ulla 0.9.3

data/website/index.txt

@@ -0,0 +1,217 @@
+h1. ulla: a program for calculating environment-specific substitution tables
+
+h2. Description
+
+'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.
+
+
+h2. Features
+
+* Environment-specific substitution table generation based on user providing environmental class definition
+* Entropy-based smoothing procedures to cope with sparse data problem
+* BLOSUM-like weighting procedures using PID threshold
+* Both unidirectional and bidirectional substitution matirces can be generated
+
+
+h2. Installation
+
+<pre>
+~user $ sudo gem install ulla
+</pre>
+
+
+h2. Requirements
+
+* ruby 1.8.7 or above (http://www.ruby-lang.org)
+* rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
+
+Following RubyGems will be automatically installed if you have rubygems installed on your machine
+
+* narray (http://narray.rubyforge.org/)
+* facets (http://facets.rubyforge.org/)
+* bio (http://bioruby.open-bio.org/)
+* simple_memoize (http://github.com/JackDanger/simple_memoize/tree/master)
+
+
+h2. Basic Usage
+
+It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/), so in most cases, you can swap 'subst' with 'ulla'.
+
+<pre>
+~user $ ulla -l TEMLIST-file -c classdef.dat
+    or
+~user $ ulla -l TEM-file -c classdef.dat
+</pre>
+
+
+h2. Options
+
+<pre>
+--tem-file (-f) FILE: a tem file
+--tem-list (-l) FILE: a list for tem files
+--classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
+--outfile (-o) FILE: output filename (default 'allmat.dat')
+--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
+--noweight: calculate substitution count with no weights
+--smooth (-s) INTEGER:
+    0 for partial smoothing (default)
+    1 for full smoothing
+--p1smooth: perform smoothing for p1 probability calculation when partial smoothing
+--nosmooth: perform no smoothing operation
+--cys (-y) INTEGER:
+    0 for using C and J only for structure (default)
+    1 for both structure and sequence
+    2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
+--output INTEGER:
+    0 for raw count (no smoothing performed)
+    1 for probabilities
+    2 for log odds ratios (default)
+--noroundoff: do not round off log odds ratio
+--scale INTEGER: log odds ratio matrices in 1/n bit units (default 3)
+--sigma DOUBLE: change the sigma value for smoothing (default 5.0)
+--autosigma: automatically adjust the sigma value for smoothing
+--add DOUBLE: add this value to raw count when deriving log odds ratios without smoothing (default 1/#classes)
+--penv: use environment-dependent frequencies for log odds ratio calculation (default false) (NOT implemented yet!!!)
+--pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
+--pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
+--verbose (-v) INTEGER
+    0 for ERROR level
+    1 for WARN or above level (default)
+    2 for INFO or above level
+    3 for DEBUG or above level
+--version: print version
+--help (-h): show help
+</pre>
+
+
+h2. Usage
+
+h4. 1. Prepare an environmental class definition file.
+
+<pre>
+~user $ cat classdef.dat
+#
+# name of feature (string); values adopted in .tem file (string); class labels assigned for each value (string);\
+# constrained or not (T or F); silent (used as masks)? (T or F)
+#
+secondary structure and phi angle;HEPC;HEPC;T;F
+solvent accessibility;TF;Aa;F;F
+hydrogen bond to other sidechain/heterogen;TF;Ss;F;F
+hydrogen bond to mainchain CO;TF;Oo;F;F
+hydrogen bond to mainchain NH;TF;Nn;F;F
+</pre>
+
+h4. 2. Prepare structural alignments and their annotations of above environmental classes in PIR format.
+
+<pre>
+~user $ cat sample1.tem
+>P1;1mnma
+sequence
+QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRNL
+IQACLNAPDD*
+>P1;1egwa
+sequence
+--GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY--
+----------*
+>P1;1mnma
+secondary structure and phi angle
+CPCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHPCCCEEEEECCCPCEEEEECCCCCHHHHCHHHHHH
+HHHHHCCCCP*
+>P1;1egwa
+secondary structure and phi angle
+--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCPCCCEEEEECCCPCEEEEECCCHHHHHHHHHHC--
+----------*
+>P1;1mnma
+solvent accessibility
+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTT
+TTTTTTTTTT*
+>P1;1egwa
+solvent accessibility
+--TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--
+----------*
+... 
+</pre>
+
+h4. 3. When you have two or more alignment files, you should make a separate file containing all the paths for the alignment files.
