<?php

class data__sequence_coordinates 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 = 'Sequence Coordinates';

  // The default description for this field.
  public static $description = 'Locations on reference sequences where the feature is located.';

  // 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' => 'data',
    // The name of the term.
    'term_name' => 'sequence_coordinates',
    // The unique ID (i.e. accession) of the term.
    'term_accession' => '2012',
    // 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 = 'data__sequence_coordinates_widget';

  // The default formatter for this field.
  public static $default_formatter = 'data__sequence_coordinates_formatter';

  // --------------------------------------------------------------------------
  //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE
  // --------------------------------------------------------------------------
  // An array containing details about the field. The format of this array
  // is the same as that returned by field_info_fields()
  protected $field;
  // An array containing details about an instance of the field. A field does
  // not have to have an instance.  But if dealing with an instance (such as
  // when using the widgetForm, formatterSettingsForm, etc.) it should be set.
  protected $instance;


  /**
   * @see TripalField::elementInfo()
   */
  public function elementInfo() {
    $field_term = $this->getFieldTermID();

    $reference_term = 'data:3002';
    $fmin_term = chado_get_semweb_term('featureloc', 'fmin');
    $fmax_term = chado_get_semweb_term('featureloc', 'fmax');
    $strand_term = chado_get_semweb_term('featureloc', 'strand');
    $phase_term = chado_get_semweb_term('featureloc', 'phase');

    return array(
      $field_term => array(
        'operations' => array(),
        'sortable' => FALSE,
        'searchable' => FALSE,
        'label' => 'Location Coordinates',
        'help' => 'The locations on other genomic sequences where this record has been aligned.',
        'type' => 'xs:complexType',
        'readonly' => TRUE,
        'elements' => array(
          $reference_term => array(
            'searchable' => TRUE,
            'label' => 'Location Reference Name',
            'help' => 'The genomic feature on which this feature is localized.',
            'operations' => array('eq', 'ne', 'contains', 'starts'),
            'sortable' => TRUE,
            'type' => 'xs:string',
            'readonly' => TRUE,
            'required' => FALSE,
          ),
          $fmin_term => array(
            'searchable' => TRUE,
            'label' => 'Location Start Position',
            'help' => 'The start position',
            'type' => 'numeric',
            'operations' => array('eq', 'gt', 'lt', 'gte' ,'lte'),
            'sortable' => TRUE,
            'type' => 'xs:integer',
            'readonly' => TRUE,
            'required' => FALSE,
          ),
          $fmax_term => array(
            'searchable' => TRUE,
            'label' => 'Location End Position',
            'help' => 'The end position',
            'type' => 'numeric',
            'operations' => array('eq', 'gt', 'lt', 'gte' ,'lte'),
            'sortable' => TRUE,
            'type' => 'xs:integer',
            'readonly' => TRUE,
            'required' => FALSE,
          ),
          $phase_term => array(
            'searchable' => TRUE,
            'type' => 'numeric',
            'label' => 'Location Phase',
            'help' => 'The phase of the feature (applicable only to coding sequences).',
            'operations' => array('eq', 'gt', 'lt', 'gte' ,'lte'),
            'sortable' => TRUE,
            'type' => 'xs:integer',
            'readonly' => TRUE,
            'required' => FALSE,
          ),
          $strand_term => array(
            'searchable' => TRUE,
            'label' => 'Location Strand',
            'help' => 'The orientation of this feature where it is localized',
            'operations' => array('eq', 'gt', 'lt', 'gte' ,'lte'),
            'sortable' => FALSE,
            'type' => 'xs:string',
            'readonly' => TRUE,
            'required' => FALSE,
          ),
        ),
      ),
    );
  }

  /**
   * @see ChadoField::query()
   */
  public function query($query, $condition) {
    $alias = $this->field['field_name'];
    $operator = $condition['operator'];

    $field_term_id = $this->getFieldTermID();
    $reference_term = $field_term_id . ',' . 'data:3002';
    $fmin_term = $field_term_id . ',' . chado_get_semweb_term('featureloc', 'fmin');
    $fmax_term = $field_term_id . ',' . chado_get_semweb_term('featureloc', 'fmax');
    $strand_term = $field_term_id . ',' . chado_get_semweb_term('featureloc', 'strand');
    $phase_term = $field_term_id . ',' . chado_get_semweb_term('featureloc', 'phase');

