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@@ -62,273 +62,264 @@ $no_hits = TRUE;
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<div class="blast-report">
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-<!-- Provide Information to the user about their blast job -->
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-<div class="blast-job-info">
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-<?php
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- $output_files = array();
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- if (file_exists($blast_job->files->result->html))
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- $output_files['html'] = array('path' => $blast_job->files->result->html, 'title' => 'Alignment');
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- if (file_exists($blast_job->files->result->tsv))
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- $output_files['tsv'] = array('path' => $blast_job->files->result->tsv, 'title' => 'Tab-Delimited');
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- if (file_exists($blast_job->files->result->gff))
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- $output_files['gff'] = array('path' => $blast_job->files->result->gff, 'title' => 'GFF3');
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- if (file_exists($blast_job->files->result->xml))
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- $output_files['xml'] = array('path' => $blast_job->files->result->xml, 'title' => 'XML');
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-?>
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- <?php if(!empty($output_files)): ?>
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- <div class="blast-download-info"><strong>Download</strong>:
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- <?php
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- $i = 0;
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- foreach($output_files as $file) {
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- $i++;
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- print l($file['title'], $file['path']);
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- if (sizeof($output_files) != $i) print ', ';
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- } ?>
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- </div>
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- <?php endif; ?>
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- <br />
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- <div class="blast-query-info"><strong>Query Information</strong>:
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- <?php print $blast_job->files->query;?></div>
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- <div class="blast-target-info"><strong>Search Target</strong>:
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- <?php print $blast_job->blastdb->db_name;?></div>
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- <div class="blast-date-info"><strong>Submission Date</strong>:
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- <?php print format_date($blast_job->date_submitted, 'medium');?></div>
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- <div class="blast-cmd-info"><strong>BLAST Command executed</strong>:
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- <?php print $blast_job->blast_cmd;?></div>
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+ <div class="blast-job-info">
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+ <!-- Provide Information to the user about their blast job -->
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+ <div class="blast-job-info">
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+ <div class="blast-download-info"><strong>Download</strong>:
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+ <a href="<?php print '../../' . $blast_job->files->result->html; ?>">Alignment</a>,
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+ <a href="<?php print '../../' . $blast_job->files->result->tsv; ?>">Tab-Delimited</a>,
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+ <a href="<?php print '../../' . $blast_job->files->result->xml; ?>">XML</a>,
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+ <a href="<?php print '../../' . $blast_job->files->result->gff; ?>">GFF3</a>
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+ </div>
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+ <br />
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+ <div class="blast-query-info"><strong>Query Information</strong>:
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+ <?php print $blast_job->files->query;?></div>
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+ <div class="blast-target-info"><strong>Search Target</strong>:
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+ <?php print $blast_job->blastdb->db_name;?></div>
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+ <div class="blast-date-info"><strong>Submission Date</strong>:
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+ <?php print format_date($blast_job->date_submitted, 'medium');?></div>
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+ <div class="blast-cmd-info"><strong>BLAST Command executed</strong>:
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+ <?php print $blast_job->blast_cmd;?></div>
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+ <br />
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+ <div class="num-results">
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+ <strong>Number of Results</strong>: <?php print $num_results; ?>
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+ </div>
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+ </div>
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+
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+ <br />
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+ <div class="num-results">
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+ <strong>Number of Results</strong>: <?php print $num_results; ?>
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+ </div>
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+ </div>
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<br />
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- <div class="num-results"><strong>Number of Results</strong>: <?php print $num_results; ?></div>
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-
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-</div>
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-<br />
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-<?php
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-
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-/**
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- * We are using the drupal table theme functionality to create this listing
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- * @see theme_table() for additional documentation
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- */
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+ <div class="report-table">
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+ <?php
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+ /**
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+ * We are using the drupal table theme functionality to create this listing
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+ * @see theme_table() for additional documentation
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+ */
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-if ($xml) {
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-?>
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+ if ($xml) {
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+ ?>
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-<p>The following table summarizes the results of your BLAST.
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-Click on a <em>triangle </em> on the left to see the alignment and a visualization of the hit,
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-and click the <em>target name </em> to get more information about the target hit.</p>
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+ <p>The following table summarizes the results of your BLAST.
