelValue=function(element,value){if(PIXEL.test(value)){return parseInt(value)||0}var scale=NEGATIVE.test(value)?-1:1;if(LENGTH.test(value)){scale*=getFontScale(element)}temp.style.width=(scale<0)?value.slice(1):value;body.appendChild(temp);value=scale*temp.offsetWidth;temp.removeNode();return parseInt(value)};var temp=createTempElement();function getFontScale(element){var scale=1;temp.style.fontFamily=element.currentStyle.fontFamily;temp.style.lineHeight=element.currentStyle.lineHeight;while(element!= body){var fontSize=element.currentStyle["ie7-font-size"];if(fontSize){if(EM.test(fontSize)){scale*=parseFloat(fontSize)}else{if(PERCENT.test(fontSize)){scale*=(parseFloat(fontSize)/100)}else{if(EX.test(fontSize)){scale*=(parseFloat(fontSize)/2)}else{temp.style.fontSize=fontSize;return 1}}}}element=element.parentElement}return scale}IE7.CSS.addFix(/cursor\s*:\s*pointer/,"cursor:hand");IE7.CSS.addFix(/display\s*:\s*list-item/,"display:block")}function fixMargin(element){if(appVersion<5.5){IE7.Layout.boxSizing(element.parentElement)}var parent=element.parentElement;var margin=parent.offsetWidth-element.offsetWidth-getPaddingWidth(parent);var autoRight=(element.currentStyle["ie7-margin"]&&element.currentStyle.marginRight=="auto")||element.currentStyle["ie7-margin-right"]=="auto";switch(parent.currentStyle.textAlign){case"right":margin=autoRight?parseInt(margin/2):0;element.runtimeStyle.marginRight=margin+"px";break;case"center":if(autoRight){margin=0}default:if(autoRight){margin /=2}element.runtimeStyle.marginLeft=parseInt(margin)+"px"}}function getPaddingWidth(element){return getPixelValue(element,element.currentStyle.paddingLeft)+getPixelValue(element,element.currentStyle.paddingRight)}IE7.CSS.addRecalc("margin(-left|-right)?","[^};]*auto",function(element){if(register(fixMargin,element,element.parentElement&&element.currentStyle.display=="block"&&element.currentStyle.marginLeft=="auto"&&element.currentStyle.position!="absolute")){fixMargin(element)}});addResize(function(){for(var i in fixMargin.elements){var element=fixMargin.elements[i];element.runtimeStyle.marginLeft=element.runtimeStyle.marginRight="";fixMargin(element)}})}IE7._isEmpty=function(element){element=element.firstChild;while(element){if(element.nodeType==3||(element.nodeType==1&&element.nodeName!="!")){return false}element=element.nextSibling}return true};IE7._isLang=function(element,code){while(element&&!element.getAttribute("lang")){element=element.parentNode}return element&&new R egExp("^"+rescape(code),"i").test(element.getAttribute("lang"))};function _nthChild(match,args,position,last){last=/last/i.test(match)?last+"+1-":"";if(!isNaN(args)){args="0n+"+args}else{if(args=="even"){args="2n"}else{if(args=="odd"){args="2n+1"}}}args=args.split("n");var a=args[0]?(args[0]=="-")?-1:parseInt(args[0]):1;var b=parseInt(args[1])||0;var negate=a<0;if(negate){a=-a;if(a==1){b++}}var query=format(a==0?"%3%7"+(last+b):"(%4%3-%2)%6%1%70%5%4%3>=%2",a,b,position,last,"&&","%","==");if(negate){query="!("+query+")"}return query}_PSEUDO_CLASSES={link:"e%1.currentStyle['ie7-link']=='link'",visited:"e%1.currentStyle['ie7-link']=='visited'",checked:"e%1.checked",contains:"e%1.innerText.indexOf('%2')!=-1",disabled:"e%1.isDisabled",empty:"IE7._isEmpty(e%1)",enabled:"e%1.disabled===false","first-child":"!IE7._getPreviousElementSibling(e%1)",lang:"IE7._isLang(e%1,'%2')","last-child":"!IE7._getNextElementSibling(e%1)","only-child":"!IE7._getPreviousElementSibling(e%1)&&!IE7._get NextElementSibling(e%1)",target:"e%1.id==location.hash.slice(1)",indeterminate:"e%1.indeterminate"};IE7._register=function(element){if(element.rows){element.ie7_length=element.rows.length;element.ie7_lookup="rowIndex"}else{if(element.cells){element.ie7_length=element.cells.length;element.ie7_lookup="cellIndex"}else{if(element.ie7_indexed!=IE7._indexed){var index=0;var child=element.firstChild;while(child){if(child.nodeType==1&&child.nodeName!="!"){child.ie7_index=++index}child=child.nextSibling}element.ie7_length=index;element.ie7_lookup="ie7_index"}}}element.ie7_indexed=IE7._indexed;return element};var keys=cssParser[_KEYS];var pseudoClass=keys[keys.length-1];keys.length--;cssParser.merge({":not\$(\\*|[\\w-]+)?([^)]*)\$":function(match,tagName,filters){var replacement=(tagName&&tagName!