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<!DOCTYPE html>
<html lang="en">
<head>
<title>WebLogo 3 - Create </title>
<!--base responsive code-->
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<!--original meta data-->
<meta name="author" content="Gavin E. Crooks">
<meta http-equiv="Content-Type" content="text/html;charset=utf-8">
<link rel="stylesheet" type="text/css" href="logo.css">
<title>WebLogo Create Layout Template</title>
<!--styling for error message for sequence input-->
<style type="text/css">
.error {
color: #900;
border-left: red solid +4pt;
}
.err_msg {
color: #900;
}
.err_msg .btn {
color: #000;
}
</style>
<!--jquery libraries-->
<script src="//code.jquery.com/jquery-1.11.0.min.js"></script>
<script src="//code.jquery.com/jquery-migrate-1.2.1.min.js"></script>
<!-- ========Start Bootstrap dependencies ==========-->
<!-- Latest compiled and minified CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
<!-- Optional theme -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap-theme.min.css">
<!-- Latest compiled and minified JavaScript -->
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script>
<!-- ========= end Bootstrap dependencies======= -->
</head>
<body>
<!--Navigation-->
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="./">WebLogo 3</a>
</div>
<div class="collapse navbar-collapse">
<ul class="nav navbar-nav">
<li><a href="./">home</a></li>
<li class="active"><a href="create.cgi">create</a></li>
<li><a href="examples.html">examples</a></li>
<li><a href="manual.html">manual</a></li>
</ul>
</div>
<!--/.nav-collapse -->
</div>
</div>
<!--end Navigation-->
<div class="container-fluid">
<!--start fluid container for responsive content-->
<div class="row">
<!--outermost row container-->
<h1><p class="text-center"> WebLogo 3: Create</p></h1>
<form enctype="multipart/form-data" action="create.cgi" name="logoform" method="post">
<!--start WebLogo form-->
<div class="row">
<!--open sequence data form row-->
<div class="col-sm-1">
<br>
</div>
<!--left margin column for sequence data form -->
<div class="col-sm-10">
<!--central column for sequence data form-->
<div class="thumbnail clearfix row" id="thumbnail-1">
<!--open thumbnail 1 div-->
<h2> Sequence Data Input:</h2>
<hr>
<div class="form-group clearfix">
<!--start clearfix div for browse & open buttons-->
<div class="col-sm-4">
<input type="file" name="sequences_file"></input>
</div>
<div class="col-sm-2"> <!--center spacing div-->
</div>
<!--start URL download container div-->
<div class="form-group col-sm-4" id="URL-upload">
<label>URL:</label>
<input type="text" name="sequences_url" placeholder="URL of sequences" id="url-upload" value="${sequences_url}">
</div>
</div> <!--end URL download container div-->
</div> <!--start clearfix div for browse & open buttons-->
<div class="form-group">
<!--open paste seqence data textbox div-->
<label class="err_msg">${error_message}</label>
<textarea type="text" class="form-control" id="sequence-data" name="sequences" style="width:100%" placeholder="Or Paste Sequence Data Here">${sequences}</textarea>
</div>
<!--close paste seqence data textbox-->
<div class="form-group row">
<!--Start div for Download and Dropbox button-->
<div class="col-sm-8">
<!--start create&clear button column-->
<div class="form-group">
<!--open create&clear button div-->
<button class="btn btn-success btn-md" type="submit" name="cmd_create">
<span class="glyphicon glyphicon-ok"></span> Create WebLogo
</button>
<button type="button" class="btn btn-default" name="cmd_clear" onclick="document.logoform.sequences.value='';"> Clear</button>
</div>
<!-- end create&clear button div-->
</div> <!--end .col-sm-8 create&clear button column-->
<div class="col-sm-4"><!--start spacing div for download checkbox-->
<div class="form-group">
<!--start download checkbox div-->
<label>
<input type="checkbox" name="download" value="false">  Download to local drive
</label>
</div>
<!--end download checkbox div div-->
</div>
</div>
<!--End clearfix row div for Download and Dropbox button-->
</div>
<!--end clearfix #thumbnail-1 div-->
</div>
<!--end col-sm-10 central column for sequence data form-->
<div class="col-sm-1"> <!--start margin row for sequence data form-->
<br>
</div><!--end margin row for sequence data form-->
</div>
<!--end sequence data form row-->
<div class="row">
<!--start row for logo options-->
<div class="col-sm-1">
<br>
</div>
<!--left column margin for logo options form-->
<div class="col-sm-10" id="wrap">
<!--central col-sm-10 logo options column-->
<div class="thumbnail col-sm-6" id="thumbnail-2">
<!--start thumbnail-2 div; left side logo options-->
<div class="form-group">
<!--open title div-->
<label>Title:</label>
<input type="text" name="logo_title" value="${logo_title}" maxlength="80" placeholder="max 80 char " id="title">