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+ Click on a <em>triangle </em> on the left to see the alignment and a visualization of the hit,
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+ and click the <em>target name </em> to get more information about the target hit.</p>
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-<?php
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- // Specify the header of the table
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- $header = array(
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- 'arrow-col' => array('data' => '', 'class' => array('arrow-col')),
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- 'number' => array('data' => '#', 'class' => array('number')),
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- 'query' => array('data' => 'Query Name (Click for alignment & visualization)', 'class' => array('query')),
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- 'hit' => array('data' => 'Target Name', 'class' => array('hit')),
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- 'evalue' => array('data' => 'E-Value', 'class' => array('evalue')),
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- );
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-
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- $rows = array();
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- $count = 0;
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-
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- // Parse the BLAST XML to generate the rows of the table
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- // where each hit results in two rows in the table: 1) A summary of the query/hit and
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- // significance and 2) additional information including the alignment
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- foreach ($xml->{'BlastOutput_iterations'}->children() as $iteration) {
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- $children_count = $iteration->{'Iteration_hits'}->children()->count();
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-
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- // Save some information needed for the hit visualization.
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- $target_name = '';
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- $q_name = $xml->{'BlastOutput_query-def'};
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- $query_size = $xml->{'BlastOutput_query-len'};
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- $target_size = $iteration->{'Iteration_stat'}->{'Statistics'}->{'Statistics_db-len'};
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-
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- if ($children_count != 0) {
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- foreach ($iteration->{'Iteration_hits'}->children() as $hit) {
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- if (is_object($hit)) {
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- $count +=1;
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- $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';
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- $no_hits = FALSE;
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-
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- // SUMMARY ROW
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- // -- Save additional information needed for the summary.
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- $score = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
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- $evalue = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
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- $query_name = (string) $iteration->{'Iteration_query-def'};
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-
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- // If the id is of the form gnl|BL_ORD_ID|### then the parseids flag
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- // to makeblastdb did a really poor job. In thhis case we want to use
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- // the def to provide the original FASTA header.
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- // @todo Deepak changed this to use just the hit_def; inquire as to why.
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- $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'};
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- // Used for the hit visualization to ensure the name isn't truncated.
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- $hit_name_short = (preg_match('/^([^\s]+)/', $hit_name, $matches)) ? $matches[1] : $hit_name;
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-
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- // Round e-value to two decimal values.
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- $rounded_evalue = '';
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- if (strpos($evalue,'e') != false) {
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- $evalue_split = explode('e', $evalue);
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- $rounded_evalue = round($evalue_split[0], 2, PHP_ROUND_HALF_EVEN);
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- $rounded_evalue .= 'e' . $evalue_split[1];
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- }
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- else {
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- $rounded_evalue = $evalue;
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- }
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-
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- // State what should be in the summary row for theme_table() later.
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- $summary_row = array(
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- 'data' => array(
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- 'arrow-col' => array('data' => '<div class="arrow"></div>', 'class' => array('arrow-col')),
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- 'number' => array('data' => $count, 'class' => array('number')),
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- 'query' => array('data' => $query_name, 'class' => array('query')),
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- 'hit' => array('data' => $hit_name, 'class' => array('hit')),
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- 'evalue' => array('data' => $rounded_evalue, 'class' => array('evalue')),
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- ),
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- 'class' => array('result-summary')
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- );
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-
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- // ALIGNMENT ROW (collapsed by default)
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- // Process HSPs
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- $HSPs = array();
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-
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- // We need to save some additional summary information in order to draw the
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- // hit visualization. First, initialize some variables...
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- $track_start = INF;
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- $track_end = -1;
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- $hsps_range = '';
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- $hit_hsps = '';
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- $hit_hsp_score = '';
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- $target_size = $hit->{'Hit_len'};
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- $Hsp_bit_score = '';
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-
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- // Then for each hit hsp, keep track of the start of first hsp and the end of
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- // the last hsp. Keep in mind that hsps might not be recorded in order.
