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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Inheritance diagram for tripal_views_handler_field_sequence:Public Member Functions | |
| init (&$view, $options) | |
| options_form (&$form, &$form_state) | |
| query () | |
| render ($values) | |
Definition at line 10 of file tripal_views_handler_field_sequence.inc.
| tripal_views_handler_field_sequence::init | ( | &$ | view, |
| $ | options | ||
| ) |
Reimplemented from chado_views_handler_field.
Definition at line 12 of file tripal_views_handler_field_sequence.inc.
{
parent::init($view, $options);
}
| tripal_views_handler_field_sequence::options_form | ( | &$ | form, |
| &$ | form_state | ||
| ) |
Defines the options form (form available to admin when they add a field to a view)
Reimplemented from chado_views_handler_field.
Definition at line 20 of file tripal_views_handler_field_sequence.inc.
{
parent::options_form($form, $form_state);
$form['display'] = array(
'#type' => 'fieldset',
'#title' => 'Format Output',
'#description' => t('Alter the way a sequence is displayed')
);
$default_num_bases_per_line = '50';
if ($this->options['display']['num_bases_per_line']) {
$default_num_bases_per_line = $this->options['display']['num_bases_per_line'];
}
$default_output_format = 'raw';
if ($this->options['display']['output_format']) {
$default_ouput_format = $this->options['display']['output_format'];
}
$form['display']['num_bases_per_line'] = array(
'#type' => 'textfield',
'#title' => t('Number of bases per line'),
'#description' => t('Specify the number of bases per line. An HTML <br> tag ' .
'will be inserted after the number of bases indicated. If no value is ' .
'provided. The sequence will be one long string (default)'),
'#default_value' => $default_num_bases_per_line,
);
$form['display']['derive_from_parent'] = array(
'#type' => 'checkbox',
'#title' => t('Derive sequence from parent'),
'#description' => t('Rather than use the sequence from the \'residues\' of this feature, you may ' .
'derive the sequence from the parent features to which it is aligned. This is useful in the case that the feature ' .
'does not have sequence associated with it and we need to get it through it\'s alignment. ' .
'Note: this will slow queries with large numbers of results on the page.'),
'#default_value' => $this->options['display']['derive_from_parent'],
);
$form['display']['aggregate'] = array(
'#type' => 'checkbox',
'#title' => t('Aggregate sub features'),
'#description' => t('If the feature has sub features (e.g. CDS of an mRNA) then check this '.
'box to filter the sequence to only include the sub features. Gaps between sub features will be '.
'excluded from the sequence. This is useful for obtaining a complete CDS from an mRNA '.
'without intronic sequence'),
'#default_value' => $this->options['display']['aggregate'],
);
$form['display']['output_format'] = array(
'#type' => 'radios',
'#title' => t('Output format'),
'#options' => array(
'raw' => 'Raw sequence data (no formatting)',
'fasta_html' => 'FASTA in HTML format',
'fasta_txt' => 'FASTA in text format',
),
'#description' => t('Select an output format. Raw output cannot be used when the sequence is derived from the parent.'),
'#default_value' => $default_ouput_format,
);
}
| tripal_views_handler_field_sequence::query | ( | ) |
We need to add a few fields to our query
Reimplemented from chado_views_handler_field.
Definition at line 79 of file tripal_views_handler_field_sequence.inc.
{
parent::query();
// if we are going to get the sequence from the parent then
// we will need to do more queries in the render function
// and we must have the feature_id to do those
if ($this->options['display']['derive_from_parent']) {
$this->ensure_my_table();
$this->query->add_field($this->table, 'feature_id');
$this->query->add_field($this->table, 'name');
}
}
| tripal_views_handler_field_sequence::render | ( | $ | values | ) |
Prior to display of results we want to format the sequence
Reimplemented from chado_views_handler_field.
Definition at line 95 of file tripal_views_handler_field_sequence.inc.
{
$residues = '';
// get the number of bases to show per line
$num_bases_per_line = $this->options['display']['num_bases_per_line'];
$output_format = $this->options['display']['output_format'];
// get the residues from the feature.residues column
$field = $this->field_alias;
// get the feature id
$feature_id = $values->feature_feature_id;
$feature_name = $values->feature_name;
// the upstream and downstream values get set by the
// tripal_views_handlers_filter_sequence.inc
$upstream = $_SESSION['upstream'];
$downstream = $_SESSION['downstream'];
if (!$upstream) {
$upstream = 0;
}
if (!$downstream) {
$downstream = 0;
}
$derive_from_parent = $this->options['display']['derive_from_parent'];
$aggregate = $this->options['display']['aggregate'];
$residues = tripal_feature_get_formatted_sequence($feature_id, $feature_name,
$num_bases_per_line, $derive_from_parent, $aggregate, $output_format,
$upstream, $downstream);
/*
// if we need to get the sequence from the parent but there is no aggregation
// then do so now.
