Warning (2): include(/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Layouts/toolbox_layout.ctp): failed to open stream: No such file or directory [CORE/Cake/View/View.php, line 971]
Code Context
        ob_start();

        include $this->__viewFile;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Layouts/toolbox_layout.ctp'
$dataForView = array(
	'sidebar_info' => array(
		'gene_id' => 'Sp2g21390',
		'species' => 'spa',
		'gene_type' => 'coding',
		'default_gf_type' => 'HOMFAM',
		'gf_info' => array(
			'has_gf' => true,
			'gf_id' => 'HOM05D007325',
			'num_genes' => array(
				[maximum depth reached]
			)
		),
		'has_msa' => true,
		'has_tree' => true,
		'igv_info' => array(
			'genome' => array(
				[maximum depth reached]
			),
			'annotation' => array(
				[maximum depth reached]
			),
			'synteny_scores' => array(
				[maximum depth reached]
			)
		)
	),
	'sidebar' => 'gene_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'only_lvl2' => true,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false,
		'has_blast_db' => true
	),
	'sidebar_information' => array(
		'type' => 'gene_id',
		'id' => 'Sp2g21390'
	),
	'gene_id' => 'Sp2g21390',
	'gene_info' => array(
		'gene_id' => 'Sp2g21390',
		'species' => 'spa',
		'transcript' => 'Sp2g21390.1',
		'coord_cds' => 'complement(join(6056110..6056415))',
		'start' => '6056110',
		'stop' => '6056415',
		'coord_transcript' => 'complement(join(6056110..6056415))',
		'seq' => 'ATGAGTGAGAAGCTCCTCTTGAGAAGCAGCACTGGCGGCGACTGTTACTGCCATGGAGCATATGGAGAGTATTTTGAGAAGAGACAGATGTTTCTAAGGAGCTACCGGTTCTCCAGGAAACAGAGCTTCTCCGAGAAGCTCACGGGATCTGTGAGGAGAGTGAAGAGATTTGTCTGGACGAGGTTGAGATCAGCGAGGAGGTTGAAACGCGTTGTCTGGTCTCGACTCAGATCGGCGTTTCTCTACCGCCGGAGACGCTTTTTCCGCCTCCTTCACTTACACGACGAACCTTCTTACTGCTTCTAA',
		'strand' => '-',
		'chr' => 'ch2-4',
		'type' => 'coding',
		'check_transcript' => 'eq',
		'check_protein' => 'eq',
		'transl_table' => '1'
	),
	'title_for_layout' => 'Dicots PLAZA 5.0 : gene pages',
	'content_for_layout' => '<h1>Sequences</h1>
<div class="col-lg-4 col-md-8 mb-4">
	<h2>Gene information</h2>
	<ul class="list-group">
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Gene</span>
			<span>
				Sp2g21390			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Chromosome</span>
			<span>
				ch2-4			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Start</span>
			<span>
				6056110			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Stop</span>
			<span>
				6056415			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Strand</span>
			<span>
				-			</span>
		</li>
	</ul>
</div>
<h2>Sequence content</h2>
<ul class="nav nav-tabs">
	<li class="nav-item">
		<a href="#DNASEQUENCES" class="nav-link active" data-bs-toggle="tab">DNA Sequences</a>
	</li>
			<li class="nav-item">
			<a href="#PROTEINSEQUENCES" class="nav-link" data-bs-toggle="tab">Protein Sequences</a>
		</li>
	</ul>
<div class="tab-content">
	<div class="tab-pane active" id="DNASEQUENCES">
		<div class="row">
			<div class="col-lg-9">
				<div id="dna_features_container" class="mt-3">
				</div>
			</div>
			<div class=" col-lg-3">
				<form method='post' name='sequence_features_form' id='sequence_features_form' class="d-flex flex-column">
					<div class="parameter_option_box mt-3">
						<h3>Parameters</h3>
						<div class="d-flex justify-content-between">
							<label>Strand</label>
							<select id="select_strand" name='strand' class='form form-select d-inline w-50'>
								<option value='+' selected='selected'>positive</option>
								<option value='-'>negative</option>
							</select>
						</div>
						<div class="d-flex justify-content-between">
							<div>
								<label>Remove overlap</label>
								</br>
								<span style='font-size:small'>(with previous/next
									gene)</span>
							</div>
							<input type='checkbox' name='overlap_removal' checked='checked' />
						</div>
						<hr>
						<div class="d-flex justify-content-between">
							<label>Exons (CDS)</label>
							<input type='checkbox' name='cds' checked='checked' />
						</div>
						<div class="d-flex justify-content-between">
							<label>Exons (UTR)</label>
							<input type='checkbox' name='utr' checked='checked' />