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- foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
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- $HSPs[] = (array) $hsp_xml;
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-
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- if ($track_start > $hsp_xml->{'Hsp_hit-from'}) {
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- $track_start = $hsp_xml->{'Hsp_hit-from'} . "";
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- }
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- if ($track_end < $hsp_xml->{'Hsp_hit-to'}) {
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- $track_end = $hsp_xml->{'Hsp_hit-to'} . "";
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- }
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-
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- // The BLAST visualization code requires the hsps to be formatted in a
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- // very specific manner. Here we build up the strings to be submitted.
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- // hits=4263001_4262263_1_742;4260037_4259524_895_1411;&scores=722;473;
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- $hit_hsps .= $hsp_xml->{'Hsp_hit-from'} . '_' .
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- $hsp_xml->{'Hsp_hit-to'} . '_' .
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- $hsp_xml->{'Hsp_query-from'} . '_' . $hsp_xml->{'Hsp_query-to'} .
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- ';';
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- $Hsp_bit_score .= $hsp_xml->{'Hsp_bit-score'} .';';
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- }
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- // Finally record the range.
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- // @todo figure out why we arbitrarily subtract 50,000 here...
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- // @more removing the 50,000 and using track start/end appears to cause no change...
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- $range_start = (int) $track_start;// - 50000;
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- $range_end = (int) $track_end;// + 50000;
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- if ($range_start < 1) $range_start = 1;
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-
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-
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- // Call the function to generate the hit image.
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- $hit_img = generate_blast_hit_image($target_name, $Hsp_bit_score, $hit_hsps,
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- $target_size, $query_size, $q_name, $hit_name_short);
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-
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-
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- // State what should be in the alignment row for theme_table() later.
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- $alignment_row = array(
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- 'data' => array(
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- 'arrow' => array(
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- 'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs, 'hit_visualization' => $hit_img)),
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- 'colspan' => 5,
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- ),
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- ),
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- 'class' => array('alignment-row', $zebra_class),
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- 'no_striping' => TRUE
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- );
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-
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- // LINK-OUTS.
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- // It was determined above whether link-outs were supported for the
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- // tripal blast database used as a search target. Thus we only want to
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- // determine a link-out if it's actually supported... ;-)
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- if ($linkout) {
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-
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- // First extract the linkout text using the regex provided through
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- // the Tripal blast database node.
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- if (preg_match($linkout_regex, $hit_name, $linkout_match)) {
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- $hit->{'linkout_id'} = $linkout_match[1];
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- $hit->{'hit_name'} = $hit_name;
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-
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- // Allow custom functions to determine the URL to support more complicated
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- // link-outs rather than just using the tripal database prefix.
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- $hit_name = call_user_func(
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- $url_function,
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- $linkout_urlprefix,
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- $hit,
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- array(
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- 'query_name' => $query_name,
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- 'score' => $score,
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- 'e-value' => $evalue,
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- 'HSPs' => $HSPs,
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- 'Target' => $blast_job->blastdb->db_name,
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- )
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+ <?php
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+ // Specify the header of the table
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+ $header = array(
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+ 'arrow-col' => array('data' => '', 'class' => array('arrow-col')),
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+ 'number' => array('data' => '#', 'class' => array('number')),
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+ 'query' => array('data' => 'Query Name (Click for alignment & visualization)', 'class' => array('query')),
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+ 'hit' => array('data' => 'Target Name', 'class' => array('hit')),
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+ 'evalue' => array('data' => 'E-Value', 'class' => array('evalue')),
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+ );
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+
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+ $rows = array();
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+ $count = 0;
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+
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+ // Parse the BLAST XML to generate the rows of the table
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+ // where each hit results in two rows in the table: 1) A summary of the query/hit and
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+ // significance and 2) additional information including the alignment
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+ foreach ($xml->{'BlastOutput_iterations'}->children() as $iteration) {
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+ $children_count = $iteration->{'Iteration_hits'}->children()->count();
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+
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+ // Save some information needed for the hit visualization.
