{%extends "genotypes/base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%from "populations/macro-display-population-card.html" import display_population_card%}

{%block title%}Genotypes{%endblock%}

{%block pagetitle%}Genotypes{%endblock%}

{%block lvl4_breadcrumbs%}
<li {%if activelink=="list-genotypes"%}
    class="breadcrumb-item active"
    {%else%}
    class="breadcrumb-item"
    {%endif%}>
  <a href="{{url_for('species.populations.genotypes.list_genotypes',
           species_id=species.SpeciesId,
           population_id=population.Id)}}">List genotypes</a>
</li>
{%endblock%}

{%block contents%}
{{flash_all_messages()}}

<div class="row">
  <p>
    The genotype encoding used for the "{{population.FullName}}" population from
    the "{{species.FullName}}" species is as shown in the table below.
  </p>
  <table class="table">
    <legend>Genotype Encoding</legend>

    <thead>
      <tr>
        <th>Allele Type</th>
        <th>Allele Symbol</th>
        <th>Allele Value</th>
      </tr>
    </thead>

    <tbody>
      {%for row in genocode%}
      <tr>
        <td>{{row.AlleleType}}</td>
        <td>{{row.AlleleSymbol}}</td>
        <td>{{row.DatabaseValue if row.DatabaseValue is not none else "NULL"}}</td>
      </tr>
      {%else%}
      <tr>
        <td colspan="7" class="text-info">
          <span class="glyphicon glyphicon-exclamation-sign"></span>
          There is no explicit genotype encoding defined for this population.
        </td>
      </tr>
      {%endfor%}
    </tbody>
  </table>
</div>

<div class="row text-danger">
  <h3>Some Important Concepts to Consider/Remember</h3>
  <ul>
    <li>Reference vs. Non-reference alleles</li>
    <li>In <em>GenoCode</em> table, items are ordered by <strong>InbredSet</strong></li>
  </ul>
  <h3>Possible references</h3>
  <ul>
    <li>https://mr-dictionary.mrcieu.ac.uk/term/genotype/</li>
  </ul>
</div>

<div class="row">
  <p>
    There are a total of {{total_markers}} genotype markers for this species.
  </p>
  <div class="row">
    <div class="col-md-2" style="text-align: start;">
      {%if start_from > 0%}
      <a href="{{url_for('species.populations.genotypes.list_genotypes',
               species_id=species.SpeciesId,
               population_id=population.Id,
               start_from=start_from-count,
               count=count)}}">
        <span class="glyphicon glyphicon-backward"></span>
        Previous
      </a>
      {%endif%}
    </div>
    <div class="col-md-8" style="text-align: center;">
      Displaying markers {{start_from+1}} to {{start_from + count}} of
      {{total_markers}}
    </div>
    <div class="col-md-2" style="text-align: end;">
      {%if start_from + count < total_markers%}
      <a href="{{url_for('species.populations.genotypes.list_genotypes',
               species_id=species.SpeciesId,
               population_id=population.Id,
               start_from=start_from+count,
               count=count)}}">
        Next
        <span class="glyphicon glyphicon-forward"></span>
      </a>
      {%endif%}
    </div>
  </div>
  <table class="table">
    <thead>
      <tr>
        <th title="">#</th>
        <th title="">Marker Name</th>
        <th title="Chromosome">Chr</th>
        <th title="Physical location of the marker in megabasepairs">
          Location (Mb)</th>
        <th title="">Source</th>
        <th title="">Source2</th>
    </thead>

    <tbody>
      {%for marker in markers%}
      <tr>
        <td>{{marker.sequence_number}}</td>
        <td>{{marker.Marker_Name}}</td>
        <td>{{marker.Chr}}</td>
        <td>{{marker.Mb}}</td>
        <td>{{marker.Source}}</td>
        <td>{{marker.Source2}}</td>
      </tr>
      {%else%}
      <tr>
        <td colspan="7" class="text-info">
          <span class="glyphicon glyphicon-exclamation-sign"></span>
          No markers to display!
        </td>
      </tr>
      {%endfor%}
    </tbody>
  </table>
</div>
{%endblock%}

{%block sidebarcontents%}
{{display_population_card(species, population)}}
{%endblock%}