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@@ -1,430 +1,376 @@
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<?php
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-/**
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- * Implements hook_info() for fields.
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- *
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- * This is a hook provided by the tripal_chado module for offloading the
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- * hook_field_info() hook for each field to specify.
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- */
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-function chado_linker__featureloc_info() {
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- return array(
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- 'label' => t('Alignments'),
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- 'description' => t('Locations on landmark sequences where the feature is aligned.'),
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- 'default_widget' => 'chado_linker__featureloc_widget',
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- 'default_formatter' => 'chado_linker__featureloc_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- );
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-}
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-/**
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- * Implements hook_attach_info().
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- *
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- * This is a hook provided by the tripal_Chado module. It allows the field
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- * to specify which bundles it will attach to and to specify thee settings.
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- *
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- * @param $entity_type
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- * @param $entity
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- * @param $term
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- *
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- * @return
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- * A field array
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- */
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-function chado_linker__featureloc_attach_info($entity_type, $bundle, $target) {
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- $field_info = array();
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-
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- $table_name = $target['data_table'];
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- $type_table = $target['type_table'];
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- $type_field = $target['field'];
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- $cv_id = $target['cv_id'];
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- $cvterm_id = $target['cvterm_id'];
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+class chado_linker__featureloc extends TripalField {
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- // If this is not the feature table then we don't want to attach.
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- if ($table_name != 'feature') {
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- return $field_info;
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+ /**
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+ * @see TripalField::field_info()
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+ */
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+ public function field_info() {
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+ return array(
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+ 'label' => t('Aligned Locations'),
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+ 'description' => t('Locations on landmark sequences where the feature is aligned.'),
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+ 'default_widget' => 'chado_linker__featureloc_widget',
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+ 'default_formatter' => 'chado_linker__featureloc_formatter',
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+ 'settings' => array(),
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+ 'storage' => array(
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+ 'type' => 'field_chado_storage',
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+ 'module' => 'tripal_chado',
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+ 'active' => TRUE
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+ ),
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+ );
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}
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- $schema = chado_get_schema('featureloc');
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- $pkey = $schema['primary key'][0];
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-
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- // Initialize the field array.
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- $field_info = array(
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- 'field_name' => 'featureloc',
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- 'field_type' => 'chado_linker__featureloc',
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- 'widget_type' => 'chado_linker__featureloc_widget',
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- 'widget_settings' => array('display_label' => 1),
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- 'description' => '',
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- 'label' => 'Alignments',
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- 'is_required' => 0,
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- 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
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- 'storage' => 'field_chado_storage',
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- 'field_settings' => array(
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- 'chado_table' => 'featureloc',
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- 'chado_column' => $pkey,
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- 'base_table' => 'feature',
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- 'semantic_web' => array(
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- 'name' => '',
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- 'accession' => '',
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- 'ns' => '',
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- 'nsurl' => '',
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+ /**
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+ * @see TripalField::attach_info()
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+ */
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+ public function attach_info($entity_type, $bundle, $target) {
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+ $field_info = array();
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+
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+ $table_name = $target['data_table'];
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+ $type_table = $target['type_table'];
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+ $type_field = $target['field'];
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+ $cv_id = $target['cv_id'];
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+ $cvterm_id = $target['cvterm_id'];
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+
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+ // If this is not the feature table then we don't want to attach.
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+ if ($table_name != 'feature') {
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+ return $field_info;
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+ }
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+
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+ $schema = chado_get_schema('featureloc');
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+ $pkey = $schema['primary key'][0];
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+
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+ // Initialize the field array.
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+ $field_info = array(
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+ 'field_name' => 'featureloc',
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+ 'field_type' => 'chado_linker__featureloc',
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+ 'widget_type' => 'chado_linker__featureloc_widget',
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+ 'widget_settings' => array('display_label' => 1),
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+ 'description' => '',
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+ 'label' => 'Aligned Locations',
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+ 'is_required' => 0,
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+ 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
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+ 'storage' => 'field_chado_storage',
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+ 'field_settings' => array(
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+ 'chado_table' => 'featureloc',
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+ 'chado_column' => $pkey,
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+ 'base_table' => 'feature',
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+ 'semantic_web' => array(
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+ 'name' => '',
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+ 'accession' => '',
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+ 'ns' => '',
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+ 'nsurl' => '',
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+ ),
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),
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- ),
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- );
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-}
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-/**
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- * Implements hook_widget_info.
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- *
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- * This is a hook provided by the tripal_chado module for offloading
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- * the hook_field_widget_info() hook for each field to specify.
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- */
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-function chado_linker__featureloc_widget_info() {
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- return array(
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- 'label' => t('Alignment Settings'),
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- 'field types' => array('chado_linker__featureloc')
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- );
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-}
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-/**
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- * Implements hook_formatter_info.