="*")?format("if(e%1.nodeName=='%2'){",_index,tagName.toUpperCase()):"";replacement+=cssParser.exec(filters);return"if(!"+replacement.slice(2,-1).replace(/\)\{if$/g,"&&")+"){"},":nth(-last 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this.store[A];return this};CookieSet.prototype.removeAll=function(A){this.store={};return this};CookieSet.prototype.contains=function(A){return(A in this.store)};CookieSet.prototype.save=function(){t=[];for(key in this.store){if(key!=""){t.push(key)}}q.cookie(this.cookie_name,t.join("|"));return this} \ No newline at end of file +function CookieSet(A){this.cookie_name=A;this.store=store={};q.each((q.cookie(A)||"").split("|"),function(C,B){store[B]=true})}CookieSet.prototype.add=function(A){this.store[A]=true;return this};CookieSet.prototype.remove=function(A){delete this.store[A];return this};CookieSet.prototype.removeAll=function(A){this.store={};return this};CookieSet.prototype.contains=function(A){return(A in this.store)};CookieSet.prototype.save=function(){t=[];for(key in this.store){if(key!=""){t.push(key)}}q.cookie(this.cookie_name,t.join("|"));return this}; \ No newline at end of file diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Thu Aug 07 11:41:59 2008 -0400 +++ b/static/scripts/packed/galaxy.base.js Thu Aug 07 19:28:42 2008 -0400 @@ -1,1 +1,1 @@ -jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))})}) \ No newline at end of file +jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[@popupmenu]").each(function(){var B={};$(this).find("a").each(function(){var C=$(this).attr("confirm"),D=$(this).attr("href"),E=$(this).attr("target");B[$(this).text()]=function(){if(!C||confirm(C)){var F=window;if(E=="_parent"){F=window.parent}F.location=D}}});var A=$("#"+$(this).attr("popupmenu"));make_popupmenu(A,B);$(this).remove();A.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){var A=$("<div id='popup-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; 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=false}else{C=jq(B).position().left;jq(A).css("left",hidden_width);if(document.recalc){document.recalc()}jq(B).removeClass("hover");jq(E).animate({left:-C},"fast");jq(B).animate({left:-1},"fast",function(){jq(this).addClass("hidden")});D=true}};jq(B).hover(function(){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(F,G){jq("#DD-helper").show()},stop:function(F,G){jq("#DD-helper").hide();return false},drag:function(F,G){x=G.position.left;x=Math.min(400,Math.max(100,x));if(D){jq(E).css("left",0);jq(B).removeClass("hidden");D=false}resize(x);G.position.left=x;G.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show()}function make_right_panel(A,E,G){var I=false;var F=false;var C=null;var D=function(J){jq(A).css("width",J);jq(E).css("right",J+9);jq(G).css("right",J).css("left","");if(document.recalc){document.recalc()}};var H=function(){if(I){jq(G).removeClass("hover");jq(G).anima 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false},drag:function(F,G){x=G.position.left;x=Math.min(400,Math.max(100,x));if(D){jq(E).css("left",0);jq(B).removeClass("hidden");D=false}resize(x);G.position.left=x;G.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show()}function make_right_panel(A,E,G){var I=false;var F=false;var C=null;var D=function(J){jq(A).css("width",J);jq(E).css("right",J+9);jq(G).css("right",J).css("left","");if(document.recalc){document.recalc()}};var H=function(){if(I){jq(G).removeClass("hover");jq(G).animate({right:C},"fast");jq(A).css("right",-C).show().animate({right:0},"fast",function(){D(C);jq(G).removeClass("hidden")});I=false}else{C=jq(document).width()-jq(G).position().left-border_tweak;jq(E).css("right",hidden_width+1);if(document.recalc){document.recalc()}jq (G).removeClass("hover");jq(A).animate({right:-C},"fast");jq(G).animate({right:-1},"fast",function(){jq(this).addClass("hidden")});I=true}F=false};var B=function(J){var K=jq(E).width()-(I?C:0);if(K<J){if(!I){H();F=true}}else{if(F){H();F=false}}};jq(G).hover(function(){jq(this).addClass("hover")},function(){jq(this).removeClass("hover")}).draggable({start:function(J,K){jq("#DD-helper").show()},stop:function(J,K){x=K.position.left;w=jq(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);D(w-x-border_tweak);jq("#DD-helper").hide();return