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@@ -27,6 +27,9 @@
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});
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</script>
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+<p>The following table summarizes the results of your BLAST. To see additional information
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+about each hit including the alignment, click on that row in the table to expand it.</p>
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+
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<?php
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// Load the XML file
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@@ -37,76 +40,79 @@ $xml = simplexml_load_file($xml_filename);
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* @see theme_table() for additional documentation
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*/
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-// Specify the header of the table
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-$header = array(
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- 'number' => array('data' => '#', 'class' => array('number')),
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- 'query' => array('data' => 'Query Name', 'class' => array('query')),
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- 'hit' => array('data' => 'Hit Name', 'class' => array('hit')),
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- 'evalue' => array('data' => 'E-Value', 'class' => array('evalue')),
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- 'arrow-col' => array('data' => '', 'class' => array('arrow-col'))
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-);
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-
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-$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 $iteration) {
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- foreach($iteration->{'Iteration_hits'}->children() as $hit) {
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- if (is_object($hit)) {
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- $count +=1;
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-
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- $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';
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-
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- // SUMMARY ROW
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- $hit_name = $hit->Hit_def;
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- if (preg_match('/(\w+)/', $hit_name, $matches)) {
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- $hit_name = $matches[1];
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- }
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- $score = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
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- $evalue = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
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- $query_name = $iteration->{'Iteration_query-def'};
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-
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- $row = array(
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- 'data' => array(
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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' => $evalue, 'class' => array('evalue')),
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- 'arrow-col' => array('data' => '<div class="arrow"></div>', 'class' => array('arrow-col'))
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- ),
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- 'class' => array('result-summary')
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- );
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- $rows[] = $row;
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-
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- // ALIGNMENT ROW (collapsed by default)
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- // Process HSPs
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- $HSPs = array();
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- foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
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- $HSPs[] = (array) $hsp_xml;
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- }
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-
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- $row = array(
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- 'data' => array(
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- 'number' => '',
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- 'query' => array(
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- 'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs)),
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- 'colspan' => 4,
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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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- $rows[] = $row;
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+if ($xml) {
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+ // Specify the header of the table
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+ $header = array(
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+ 'number' => array('data' => '#', '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' => 'E-Value', 'class' => array('evalue')),
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+ 'arrow-col' => array('data' => '', 'class' => array('arrow-col'))
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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 $iteration) {
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+ foreach($iteration->{'Iteration_hits'}->children() as $hit) {
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+ if (is_object($hit)) {
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+ $count +=1;
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+
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+ $zebra_class = ($count % 2 == 0) ? 'even' : 'odd';
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+
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+ // SUMMARY ROW
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+ $hit_name = $hit->Hit_id;
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+ $score = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_score'};
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+ $evalue = $hit->{'Hit_hsps'}->{'Hsp'}->{'Hsp_evalue'};
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+ $query_name = $iteration->{'Iteration_query-def'};
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+
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+ $row = array(
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+ 'data' => array(
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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' => $evalue, 'class' => array('evalue')),
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+ 'arrow-col' => array('data' => '<div class="arrow"></div>', 'class' => array('arrow-col'))
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+ ),
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+ 'class' => array('result-summary')
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+ );
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+ $rows[] = $row;
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+
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+ // ALIGNMENT ROW (collapsed by default)
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+ // Process HSPs
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+ $HSPs = array();
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+ foreach ($hit->{'Hit_hsps'}->children() as $hsp_xml) {
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+ $HSPs[] = (array) $hsp_xml;
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+ }
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+
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+ $row = array(
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+ 'data' => array(
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+ 'number' => '',
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+ 'query' => array(
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+ 'data' => theme('blast_report_alignment_row', array('HSPs' => $HSPs)),
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+ 'colspan' => 4,
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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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+ $rows[] = $row;
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+ }
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}
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}
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-}
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-print theme('table', array(
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- 'header' => $header,
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- 'rows' => $rows,
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- 'attributes' => array('id' => 'blast_report'),
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- ));
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+ print theme('table', array(
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+ 'header' => $header,
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+ 'rows' => $rows,
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+ 'attributes' => array('id' => 'blast_report'),
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+ ));
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+}
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+else {
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+ drupal_set_title('BLAST: Error Encountered');
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+ print '<p>We encountered an error and are unable to load your BLAST results.</p>';
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+}
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?>
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Lacey Sanderson