						</div>
						<div class="d-flex justify-content-between">
							<label>Intron</label>
							<input type='checkbox' name='intron' checked='checked' />
						</div>
						<div class="d-flex justify-content-between">
							<label>Upstream</label>
							<select id="select_upstream" name='upstream' class='form form-select d-inline w-50'>
								<option value='off' selected='selected'>None</option>
								<option value='1000'>1kb</option>
								<option value='2000'>2kb</option>
							</select>
						</div>

						<div class="d-flex justify-content-between">
							<label>Downstream</label>
							<select id="select_downstream" name='downstream' class='form form-select d-inline w-50'>
								<option value='off' selected='selected'>None</option>
								<option value='1000'>1kb</option>
								<option value='2000'>2kb</option>
							</select>
						</div>
						<hr>
						<div class="d-flex justify-content-between">
							<label>Output</label>
							<select id="select_output" name='output_format' class='form form-select d-inline w-50'>
								<option value='text' selected='selected'>Text</option>
								<option value='fasta'>Fasta</option>
							</select>
						</div>
						<input type='button' value='Update sequence view' class='btn btn-primary mt-2' id='feature_submit_btn' />
					</div>
				</form>
			</div>
		</div>
	</div>
			<div class="tab-pane" id="PROTEINSEQUENCES">
			<div class="mt-4">
				<div id="aa_features_container"></div>
			</div>
		</div>
	</div>
</div>


<script type="text/javascript">
	//<![CDATA[
	function update_dna_features() {
		var container_id = "dna_features_container";
		var url = '/plaza.dev/_dev_instances/feedback/genes/get_dnasequence_features/Sp2g21390';
		var post_data = jQuery("#sequence_features_form").serialize(true);
		//console.log(post_data);
		jQuery("#" + container_id).html('<div class="spinner-border position-relative start-50" role="status"><span class="visually-hidden">Loading...</span></div>');
		jQuery.ajax({
			url: url,
			method: "POST",
			data: post_data,
			success: function(data) {
				//console.log(data);
				jQuery("#" + container_id).html(data);
			},
			error: function(e){
				console.log(e);
			}
		});
	}

	function update_aa_features() {
		var container_id = "aa_features_container";
		var url = '/plaza.dev/_dev_instances/feedback/genes/get_aasequence_features/Sp2g21390';
		jQuery("#" + container_id).html('<div class="spinner-border position-relative start-50" role="status"><span class="visually-hidden">Loading...</span></div>');
		jQuery.ajax({
			url: url,
			success: function(data) {
				jQuery("#" + container_id).html(data);
			}
		});
	}

	function checbox_changed() {
		if (this.checked) {
			console.log("checked");
		} else {
			console.log("not checked");
		}
	}

	jQuery("#feature_submit_btn").click(function(event) {
		update_dna_features();
	});

	jQuery(document).ready(function() {
		update_dna_features();
					update_aa_features();
		
		// Disable select for upstream/downstream when deselected

		$("#checkbox_upstream").click(function() {
			if (!this.checked) {
				$("#select_upstream").prop('disabled', true);
			} else {
				$("#select_upstream").prop('disabled', false);
			}
		});

		$("#checkbox_downstream").click(function() {
			if (!this.checked) {
				$("#select_downstream").prop('disabled', true);
			} else {
				$("#select_downstream").prop('disabled', false);
			}
		});
	});