</div>
<!--close title div-->
<div class="form-group clearfix">
<!--open output format div-->
<label>Output Format:</label>
<!--open div for format options-->
<select name="format">
<option ${png_print} value="png_print">PNG</option>
<option ${jpeg} value="jpeg">JPEG (low res.)</option>
<option ${eps} value="eps">EPS (vector)</option>
<option ${pdf} value="pdf">PDF (vector)</option>
<option ${svg} value="svg">SVG (vector)</option>
<option ${logodata} value="logodata">Data (plain text)</option>
<option ${csv} value="csv">CSV (plain text)</option>
</select>
<!--close div for format options-->
</div>
<!--close output format div-->
<!--open div for sequence type option-->
<div class="form-group">
<label ${alphabet_err}>Sequence type </label>
<select type="submit" name="alphabet">
<option ${alphabet_auto} value="alphabet_auto" >auto</option>
<option ${alphabet_protein} value="alphabet_protein">protein</option>
<option ${alphabet_dna} value="alphabet_dna">dna</option>
<option ${alphabet_rna} value="alphabet_rna">rna</option>
</select>
</div> <!--close dive for sequence type option-->
<div class="form-group">
<!--open logo-size div-->
<label ${size_err}>Logo-size: </label>
<select type="submit" name="stack_width">
<option ${small}>small</option>
<option ${medium}>medium</option>
<option ${large}>large</option>
</select>
</div>
<!--close logo-size div-->
<div class="form-group">
<!--open Stacks per Line div-->
<label ${stacks_per_line_err}>Stacks per Line:</label>
<input type="text" name="stacks_per_line" size="8" value="${stacks_per_line}" placeholder="40">
</div>
<!--close div for format options-->
<div class="form-group">
<!--open Ignore lower case div-->
<label>Ignore lower case:
<input type="checkbox" name="ignore_lower_case" value="true" ${ignore_lower_case}>
</label>
</div>
<!--close ignore lower case div-->
<div class="form-group">
<!--open Units div-->
<label>Units: </label>
<select name="unit_name">
<option ${probability}>probability</option>
<option ${bits}>bits</option>
<option ${nats}>nats</option>
<option ${kT}>kT</option>
<option ${kJ_mol}>kJ/mol</option>
<option ${kcal_mol}>kcal/mol</option>
</select>
</div>
<!--close Units div-->
<div class="form-group">
<!--open first position number div-->
<label ${first_index_err}> First position number: </label>
<input type="text" name="first_index" placeholder="max length 80" size="4" maxlength="80" value="${first_index}">
</div>
<!--close first position div-->
<div class="form-group">
<!--open logo range div-->
<label ${logo_range_err}> Logo range: </label>
<input type="text" placeholder="logo start" name="logo_start" value="${logo_start}" size="4" maxlength="80"> -
<input type="text" placeholder="logo end" name="logo_end" value="${logo_end}" id="formGroupInputSmall" size="4" maxlength="80">
</div>
<!--close logo range div-->
<div class="form-group">
<!--open figure label div-->
<label>Figure label:</label>
<input type="text" name="logo_label" value="${logo_label}" maxlength="100">
</div>
<!--close figure label div-->
<div class="form-group">
<!--open scale stack div-->
<label>Scale stack widths: </label>
<input type="checkbox" name="scale_width" value="true" ${scale_width}>
</div>
<!--close scale stack div-->
<div class="form-group">
<!--open composition div-->
<label ${composition_err}>Composition:</label>
<select name="composition">
<option ${comp_none} value="comp_none">No adjustment for composition</option>
<option ${comp_auto} value="comp_auto">auto</option>
<option ${comp_equiprobable} value="comp_equiprobable">equiprobable</option>
<option ${comp_CG} value="comp_CG">Percentage CG ⇒</option>
<option ${comp_Celegans} value="comp_Celegans">C. elegans (36%) </option>
<option ${comp_Dmelanogaster} value="comp_Dmelanogaster">D. melanogaster (43%)</option>
<option ${comp_Ecoli} value="comp_Ecoli">E. coli (50.5%) </option>
<option ${comp_Hsapiens} value="comp_Hsapiens">H. sapiens (40%) </option>
<option ${comp_Mmusculus} value="comp_Mmusculus">M. musculus (42%)</option>
<option ${comp_Scerevisiae} value="comp_Scerevisiae">S. cerevisiae (38%)</option>
</select>
<span>or</span>
<input type="text" name="percentCG" value="${percentCG}" size="4" maxlength="8">
<span> % CG </span>
</div>
<!--close composition div-->
<div id="padding-div">
<br>
</div>
</div>
<!--close 2nd thumbnail column-->
<div class="thumbnail col-sm-6" id="thumbnail-3">
<!--start third thumbnail ; right side logo options-->
<!--start error bars div-->
<div class="form-group">
<label>Error bars: </label>
<input type="checkbox" name="show_errorbars" value="true" ${show_errorbars} checked>
</div>
<!--end error bars div-->
<div class="form-group">
<!--start Sequence Ends labels:div-->
<label>Show Sequence Ends labels:</label>
<input type="checkbox" name="show_ends" value="true" ${show_ends}>
