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finished sequence page
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@proost
proost committed Oct 27, 2016
1 parent 93bb3a5 commit c8c7596
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Showing 3 changed files with 43 additions and 52 deletions.
26 changes: 21 additions & 5 deletions planet/static/css/main.css
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,9 @@ textarea.form-control {
margin-top: 5px;
}

/*
Cytoscape
*/

#cy {
min-height: 800px;
Expand All @@ -88,6 +91,12 @@ textarea.form-control {
top: 1em;
}

#legend {
display:none;
margin-top:800px;
}


.panel-scroll { height:250px; max-height: 250px; width: 100%; margin: 0; overflow-y: auto; }

/*
Expand Down Expand Up @@ -302,11 +311,18 @@ submenu
border-radius: 6px 0 6px 6px;
}

#legend {
display:none;
margin-top:800px;
}

/* Breadcrumb */
.breadcrumb {
margin-top:15px
}

/* Headers */

.banner-blue {
color: white;
padding: 8px 15px;
margin-bottom: 15px;
list-style: none;
background-color: #428bca;
border-radius: 4px;
}
4 changes: 2 additions & 2 deletions planet/templates/modals/sequence.html
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
<div class="modal-header">
{% if coding %}
<h4 class="modal-title" id="myModalLabel"><strong>{{ sequence.name }}</strong> coding sequence<small>(length: {{ sequence.coding_sequence|length }} bp)</small></h4>
<h4 class="modal-title" id="myModalLabel"><strong>{{ sequence.name }}</strong> coding sequence<small> (length: {{ sequence.coding_sequence|length }} bp)</small></h4>
{% else %}
<h4 class="modal-title" id="myModalLabel"><strong>{{ sequence.name }}</strong> protein sequence<small>(length: {{ sequence.protein_sequence|length }} aa)</small></h4>
<h4 class="modal-title" id="myModalLabel"><strong>{{ sequence.name }}</strong> protein sequence<small> (length: {{ sequence.protein_sequence|length }} aa)</small></h4>
{% endif %}

</div>
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65 changes: 20 additions & 45 deletions planet/templates/sequence.html
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Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,16 @@
{% if sequence %}
<ol class="breadcrumb">
<li><a href="{{ url_for('main.screen') }}">Home</a></li>
<li><a href="{{ url_for('species.species_overview') }}">Species</a></li>
<li><a href="{{ url_for('species.species_view', species_id=sequence.species.id) }}"><em>{{ sequence.species.name }}</em></a></li>
<li>Sequence</li>
<li class="active"><strong>{{ sequence.name }}</strong></li>
</ol>
<h1><strong>{{ sequence.name }}</strong> <small>({{ sequence.readable_type }})</small></h1>
<br />

{%- if sequence.aliases -%}
<p><strong>Aliases : </strong>{{sequence.aliases}}</p>
{%endif%}
{% if sequence.description %}

<p><strong>Description: </strong> {{sequence.description}}</p>
Expand All @@ -27,16 +30,21 @@ <h1><strong>{{ sequence.name }}</strong> <small>({{ sequence.readable_type }})</

<br />
<div>
<p>Sequence: <a href="{{ url_for('sequence.sequence_modal_coding', sequence_id=sequence.id) }}" data-target="#profileModal">coding</a> (<a href="{{ url_for('sequence.sequence_fasta_coding', sequence_id=sequence.id) }}">download</a>) {%- if sequence.type == 'protein_coding' -%}, <a href="{{ url_for('sequence.sequence_modal_protein', sequence_id=sequence.id) }}" data-target="#profileModal">protein</a> (<a href="{{ url_for('sequence.sequence_fasta_protein', sequence_id=sequence.id) }}">download</a>) {% endif %}</p>
<p><strong><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='gene_family') }}" data-target="#helpModal">Gene families</abbr>: </strong>{%- if families|count > 0 -%}{%- for family in families -%}
<a href="{{ url_for('family.family_view', family_id=family.id) }}">{{ family.name }}</a> ({{ family.method.method }}) {%- if not loop.last -%}, {% endif %}
{% endfor %} {% else %}<em>No families found for this sequence</em>{% endif %}</p>
<p><strong>Sequence:</strong> <a href="{{ url_for('sequence.sequence_modal_coding', sequence_id=sequence.id) }}" data-target="#profileModal">coding</a> (<a href="{{ url_for('sequence.sequence_fasta_coding', sequence_id=sequence.id) }}">download</a>) {%- if sequence.type == 'protein_coding' -%}, <a href="{{ url_for('sequence.sequence_modal_protein', sequence_id=sequence.id) }}" data-target="#profileModal">protein</a> (<a href="{{ url_for('sequence.sequence_fasta_protein', sequence_id=sequence.id) }}">download</a>) {% endif %}</p>
</div>