	//]]>
</script>',
	'scripts_for_layout' => ''
)
$sidebar_info = array(
	'gene_id' => 'Sp2g21390',
	'species' => 'spa',
	'gene_type' => 'coding',
	'default_gf_type' => 'HOMFAM',
	'gf_info' => array(
		'has_gf' => true,
		'gf_id' => 'HOM05D007325',
		'num_genes' => array(
			'num_genes' => '106',
			'num_species' => '54'
		)
	),
	'has_msa' => true,
	'has_tree' => true,
	'igv_info' => array(
		'genome' => array(
			'content' => array(
				[maximum depth reached]
			),
			'index' => array(
				[maximum depth reached]
			),
			'compressed_index' => array(
				[maximum depth reached]
			)
		),
		'annotation' => array(
			'content' => array(
				[maximum depth reached]
			)
		),
		'synteny_scores' => array(
			'content' => array(
				[maximum depth reached]
			)
		)
	)
)
$sidebar = 'gene_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'only_lvl2' => true,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false,
	'has_blast_db' => true
)
$sidebar_information = array(
	'type' => 'gene_id',
	'id' => 'Sp2g21390'
)
$gene_id = 'Sp2g21390'
$gene_info = array(
	'gene_id' => 'Sp2g21390',
	'species' => 'spa',
	'transcript' => 'Sp2g21390.1',
	'coord_cds' => 'complement(join(6056110..6056415))',
	'start' => '6056110',
	'stop' => '6056415',
	'coord_transcript' => 'complement(join(6056110..6056415))',
	'seq' => 'ATGAGTGAGAAGCTCCTCTTGAGAAGCAGCACTGGCGGCGACTGTTACTGCCATGGAGCATATGGAGAGTATTTTGAGAAGAGACAGATGTTTCTAAGGAGCTACCGGTTCTCCAGGAAACAGAGCTTCTCCGAGAAGCTCACGGGATCTGTGAGGAGAGTGAAGAGATTTGTCTGGACGAGGTTGAGATCAGCGAGGAGGTTGAAACGCGTTGTCTGGTCTCGACTCAGATCGGCGTTTCTCTACCGCCGGAGACGCTTTTTCCGCCTCCTTCACTTACACGACGAACCTTCTTACTGCTTCTAA',
	'strand' => '-',
	'chr' => 'ch2-4',
	'type' => 'coding',
	'check_transcript' => 'eq',
	'check_protein' => 'eq',
	'transl_table' => '1'
)
$title_for_layout = 'Dicots PLAZA 5.0 : gene pages'
$content_for_layout = '<h1>Sequences</h1>
<div class="col-lg-4 col-md-8 mb-4">
	<h2>Gene information</h2>
	<ul class="list-group">
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Gene</span>
			<span>
				Sp2g21390			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Chromosome</span>
			<span>
				ch2-4			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Start</span>
			<span>
				6056110			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Stop</span>
			<span>
				6056415			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Strand</span>
			<span>
				-			</span>
		</li>
	</ul>
</div>
<h2>Sequence content</h2>
<ul class="nav nav-tabs">
	<li class="nav-item">
		<a href="#DNASEQUENCES" class="nav-link active" data-bs-toggle="tab">DNA Sequences</a>
	</li>
			<li class="nav-item">
			<a href="#PROTEINSEQUENCES" class="nav-link" data-bs-toggle="tab">Protein Sequences</a>
		</li>
	</ul>
<div class="tab-content">
	<div class="tab-pane active" id="DNASEQUENCES">
		<div class="row">
			<div class="col-lg-9">
				<div id="dna_features_container" class="mt-3">
				</div>
			</div>
			<div class=" col-lg-3">
				<form method='post' name='sequence_features_form' id='sequence_features_form' class="d-flex flex-column">
					<div class="parameter_option_box mt-3">
						<h3>Parameters</h3>
						<div class="d-flex justify-content-between">
							<label>Strand</label>
							<select id="select_strand" name='strand' class='form form-select d-inline w-50'>
								<option value='+' selected='selected'>positive</option>
								<option value='-'>negative</option>
							</select>
						</div>
						<div class="d-flex justify-content-between">
							<div>
								<label>Remove overlap</label>
								</br>
								<span style='font-size:small'>(with previous/next
									gene)</span>
							</div>
							<input type='checkbox' name='overlap_removal' checked='checked' />
						</div>
						<hr>
						<div class="d-flex justify-content-between">
							<label>Exons (CDS)</label>
							<input type='checkbox' name='cds' checked='checked' />
						</div>
						<div class="d-flex justify-content-between">
							<label>Exons (UTR)</label>
							<input type='checkbox' name='utr' checked='checked' />