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- *
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- * This is a hook provided by the tripal_chado module for
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- * offloading the hook_field_formatter_info() for each field
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- * to specify.
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- *
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- */
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-function chado_linker__featureloc_formatter_info() {
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- return array(
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- 'label' => t('Alignments'),
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- 'field types' => array('chado_linker__featureloc'),
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- 'settings' => array(
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- ),
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- );
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-}
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+ );
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-/**
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- * Implements hook_formatter_settings_summary.
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- *
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- * This is a hook provided by the tripal_chado module for
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- * offloading the hook_field_formatter_settings_summary() for each field
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- * to specify.
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- *
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- */
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-function chado_linker__featureloc_formatter_settings_summary($field, $instance,
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- $view_mode) {
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+ return $field_info;
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+ }
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-}
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+ /**
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+ * @see TripalField::widget_info()
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+ */
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+ public function widget_info() {
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+ return array(
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+ 'label' => t('Aligned Locations'),
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+ 'field types' => array('chado_linker__featureloc')
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+ );
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+ }
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-/**
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- * Provides a settings form for the formatter.
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- *
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- * This is a hook provided by the tripal_chado module for
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- * offloading the hook_field_formatter_settings_form() for each field
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- * to specify.
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- */
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-function chado_linker__featureloc_formatter_settings_form($field, $instance,
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- $view_mode, $form, &$form_state) {
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+ /**
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+ * @see TripalField::formatter_info()
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+ */
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+ public function formatter_info() {
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+ return array(
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+ 'label' => t('Aligned Locations'),
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+ 'field types' => array('chado_linker__featureloc'),
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+ 'settings' => array(
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+ ),
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+ );
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+ }
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+ /**
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+ * @see TripalField::formatter_settings_summary()
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+ */
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+ public function formatter_settings_summary($field, $instance,
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+ $view_mode) {
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+ }
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-}
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+ /**
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+ * @see TripalField::formatter_settings_form()
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+ */
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+ public function formatter_settings_form($field, $instance,
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+ $view_mode, $form, &$form_state) {
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-/**
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- * Validation function for the chado_linker_featureloc_formatter_settings_form.
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- */
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-function chado_linker__featureloc_formatter_settings_form_validate(&$form, &$form_state) {
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- // Place here as an example for validating the settings form.
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-}
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-/**
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- *
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- */
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-function chado_linker__featureloc_formatter(&$element, $entity_type, $entity,
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- $field, $instance, $langcode, $items, $display) {
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-
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- // Get the settings
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- $settings = $display['settings'];
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-
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- foreach ($items as $delta => $item) {
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- $alignments = $item['featurelocs'];
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- if (count($alignments) > 0){
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-
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- // the $headers array is an array of fields to use as the colum headers.
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- // additional documentation can be found here
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- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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- $headers = array('Aligned Feature' ,'Feature Type', 'Alignment Location');
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-
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- // the $rows array contains an array of rows where each row is an array
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- // of values for each column of the table in that row. Additional documentation
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- // can be found here:
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- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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- $rows = array();
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-
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- foreach ($alignments as $alignment){
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- $feature_name = $alignment->name;
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- if (property_exists($alignment, 'nid')) {
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- $feature_name = l($feature_name, "node/" . $alignment->nid);
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- }
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- $feature_loc = '';
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- $strand = '.';
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- if ($alignment->strand == -1) {
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- $strand = '-';
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- }
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- elseif ($alignment->strand == 1) {
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- $strand = '+';
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- }
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- // if this is a match then make the other location
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- if(property_exists($alignment, 'right_feature')){
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- $rstrand = '.';
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- if ($alignment->right_strand == -1) {
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- $rstrand = '-';
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- }
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- elseif ($alignment->right_strand == 1) {
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- $rstrand = '+';
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- }
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- $feature_loc = $feature->name .":". ($alignment->fmin + 1) . ".." . $alignment->fmax . " " . $strand;
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- $feature_loc .= "<br>" . $alignment->name .":". ($alignment->right_fmin + 1) . ".." . $alignment->right_fmax . " " . $rstrand;
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+ }
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+
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+ /**
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+ * @see TripalField::formatter_view()