+
+<pre>
+~user $ ls -1 *.tem > TEMLIST
+~user $ cat TEMLIST
+sample1.tem
+sample2.tem
+...
+</pre>
+
+h4. 4. To produce substitution count matrices, type
+
+<pre>
+~user $ ulla -l TEMLIST --output 0 -o substcount.mat
+</pre>
+
+h4. 5. To produce substitution probability matrices, type
+
+<pre>
+~user $ ulla -l TEMLIST --output 1 -o substprob.mat
+</pre>
+
+h4. 6. To produce log odds ratio matrices, type
+
+<pre>
+~user $ ulla -l TEMLIST --output 2 -o substlogo.mat
+</pre>
+
+h4. 7. To produce substitution data only from the sequence pairs within a given PID range, type (if you don't provide any name for output, 'allmat.dat' will be used.)
+
+<pre>
+~user $ ulla -l TEMLIST --pidmin 60 --pidmax 80 --output 1
+</pre>
+
+h4. 8. To change the clustering level (default 60), type
+
+<pre>
+~user $ ulla -l TEMLIST --weight 80 --output 2
+</pre>
+
+h4. 9. In case any positions are masked with the character 'X' in any environmental feature will be excluded from the calculation of substitution counts.
+
+
+h2. Repository
+
+You can download a pre-built RubyGems package from
+
+* rubyforge: "http://rubyforge.org/projects/ulla":http://rubyforge.org/projects/ulla
+
+or, You can fetch the source from
+
+* github: "http://github.com/semin/ulla/tree/master":http://github.com/semin/ulla/tree/master
+
+
+h2. Contact
+
+Comments are welcome, please send an email to me (seminlee at gmail dot com). 
+
+
+h2. License
+
+(The MIT License)
+
+Copyright (c) 2008 Semin Lee
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+'Software'), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/website/javascripts/rounded_corners_lite.inc.js

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+ /****************************************************************
+  *                                                              *
+  *  curvyCorners                                                *
+  *  ------------                                                *
+  *                                                              *
+  *  This script generates rounded corners for your divs.        *
+  *                                                              *
+  *  Version 1.2.9                                               *
+  *  Copyright (c) 2006 Cameron Cooke                            *
+  *  By: Cameron Cooke and Tim Hutchison.                        *
+  *                                                              *
+  *                                                              *
+  *  Website: http://www.curvycorners.net                        *
+  *  Email:   info@totalinfinity.com                             *
+  *  Forum:   http://www.curvycorners.net/forum/                 *
+  *                                                              *
+  *                                                              *
+  *  This library is free software; you can redistribute         *
+  *  it and/or modify it under the terms of the GNU              *
+  *  Lesser General Public License as published by the           *
+  *  Free Software Foundation; either version 2.1 of the         *
+  *  License, or (at your option) any later version.             *
+  *                                                              *
+  *  This library is distributed in the hope that it will        *
+  *  be useful, but WITHOUT ANY WARRANTY; without even the       *
+  *  implied warranty of MERCHANTABILITY or FITNESS FOR A        *
+  *  PARTICULAR PURPOSE. See the GNU Lesser General Public       *
+  *  License for more details.                                   *
+  *                                                              *
+  *  You should have received a copy of the GNU Lesser           *
+  *  General Public License along with this library;             *
+  *  Inc., 59 Temple Place, Suite 330, Boston,                   *