						</div>
						<div class="d-flex justify-content-between">
							<label>Intron</label>
							<input type='checkbox' name='intron' checked='checked' />
						</div>
						<div class="d-flex justify-content-between">
							<label>Upstream</label>
							<select id="select_upstream" name='upstream' class='form form-select d-inline w-50'>
								<option value='off' selected='selected'>None</option>
								<option value='1000'>1kb</option>
								<option value='2000'>2kb</option>
							</select>
						</div>

						<div class="d-flex justify-content-between">
							<label>Downstream</label>
							<select id="select_downstream" name='downstream' class='form form-select d-inline w-50'>
								<option value='off' selected='selected'>None</option>
								<option value='1000'>1kb</option>
								<option value='2000'>2kb</option>
							</select>
						</div>
						<hr>
						<div class="d-flex justify-content-between">
							<label>Output</label>
							<select id="select_output" name='output_format' class='form form-select d-inline w-50'>
								<option value='text' selected='selected'>Text</option>
								<option value='fasta'>Fasta</option>
							</select>
						</div>
						<input type='button' value='Update sequence view' class='btn btn-primary mt-2' id='feature_submit_btn' />
					</div>
				</form>
			</div>
		</div>
	</div>
			<div class="tab-pane" id="PROTEINSEQUENCES">
			<div class="mt-4">
				<div id="aa_features_container"></div>
			</div>
		</div>
	</div>
</div>


<script type="text/javascript">
	//<![CDATA[
	function update_dna_features() {
		var container_id = "dna_features_container";
		var url = '/plaza.dev/_dev_instances/feedback/genes/get_dnasequence_features/Sp2g21390';
		var post_data = jQuery("#sequence_features_form").serialize(true);
		//console.log(post_data);
		jQuery("#" + container_id).html('<div class="spinner-border position-relative start-50" role="status"><span class="visually-hidden">Loading...</span></div>');
		jQuery.ajax({
			url: url,
			method: "POST",
			data: post_data,
			success: function(data) {
				//console.log(data);
				jQuery("#" + container_id).html(data);
			},
			error: function(e){
				console.log(e);
			}
		});
	}

	function update_aa_features() {
		var container_id = "aa_features_container";
		var url = '/plaza.dev/_dev_instances/feedback/genes/get_aasequence_features/Sp2g21390';
		jQuery("#" + container_id).html('<div class="spinner-border position-relative start-50" role="status"><span class="visually-hidden">Loading...</span></div>');
		jQuery.ajax({
			url: url,
			success: function(data) {
				jQuery("#" + container_id).html(data);
			}
		});
	}

	function checbox_changed() {
		if (this.checked) {
			console.log("checked");
		} else {
			console.log("not checked");
		}
	}

	jQuery("#feature_submit_btn").click(function(event) {
		update_dna_features();
	});

	jQuery(document).ready(function() {
		update_dna_features();
					update_aa_features();
		
		// Disable select for upstream/downstream when deselected

		$("#checkbox_upstream").click(function() {
			if (!this.checked) {
				$("#select_upstream").prop('disabled', true);
			} else {
				$("#select_upstream").prop('disabled', false);
			}
		});

		$("#checkbox_downstream").click(function() {
			if (!this.checked) {
				$("#select_downstream").prop('disabled', true);
			} else {
				$("#select_downstream").prop('disabled', false);
			}
		});
	});

	//]]>
</script>'
$scripts_for_layout = ''
include - CORE/Cake/View/View.php, line 971
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::renderLayout() - CORE/Cake/View/View.php, line 546
View::render() - CORE/Cake/View/View.php, line 481
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 151