{% if expression_profiles|count > 0 %}
<h3 class="banner-blue">Expression Profile</h3>
{% for profile in expression_profiles %}
{% if loop.first %}
<h3>Expression Profile <small>(<a href="{{ url_for('expression_profile.expression_profile_view', profile_id=profile.id) }}">view details</a>)</small></h3>
<div style="height:350px; max-height:350px; margin-top:30px">
<canvas id="expression-profile" class="center-block" height="350"/>
</div>
<br />
<p><strong>Note:</strong>Only the main profile, including all conditions, is shown. Additional statistics and tissue specific profiles are available <a href="{{ url_for('expression_profile.expression_profile_view', profile_id=profile.id) }}">here</a>.</p>
{% endif %}
{% endfor %}
{% if expression_profiles|count > 1 %}
Expand All @@ -61,12 +69,11 @@ <h3>Expression Profile <small>(<a href="{{ url_for('expression_profile.expressio
</div>
{% endif %}
{% else %}
<h3>Expression Profile</h3>
<p><span class="text-muted"><em>No expression profile available</em></span></p>
{% endif %}
<br />
<div>
<h3>Co-expression Networks</h3>
<h3 class="banner-blue">Co-expression Networks</h3>
{% if network_nodes|count > 0 or coexpression_clusters|count > 0 %}
<div class="table-responsive">
<table class="table table-striped" id="coexpression_table">
Expand Down Expand Up @@ -100,7 +107,7 @@ <h3>Co-expression Networks</h3>
{% endif %}
</div>
<br />
<h3>Expression Context Conservation (<abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='ecc') }}" data-target="#helpModal">ECC</abbr>)</h3>
<h3 class="banner-blue">Expression Context Conservation (<abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='ecc') }}" data-target="#helpModal">ECC</abbr>)</h3>
<div class="table-responsive">
<table class="table table-striped" id="ecc_hits_table">
<thead>
Expand Down Expand Up @@ -129,15 +136,15 @@ <h3>Expression Context Conservation (<abbr title="Click to show help" href="{{ u
</table>
</div>
<br />
<h3>Functional Annotation</h3>
<h3 class="banner-blue">Functional Annotation</h3>
<div class="panel with-nav-tabs panel-default">
<div class="panel-heading">
<ul class="nav nav-tabs">
<li class="active"><a href="#tab1default" data-toggle="tab">GO</a></li>
<li><a href="#tab2default" data-toggle="tab">InterPro</a></li>
</ul>
</div>
<div class="panel-body">
<div>
<div class="tab-content">
<div class="tab-pane fade in active" id="tab1default">
{% if go_associations|count > 0 %}
Expand Down Expand Up @@ -166,7 +173,9 @@ <h3>Functional Annotation</h3>
</tbody>
</table>
</div>
<a href="#" id="go_toggle">Toggle parental</a>
<div class="panel-body">
<a href="#" id="go_toggle">Toggle parental</a>
</div>
{% else %}
<p>No GO annotation available for this sequence</p>
{% endif %}
Expand Down Expand Up @@ -212,41 +221,8 @@ <h3>Functional Annotation</h3>
</div>
</div>
</div>

<div class="col-lg-4 col-md-6 col-sm-12">
<div class="panel panel-default">
<div class="panel-heading"><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='gene_family') }}" data-target="#helpModal">Gene Families</abbr></div>
{% if families|count > 0 %}
<div class="panel-scroll">
<div class="table-responsive">
<table class="table table-striped" id="family_table">
<thead>
<tr>
<th data-sort="string-ins">Name</th>
<th data-sort="string-ins">Method</th>
</tr>
</thead>
<tbody>
{% for family in families %}
<tr>
<td><a href="{{ url_for('family.family_view', family_id=family.id) }}">{{ family.name }}</a></td>
<td>{{ family.method.method }}</td>
</tr>
{% endfor %}
</tbody>
</table>
</div>
</div>
{% else %}
<div class="panel-body panel-scroll">
<p>This sequence isn't a member of any gene families</p>
</div>
{% endif %}
</div>
</div> <!-- end col -->


<div class="col-lg-4 col-md-6 col-sm-12">
<div class="row">
<div class="col-lg-12 col-md-12 col-sm-12">
<div class="panel panel-default">
<div class="panel-heading">External Links</div>
{% if sequence.xrefs|count > 0 %}
Expand Down Expand Up @@ -304,7 +280,6 @@ <h3>Functional Annotation</h3>
$(function () {
$("#go_table").stupidtable();
$("#interpro_table").stupidtable();
$("#family_table").stupidtable();
$("#ecc_hits_table").stupidtable();
$("#coexpression_table").stupidtable();

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