+  *  MA 02111-1307 USA                                           *
+  *                                                              *
+  ****************************************************************/
+  
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+this.box.style.backgroundPosition = "0px -" + (topMaxRadius - this.borderWidth) + "px";}
+break; case "b":
+if(this.bottomContainer)
+{ if(this.settings.bl.radius && this.settings.br.radius)
+{ newFillerBar.style.height = botMaxRadius - this.borderWidth + "px"; newFillerBar.style.marginLeft = this.settings.bl.radius - this.borderWidth + "px"; newFillerBar.style.marginRight = this.settings.br.radius - this.borderWidth + "px"; newFillerBar.style.borderBottom = this.borderString; if(this.backgroundImage != "")
+newFillerBar.style.backgroundPosition = "-" + (botMaxRadius + this.borderWidth) + "px -" + (this.boxHeight + (topMaxRadius + this.borderWidth)) + "px"; this.bottomContainer.appendChild(newFillerBar);}
+}
+break;}
+}
+}
+if(this.settings.autoPad == true && this.boxPadding > 0)
+{ var contentContainer = document.createElement("DIV"); contentContainer.style.position = "relative"; contentContainer.innerHTML = this.boxContent; contentContainer.className = "autoPadDiv"; var topPadding = Math.abs(topMaxRadius - this.boxPadding); var botPadding = Math.abs(botMaxRadius - this.boxPadding); if(topMaxRadius < this.boxPadding)
+contentContainer.style.paddingTop = topPadding + "px"; if(botMaxRadius < this.boxPadding)
+contentContainer.style.paddingBottom = botMaxRadius + "px"; contentContainer.style.paddingLeft = this.boxPadding + "px"; contentContainer.style.paddingRight = this.boxPadding + "px"; this.contentDIV = this.box.appendChild(contentContainer);}
+}
+this.drawPixel = function(intx, inty, colour, transAmount, height, newCorner, image, cornerRadius)
+{ var pixel = document.createElement("DIV"); pixel.style.height = height + "px"; pixel.style.width = "1px"; pixel.style.position = "absolute"; pixel.style.fontSize = "1px"; pixel.style.overflow = "hidden"; var topMaxRadius = Math.max(this.settings["tr"].radius, this.settings["tl"].radius); if(image == -1 && this.backgroundImage != "")
+{ pixel.style.backgroundImage = this.backgroundImage; pixel.style.backgroundPosition = "-" + (this.boxWidth - (cornerRadius - intx) + this.borderWidth) + "px -" + ((this.boxHeight + topMaxRadius + inty) -this.borderWidth) + "px";}
+else
+{ pixel.style.backgroundColor = colour;}
+if (transAmount != 100)
+setOpacity(pixel, transAmount); pixel.style.top = inty + "px"; pixel.style.left = intx + "px"; newCorner.appendChild(pixel);}
+}
+function insertAfter(parent, node, referenceNode)
+{ parent.insertBefore(node, referenceNode.nextSibling);}
+function BlendColour(Col1, Col2, Col1Fraction)
+{ var red1 = parseInt(Col1.substr(1,2),16); var green1 = parseInt(Col1.substr(3,2),16); var blue1 = parseInt(Col1.substr(5,2),16); var red2 = parseInt(Col2.substr(1,2),16); var green2 = parseInt(Col2.substr(3,2),16); var blue2 = parseInt(Col2.substr(5,2),16); if(Col1Fraction > 1 || Col1Fraction < 0) Col1Fraction = 1; var endRed = Math.round((red1 * Col1Fraction) + (red2 * (1 - Col1Fraction))); if(endRed > 255) endRed = 255; if(endRed < 0) endRed = 0; var endGreen = Math.round((green1 * Col1Fraction) + (green2 * (1 - Col1Fraction))); if(endGreen > 255) endGreen = 255; if(endGreen < 0) endGreen = 0; var endBlue = Math.round((blue1 * Col1Fraction) + (blue2 * (1 - Col1Fraction))); if(endBlue > 255) endBlue = 255; if(endBlue < 0) endBlue = 0; return "#" + IntToHex(endRed)+ IntToHex(endGreen)+ IntToHex(endBlue);}
+function IntToHex(strNum)
+{ base = strNum / 16; rem = strNum % 16; base = base - (rem / 16); baseS = MakeHex(base); remS = MakeHex(rem); return baseS + '' + remS;}
+function MakeHex(x)
+{ if((x >= 0) && (x <= 9))
+{ return x;}
+else
+{ switch(x)
