<%args>
    $sequenceset_html => undef
    $organism_html    => undef
    $sequence_input   => undef
    $admin            => 0
    $sequence_data_dir
</%args>
<script type="text/javascript" src="/js/mimosa-grid.js"></script>

<div id="tabs1">
 <div id="t1_content">
    <div id="pagetitle">
        <h2>Mimosa - Miniature Model Organism Sequence Aligner</h2>
    </div>

    <div id="mimosa-grid">
    </div>

<table border="0">
<form method="post" enctype="multipart/form-data" action="/submit" name="main_input_form">
  <input type="hidden" id="mimosa_sequence_set_ids" name="mimosa_sequence_set_ids" value="0" />
  <input type="hidden" name="interface_type" value="simple" />
  <input type="hidden" name="outformat" value="0" />
  <br>
<tr><td>
  Program:</td><td> <select id="program_selector"   name="program">
<option value="none">Choose a BLAST program</option>
<option selected="true" value="blastn">BLASTN (nucleotide to nucleotide)</option>
<option value="tblastx">TBLASTX (protein to protein; both database and query are translated)</option>
<option value="tblastn">TBLASTN (protein to nucleotide; database translated to protein)</option>
</select>
</td></tr>
    <tr><td>Name:</td><td> <input type="text" name="search_name" size="20" id="search_name"></td></tr>
    <tr><td>Description:</td><td> <input type="text" name="search_description" size="20" id="search_description"></td></tr>

    <tr><td><b>Query sequence</b></td></tr>
    <tr><td colspan="2">
    <textarea name="sequence" id="sequence_input" rows="8" cols="80"><% $sequence_input %></textarea></td></tr>
    <tr><td>Upload query sequence file:</td><td> <input type="file" name="sequence_input_file" size="40"></td></tr>
    </table>
       <br/>
        <input value="unchecked" type="checkbox" name="advanced" id="advanced_control" onclick="$('#advanced').toggle('slow', 'swing')">
        <label for="advanced_control">Advanced Options</label>
    <div class="info_table_fieldval">

         <div id="advanced" style="display:none; width: 700px;">
  Filter Query?: <input type="checkbox" checked="checked" name="filtered" value="T" /><br/>

    <div class="info_table_fieldval">
    Expect (e-value) Threshold
      <input type="text" size="6" value="1e-10" name="evalue" />
    <br/>
    </div>

    <div>
    Alignment View
    <select id="alignment_views" name="alignment_view">
    <option value="0">Pairwise</option>
    <option value="1">Query-anchored showing identities</option>
    <option value="2">Query-anchored no identities</option>
    <option value="3">Flat query-anchored, show identities</option>
    <option value="4">Flat query-anchored, no identities</option>
    <option value="5">Query-anchored no identities and blunt ends</option>
    <option value="6">Flat query-anchored, no identities and blunt ends</option>
    <option value="7">XML Blast output</option>
    <option value="8">Tabular</option>
    <option value="9">Tabular with comment lines</option>
    <option value="10">ASN text</option>
    </select>
    </div>

    <div class="info_table_fieldval">
    Substitution Matrix
      <select id="simple_selectbox_2"   name="matrix">
            <option value="BLOSUM62">BLOSUM62 (default)</option>
            <option value="BLOSUM80">BLOSUM80 (recent divergence)</option>
            <option value="BLOSUM45">BLOSUM80 (ancient divergence)</option>
            <option value="PAM30">PAM30</option>
            <option value="PAM70">PAM70</option>
    </select>
    </div>

    <div class="info_table_fieldval">
    Show Graphics
      <select id="simple_selectbox_3"   name="output_graphs">
        <option value="bioperl_histogram">all</option>
        <option value="none">none</option>
        <option value="bioperl_only">alignment summary only</option>
    </select>
    </div>
    <div class="info_table_fieldval">
    Max hits to show: <input type="text" name="maxhits" size="6" value="100" />
    </div>
    </div> <!-- advanced -->
      <div><br/><input type="reset" value="Clear" onclick="clearField(); "> <input type="submit" name="search" value="Align" ></div>
    </div>
</form>

</div> <!-- t1_content -->

    <& tabs.mason, sequence_data_dir => $sequence_data_dir &>

</div>