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+ */
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+ function formatter_view(&$element, $entity_type, $entity,
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+ $field, $instance, $langcode, $items, $display) {
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+
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+ // Get the settings
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+ $settings = $display['settings'];
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+
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+ $rows = array();
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+ $headers = array('Aligned Feature' ,'Feature Type', 'Alignment Location');
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+
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+ foreach ($items as $delta => $item) {
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+ $alignment = $item['value'];
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+ $feature_name = $alignment['name'];
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+ $feature_loc = '';
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+ $strand = '.';
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+ if ($alignment['strand'] == -1) {
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+ $strand = '-';
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+ }
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+ elseif ($alignment['strand'] == 1) {
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+ $strand = '+';
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+ }
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+ // if this is a match then make the other location
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+ if(array_key_exists($alignment, 'right_feature')){
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+ $rstrand = '.';
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+ if ($alignment['right_strand'] == -1) {
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+ $rstrand = '-';
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}
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- else {
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- $feature_loc = $alignment->name .":". ($alignment->fmin + 1) . ".." . $alignment->fmax . " " . $strand;
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+ elseif ($alignment['right_strand'] == 1) {
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+ $rstrand = '+';
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}
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-
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- $rows[] = array(
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- $feature_name,
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- $alignment->type,
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- $feature_loc
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- );
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+ $feature_loc = $feature['name'] .":". ($alignment['fmin'] + 1) . ".." . $alignment['fmax'] . " " . $strand;
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+ $feature_loc .= "<br>" . $alignment['name'] .":". ($alignment['right_fmin'] + 1) . ".." . $alignment['right_fmax'] . " " . $rstrand;
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+ }
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+ else {
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+ $feature_loc = $alignment['name'] .":". ($alignment['fmin'] + 1) . ".." . $alignment['fmax'] . " " . $strand;
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}
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- // the $table array contains the headers and rows array as well as other
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- // options for controlling the display of the table. Additional
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- // documentation can be found here:
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- // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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- $table = array(
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- 'header' => $headers,
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- 'rows' => $rows,
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- 'attributes' => array(
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- 'id' => 'tripal_feature-table-alignments',
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- 'class' => 'tripal-data-table'
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- ),
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- 'sticky' => FALSE,
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- 'caption' => '',
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- 'colgroups' => array(),
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- 'empty' => '',
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- );
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-
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- // once we have our table array structure defined, we call Drupal's theme_table()
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- // function to generate the table.
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- $element[$delta] = array(
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- '#type' => 'markup',
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- '#markup' => theme_table($table),
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+ $rows[] = array(
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+ $feature_name,
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+ $alignment['type'],
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+ $feature_loc
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);
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}
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- }
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-}
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-/**
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- * Loads the field values with appropriate data.
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- *
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- * This function is called by the tripal_chado_field_storage_load() for
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- * each property managed by the field_chado_storage storage type. This is
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- * an optional hook function that is only needed if the field has
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- * multiple form elements.
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- */
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-function chado_linker__featureloc_load($field, $entity, $base_table, $record) {
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- $field_name = $field['field_name'];
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-
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- $options = array(
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- 'return_array' => 1,
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- 'include_fk' => array(
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- 'srcfeature_id' => array(
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- 'type_id' => 1,
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- ),
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- 'feature_id' => array(
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- 'type_id' => 1
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+
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+ // the $table array contains the headers and rows array as well as other
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+ // options for controlling the display of the table. Additional
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+ // documentation can be found here:
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+ // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
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+ $table = array(
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+ 'header' => $headers,
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+ 'rows' => $rows,
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+ 'attributes' => array(
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+ 'id' => 'tripal_feature-table-alignments',
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+ 'class' => 'tripal-data-table'
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),
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- )
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- );
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- $feature = chado_expand_var($record, 'table', 'featureloc', $options);
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-
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- // get alignments as child
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- $cfeaturelocs = $feature->featureloc->feature_id;
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- if (!$cfeaturelocs) {
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- $cfeaturelocs = array();
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- }
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- // get alignment as parent
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- $pfeaturelocs = $feature->featureloc->srcfeature_id;
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- if (!$pfeaturelocs) {
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- $pfeaturelocs = array();
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+ 'sticky' => FALSE,
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+ 'caption' => '',
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+ 'colgroups' => array(),
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+ 'empty' => '',
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+ );
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+
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+ // once we have our table array structure defined, we call Drupal's theme_table()
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+ // function to generate the table.