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+ $target_name = '';
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+ $q_name = $xml->{'BlastOutput_query-def'};
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+ $query_size = $xml->{'BlastOutput_query-len'};
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+ $target_size = $iteration->{'Iteration_stat'}->{'Statistics'}->{'Statistics_db-len'};
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+
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+ if ($children_count != 0) {
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+ foreach ($iteration->{'Iteration_hits'}->children() as $hit) {
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+ if (is_object($hit)) {
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+ $count +=1;
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+ $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';
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+ $no_hits = FALSE;
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+
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+ // SUMMARY ROW
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+ // -- Save additional information needed for the summary.
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+ $score = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
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+ $evalue = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
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+ $query_name = (string) $iteration->{'Iteration_query-def'};
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+
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+ // If the id is of the form gnl|BL_ORD_ID|### then the parseids flag
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+ // to makeblastdb did a really poor job. In thhis case we want to use
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+ // the def to provide the original FASTA header.
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+ // @todo Deepak changed this to use just the hit_def; inquire as to why.
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+ $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'};
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+ // Used for the hit visualization to ensure the name isn't truncated.
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+ $hit_name_short = (preg_match('/^([^\s]+)/', $hit_name, $matches)) ? $matches[1] : $hit_name;
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+
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+ // Round e-value to two decimal values.
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+ $rounded_evalue = '';
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+ if (strpos($evalue,'e') != false) {
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+ $evalue_split = explode('e', $evalue);
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+ $rounded_evalue = round($evalue_split[0], 2, PHP_ROUND_HALF_EVEN);
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+ $rounded_evalue .= 'e' . $evalue_split[1];
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+ }
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+ else {
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+ $rounded_evalue = $evalue;
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+ }
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+
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+ // State what should be in the summary row for theme_table() later.
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+ $summary_row = array(
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+ 'data' => array(
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+ 'arrow-col' => array('data' => '<div class="arrow"></div>', 'class' => array('arrow-col')),
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+ 'number' => array('data' => $count, 'class' => array('number')),
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+ 'query' => array('data' => $query_name, 'class' => array('query')),
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+ 'hit' => array('data' => $hit_name, 'class' => array('hit')),
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+ 'evalue' => array('data' => $rounded_evalue, 'class' => array('evalue')),
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+ ),
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+ 'class' => array('result-summary')
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);
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- }
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-
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- // Replace the target name with the link.
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- $summary_row['data']['hit']['data'] = $hit_name;
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- }
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-
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- // ADD TO TABLE ROWS
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- $rows[] = $summary_row;
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- $rows[] = $alignment_row;
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-
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- }//end of if - checks $hit
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- }//end of foreach - iteration_hits
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- }//end of if - check for iteration_hits
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- else {
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- // Currently where the "no results" is added.
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- $query_name = $iteration->{'Iteration_query-def'};
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- $query_with_no_hits[] = $query_name;
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-
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- }//no results
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- }//end of foreach - BlastOutput_iterations
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+ // ALIGNMENT ROW (collapsed by default)
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+ // Process HSPs
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+ $HSPs = array();
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+
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+ // We need to save some additional summary information in order to draw the
|
|
|
+ // hit visualization. First, initialize some variables...
|
|
|
+ $track_start = INF;
|
|
|
+ $track_end = -1;
|
|
|
+ $hsps_range = '';
|
|
|
+ $hit_hsps = '';
|
|
|
+ $hit_hsp_score = '';
|
|
|
+ $target_size = $hit->{'Hit_len'};
|
|
|
+ $Hsp_bit_score = '';
|
|
|
+
|
|
|
+ // Then for each hit hsp, keep track of the start of first hsp and the end of
|
|
|
+ // the last hsp. Keep in mind that hsps might not be recorded in order.
|
|
|
+ foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
|
|
|
+ $HSPs[] = (array) $hsp_xml;
|
|
|
+
|
|
|
+ if ($track_start > $hsp_xml->{'Hsp_hit-from'}) {
|
|
|
+ $track_start = $hsp_xml->{'Hsp_hit-from'} . "";
|
|
|
+ }
|
|
|
+ if ($track_end < $hsp_xml->{'Hsp_hit-to'}) {
|
|
|
+ $track_end = $hsp_xml->{'Hsp_hit-to'} . "";
|
|
|
+ }
|
|
|
+
|
|
|
+ // The BLAST visualization code requires the hsps to be formatted in a
|
|
|
+ // very specific manner. Here we build up the strings to be submitted.