    // Join to the organism table for this field.
    $this->queryJoinOnce($query, 'featureloc', $alias, "base.feature_id = $alias.feature_id");
    if ($condition['column'] == $reference_term) {
      $salias = $alias . '_src';
      $this->queryJoinOnce($query, 'feature', $salias, "$alias.srcfeature_id = $salias.feature_id");
      $query->condition("$salias.name", $condition['value'], $operator);
    }
    if ($condition['column'] == $strand_term) {
      $strand = '';
      if ($condition['value'] == '-') {
        $strand = -1;
      }
      if ($condition['value'] == '+') {
        $strand = 1;
      }
      $query->condition("$alias.strand", $strand, $operator);
    }
    if ($condition['column'] == $fmin_term) {
      $query->condition("$alias.fmin", $condition['value'] - 1, $operator);
    }
    if ($condition['column'] == $fmax_term) {
      $query->condition("$alias.fmax", $condition['value'], $operator);
    }
    if ($condition['column'] == $phase_term) {
      $query->condition("$alias.phase", $condition['value'], $operator);
    }
  }

  /**
   * @see ChadoField::queryOrder()
   */
  public function queryOrder($query, $order) {
    $alias = $this->field['field_name'];

    $field_term_id = $this->getFieldTermID();
    $reference_term = $field_term_id . ',' . 'data:3002';
    $fmin_term = $field_term_id . ',' . chado_get_semweb_term('featureloc', 'fmin');
    $fmax_term = $field_term_id . ',' . chado_get_semweb_term('featureloc', 'fmax');
    $strand_term = $field_term_id . ',' . chado_get_semweb_term('featureloc', 'strand');
    $phase_term = $field_term_id . ',' . chado_get_semweb_term('featureloc', 'phase');

    $this->queryJoinOnce($query, 'featureloc', $alias, "base.feature_id = $alias.feature_id", "LEFT OUTER");
    if ($order['column'] == $reference_term) {
      $salias = $alias . '_src';
      $this->queryJoinOnce($query, 'feature', $salias, "$alias.srcfeature_id = $salias.feature_id", "LEFT OUTER");
      $query->orderBy("$salias.name", $order['direction']);
    }
    if ($order['column'] == $fmin_term) {
      $query->orderBy("$alias.fmin", $order['direction']);
    }
    if ($order['column'] == $fmax_term) {
      $query->orderBy("$alias.fmax", $order['direction']);
    }
    if ($order['column'] == $phase_term) {
      $query->orderBy("$alias.phase", $order['direction']);
    }
  }

  /**
   *
   * @see TripalField::load()
   */
  public function load($entity) {
    $field_name = $this->field['field_name'];
    $feature = $entity->chado_record;
    $num_seqs = 0;

    $description = 'schema:description';
    $reference_term = 'data:3002';
    $fmin_term = chado_get_semweb_term('featureloc', 'fmin');
    $fmax_term = chado_get_semweb_term('featureloc', 'fmax');
    $strand_term = chado_get_semweb_term('featureloc', 'strand');
    $phase_term = chado_get_semweb_term('featureloc', 'phase');

    $options = array(
      'return_array' => TRUE,
      'order_by' => array('rank' => 'ASC'),
    );
    $feature = chado_expand_var($feature, 'table', 'featureloc', $options);

    // Set some defauls for the empty record
    $entity->{$field_name}['und'][0] = array(
      'value' => '',
    );

    // Get the featureloc records that this feature is aligned to.
    $aligned = $feature->featureloc->feature_id;
    if ($aligned) {
      foreach ($aligned as $index => $featureloc) {
        $srcfeature = $featureloc->srcfeature_id->name;
        $strand = '';
        if ($featureloc->strand == 1) {
          $strand = '+';
        }
        elseif ($featureloc->strand == -1) {
          $strand = '-';
        }
        else {
          $strand = '';
        }
        $fmin = $featureloc->fmin + 1;
        $fmax = $featureloc->fmax;
        $entity->{$field_name}['und'][$index] = array(
          'value' => array(
            $description => $srcfeature . ':' . $fmin . '-' . $fmax . $strand,
            $reference_term => $srcfeature,
            $fmin_term => $fmin,
            $fmax_term => $fmax,
            $strand_term => $strand,
            $phase_term => $featureloc->phase,
          ),
        );
        $sentity_id = chado_get_record_entity_by_table('feature_id', $featureloc->srcfeature_id->feature_id);
        if ($sentity_id) {
          $entity->{$field_name}['und'][0]['value']['entity'] = 'TripalEntity:' . $sentity_id;
        }
      }
    }
  }
}