Warning (2): include() [<a href='http://php.net/function.include'>function.include</a>]: Failed opening '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Layouts/toolbox_layout.ctp' for inclusion (include_path='/www/bioinformatics01_ro/plaza/_dev_instances/feedback/lib:.:/opt/remi/php74/root/usr/share/pear:/opt/remi/php74/root/usr/share/php:/usr/share/pear:/usr/share/php') [CORE/Cake/View/View.php, line 971]
Code Context
        ob_start();

        include $this->__viewFile;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Layouts/toolbox_layout.ctp'
$dataForView = array(
	'sidebar_info' => array(
		'gene_id' => 'Sp2g21390',
		'species' => 'spa',
		'gene_type' => 'coding',
		'default_gf_type' => 'HOMFAM',
		'gf_info' => array(
			'has_gf' => true,
			'gf_id' => 'HOM05D007325',
			'num_genes' => array(
				[maximum depth reached]
			)
		),
		'has_msa' => true,
		'has_tree' => true,
		'igv_info' => array(
			'genome' => array(
				[maximum depth reached]
			),
			'annotation' => array(
				[maximum depth reached]
			),
			'synteny_scores' => array(
				[maximum depth reached]
			)
		)
	),
	'sidebar' => 'gene_sidebar',
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 1,
		'num_colinearity_with_dating_runs' => (int) 0,
		'only_lvl2' => true,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false,
		'has_blast_db' => true
	),
	'sidebar_information' => array(
		'type' => 'gene_id',
		'id' => 'Sp2g21390'
	),
	'gene_id' => 'Sp2g21390',
	'gene_info' => array(
		'gene_id' => 'Sp2g21390',
		'species' => 'spa',
		'transcript' => 'Sp2g21390.1',
		'coord_cds' => 'complement(join(6056110..6056415))',
		'start' => '6056110',
		'stop' => '6056415',
		'coord_transcript' => 'complement(join(6056110..6056415))',
		'seq' => 'ATGAGTGAGAAGCTCCTCTTGAGAAGCAGCACTGGCGGCGACTGTTACTGCCATGGAGCATATGGAGAGTATTTTGAGAAGAGACAGATGTTTCTAAGGAGCTACCGGTTCTCCAGGAAACAGAGCTTCTCCGAGAAGCTCACGGGATCTGTGAGGAGAGTGAAGAGATTTGTCTGGACGAGGTTGAGATCAGCGAGGAGGTTGAAACGCGTTGTCTGGTCTCGACTCAGATCGGCGTTTCTCTACCGCCGGAGACGCTTTTTCCGCCTCCTTCACTTACACGACGAACCTTCTTACTGCTTCTAA',
		'strand' => '-',
		'chr' => 'ch2-4',
		'type' => 'coding',
		'check_transcript' => 'eq',
		'check_protein' => 'eq',
		'transl_table' => '1'
	),
	'title_for_layout' => 'Dicots PLAZA 5.0 : gene pages',
	'content_for_layout' => '<h1>Sequences</h1>
<div class="col-lg-4 col-md-8 mb-4">
	<h2>Gene information</h2>
	<ul class="list-group">
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Gene</span>
			<span>
				Sp2g21390			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Chromosome</span>
			<span>
				ch2-4			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Start</span>
			<span>
				6056110			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Stop</span>
			<span>
				6056415			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Strand</span>
			<span>
				-			</span>
		</li>
	</ul>
</div>
<h2>Sequence content</h2>
<ul class="nav nav-tabs">
	<li class="nav-item">
		<a href="#DNASEQUENCES" class="nav-link active" data-bs-toggle="tab">DNA Sequences</a>
	</li>
			<li class="nav-item">
			<a href="#PROTEINSEQUENCES" class="nav-link" data-bs-toggle="tab">Protein Sequences</a>
		</li>
	</ul>
<div class="tab-content">
	<div class="tab-pane active" id="DNASEQUENCES">
		<div class="row">
			<div class="col-lg-9">
				<div id="dna_features_container" class="mt-3">
				</div>
			</div>
			<div class=" col-lg-3">
				<form method='post' name='sequence_features_form' id='sequence_features_form' class="d-flex flex-column">
					<div class="parameter_option_box mt-3">
						<h3>Parameters</h3>
						<div class="d-flex justify-content-between">
							<label>Strand</label>
							<select id="select_strand" name='strand' class='form form-select d-inline w-50'>
								<option value='+' selected='selected'>positive</option>
								<option value='-'>negative</option>
							</select>
						</div>
						<div class="d-flex justify-content-between">
							<div>
								<label>Remove overlap</label>
								</br>
								<span style='font-size:small'>(with previous/next
									gene)</span>
							</div>
							<input type='checkbox' name='overlap_removal' checked='checked' />
						</div>
						<hr>
						<div class="d-flex justify-content-between">
							<label>Exons (CDS)</label>
							<input type='checkbox' name='cds' checked='checked' />
						</div>
						<div class="d-flex justify-content-between">
							<label>Exons (UTR)</label>
							<input type='checkbox' name='utr' checked='checked' />