|
|
|
+ // hits=4263001_4262263_1_742;4260037_4259524_895_1411;&scores=722;473;
|
|
|
+ $hit_hsps .= $hsp_xml->{'Hsp_hit-from'} . '_' .
|
|
|
+ $hsp_xml->{'Hsp_hit-to'} . '_' .
|
|
|
+ $hsp_xml->{'Hsp_query-from'} . '_' . $hsp_xml->{'Hsp_query-to'} .
|
|
|
+ ';';
|
|
|
+ $Hsp_bit_score .= $hsp_xml->{'Hsp_bit-score'} .';';
|
|
|
+ }
|
|
|
+
|
|
|
+ // Finally record the range.
|
|
|
+ // @todo figure out why we arbitrarily subtract 50,000 here...
|
|
|
+ // @more removing the 50,000 and using track start/end appears to cause no change...
|
|
|
+ $range_start = (int) $track_start;// - 50000;
|
|
|
+ $range_end = (int) $track_end;// + 50000;
|
|
|
+ if ($range_start < 1) $range_start = 1;
|
|
|
+
|
|
|
+ // Call the function to generate the hit image.
|
|
|
+ $hit_img = generate_blast_hit_image($target_name, $Hsp_bit_score, $hit_hsps,
|
|
|
+ $target_size, $query_size, $q_name, $hit_name_short);
|
|
|
+
|
|
|
+ // State what should be in the alignment row for theme_table() later.
|
|
|
+ $alignment_row = array(
|
|
|
+ 'data' => array(
|
|
|
+ 'arrow' => array(
|
|
|
+ 'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs, 'hit_visualization' => $hit_img)),
|
|
|
+ 'colspan' => 5,
|
|
|
+ ),
|
|
|
+ ),
|
|
|
+ 'class' => array('alignment-row', $zebra_class),
|
|
|
+ 'no_striping' => TRUE
|
|
|
+ );
|
|
|
|
|
|
- if ($no_hits) {
|
|
|
- print '<p class="no-hits-message">No results found.</p>';
|
|
|
- }
|
|
|
- else {
|
|
|
- // We want to warn the user if some of their query sequences had no hits.
|
|
|
- if (!empty($query_with_no_hits)) {
|
|
|
- print '<p class="no-hits-message">Some of your query sequences did not '
|
|
|
- . 'match to the database/template. They are: '
|
|
|
- . implode(', ', $query_with_no_hits) . '.</p>';
|
|
|
+ // LINK-OUTS.
|
|
|
+ // It was determined above whether link-outs were supported for the
|
|
|
+ // tripal blast database used as a search target. Thus we only want to
|
|
|
+ // determine a link-out if it's actually supported... ;-)
|
|
|
+ if ($linkout) {
|
|
|
+
|
|
|
+ // First extract the linkout text using the regex provided through
|
|
|
+ // the Tripal blast database node.
|
|
|
+ if (preg_match($linkout_regex, $hit_name, $linkout_match)) {
|
|
|
+ $hit->{'linkout_id'} = $linkout_match[1];
|
|
|
+ $hit->{'hit_name'} = $hit_name;
|
|
|
+
|
|
|
+ // Allow custom functions to determine the URL to support more complicated
|
|
|
+ // link-outs rather than just using the tripal database prefix.
|
|
|
+ $hit_name = call_user_func(
|
|
|
+ $url_function,
|
|
|
+ $linkout_urlprefix,
|
|
|
+ $hit,
|
|
|
+ array(
|
|
|
+ 'query_name' => $query_name,
|
|
|
+ 'score' => $score,
|
|
|
+ 'e-value' => $evalue,
|
|
|
+ 'HSPs' => $HSPs,
|
|
|
+ 'Target' => $blast_job->blastdb->db_name,
|
|
|
+ )
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+ // Replace the target name with the link.
