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@@ -8,7 +8,7 @@ $linkout = FALSE;
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if ($blast_job->blastdb->linkout->none === FALSE) {
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if ($blast_job->blastdb->linkout->none === FALSE) {
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$linkout_type = $blast_job->blastdb->linkout->type;
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$linkout_type = $blast_job->blastdb->linkout->type;
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$linkout_regex = $blast_job->blastdb->linkout->regex;
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$linkout_regex = $blast_job->blastdb->linkout->regex;
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-
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+
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// Note that URL prefix is not required if linkout type is 'custom'
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// Note that URL prefix is not required if linkout type is 'custom'
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if (isset($blast_job->blastdb->linkout->db_id->urlprefix) && !empty($blast_job->blastdb->linkout->db_id->urlprefix)) {
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if (isset($blast_job->blastdb->linkout->db_id->urlprefix) && !empty($blast_job->blastdb->linkout->db_id->urlprefix)) {
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$linkout_urlprefix = $blast_job->blastdb->linkout->db_id->urlprefix;
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$linkout_urlprefix = $blast_job->blastdb->linkout->db_id->urlprefix;
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@@ -64,22 +64,35 @@ $no_hits = TRUE;
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<!-- Provide Information to the user about their blast job -->
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<!-- Provide Information to the user about their blast job -->
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<div class="blast-job-info">
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<div class="blast-job-info">
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-<?php if($xml): ?>
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+<?php if($xml):
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+ $output_files = array();
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+ if (file_exists($blast_job->files->result->html))
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+ $output_files['html'] = array('path' => url($blast_job->files->result->html), 'title' => 'Alignment');
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+ if (file_exists($blast_job->files->result->tsv))
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+ $output_files['tsv'] = array('path' => url($blast_job->files->result->tsv), 'title' => 'Tab-Delimited');
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+ if (file_exists($blast_job->files->result->gff))
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+ $output_files['gff'] = array('path' => url($blast_job->files->result->gff), 'title' => 'GFF3');
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+ if (file_exists($blast_job->files->result->xml))
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+ $output_files['xml'] = array('path' => url($blast_job->files->result->xml), 'title' => 'XML');
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+?>
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<div class="blast-download-info"><strong>Download</strong>:
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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; ?>">GFF</a>
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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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</div>
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<?php endif; ?>
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<?php endif; ?>
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<br />
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<br />
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- <div class="blast-query-info"><strong>Query Information</strong>:
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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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<?php print $blast_job->files->query;?></div>
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- <div class="blast-target-info"><strong>Search Target</strong>:
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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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<?php print $blast_job->blastdb->db_name;?></div>
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- <div class="blast-date-info"><strong>Submission Date</strong>:
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+ <div class="blast-date-info"><strong>Submission Date</strong>:
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<?php print format_date($blast_job->date_submitted, 'medium');?></div>
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<?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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+ <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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<?php print $blast_job->blast_cmd;?></div>
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</div>
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</div>
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<br />
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<br />
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@@ -94,8 +107,8 @@ $no_hits = TRUE;
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if ($xml) {
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if ($xml) {
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?>
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?>
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-<p>The following table summarizes the results of your BLAST.
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-Click on a <em>triangle </em> on the left to see the alignment and a visualization of the hit,
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+<p>The following table summarizes the results of your BLAST.