						</div>
						<div class="d-flex justify-content-between">
							<label>Intron</label>
							<input type='checkbox' name='intron' checked='checked' />
						</div>
						<div class="d-flex justify-content-between">
							<label>Upstream</label>
							<select id="select_upstream" name='upstream' class='form form-select d-inline w-50'>
								<option value='off' selected='selected'>None</option>
								<option value='1000'>1kb</option>
								<option value='2000'>2kb</option>
							</select>
						</div>

						<div class="d-flex justify-content-between">
							<label>Downstream</label>
							<select id="select_downstream" name='downstream' class='form form-select d-inline w-50'>
								<option value='off' selected='selected'>None</option>
								<option value='1000'>1kb</option>
								<option value='2000'>2kb</option>
							</select>
						</div>
						<hr>
						<div class="d-flex justify-content-between">
							<label>Output</label>
							<select id="select_output" name='output_format' class='form form-select d-inline w-50'>
								<option value='text' selected='selected'>Text</option>
								<option value='fasta'>Fasta</option>
							</select>
						</div>
						<input type='button' value='Update sequence view' class='btn btn-primary mt-2' id='feature_submit_btn' />
					</div>
				</form>
			</div>
		</div>
	</div>
			<div class="tab-pane" id="PROTEINSEQUENCES">
			<div class="mt-4">
				<div id="aa_features_container"></div>
			</div>
		</div>
	</div>
</div>


<script type="text/javascript">
	//<![CDATA[
	function update_dna_features() {
		var container_id = "dna_features_container";
		var url = '/plaza.dev/_dev_instances/feedback/genes/get_dnasequence_features/Sp2g21390';
		var post_data = jQuery("#sequence_features_form").serialize(true);
		//console.log(post_data);
		jQuery("#" + container_id).html('<div class="spinner-border position-relative start-50" role="status"><span class="visually-hidden">Loading...</span></div>');
		jQuery.ajax({
			url: url,
			method: "POST",
			data: post_data,
			success: function(data) {
				//console.log(data);
				jQuery("#" + container_id).html(data);
			},
			error: function(e){
				console.log(e);
			}
		});
	}

	function update_aa_features() {
		var container_id = "aa_features_container";
		var url = '/plaza.dev/_dev_instances/feedback/genes/get_aasequence_features/Sp2g21390';
		jQuery("#" + container_id).html('<div class="spinner-border position-relative start-50" role="status"><span class="visually-hidden">Loading...</span></div>');
		jQuery.ajax({
			url: url,
			success: function(data) {
				jQuery("#" + container_id).html(data);
			}
		});
	}

	function checbox_changed() {
		if (this.checked) {
			console.log("checked");
		} else {
			console.log("not checked");
		}
	}

	jQuery("#feature_submit_btn").click(function(event) {
		update_dna_features();
	});

	jQuery(document).ready(function() {
		update_dna_features();
					update_aa_features();
		
		// Disable select for upstream/downstream when deselected

		$("#checkbox_upstream").click(function() {
			if (!this.checked) {
				$("#select_upstream").prop('disabled', true);
			} else {
				$("#select_upstream").prop('disabled', false);
			}
		});

		$("#checkbox_downstream").click(function() {
			if (!this.checked) {
				$("#select_downstream").prop('disabled', true);
			} else {
				$("#select_downstream").prop('disabled', false);
			}
		});
	});