|
|
|
+ $summary_row['data']['hit']['data'] = $hit_name;
|
|
|
+ }
|
|
|
+
|
|
|
+ // ADD TO TABLE ROWS
|
|
|
+ $rows[] = $summary_row;
|
|
|
+ $rows[] = $alignment_row;
|
|
|
+
|
|
|
+ }//end of if - checks $hit
|
|
|
+ }//end of foreach - iteration_hits
|
|
|
+ }//end of if - check for iteration_hits
|
|
|
+
|
|
|
+ else {
|
|
|
+ // Currently where the "no results" is added.
|
|
|
+ $query_name = $iteration->{'Iteration_query-def'};
|
|
|
+ $query_with_no_hits[] = $query_name;
|
|
|
+
|
|
|
+ }//no results
|
|
|
+ }//end of foreach - BlastOutput_iterations
|
|
|
+
|
|
|
+ if ($no_hits) {
|
|
|
+ print '<p class="no-hits-message">No results found.</p>';
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ // We want to warn the user if some of their query sequences had no hits.
|
|
|
+ if (!empty($query_with_no_hits)) {
|
|
|
+ print '<p class="no-hits-message">Some of your query sequences did not '
|
|
|
+ . 'match to the database/template. They are: '
|
|
|
+ . implode(', ', $query_with_no_hits) . '.</p>';
|
|
|
+ }
|
|
|
+
|
|
|
+ // Actually print the table.
|
|
|
+ if (!empty($rows)) {
|
|
|
+ print theme('table', array(
|
|
|
+ 'header' => $header,
|
|
|
+ 'rows' => $rows,
|
|
|
+ 'attributes' => array('id' => 'blast_report'),
|
|
|
+ 'sticky' => FALSE
|
|
|
+ ));
|
|
|
+ }
|
|
|
+ }//handle no hits
|
|
|
+ }//XML exists
|
|
|
+ elseif ($too_many_results) {
|
|
|
+ print '<div class="messages error">Your BLAST resulted in '. number_format(floatval($num_results)) .' results which is too many to reasonably display. We have provided the result files for Download at the top of this page; however, we suggest you re-submit your query using a more stringent e-value (i.e. a smaller number).</div>';
|
|
|
}
|
|
|
-
|
|
|
- // Actually print the table.
|
|
|
- if (!empty($rows)) {
|
|
|
- print theme('table', array(
|
|
|
- 'header' => $header,
|
|
|
- 'rows' => $rows,
|
|
|
- 'attributes' => array('id' => 'blast_report'),
|
|
|
- 'sticky' => FALSE
|
|
|
- ));
|
|
|
+ else {
|
|
|
+ drupal_set_title('BLAST: Error Encountered');
|
|
|
+ print '<div class="messages error">We encountered an error and are unable to load your BLAST results.</div>';
|
|
|
}
|
|
|
- }//handle no hits
|
|
|
-}//XML exists
|
|
|
-elseif ($too_many_results) {
|
|
|
- print '<div class="messages error">Your BLAST resulted in '. number_format(floatval($num_results)) .' results which is too many to reasonably display. We have provided the result files for Download at the top of this page; however, we suggest you re-submit your query using a more stringent e-value (i.e. a smaller number).</div>';
|
|
|
-}
|
|
|
-else {
|
|
|
- drupal_set_title('BLAST: Error Encountered');
|
|
|
- print '<div class="messages error">We encountered an error and are unable to load your BLAST results.</div>';
|
|
|
-}
|
|
|
-?>
|
|
|
+ ?>
|
|
|
|
|
|
-<p><?php print l(
|
|
|
- 'Edit this query and re-submit',
|
|
|
- $blast_form_url,
|
|
|
- array('query' => array('resubmit' => blast_ui_make_secret($job_id))));
|
|
|
-?></p>
|
|
|
+ <p><?php print l(
|
|
|
+ 'Edit this query and re-submit',
|
|
|
+ $blast_form_url,
|
|
|
+ array('query' => array('resubmit' => blast_ui_make_secret($job_id))));
|
|
|
+ ?></p>
|
|
|
</div>
|
|
|
|
|
|
<?php print theme('blast_recent_jobs', array()); ?>
|
E.Cannon