<?php
class data__sequence 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 label for this field.
public static $default_label = 'Sequence';
// The default description for this field.
public static $description = 'A field for managing nucleotide and protein residues.';
// Provide a list of instance specific settings. These can be accessed within
// the instanceSettingsForm. When the instanceSettingsForm is submitted
// then Drupal will automatically change these settings for the instance.
// 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 = [
// The short name for the vocabulary (e.g. schema, SO, GO, PATO, etc.).
'term_vocabulary' => 'data',
// The name of the term.
'term_name' => 'sequence',
// The unique ID (i.e. accession) of the term.
'term_accession' => '2044',
// 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,
];
// Indicates the download formats for this field. The list must be the
// name of a child class of the TripalFieldDownloader.
public static $download_formatters = [
'TripalTabDownloader',
'TripalCSVDownloader',
'TripalNucFASTADownloader',
];
// The default widget for this field.
public static $default_widget = 'data__sequence_widget';
// The default formatter for this field.
public static $default_formatter = 'data__sequence_formatter';
/**
* @see TripalField::elementInfo()
*/
public function elementInfo() {
$field_term = $this->getFieldTermID();
return [
$field_term => [
'operations' => [],
'sortable' => FALSE,
'searchable' => FALSE,
'type' => 'xs:string',
'readonly' => FALSE,
],
];
}
/**
* @see TripalField::load()
*/
public function load($entity) {
$field_name = $this->field['field_name'];
$feature = $entity->chado_record;
$feature = chado_expand_var($feature, 'field', 'feature.residues');
$entity->{$field_name}['und'][0]['value'] = $feature->residues;
/* // Add in sequences from alignments.
$options = array(
'return_array' => 1,
'include_fk' => array(
'srcfeature_id' => array(
'type_id' => 1
),
'feature_id' => array(
'type_id' => 1
),
),
);
$feature = chado_expand_var($feature, 'table', 'featureloc', $options);
$featureloc_sequences = $this->get_featureloc_sequences($feature->feature_id, $feature->featureloc->feature_id);
// Add in the coding sequences. It's faster to provide the SQL rather than
// to use chado_generate_var based on the type.
$sql = "
SELECT F.*
FROM {feature_relationship} FR
INNER JOIN {feature} F on FR.subject_id = F.feature_id
INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
INNER JOIN {cvterm} RCVT on RCVT.cvterm_id = FR.type_id
INNER JOIN {featureloc} FL on FL.feature_id = F.feature_id
WHERE
FR.object_id = :feature_id and
CVT.name = 'CDS' and
RCVT.name = 'part_of'
ORDER BY FR.rank ASC
";
$results = chado_query($sql, array(':feature_id' => $feature->feature_id));
$coding_seq = '';
while ($CDS = $results->fetchObject()) {
if ($CDS->residues) {
$coding_seq .= $CDS->residues;
}
}
if ($coding_seq) {
$entity->{$field_name}['und'][$num_seqs++]['value'] = array(
'@type' => 'SO:0000316',
'type' => 'coding_sequence',
'label' => 'Coding sequence (CDS)',
'defline' => chado_get_fasta_defline($feature, 'CDS', NULL, '', strlen($coding_seq)),
'residues' => $coding_seq,
);
}
foreach($featureloc_sequences as $src => $attrs){
// the $attrs array has the following keys
// * id: a unique identifier combining the feature id with the cvterm id
// * type: the type of sequence (e.g. mRNA, etc)
// * location: the alignment location
// * defline: the definition line
// * formatted_seq: the formatted sequences
// * featureloc: the feature object aligned to
$entity->{$field_name}['und'][$num_seqs++]['value'] = array(
'residues' => $attrs['residues'],
'@type' => 'SO:0000110',
'type' => 'sequence_feature',
'defline' => chado_get_fasta_defline($feature, '', $attrs['featureloc'], 'CDS', strlen($attrs['residues'])),
'label' => 'Sequence from alignment at ' . $attrs['location'],
);
// check to see if this alignment has any CDS. If so, generate a CDS sequence
$cds_sequence = chado_get_feature_sequences(
array(
'feature_id' => $feature->feature_id,
'parent_id' => $attrs['featureloc']->srcfeature_id->feature_id,
'name' => $feature->name,
'featureloc_id' => $attrs['featureloc']->featureloc_id,
),
array(
'derive_from_parent' => 1, // CDS are in parent-child relationships so we want to use the sequence from the parent
'aggregate' => 1, // we want to combine all CDS for this feature into a single sequence
'sub_feature_types' => array('CDS'), // we're looking for CDS features
'is_html' => 0
)
);
if (count($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'] = array(
'residues' => $cds_sequence[0]['residues'],
'@type' => 'SO:0000316',
'type' => 'coding_sequence',
'defline' => chado_get_fasta_defline($feature, '', $attrs['featureloc'], 'CDS', $cds_sequence[0]['length']),
'label' => 'Coding sequence (CDS) from alignment at ' . $attrs['location'],
);
}
}
} */
}
}