	//]]>
</script>',
	'scripts_for_layout' => ''
)
$sidebar_info = array(
	'gene_id' => 'Sp2g21390',
	'species' => 'spa',
	'gene_type' => 'coding',
	'default_gf_type' => 'HOMFAM',
	'gf_info' => array(
		'has_gf' => true,
		'gf_id' => 'HOM05D007325',
		'num_genes' => array(
			'num_genes' => '106',
			'num_species' => '54'
		)
	),
	'has_msa' => true,
	'has_tree' => true,
	'igv_info' => array(
		'genome' => array(
			'content' => array(
				[maximum depth reached]
			),
			'index' => array(
				[maximum depth reached]
			),
			'compressed_index' => array(
				[maximum depth reached]
			)
		),
		'annotation' => array(
			'content' => array(
				[maximum depth reached]
			)
		),
		'synteny_scores' => array(
			'content' => array(
				[maximum depth reached]
			)
		)
	)
)
$sidebar = 'gene_sidebar'
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 1,
	'num_colinearity_with_dating_runs' => (int) 0,
	'only_lvl2' => true,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false,
	'has_blast_db' => true
)
$sidebar_information = array(
	'type' => 'gene_id',
	'id' => 'Sp2g21390'
)
$gene_id = 'Sp2g21390'
$gene_info = array(
	'gene_id' => 'Sp2g21390',
	'species' => 'spa',
	'transcript' => 'Sp2g21390.1',
	'coord_cds' => 'complement(join(6056110..6056415))',
	'start' => '6056110',
	'stop' => '6056415',
	'coord_transcript' => 'complement(join(6056110..6056415))',
	'seq' => 'ATGAGTGAGAAGCTCCTCTTGAGAAGCAGCACTGGCGGCGACTGTTACTGCCATGGAGCATATGGAGAGTATTTTGAGAAGAGACAGATGTTTCTAAGGAGCTACCGGTTCTCCAGGAAACAGAGCTTCTCCGAGAAGCTCACGGGATCTGTGAGGAGAGTGAAGAGATTTGTCTGGACGAGGTTGAGATCAGCGAGGAGGTTGAAACGCGTTGTCTGGTCTCGACTCAGATCGGCGTTTCTCTACCGCCGGAGACGCTTTTTCCGCCTCCTTCACTTACACGACGAACCTTCTTACTGCTTCTAA',
	'strand' => '-',
	'chr' => 'ch2-4',
	'type' => 'coding',
	'check_transcript' => 'eq',
	'check_protein' => 'eq',
	'transl_table' => '1'
)
$title_for_layout = 'Dicots PLAZA 5.0 : gene pages'
$content_for_layout = '<h1>Sequences</h1>
<div class="col-lg-4 col-md-8 mb-4">
	<h2>Gene information</h2>
	<ul class="list-group">
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Gene</span>
			<span>
				Sp2g21390			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Chromosome</span>
			<span>
				ch2-4			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Start</span>
			<span>
				6056110			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Stop</span>
			<span>
				6056415			</span>
		</li>
		<li class="d-flex justify-content-between list-group-item list-group-item-light">
			<span class="list_group_label">Strand</span>
			<span>
				-			</span>
		</li>
	</ul>
</div>
<h2>Sequence content</h2>
<ul class="nav nav-tabs">
	<li class="nav-item">
		<a href="#DNASEQUENCES" class="nav-link active" data-bs-toggle="tab">DNA Sequences</a>
	</li>
			<li class="nav-item">
			<a href="#PROTEINSEQUENCES" class="nav-link" data-bs-toggle="tab">Protein Sequences</a>
		</li>
	</ul>
<div class="tab-content">
	<div class="tab-pane active" id="DNASEQUENCES">
		<div class="row">
			<div class="col-lg-9">
				<div id="dna_features_container" class="mt-3">
				</div>
			</div>
			<div class=" col-lg-3">
				<form method='post' name='sequence_features_form' id='sequence_features_form' class="d-flex flex-column">
					<div class="parameter_option_box mt-3">
						<h3>Parameters</h3>
						<div class="d-flex justify-content-between">
							<label>Strand</label>
							<select id="select_strand" name='strand' class='form form-select d-inline w-50'>
								<option value='+' selected='selected'>positive</option>
								<option value='-'>negative</option>
							</select>
						</div>
						<div class="d-flex justify-content-between">
							<div>
								<label>Remove overlap</label>
								</br>
								<span style='font-size:small'>(with previous/next
									gene)</span>
							</div>
							<input type='checkbox' name='overlap_removal' checked='checked' />
						</div>
						<hr>
						<div class="d-flex justify-content-between">
							<label>Exons (CDS)</label>
							<input type='checkbox' name='cds' checked='checked' />
						</div>
						<div class="d-flex justify-content-between">
							<label>Exons (UTR)</label>
							<input type='checkbox' name='utr' checked='checked' />

