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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">
+ <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>
+ <p>You can also create a new genotype dataset by clicking the button below.
+ <br />
+ <a href="#create-new-genotype-dataset"
+ 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>
+
+ {%if datasets | length > 0%}
+ <table class="table">
+ </table>
+ {%else%}
+ <p class="text-warning">
+ <span class="glyphicon glyphicon-exclamation-sign"></span>
+ There are no genotype datasets to display, yet!
+ </p>
+ {%endif%}
+</div>
+{%endblock%}
+
+{%block sidebarcontents%}
+{{display_population_card(species, population)}}
+{%endblock%}