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{%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%}
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