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+Click on a <em>triangle </em> on the left to see the alignment and a visualization of the hit,
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and click the <em>target name </em> to get more information about the target hit.</p>
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and click the <em>target name </em> to get more information about the target hit.</p>
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<?php
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<?php
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@@ -122,7 +135,7 @@ and click the <em>target name </em> to get more information about the target hit
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$q_name = $xml->{'BlastOutput_query-def'};
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$q_name = $xml->{'BlastOutput_query-def'};
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$query_size = $xml->{'BlastOutput_query-len'};
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$query_size = $xml->{'BlastOutput_query-len'};
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$target_size = $iteration->{'Iteration_stat'}->{'Statistics'}->{'Statistics_db-len'};
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$target_size = $iteration->{'Iteration_stat'}->{'Statistics'}->{'Statistics_db-len'};
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-
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+
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if ($children_count != 0) {
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if ($children_count != 0) {
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foreach ($iteration->{'Iteration_hits'}->children() as $hit) {
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foreach ($iteration->{'Iteration_hits'}->children() as $hit) {
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if (is_object($hit)) {
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if (is_object($hit)) {
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@@ -135,12 +148,12 @@ and click the <em>target name </em> to get more information about the target hit
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$score = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
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$score = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
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$evalue = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
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$evalue = (float) $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
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$query_name = (string) $iteration->{'Iteration_query-def'};
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$query_name = (string) $iteration->{'Iteration_query-def'};
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-
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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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// 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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// 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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// 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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// @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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+ $hit_name = (preg_match('/BL_ORD_ID/', $hit->{'Hit_id'})) ? $hit->{'Hit_def'} : $hit->{'Hit_id'};
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// Used for the hit visualization to ensure the name isn't truncated.
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// Used for the hit visualization to ensure the name isn't truncated.
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$hit_name_short = (preg_match('/^([^\s]+)/', $hit_name, $matches)) ? $matches[1] : $hit_name;
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$hit_name_short = (preg_match('/^([^\s]+)/', $hit_name, $matches)) ? $matches[1] : $hit_name;
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@@ -148,13 +161,13 @@ and click the <em>target name </em> to get more information about the target hit
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$rounded_evalue = '';
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$rounded_evalue = '';
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if (strpos($evalue,'e') != false) {
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if (strpos($evalue,'e') != false) {
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$evalue_split = explode('e', $evalue);
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$evalue_split = explode('e', $evalue);
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- $rounded_evalue = round($evalue_split[0], 2, PHP_ROUND_HALF_EVEN);
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+ $rounded_evalue = round($evalue_split[0], 2, PHP_ROUND_HALF_EVEN);
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$rounded_evalue .= 'e' . $evalue_split[1];
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$rounded_evalue .= 'e' . $evalue_split[1];
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}
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}
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- else {
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+ else {
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$rounded_evalue = $evalue;
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$rounded_evalue = $evalue;
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}
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}
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-
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+
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// State what should be in the summary row for theme_table() later.
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// State what should be in the summary row for theme_table() later.
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$summary_row = array(
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$summary_row = array(
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'data' => array(
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'data' => array(
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@@ -166,7 +179,7 @@ and click the <em>target name </em> to get more information about the target hit
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),
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),
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'class' => array('result-summary')
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'class' => array('result-summary')
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);
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);
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-
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+
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// ALIGNMENT ROW (collapsed by default)
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// ALIGNMENT ROW (collapsed by default)
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// Process HSPs
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// Process HSPs
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$HSPs = array();
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$HSPs = array();
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@@ -180,12 +193,12 @@ and click the <em>target name </em> to get more information about the target hit
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$hit_hsp_score = '';
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$hit_hsp_score = '';
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$target_size = $hit->{'Hit_len'};
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$target_size = $hit->{'Hit_len'};
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$Hsp_bit_score = '';
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$Hsp_bit_score = '';
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-
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+
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// Then for each hit hsp, keep track of the start of first hsp and the end of
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// Then for each hit hsp, keep track of the start of first hsp and the end of
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// the last hsp. Keep in mind that hsps might not be recorded in order.
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// the last hsp. Keep in mind that hsps might not be recorded in order.
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foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
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foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
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$HSPs[] = (array) $hsp_xml;
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$HSPs[] = (array) $hsp_xml;
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-
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+
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if ($track_start > $hsp_xml->{'Hsp_hit-from'}) {
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if ($track_start > $hsp_xml->{'Hsp_hit-from'}) {
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$track_start = $hsp_xml->{'Hsp_hit-from'} . "";
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$track_start = $hsp_xml->{'Hsp_hit-from'} . "";
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}
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}
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@@ -196,22 +209,22 @@ and click the <em>target name </em> to get more information about the target hit
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// The BLAST visualization code requires the hsps to be formatted in a
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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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// 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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// 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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+ $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 .= $hsp_xml->{'Hsp_bit-score'} .';';
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}
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}
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// Finally record the range.