+{ case 10: return "A"; case 11: return "B"; case 12: return "C"; case 13: return "D"; case 14: return "E"; case 15: return "F";}
+}
+}
+function pixelFraction(x, y, r)
+{ var pixelfraction = 0; var xvalues = new Array(1); var yvalues = new Array(1); var point = 0; var whatsides = ""; var intersect = Math.sqrt((Math.pow(r,2) - Math.pow(x,2))); if ((intersect >= y) && (intersect < (y+1)))
+{ whatsides = "Left"; xvalues[point] = 0; yvalues[point] = intersect - y; point = point + 1;}
+var intersect = Math.sqrt((Math.pow(r,2) - Math.pow(y+1,2))); if ((intersect >= x) && (intersect < (x+1)))
+{ whatsides = whatsides + "Top"; xvalues[point] = intersect - x; yvalues[point] = 1; point = point + 1;}
+var intersect = Math.sqrt((Math.pow(r,2) - Math.pow(x+1,2))); if ((intersect >= y) && (intersect < (y+1)))
+{ whatsides = whatsides + "Right"; xvalues[point] = 1; yvalues[point] = intersect - y; point = point + 1;}
+var intersect = Math.sqrt((Math.pow(r,2) - Math.pow(y,2))); if ((intersect >= x) && (intersect < (x+1)))
+{ whatsides = whatsides + "Bottom"; xvalues[point] = intersect - x; yvalues[point] = 0;}
+switch (whatsides)
+{ case "LeftRight":
+pixelfraction = Math.min(yvalues[0],yvalues[1]) + ((Math.max(yvalues[0],yvalues[1]) - Math.min(yvalues[0],yvalues[1]))/2); break; case "TopRight":
+pixelfraction = 1-(((1-xvalues[0])*(1-yvalues[1]))/2); break; case "TopBottom":
+pixelfraction = Math.min(xvalues[0],xvalues[1]) + ((Math.max(xvalues[0],xvalues[1]) - Math.min(xvalues[0],xvalues[1]))/2); break; case "LeftBottom":
+pixelfraction = (yvalues[0]*xvalues[1])/2; break; default:
+pixelfraction = 1;}
+return pixelfraction;}
+function rgb2Hex(rgbColour)
+{ try{ var rgbArray = rgb2Array(rgbColour); var red = parseInt(rgbArray[0]); var green = parseInt(rgbArray[1]); var blue = parseInt(rgbArray[2]); var hexColour = "#" + IntToHex(red) + IntToHex(green) + IntToHex(blue);}
+catch(e){ alert("There was an error converting the RGB value to Hexadecimal in function rgb2Hex");}
+return hexColour;}
+function rgb2Array(rgbColour)
+{ var rgbValues = rgbColour.substring(4, rgbColour.indexOf(")")); var rgbArray = rgbValues.split(", "); return rgbArray;}
+function setOpacity(obj, opacity)
+{ opacity = (opacity == 100)?99.999:opacity; if(isSafari && obj.tagName != "IFRAME")
+{ var rgbArray = rgb2Array(obj.style.backgroundColor); var red = parseInt(rgbArray[0]); var green = parseInt(rgbArray[1]); var blue = parseInt(rgbArray[2]); obj.style.backgroundColor = "rgba(" + red + ", " + green + ", " + blue + ", " + opacity/100 + ")";}
+else if(typeof(obj.style.opacity) != "undefined")
+{ obj.style.opacity = opacity/100;}
+else if(typeof(obj.style.MozOpacity) != "undefined")
+{ obj.style.MozOpacity = opacity/100;}
+else if(typeof(obj.style.filter) != "undefined")
+{ obj.style.filter = "alpha(opacity:" + opacity + ")";}
+else if(typeof(obj.style.KHTMLOpacity) != "undefined")
+{ obj.style.KHTMLOpacity = opacity/100;}
+}
+function inArray(array, value)
+{ for(var i = 0; i < array.length; i++){ if (array[i] === value) return i;}
+return false;}
+function inArrayKey(array, value)
+{ for(key in array){ if(key === value) return true;}
+return false;}
+function addEvent(elm, evType, fn, useCapture) { if (elm.addEventListener) { elm.addEventListener(evType, fn, useCapture); return true;}
+else if (elm.attachEvent) { var r = elm.attachEvent('on' + evType, fn); return r;}
+else { elm['on' + evType] = fn;}
+}
+function removeEvent(obj, evType, fn, useCapture){ if (obj.removeEventListener){ obj.removeEventListener(evType, fn, useCapture); return true;} else if (obj.detachEvent){ var r = obj.detachEvent("on"+evType, fn); return r;} else { alert("Handler could not be removed");}
+}
+function format_colour(colour)
+{ var returnColour = "#ffffff"; if(colour != "" && colour != "transparent")
+{ if(colour.substr(0, 3) == "rgb")