false},click:function(){H()},drag:function(J,K){x=K.position.left;w=jq(window).width();x=Math.min(w-100,x);x=Math.max(w-400,x);if(I){jq(A).css("right",0);jq(G).removeClass("hidden");I=false}D(w-x-border_tweak);K.position.left=x;K.position.top=$(this).data("draggable").originalPosition.top}}).find("div").show();return{handle_minwidth_hint:B}}function make_popupmenu(D,B){var A=$("<div class='popupmenu'><div class='popupmenu-top'><div class='p opupmenu-top-inner'/></div></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(){var F=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.top+$(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)}; \ No newline at end of file diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/galaxy.ui.scrollPanel.js --- a/static/scripts/packed/galaxy.ui.scrollPanel.js Thu Aug 07 11:41:59 2008 -0400 +++ b/static/scripts/packed/galaxy.ui.scrollPanel.js Thu Aug 07 19:28:42 2008 -0400 @@ -1,1 +1,1 @@ -$.ui.plugin.add("draggable","scrollPanel",{drag:function(G,H){var J=$(this).data("draggable");clearTimeout(J.timeout);var B=H.options,D=J.element,A=B.panel,C=A.position(),I=A.width(),E=A.height();viewport=A.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),element_w=D.width(),element_h=D.height(),moved=false,close=5,nudge=23,p_min_x=-(I-viewport_w),p_min_y=-(E-viewport_h),p_max_x=0,p_max_y=0,min_vis_x=-C.left,max_vis_x=min_vis_x+viewport_w,min_vis_y=-C.top,max_vis_y=min_vis_y+viewport_h,mouse_x=H.position.left+J.offset.click.left;mouse_y=H.position.top+J.offset.click.top;if((C.left<p_max_x)&&(mouse_x-close<min_vis_x)){var K=Math.min(nudge,p_max_x-C.left);A.css("left",C.left+K);moved=true;J.offset.parent.left+=K;H.position.left-=K}if((!moved)&&(C.left>p_min_x)&&(mouse_x+close>max_vis_x)){var K=Math.min(nudge,C.left-p_min_x);A.css("left",C.left-K);moved=true;J.offset.parent.left-=K;H.position.left+=K}if((!moved)&&(C.top<p_max_y)&&(mouse_y-close<min_vis_y)){var K=Math.min(nudge,p_max_y-C.top);A.css("top",C.top+K);var F=A.position().top-C.top;J.offset.parent.top+=F;H.position.top-=F;moved=true}if((!moved)&&(C.top>p_min_y)&&(mouse_y+close>max_vis_y)){var K=Math.min(nudge,C.top-p_min_x);A.css("top",(C.top-K)+"px");var F=C.top-A.position().top;J.offset.parent.top-=F;H.position.top+=F;moved=true}if(moved){$.ui.ddmanager.prepareOffsets(J,G)}H.position.left=Math.max(H.position.left,0);H.position.top=Math.max(H.position.top,0);H.position.left=Math.min(H.position.left,I-element_w);H.position.top=Math.min(H.position.top,E-element_h);if(moved){J.old_e=G;J.timeout=setTimeout(function(){J.mouseMove(G)},50)}}}); \ No newline at end of file +$.ui.plugin.add("draggable","scrollPanel",{drag:function(G,H){var J=$(this).data("draggable");clearTimeout(J.timeout);var B=H.options,D=J.element,A=B.panel,C=A.position(),I=A.width(),E=A.height();viewport=A.parent();viewport_w=viewport.width(),viewport_h=viewport.height(),element_w=D.width(),element_h=D.height(),moved=false,close=5,nudge=23,p_min_x=-(I-viewport_w),p_min_y=-(E-viewport_h),p_max_x=0,p_max_y=0,min_vis_x=-C.left,max_vis_x=min_vis_x+viewport_w,min_vis_y=-C.top,max_vis_y=min_vis_y+viewport_h,mouse_x=H.position.left+J.offset.click.left;mouse_y=H.position.top+J.offset.click.top;if((C.left<p_max_x)&&(mouse_x-close<min_vis_x)){var K=Math.min(nudge,p_max_x-C.left);A.css("left",C.left+K);moved=true;J.offset.parent.left+=K;H.position.left-=K}if((!moved)&&(C.left>p_min_x)&&(mouse_x+close>max_vis_x)){var K=Math.min(nudge,C.left-p_min_x);A.css("left",C.left-K);moved=true;J.offset.parent.left-=K;H.position.left+=K}if((!moved)&&(C.top<p_max_y)&&(mouse_y-close<min_vis_y)){var K=Math.min(nudge,p_max_y-C.top);A.css("top",C.top+K);var F=A.position().top-C.top;J.offset.parent.top+=F;H.position.top-=F;moved=true}if((!moved)&&(C.top>p_min_y)&&(mouse_y+close>max_vis_y)){var K=Math.min(nudge,C.top-p_min_x);A.css("top",(C.top-K)+"px");var F=C.top-A.position().top;J.offset.parent.top-=F;H.position.top+=F;moved=true}H.position.left=Math.max(H.position.left,0);H.position.top=Math.max(H.position.top,0);H.position.left=Math.min(H.position.left,I-element_w);H.position.top=Math.min(H.position.top,E-element_h);if(moved){$.ui.ddmanager.prepareOffsets(J,G)}if(moved){J.old_e=G;J.timeout=setTimeout(function(){J.mouseMove(G)},50)}},stop:function(C,B){var A=$(this).data("draggable");clearTimeout(A.timeout)}}); \ No newline at end of file diff -r 95e3285790d1 -r c17db2e5f334 static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Aug 07 11:41:59 2008 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Thu Aug 07 19:28:42 2008 -0400 @@ -1,1 +1,1 @@ -function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype.__proto__=Terminal.prototype;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype={__proto__:Terminal.prototype,can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}};function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototype ,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.style.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("h eight",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H= E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).fadeOut("fast",function(){$(this).remove()})});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).fadeIn("fast")}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);E.terminal=new OutputTerm inal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors=D.tool_errors;if(this.tool_error s){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'/>").appendTo(A);$.each(D.data_inputs,function(G,F){t=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(t,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(t))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(D){var B=$(this.element),C=this;this.tool_state=D.state;this.form_html=D.form_html;this.tool_errors=D.tool_errors;if(this.tool_errors){B.a ddClass("tool-node-error")}else{B.removeClass("tool-node-error")}var E=B.find("div.inputs");var A=$("<div class='inputs'/>");old=E.find("div.input-data-row");$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");C.enable_input_terminal(G,F.name,F.extensions);E.find("div[name="+F.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var I=this.terminal.connectors[0];if(I){G[0].terminal.connectors[0]=I;I.handle2=G[0].terminal}});$(this).remove()});A.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(G))});E.replaceWith(A);E.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; text-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_changed(this)},changed:function(){workflow.node _changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,function(E,D){var C=prebuild_node("tool",D.name, D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive()}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A},node_changed:function(A){this.has_changes=true;if(this.active_node==A){this.activate_node(A)}}});function prebuild_node(H,F,K){var E=$("<div class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectable'>"+F+"</div>");E.append(J);E.css("left ",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10,scrollSpeed:20,click:function(L,N){var M=$(this).data("draggable").element.get(0);(function(O){O.removeChild(M);O.appendChild(M)})(M.parentNode);workflow.activate_node (C)},start:function(){workflow.activate_node(C);$(this).css("z-index","1000")},drag:function(){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(L,N){var M=$(this).data("draggable").element.get(0);(function(O){O.removeChild(M);O.appendChild(M)})(M.parentNode);$(this).css("z-index","100");$(this).find(".terminal").each(function(){this.terminal.redraw()})}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes}; \ No newline at end of file +function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype.__proto__=Terminal.prototype;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype={__proto__:Terminal.prototype,can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}};function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototype ,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.style.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("h eight",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H= E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).fadeOut("fast",function(){$(this).remove()})});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).fadeIn("fast")}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);E.terminal=new OutputTerm 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1 0

