{%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">
  <h2>Genetic Markers</h2>
  <p>There are a total of {{total_markers}} currently registered genetic markers
    for the "{{species.FullName}}" species. You can click
    <a href="{{url_for('species.populations.genotypes.list_markers',
             species_id=species.SpeciesId)}}"
       title="View genetic markers for species '{{species.FullName}}">
      this link to view the genetic markers
    </a>.
  </p>
</div>

<div class="row">
  <h2>Genotype Encoding</h2>
  <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">

    <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>

  {%if genocode | length < 1%}
  <a href="#add-genotype-encoding"
     title="Add a genotype encoding system for this population"
     class="btn btn-primary">
    add genotype encoding
    </a>
  {%endif%}
</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>
    <li>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7363099/</li>
  </ul>
</div>

<div class="row">
  <h2>Genotype Datasets</h2>

  <p>The genotype data is organised under various genotype datasets. You can
    click on the link for the relevant dataset to view a little more information
    about it.</p>

  {%if dataset is not none%}
    <table class="table">
      <thead>
        <tr>
          <th>Name</th>
          <th>Full Name</th>
        </tr>
      </thead>

      <tbody>
        <tr>
          <td>{{dataset.Name}}</td>
          <td><a href="{{url_for('species.populations.genotypes.view_dataset',
                       species_id=species.SpeciesId,
                       population_id=population.Id,
                       dataset_id=dataset.Id)}}"
                 title="View details regarding and manage dataset '{{dataset.FullName}}'">
              {{dataset.FullName}}</a></td>
        </tr>
      </tbody>
    </table>
  {%else%}
  <p class="text-warning">
    <span class="glyphicon glyphicon-exclamation-sign"></span>
    There is no genotype dataset defined for this population.
  </p>
  <p>
    <a href="{{url_for('species.populations.genotypes.create_dataset',
             species_id=species.SpeciesId,
             population_id=population.Id)}}"
       title="Create a new genotype dataset for the '{{population.FullName}}' population for the '{{species.FullName}}' species."
       class="btn btn-primary">
      create new genotype dataset</a></p>
  {%endif%}
</div>
<div class="row text-warning">
  <p>
    <span class="glyphicon glyphicon-exclamation-sign"></span>
    <strong>NOTE</strong>: Currently the GN2 (and related) system(s) expect a
    single genotype dataset. If there is more than one, the system apparently
    fails in unpredictable ways.
  </p>
  <p>Fix this to allow multiple datasets, each with a different assembly from
    all the rest.</p>
</div>
{%endblock%}

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