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// Finally record the range.
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// @todo figure out why we arbitrarily subtract 50,000 here...
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// @todo figure out why we arbitrarily subtract 50,000 here...
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// @more removing the 50,000 and using track start/end appears to cause no change...
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// @more removing the 50,000 and using track start/end appears to cause no change...
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$range_start = (int) $track_start;// - 50000;
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$range_start = (int) $track_start;// - 50000;
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$range_end = (int) $track_end;// + 50000;
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$range_end = (int) $track_end;// + 50000;
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- if ($range_start < 1) $range_start = 1;
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-
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+ if ($range_start < 1) $range_start = 1;
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+
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// Call the function to generate the hit image.
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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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+ $hit_img = generate_blast_hit_image($target_name, $Hsp_bit_score, $hit_hsps,
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$target_size, $query_size, $q_name, $hit_name_short);
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$target_size, $query_size, $q_name, $hit_name_short);
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@@ -226,19 +239,19 @@ and click the <em>target name </em> to get more information about the target hit
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'class' => array('alignment-row', $zebra_class),
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'class' => array('alignment-row', $zebra_class),
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'no_striping' => TRUE
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'no_striping' => TRUE
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);
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);
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-
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+
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// LINK-OUTS.
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// LINK-OUTS.
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// It was determined above whether link-outs were supported for the
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// It was determined above whether link-outs were supported for the
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- // tripal blast database used as a search target. Thus we only want to
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+ // tripal blast database used as a search target. Thus we only want to
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// determine a link-out if it's actually supported... ;-)
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// determine a link-out if it's actually supported... ;-)
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if ($linkout) {
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if ($linkout) {
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-
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+
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// First extract the linkout text using the regex provided through
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// First extract the linkout text using the regex provided through
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// the Tripal blast database node.
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// the Tripal blast database node.
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if (preg_match($linkout_regex, $hit_name, $linkout_match)) {
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if (preg_match($linkout_regex, $hit_name, $linkout_match)) {
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$hit->{'linkout_id'} = $linkout_match[1];
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$hit->{'linkout_id'} = $linkout_match[1];
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$hit->{'hit_name'} = $hit_name;
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$hit->{'hit_name'} = $hit_name;
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-
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+
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// Allow custom functions to determine the URL to support more complicated
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// Allow custom functions to determine the URL to support more complicated
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// link-outs rather than just using the tripal database prefix.
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// link-outs rather than just using the tripal database prefix.
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$hit_name = call_user_func(
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$hit_name = call_user_func(
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@@ -254,11 +267,11 @@ and click the <em>target name </em> to get more information about the target hit
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)
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)
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);
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);
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}
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}
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-
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+
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// Replace the target name with the link.
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// Replace the target name with the link.
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$summary_row['data']['hit']['data'] = $hit_name;
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$summary_row['data']['hit']['data'] = $hit_name;
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}
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}
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-
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+
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// ADD TO TABLE ROWS
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// ADD TO TABLE ROWS
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$rows[] = $summary_row;
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$rows[] = $summary_row;
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$rows[] = $alignment_row;
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$rows[] = $alignment_row;
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@@ -266,7 +279,7 @@ and click the <em>target name </em> to get more information about the target hit
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}//end of if - checks $hit
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}//end of if - checks $hit
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}//end of foreach - iteration_hits
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}//end of foreach - iteration_hits
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}//end of if - check for iteration_hits
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}//end of if - check for iteration_hits
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-
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+
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else {
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else {
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// Currently where the "no results" is added.
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// Currently where the "no results" is added.
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$query_name = $iteration->{'Iteration_query-def'};
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$query_name = $iteration->{'Iteration_query-def'};
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@@ -305,7 +318,7 @@ else {
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?>
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?>
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<p><?php print l(
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<p><?php print l(
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- 'Edit this query and re-submit',
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+ 'Edit this query and re-submit',
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$blast_form_url,
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$blast_form_url,
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array('query' => array('resubmit' => blast_ui_make_secret($job_id))));
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array('query' => array('resubmit' => blast_ui_make_secret($job_id))));
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?></p>
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?></p>
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