if ($this->options['display']['derive_from_parent']) {
// execute our prepared statement
if (tripal_core_is_sql_prepared('sequence_by_parent')) {
$sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
$parents = chado_query($sql, $upstream, $downstream, $feature_id);
}
while ($parent = db_fetch_object($parents)) {
$seq = ''; // initialize the sequence for each parent
// if we are to aggregate then we will ignore the feature returned
// by the query above and rebuild it using the sub features
if ($this->options['display']['aggregate']){
// now get the sub features that are located on the parent.
$sql = "EXECUTE sub_features (%d, %d)";
$children = chado_query($sql, $feature_id, $parent->srcfeature_id);
$sql = "EXECUTE count_sub_features (%d, %d)";
$num_children = db_fetch_object(chado_query($sql, $feature_id, $parent->srcfeature_id));
// iterate through the sub features and concat their sequences. They
// should already be in order.
$types = array();
$i = 0;
while($child = db_fetch_object($children)) {
// keep up with the types
if (!in_array($child->type_name,$types)) {
$types[] = $child->type_name;
}
$sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
// if the first sub feature we need to include the upstream bases
if ($i == 0 and $parent->strand >= 0) {
// -------------------------- ref
// ....----> ---->
// up 1 2
$q = chado_query($sql, $upstream, 0, $child->feature_id);
}
elseif ($i == 0 and $parent->strand < 0) {
// -------------------------- ref
// ....<---- <----
// down 1 2
$q = chado_query($sql, 0, $downstream, $child->feature_id);
}
// if the last sub feature we need to include the downstream bases
elseif ($i == $num_children->num_children - 1 and $parent->strand >= 0) {
// -------------------------- ref
// ----> ---->....
// 1 2 down
$q = chado_query($sql, 0, $downstream, $child->feature_id);
}
elseif ($i == $num_children->num_children - 1 and $parent->strand < 0) {
// -------------------------- ref
// <---- <----....
// 1 2 up
$q = chado_query($sql, $upstream, 0, $child->feature_id);
}
// for internal sub features we don't want upstream or downstream bases
else {
$sql = "EXECUTE sequence_by_parent (%d, %d, %d)";
$q = chado_query($sql, 0, 0, $child->feature_id);
}
while($subseq = db_fetch_object($q)){
// concatenate the sequences of all the sub features
if($subseq->srcfeature_id == $parent->srcfeature_id){
$seq .= $subseq->residues;
}
}
$i++;
}
}
// if this isn't an aggregate then use the parent residues
else {
$seq = $parent->residues;
}
// get the reverse compliment if feature is on the reverse strand
$dir = 'forward';
if ($parent->strand < 0) {
$seq = trpial_feature_reverse_complement($seq);
$dir = 'reverse';
}
// now format for display
if ($output_format == 'fasta_html') {
$seq = wordwrap($seq, $num_bases_per_line, "<br>", TRUE);
}
elseif ($output_format == 'fasta_txt') {
$seq = wordwrap($seq, $num_bases_per_line, "\n", TRUE);
}
$residues .= ">$feature_name ($parent->typename) $parent->srcname:" . ($parent->adjfmin + 1) . ".." . $parent->adjfmax ." ($dir). ";
if (count($types) > 0) {
$residues .= "Excludes all bases but those of type(s): " . implode(', ',$types) . ". " ;
}
if ($parent->upstream > 0) {
$residues .= "Includes " . $parent->upstream . " bases upstream. ";
}
if ($parent->downstream > 0) {
$residues .= "Includes " . $parent->downstream . " bases downstream. ";
}
if (!$seq) {
$residues .= "No sequence available\n<br>";
}
else {
if ($output_format == 'fasta_html') {
$residues .= "<br>";
}
$residues .= "\n" . $seq . "\n";
if ($output_format == 'fasta_html') {
$residues .= "<br>";
}
}
}
}
// if we are not getting the sequence from the parent sequence then
// use what comes through from the feature record
else {
$residues = $values->$field;
if ($output_format == 'fasta_html') {
$residues = wordwrap($residues, $num_bases_per_line, "<br>", TRUE);
}
elseif ($output_format == 'fasta_txt') {
$residues = wordwrap($residues, $num_bases_per_line, "\n", TRUE);
}
}
// format the residues for display
if($residues and $num_bases_per_line){
if ($output_format == 'fasta_html') {
$residues = '<span style="font-family: monospace;">' . $residues . '</span>';
}
} */
return $residues;
}
1.7.4