[hg] galaxy 1467: Fix for dynamic select lists generated from co...
by Nate Coraor 07 Aug '08

07 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/95e3285790d1 changeset: 1467:95e3285790d1 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Aug 07 11:41:59 2008 -0400 description: Fix for dynamic select lists generated from contents of input file when no valid datasets exist in the history. 1 file(s) affected in this change: lib/galaxy/tools/parameters/dynamic_options.py diffs (11 lines): diff -r 91c63a82359a -r 95e3285790d1 lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py Mon Aug 04 10:20:23 2008 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Thu Aug 07 11:41:59 2008 -0400 @@ -363,6 +363,7 @@ if self.dataset_ref_name: dataset = other_values.get( self.dataset_ref_name, None ) assert dataset is not None, "Required dataset '%s' missing from input" % self.dataset_ref_name + if not dataset: return [] #no valid dataset in history options = self.parse_file_fields( open( dataset.file_name ) ) else: options = list( self.file_fields )

1 0

Main is at rev 1466:91c63a82359a
by Nate Coraor 07 Aug '08

07 Aug '08

With Workflows enabled.

1 0

[hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1460:...
by hg＠bx.psu.edu 06 Aug '08

06 Aug '08

details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ… changeset: 1460:837f8b7698c4 user: James Taylor <james(a)jamestaylor.org> date: Thu Jul 31 17:55:41 2008 -0400 description: Fix for preserving values of parameters after a repeat/conditional in Tool.update_state. This should fix the problem reported by Dan with the subject "Re: [galaxy-bugs] Galaxy tool error report from cathy(a)bx.psu.edu". Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1461: Compensatory bug in conditional parameters that was revealed by previous details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ… changeset: 1461:6bbf70be8b03 user: James Taylor <james(a)jamestaylor.org> date: Thu Jul 31 20:49:06 2008 -0400 description: Compensatory bug in conditional parameters that was revealed by previous commit. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1462: Fix for JobWrapper.finish, dataset state no longer flushed prior to other attributes ( e.g., metadata) being flushed. details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ… changeset: 1462:777d9bdfd7d3 user: greg date: Fri Aug 01 14:25:42 2008 -0400 description: Fix for JobWrapper.finish, dataset state no longer flushed prior to other attributes ( e.g., metadata) being flushed. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1463: Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params. details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ… changeset: 1463:66be239241bc user: greg date: Fri Aug 01 14:34:16 2008 -0400 description: Fix for gops metadata param parser when strand column not included in input dataset, added new test for gops intersect. Fix for datatype converters - now use new approach to metadata params. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1464: Fix for the creation of workflows from shared histories. details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ… changeset: 1464:c7acaa1bb88f user: dan(a)scofield.bx.psu.edu date: Fri Aug 01 15:05:54 2008 -0400 description: Fix for the creation of workflows from shared histories. Added a column 'copied_from_history_dataset_association' to history_dataset_association. This requires a db change. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1465: Remove a couple templates that I missed in the rollback. details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ… changeset: 1465:3b35cdf1689a user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Aug 01 15:26:02 2008 -0400 description: Remove a couple templates that I missed in the rollback. Subject: [hg: /afs/bx.psu.edu/misc/projects/universe/clones/public] 1466: Better fix for gops command line parser, now properly handles no strand column. details: http://www.bx.psu.edu/hg//afs/bx.psu.edu/misc/projects/universe/clones/publ… changeset: 1466:91c63a82359a user: greg date: Mon Aug 04 10:20:23 2008 -0400 description: Better fix for gops command line parser, now properly handles no strand column. diffs (371 lines): diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml --- a/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml Mon Aug 04 10:20:23 2008 -0400 @@ -1,5 +1,5 @@ <tool id="CONVERTER_fastqsolexa_to_qual_0" name="Convert Fastqsolexa to Qual"> - <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 $input1.extension</command> + <command interpreter="python">fastqsolexa_to_qual_converter.py $input1 $output1 ${input1.extension}</command> <inputs> <param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/> </inputs> diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/interval_to_bed_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Aug 04 10:20:23 2008 -0400 @@ -1,7 +1,7 @@ <tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED">   - <command interpreter="python">interval_to_bed_converter.py $output1 $input1 $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol</command> + <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command> <inputs> <page> <param format="interval" name="input1" type="data" label="Choose intervals"/> diff -r b301cae30997 -r 91c63a82359a lib/galaxy/datatypes/converters/maf_to_interval_converter.xml --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Mon Aug 04 10:20:23 2008 -0400 @@ -1,6 +1,6 @@ <tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals">  - <command interpreter="python">maf_to_interval_converter.py $output1 $input1 $input1_dbkey</command> + <command interpreter="python">maf_to_interval_converter.py $output1 $input1 ${input1.metadata.dbkey}</command> <inputs> <page> <param format="maf" name="input1" type="data" label="Choose MAF file"/> diff -r b301cae30997 -r 91c63a82359a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/jobs/__init__.py Mon Aug 04 10:20:23 2008 -0400 @@ -400,11 +400,6 @@ else: job.state = 'ok' for dataset_assoc in job.output_datasets: - if stderr: - dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR - else: - dataset_assoc.dataset.dataset.state = model.Dataset.states.OK - dataset_assoc.dataset.dataset.flush() for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running dataset.blurb = 'done' dataset.peek = 'no peek' @@ -424,6 +419,11 @@ else: dataset.blurb = "empty" dataset.flush() + if stderr: + dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR + else: + dataset_assoc.dataset.dataset.state = model.Dataset.states.OK + dataset_assoc.dataset.dataset.flush() # Save stdout and stderr if len( stdout ) > 32768: diff -r b301cae30997 -r 91c63a82359a lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/model/__init__.py Mon Aug 04 10:20:23 2008 -0400 @@ -104,7 +104,7 @@ class HistoryDatasetAssociation( object ): def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, - parent_id=None, validation_errors=None, visible=True, create_dataset = False ): + parent_id=None, copied_from_history_dataset_association = None, validation_errors=None, visible=True, create_dataset = False ): self.name = name or "Unnamed dataset" self.id = id self.hid = hid @@ -125,6 +125,7 @@ self.dataset = dataset self.parent_id = parent_id self.validation_errors = validation_errors + self.copied_from_history_dataset_association = copied_from_history_dataset_association @property def ext( self ): @@ -252,7 +253,7 @@ return self.datatype.get_converter_types( self, datatypes_registry) def copy( self, copy_children = False, parent_id = None ): - des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id ) + des = HistoryDatasetAssociation( hid=self.hid, name=self.name, info=self.info, blurb=self.blurb, peek=self.peek, extension=self.extension, dbkey=self.dbkey, metadata=self._metadata, dataset = self.dataset, visible=self.visible, deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association = self ) des.flush() if copy_children: for child in self.children: diff -r b301cae30997 -r 91c63a82359a lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/model/mapping.py Mon Aug 04 10:20:23 2008 -0400 @@ -72,6 +72,7 @@ Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ), Column( "hid", Integer ), Column( "name", TrimmedString( 255 ) ), Column( "info", TrimmedString( 255 ) ), @@ -250,13 +251,17 @@ history=relation( History, primaryjoin=( History.table.c.id == HistoryDatasetAssociation.table.c.history_id ) ), + copied_to_history_dataset_associations=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), + backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id] ) ), implicitly_converted_datasets=relation( ImplicitlyConvertedDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), children=relation( HistoryDatasetAssociation, primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), - backref=backref( "parent", remote_side=[HistoryDatasetAssociation.table.c.id] ) ) + backref=backref( "parent", primaryjoin=( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id] ) ) ) ) assign_mapper( context, Dataset, Dataset.table, diff -r b301cae30997 -r 91c63a82359a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Aug 04 10:20:23 2008 -0400 @@ -731,7 +731,7 @@ for i, rep_state in enumerate( group_state ): rep_index = rep_state['__index__'] max_index = max( max_index, rep_index ) - prefix = "%s_%d|" % ( key, rep_index ) + rep_prefix = "%s_%d|" % ( key, rep_index ) if group_old_errors: rep_old_errors = group_old_errors[i] else: @@ -740,7 +740,7 @@ input.inputs, rep_state, incoming, - prefix=prefix, + prefix=rep_prefix, context=context, update_only=update_only, old_errors=rep_old_errors, @@ -765,9 +765,9 @@ group_state = state[input.name] group_old_errors = old_errors.get( input.name, {} ) old_current_case = group_state['__current_case__'] - prefix = "%s|" % ( key ) + group_prefix = "%s|" % ( key ) # Deal with the 'test' element and see if it's value changed - test_param_key = prefix + input.test_param.name + test_param_key = group_prefix + input.test_param.name test_param_error = None test_incoming = incoming.get( test_param_key, None ) if test_param_key not in incoming \ @@ -797,7 +797,7 @@ input.cases[current_case].inputs, group_state, incoming, - prefix=prefix, + prefix=group_prefix, context=context, update_only=update_only, old_errors=group_old_errors, diff -r b301cae30997 -r 91c63a82359a lib/galaxy/tools/util/galaxyops/__init__.py --- a/lib/galaxy/tools/util/galaxyops/__init__.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/tools/util/galaxyops/__init__.py Mon Aug 04 10:20:23 2008 -0400 @@ -13,13 +13,18 @@ print >> sys.stderr, msg sys.exit( 1 ) -# Default chrom, start, end, stran cols for a bed file +# Default chrom, start, end, strand cols for a bed file BED_DEFAULT_COLS = 0, 1, 2, 5 def parse_cols_arg( cols ): """Parse a columns command line argument into a four-tuple""" if cols: - return map( lambda x: int( x ) - 1, cols.split(",") ) + # Handle case where no strand column included - in this case, cols + # looks something like 1,2,3, + if cols.endswith( ',' ): + cols += '0' + col_list = map( lambda x: int( x ) - 1, cols.split(",") ) + return col_list else: return BED_DEFAULT_COLS diff -r b301cae30997 -r 91c63a82359a lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Wed Jul 30 17:15:40 2008 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Mon Aug 04 10:20:23 2008 -0400 @@ -676,9 +676,16 @@ if dataset.state in ( 'new', 'running', 'queued' ): warnings.add( "Some datasets still queued or running were ignored" ) continue - if not dataset.creating_job_associations: - jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] - for assoc in dataset.creating_job_associations: + + #if this hda was copied from another, we need to find the job that created the origial hda + job_hda = dataset + while job_hda.copied_from_history_dataset_association: + job_hda = job_hda.copied_from_history_dataset_association + + if not job_hda.creating_job_associations: + jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ] + + for assoc in job_hda.creating_job_associations: job = assoc.job if job in jobs: jobs[ job ].append( ( assoc.name, dataset ) ) diff -r b301cae30997 -r 91c63a82359a templates/history/permissions.mako --- a/templates/history/permissions.mako Wed Jul 30 17:15:40 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">Change Default History Permissions</%def> - -%if trans.user: - <div class="toolForm"> - <div class="toolFormTitle">Change Default History Permissions</div> - <div class="toolFormBody"> - <form name="set_permissions" method="post"> - <div class="form-row"> - <% user_groups = [ assoc.group for assoc in trans.user.groups ] %> - <% cur_groups = [ assoc.group for assoc in trans.get_history().default_groups ] %> - <div style="float: left; width: 250px; margin-right: 10px;"> - <table> - <tr><th>Group</th><th>In</th><th>Out</th></tr> - %for group in user_groups: - <tr><td>${group.name}</td><td><input type="radio" name="group_${group.id}" value="in" - %if group in cur_groups: - checked - %endif - ></td><td><input type="radio" name="group_${group.id}" value="out" - %if group not in cur_groups: - checked - %endif - ></td></tr> - %endfor - </table> - </div> - - <div style="clear: both"></div> - - <div class="toolParamHelp" style="clear: both;"> - This will change the default permissions assigned to new datasets for your current history. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="set_permissions" value="Save"> - </div> - </form> - </div> - </div> -%endif \ No newline at end of file diff -r b301cae30997 -r 91c63a82359a templates/tool_form.tmpl --- a/templates/tool_form.tmpl Wed Jul 30 17:15:40 2008 -0400 +++ b/templates/tool_form.tmpl Mon Aug 04 10:20:23 2008 -0400 @@ -57,9 +57,9 @@ #set group_state = $tool_state[$input.name] #set group_errors = $errors.get( $input.name, {} ) #set current_case = $group_state['__current_case__'] - #set prefix = $prefix + $input.name + "|" - $row_for_param( $prefix, $input.test_param, $group_state, $group_errors, $context ) - $do_inputs( $input.cases[$current_case].inputs, $group_state, $group_errors, $prefix, $context ) + #set group_prefix = $prefix + $input.name + "|" + $row_for_param( $group_prefix, $input.test_param, $group_state, $group_errors, $context ) + $do_inputs( $input.cases[$current_case].inputs, $group_state, $group_errors, $group_prefix, $context ) #else $row_for_param( $prefix, $input, $tool_state, $errors, $context ) #end if diff -r b301cae30997 -r 91c63a82359a templates/user/permissions.mako --- a/templates/user/permissions.mako Wed Jul 30 17:15:40 2008 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ -<%inherit file="/base.mako"/> -<%def name="title()">Change Default History Permissions</%def> - -%if trans.user: - <div class="toolForm"> - <div class="toolFormTitle">Change Default Permissions for new Histories </div> - <div class="toolFormBody"> - <form name="set_permissions" method="post"> - <div class="form-row"> - <% user_groups = [ assoc.group for assoc in trans.user.groups ] %> - <% cur_groups = [ assoc.group for assoc in trans.user.default_groups ] %> - <div style="float: left; width: 250px; margin-right: 10px;"> - <table> - <tr><th>Group</th><th>In</th><th>Out</th></tr> - %for group in user_groups: - <tr><td>${group.name}</td><td><input type="radio" name="group_${group.id}" value="in" - %if group in cur_groups: - checked - %endif - ></td><td><input type="radio" name="group_${group.id}" value="out" - %if group not in cur_groups: - checked - %endif - ></td></tr> - %endfor - </table> - </div> - - <div style="clear: both"></div> - - <div class="toolParamHelp" style="clear: both;"> - This will change the default permissions assigned to new datasets for new histories. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="set_permissions" value="Save"> - </div> - </form> - </div> - </div> -%endif \ No newline at end of file diff -r b301cae30997 -r 91c63a82359a templates/workflow/editor_tool_form.mako --- a/templates/workflow/editor_tool_form.mako Wed Jul 30 17:15:40 2008 -0400 +++ b/templates/workflow/editor_tool_form.mako Mon Aug 04 10:20:23 2008 -0400 @@ -23,10 +23,10 @@ %elif input.type == "conditional": <% group_values = values[input.name] %> <% current_case = group_values['__current_case__'] %> - <% prefix = prefix + input.name + "|" %> + <% group_prefix = prefix + input.name + "|" %> <% group_errors = errors.get( input.name, {} ) %> - ${row_for_param( input.test_param, group_values[ input.test_param.name ], group_errors, prefix )} - ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, prefix )} + ${row_for_param( input.test_param, group_values[ input.test_param.name ], group_errors, group_prefix )} + ${do_inputs( input.cases[ current_case ].inputs, group_values, group_errors, group_prefix )} %else: ${row_for_param( input, values[ input.name ], errors, prefix )} %endif diff -r b301cae30997 -r 91c63a82359a test-data/12.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12.bed Mon Aug 04 10:20:23 2008 -0400 @@ -0,0 +1,10 @@ +chr1 147962192 147962580 +chr1 115468538 115468624 +chr1 115483024 115483277 +chr1 115484165 115484501 +chr1 115485764 115485980 +chr1 115486322 115486481 +chr1 115491298 115491487 +chr1 115468538 115468624 +chr1 115483024 115483277 +chr1 115484165 115484501 diff -r b301cae30997 -r 91c63a82359a test-data/gops_intersect_no_strand_out.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gops_intersect_no_strand_out.bed Mon Aug 04 10:20:23 2008 -0400 @@ -0,0 +1,1 @@ +chr1 147962192 147962580 diff -r b301cae30997 -r 91c63a82359a tools/new_operations/intersect.xml --- a/tools/new_operations/intersect.xml Wed Jul 30 17:15:40 2008 -0400 +++ b/tools/new_operations/intersect.xml Mon Aug 04 10:20:23 2008 -0400 @@ -50,6 +50,13 @@ <param name="returntype" value="" /> <output name="output" file="gops_intersect_bigint_out.interval" /> </test> + <test> + <param name="input1" value="12.bed" ftype="bed" /> + <param name="input2" value="1.bed" ftype="bed" /> + <param name="min" value="1" /> + <param name="returntype" value="" /> + <output name="output" file="gops_intersect_no_strand_out.bed" /> + </test> </tests> <help>

1 0

Test is at rev 1470:91c63a82359a, but...
by Greg Von Kuster 04 Aug '08

04 Aug '08

I cannot run cfrun from thumper with my account, so we'll have to wait until it runs automatically...

1 0

Test is at hg Changeset: 1453:e5bbb85083dc
by Greg Von Kuster 01 Aug '08

01 Aug '08

1 0