+{ returnColour = rgb2Hex(colour);}
+else if(colour.length == 4)
+{ returnColour = "#" + colour.substring(1, 2) + colour.substring(1, 2) + colour.substring(2, 3) + colour.substring(2, 3) + colour.substring(3, 4) + colour.substring(3, 4);}
+else
+{ returnColour = colour;}
+}
+return returnColour;}
+function get_style(obj, property, propertyNS)
+{ try
+{ if(obj.currentStyle)
+{ var returnVal = eval("obj.currentStyle." + property);}
+else
+{ if(isSafari && obj.style.display == "none")
+{ obj.style.display = ""; var wasHidden = true;}
+var returnVal = document.defaultView.getComputedStyle(obj, '').getPropertyValue(propertyNS); if(isSafari && wasHidden)
+{ obj.style.display = "none";}
+}
+}
+catch(e)
+{ }
+return returnVal;}
+function getElementsByClass(searchClass, node, tag)
+{ var classElements = new Array(); if(node == null)
+node = document; if(tag == null)
+tag = '*'; var els = node.getElementsByTagName(tag); var elsLen = els.length; var pattern = new RegExp("(^|\s)"+searchClass+"(\s|$)"); for (i = 0, j = 0; i < elsLen; i++)
+{ if(pattern.test(els[i].className))
+{ classElements[j] = els[i]; j++;}
+}
+return classElements;}
+function newCurvyError(errorMessage)
+{ return new Error("curvyCorners Error:\n" + errorMessage)
+}

data/website/stylesheets/screen.css

@@ -0,0 +1,158 @@
+body {
+  background-color: #8DBD82;
+  font-family: "Georgia", sans-serif;
+  font-size: 16px;
+  line-height: 1.6em;
+  padding: 1.6em 0 0 0;
+  color: #333;
+}
+h1, h2, h3, h4, h5, h6 {
+  color: #444;
+}
+h1 { 
+  font-family: sans-serif;
+  font-weight: normal;
+  font-size: 4em;
+  line-height: 0.8em;
+  letter-spacing: -0.1ex;
+	margin: 5px;
+}
+li {
+  padding: 0;
+  margin: 0;
+  list-style-type: square;
+}
+a {
+  color: #5E5AFF;
+	background-color: #A1DDB1;
+  font-weight: normal;
+  text-decoration: underline;
+}
+blockquote {
+  font-size: 90%;
+  font-style: italic;
+  border-left: 1px solid #111;
+  padding-left: 1em;
+}
+.caps {
+  font-size: 80%;
+}
+
+#main {
+  width: 55em;
+  padding: 0;
+  margin: 0 auto;
+}
+.coda {
+  text-align: right;
+  color: #77f;
+  font-size: smaller;
+}
+
+table {
+  font-size: 90%;
+  line-height: 1.4em;
+  color: #ff8;
+  background-color: #111;
+  padding: 2px 10px 2px 10px;
+	border-style: dashed;
+}
+
+th {
+	color: #fff;
+}
+
+td {
+  padding: 2px 10px 2px 10px;
+}
+
+.success {
+	color: #0CC52B;
+}
+
+.failed {
+	color: #E90A1B;
+}
+
+.unknown {
+	color: #995000;
+}
+pre, code {
+  font-family: monospace;
+  font-size: 90%;
+  line-height: 1.4em;
+  color: #ff8;
+  background-color: #111;
+  padding: 2px 10px 2px 10px;
+}
+.comment { color: #aaa; font-style: italic; }
+.keyword { color: #eff; font-weight: bold; }
+.punct { color: #eee; font-weight: bold; }
+.symbol { color: #0bb; }
+.string { color: #6b4; }
+.ident { color: #ff8; }
+.constant { color: #66f; }
+.regex { color: #ec6; }
+.number { color: #F99; }
+.expr { color: #227; }
+
+.sidebar {
+  float: right;
+}
+
+#version {
+  width: 217px;
+  text-align: right;
+  font-family: sans-serif;
+  font-weight: normal;
+  color: #141331;
+  padding: 15px 20px 10px 20px;
+  margin: 0 auto;
+	margin-top: 15px;
+  background-color: #9A5535;
+  border: 3px solid #7E393E;
+}
+
+#version .numbers {
+  display: block;
+  font-size: 4em;
+  line-height: 0.8em;
+  letter-spacing: -0.1ex;
+	margin-bottom: 15px;
+}
+
+#version p {
+  text-decoration: none;
+	color: #F1F4FF;
+	background-color: #9A5535;
+	margin: 0;
+	padding: 0;
+}
+
+#version a {
+  text-decoration: none;
+	color: #F1F4FF;
+	background-color: #9A5535;
+}
+
+.clickable {
+	cursor:	pointer; 
+	cursor:	hand;
+}
+
+#twitter_search {
+	margin: 40px 0 10px 15px;
+  color: #F1F4FF;
+  background-color: #9A5535;
+  border: 3px solid #7E393E;
+}
+
+#twitter_search h3 {
+  color: #F1F4FF;
+	margin-bottom: 0px;
+}
+
+#twitter_search center b {
+	display: none;
+}
+