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- <?php
- class so__cds extends ChadoField {
- // --------------------------------------------------------------------------
- // EDITABLE STATIC CONSTANTS
- //
- // The following constants SHOULD be set for each descendent class. They are
- // used by the static functions to provide information to Drupal about
- // the field and it's default widget and formatter.
- // --------------------------------------------------------------------------
- // The default lable for this field.
- public static $default_label = 'Coding Sequence';
- // The default description for this field.
- public static $description = 'A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.';
- // Provide a list of instance specific settings. These can be access within
- // the instanceSettingsForm. When the instanceSettingsForm is submitted
- // then Drupal with automatically change these settings for the instnace.
- // It is recommended to put settings at the instance level whenever possible.
- // If you override this variable in a child class be sure to replicate the
- // term_name, term_vocab, term_accession and term_fixed keys as these are
- // required for all TripalFields.
- public static $default_instance_settings = array(
- // The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).
- 'term_vocabulary' => 'SO',
- // The name of the term.
- 'term_name' => 'CDS',
- // The unique ID (i.e. accession) of the term.
- 'term_accession' => '0000316',
- // Set to TRUE if the site admin is allowed to change the term
- // type. This will create form elements when editing the field instance
- // to allow the site admin to change the term settings above.
- 'term_fixed' => FALSE,
- );
- // The default widget for this field.
- public static $default_widget = 'so__cds_widget';
- // The default formatter for this field.
- public static $default_formatter = 'so__cds_formatter';
- /**
- * @see TripalField::elementInfo()
- */
- public function elementInfo() {
- $field_term = $this->getFieldTermID();
- return array(
- $field_term => array(
- 'sortable' => FALSE,
- 'searchable' => FALSE,
- 'type' => 'xs:string',
- 'readonly' => TRUE,
- ),
- );
- }
- /**
- * @see TripalField::load()
- */
- public function load($entity) {
- $field_name = $this->field['field_name'];
- $feature = $entity->chado_record;
- $num_seqs = 0;
- // Set some defauls for the empty record
- $entity->{$field_name}['und'][0] = array(
- 'value' => '',
- );
- $options = array(
- 'return_array' => TRUE,
- 'order_by' => array('rank' => 'ASC'),
- );
- $feature = chado_expand_var($feature, 'table', 'featureloc', $options);
- $featurelocs = $feature->featureloc->feature_id;
- foreach($featurelocs as $featureloc){
- // Generate a CDS sequence if one exsits for this feature alignment.
- $cds_sequence = chado_get_feature_sequences(
- array(
- 'feature_id' => $feature->feature_id,
- 'parent_id' => $featureloc->srcfeature_id->feature_id,
- 'name' => $feature->name,
- 'featureloc_id' => $featureloc->featureloc_id,
- ),
- array(
- // CDS are in parent-child relationships so we want to use the
- // sequence from the parent
- 'derive_from_parent' => 1,
- // we want to combine all CDS for this feature into a single sequence
- 'aggregate' => 1,
- // we're looking for CDS features
- 'sub_feature_types' => array('CDS'),
- 'is_html' => 0
- )
- );
- if (count($cds_sequence) > 0) {
- // the chado_get_feature_sequences() function can return multiple sequences
- // if a feature is aligned to multiple places. In the case of CDSs we expect
- // that one mRNA is only aligned to a single location on the assembly so we
- // can access the CDS sequence with index 0.
- if ($cds_sequence[0]['residues']) {
- $entity->{$field_name}['und'][$num_seqs++]['value'] = $cds_sequence[0]['residues'];
- }
- }
- }
- }
- }
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