						</div>
						<div class="d-flex justify-content-between">
							<label>Intron</label>
							<input type='checkbox' name='intron' checked='checked' />
						</div>
						<div class="d-flex justify-content-between">
							<label>Upstream</label>
							<select id="select_upstream" name='upstream' class='form form-select d-inline w-50'>
								<option value='off' selected='selected'>None</option>
								<option value='1000'>1kb</option>
								<option value='2000'>2kb</option>
							</select>
						</div>

						<div class="d-flex justify-content-between">
							<label>Downstream</label>
							<select id="select_downstream" name='downstream' class='form form-select d-inline w-50'>
								<option value='off' selected='selected'>None</option>
								<option value='1000'>1kb</option>
								<option value='2000'>2kb</option>
							</select>
						</div>
						<hr>
						<div class="d-flex justify-content-between">
							<label>Output</label>
							<select id="select_output" name='output_format' class='form form-select d-inline w-50'>
								<option value='text' selected='selected'>Text</option>
								<option value='fasta'>Fasta</option>
							</select>
						</div>
						<input type='button' value='Update sequence view' class='btn btn-primary mt-2' id='feature_submit_btn' />
					</div>
				</form>
			</div>
		</div>
	</div>
			<div class="tab-pane" id="PROTEINSEQUENCES">
			<div class="mt-4">
				<div id="aa_features_container"></div>
			</div>
		</div>
	</div>
</div>


<script type="text/javascript">
	//<![CDATA[
	function update_dna_features() {
		var container_id = "dna_features_container";
		var url = '/plaza.dev/_dev_instances/feedback/genes/get_dnasequence_features/Sp2g21390';
		var post_data = jQuery("#sequence_features_form").serialize(true);
		//console.log(post_data);
		jQuery("#" + container_id).html('<div class="spinner-border position-relative start-50" role="status"><span class="visually-hidden">Loading...</span></div>');
		jQuery.ajax({
			url: url,
			method: "POST",
			data: post_data,
			success: function(data) {
				//console.log(data);
				jQuery("#" + container_id).html(data);
			},
			error: function(e){
				console.log(e);
			}
		});
	}

	function update_aa_features() {
		var container_id = "aa_features_container";
		var url = '/plaza.dev/_dev_instances/feedback/genes/get_aasequence_features/Sp2g21390';
		jQuery("#" + container_id).html('<div class="spinner-border position-relative start-50" role="status"><span class="visually-hidden">Loading...</span></div>');
		jQuery.ajax({
			url: url,
			success: function(data) {
				jQuery("#" + container_id).html(data);
			}
		});
	}

	function checbox_changed() {
		if (this.checked) {
			console.log("checked");
		} else {
			console.log("not checked");
		}
	}

	jQuery("#feature_submit_btn").click(function(event) {
		update_dna_features();
	});

	jQuery(document).ready(function() {
		update_dna_features();
					update_aa_features();
		
		// Disable select for upstream/downstream when deselected

		$("#checkbox_upstream").click(function() {
			if (!this.checked) {
				$("#select_upstream").prop('disabled', true);
			} else {
				$("#select_upstream").prop('disabled', false);
			}
		});

		$("#checkbox_downstream").click(function() {
			if (!this.checked) {
				$("#select_downstream").prop('disabled', true);
			} else {
				$("#select_downstream").prop('disabled', false);
			}
		});
	});

	//]]>
</script>'
$scripts_for_layout = ''
include - CORE/Cake/View/View.php, line 971
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::renderLayout() - CORE/Cake/View/View.php, line 546
View::render() - CORE/Cake/View/View.php, line 481
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 151