</div>
<!--end Sequence Ends labels:div-->
<div class="form-group">
<!--start Version fineprint: -->
<label>Version fineprint: </label>
<input type="checkbox" name="show_fineprint" value="true" checked ${show_fineprint}>
</div>
<!--end Version fineprint: -->
<div class="form-group">
<!--start x-axis div-->
<label>X-axis</label>
<input type="checkbox" name="show_xaxis" value="true" ${show_xaxis}>
<span>Label: </span>
<input type="text" name="xaxis_label" value="${xaxis_label}" size="20" maxlength="100">
</div>
<!--end x-axis div-->
<div class="form-group">
<!--start y-axis div-->
<label>Y-axis</label>
<input type="checkbox" name="show_yaxis" value="true" ${show_yaxis}>
<span>Label: </span>
<input type="text" name="yaxis_label" value="${yaxis_label}" size="20" maxlength="32">
</div>
<!--end y-axis div-->
<div class="form-group">
<!--start y-axis scale div-->
<label>Y-axis scale:</label>
<input type="text" name="yaxis_scale" value="${yaxis_scale}" size="4" maxlength="100" placeholder="100 character max">
</div>
<!--end y-axis scale div-->
<div class="form-group">
<!--Y-axis tic spacing-->
<label>Y-axis tic spacing:</label>
<input type="text" name="yaxis_tic_interval" value="${yaxis_tic_interval}" placeholder="Y-axis tic spacing" size="4" maxlength="100">
</div>
<div class="form-group" >
<!--start color scheme div-->
<label ${color_scheme_err}>Color scheme: </label>
<select name="color_scheme">
<option ${color_auto} value="color_auto">Auto</option>
<option ${color_monochrome} value="color_monochrome">Monochrome</option>
<option ${color_base_pairing} value="color_base_pairing">Base pairing (NA default)</option>
<option ${color_classic} value="color_classic">Classic (NA)</option>
<option ${color_hydrophobicity} value="color_hydrophobicity">Hydrophobicity (AA default)</option>
<option ${color_chemistry} value="color_chemistry">Chemistry (AA)</option>
<option ${color_charge} value="color_charge">Charge (AA)</option>
<option ${color_custom} value="color_custom">Custom (Specify below)</option>
</select>
<!-- Color key:
<input type="checkbox" name="show_color_key" value="true" ${show_color_key} disabled >
-->
</div>
<!--end color scheme div-->
<div class="row">
<div class="col-sm-5">
<div class="form-group stacked-textfields" id="Symbols">
<!--start symbols div-->
<div>
<label>Symbols:</label>
</div>
<div>
<!--start symbol options-->
<input name="symbols0" type="text" maxlength="64" value="${symbols0}">
<input name="symbols1" type="text" maxlength="64" value="${symbols1}">
<input name="symbols2" type="text" maxlength="64" value="${symbols2}">
<input name="symbols3" type="text" maxlength="64" value="${symbols3}">
<input name="symbols4" type="text" maxlength="64" value="${symbols4}">
</div>
<!--end symbol options-->
</div>
</div>
<!--end symbols div-->
<div class="col-sm-5">
<div class="form-group stacked-textfields" id="Colors">
<!--start colors div-->
<div>
<label>Color:</label>
</div>
<div>
<input name="color0" type="text" maxlength="64" value="${color0}">
<input name="color1" type="text" maxlength="64" value="${color1}">
<input name="color2" type="text" maxlength="64" value="${color2}">
<input name="color3" type="text" maxlength="64" value="${color3}">
<input name="color4" type="text" maxlength="64" value="${color4}">
</div>
</div>
</div>
</div> <!--end row for color and symbols div-->
<!--end colors div-->
<div class="form-group">
<!--start reset defaults div-->
<!--Reset defaults must come after create_logo so that hitting enter creates a logo-->
<input type="submit" class="btn btn-default btn-sm" name="cmd_reset" value= "Reset Defaults">
</div>
<!--end reset defaults div-->
</div>
<!--close 3rd thumbnail group-->
<!--start 4th thumbnail group-->
<div class="thumbnail clearfix" id="thumbnail-4">
<div class="form-group">
<!--start create weblogo bottom button div-->
<button class="btn btn-success btn-lg" type="submit" name="cmd_create" id="last-button">
<span class="glyphicon glyphicon-ok"></span> Create WebLogo </button>
</div>
<!--end create weblogo bottom button div-->
</div>
<!--end 4th thumbnail group-->
</div>
<!--end col-sm-10 central logo options column-->
<div class="col-sm-1">
<br>
</div>
<!--right column margin for logo options form-->
</div>
<!--end row for logo options-->
</form>
<!--end WebLogo form-->
<div class="footer row" id="footer">
<br>
</div>
</div>
<!--end outermost row container-->
</div>
<!--end fluid container for responsive content-->
<!--fallback to server-hosted files in case CDNs fail-->
<!--Google analytics-->
<script type="text/javascript">
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
</script>
<script type="text/javascript">
var pageTracker = _gat._getTracker("UA-5951066-1");
pageTracker._trackPageview();
</script>
</body>
</html>
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