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+ $element[$delta] = array(
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|
|
+ '#type' => 'markup',
|
|
|
+ '#markup' => theme_table($table),
|
|
|
+ );
|
|
|
}
|
|
|
|
|
|
- // get matched alignments (those with an itermediate 'match' or 'EST_match', etc
|
|
|
- $mfeaturelocs = chado_linker__featureloc_get_matched_alignments($feature);
|
|
|
- $feature->matched_featurelocs = $mfeaturelocs;
|
|
|
-
|
|
|
- // combine all three alignments into a single array for printing together in
|
|
|
- // a single list
|
|
|
- $alignments = array();
|
|
|
- foreach ($pfeaturelocs as $featureloc) {
|
|
|
- // if type is a 'match' then ignore it. We will handle those below
|
|
|
- if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) {
|
|
|
- continue;
|
|
|
+ /**
|
|
|
+ * @see TripalField::load()
|
|
|
+ */
|
|
|
+ function load($field, $entity, $details) {
|
|
|
+ $record = $details['record'];
|
|
|
+ $settings = $field['settings'];
|
|
|
+
|
|
|
+ $field_name = $field['field_name'];
|
|
|
+ $field_type = $field['type'];
|
|
|
+
|
|
|
+ $options = array(
|
|
|
+ 'return_array' => TRUE,
|
|
|
+ 'include_fk' => array(
|
|
|
+ 'srcfeature_id' => array(
|
|
|
+ 'type_id' => 1,
|
|
|
+ ),
|
|
|
+ 'feature_id' => array(
|
|
|
+ 'type_id' => 1
|
|
|
+ ),
|
|
|
+ )
|
|
|
+ );
|
|
|
+ $feature = chado_expand_var($record, 'table', 'featureloc', $options);
|
|
|
+
|
|
|
+ // Get alignments as child
|
|
|
+ $cfeaturelocs = $feature->featureloc->feature_id;
|
|
|
+ if (!$cfeaturelocs) {
|
|
|
+ $cfeaturelocs = array();
|
|
|
}
|
|
|
- $alignment = new stdClass();
|
|
|
- $alignment->record = $featureloc;
|
|
|
- $alignment->name = $featureloc->feature_id->name;
|
|
|
- $alignment->type = $featureloc->feature_id->type_id->name;
|
|
|
- $alignment->fmin = $featureloc->fmin;
|
|
|
- $alignment->fmax = $featureloc->fmax;
|
|
|
- $alignment->phase = $featureloc->phase;
|
|
|
- $alignment->strand = $featureloc->strand;
|
|
|
- $alignments[] = $alignment;
|
|
|
- if (property_exists($featureloc->feature_id, 'nid')) {
|
|
|
- $alignment->nid = $featureloc->feature_id->nid;
|
|
|
+ // Get alignment as parent
|
|
|
+ $pfeaturelocs = $feature->featureloc->srcfeature_id;
|
|
|
+ if (!$pfeaturelocs) {
|
|
|
+ $pfeaturelocs = array();
|
|
|
}
|
|
|
- }
|
|
|
- foreach ($cfeaturelocs as $featureloc) {
|
|
|
- // if type is a 'match' then ignore it. We will handle those below
|
|
|
- if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) {
|
|
|
- continue;
|
|
|
+
|
|
|
+ // Get matched alignments (those with an itermediate 'match' or 'EST_match', etc
|
|
|
+ $mfeaturelocs = $this->get_matched_alignments($feature);
|
|
|
+ $feature->matched_featurelocs = $mfeaturelocs;
|
|
|
+
|
|
|
+ // Combine all three alignments into a single array for printing together in
|
|
|
+ // a single list
|
|
|
+ $alignments = array();
|
|
|
+ foreach ($pfeaturelocs as $featureloc) {
|
|
|
+ // if type is a 'match' then ignore it. We will handle those below
|
|
|
+ if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ $alignments[] = array(
|
|
|
+ 'name' => $featureloc->feature_id->name,
|
|
|
+ 'type' => $featureloc->feature_id->type_id->name,
|
|
|
+ 'fmin' => $featureloc->fmin,
|
|
|
+ 'fmax' => $featureloc->fmax,
|
|
|
+ 'phase' => $featureloc->phase,
|
|
|
+ 'strand' => $featureloc->strand,
|
|
|
+ );
|
|
|
}
|
|
|
- $alignment = new stdClass();
|
|
|
- $alignment->record = $featureloc;
|
|
|
- $alignment->name = $featureloc->srcfeature_id->name;
|
|
|
- $alignment->type = $featureloc->srcfeature_id->type_id->name;
|
|
|
- $alignment->fmin = $featureloc->fmin;
|
|
|
- $alignment->is_fmin_partial = $featureloc->is_fmin_partial;
|
|
|
- $alignment->fmax = $featureloc->fmax;
|
|
|
- $alignment->is_fmax_partial = $featureloc->is_fmax_partial;
|
|
|
- $alignment->phase = $featureloc->phase;
|
|
|
- $alignment->strand = $featureloc->strand;
|
|
|
- $alignments[] = $alignment;
|
|
|
- if (property_exists($featureloc->srcfeature_id, 'nid')) {
|
|
|
- $alignment->nid = $featureloc->srcfeature_id->nid;
|
|
|
+ foreach ($cfeaturelocs as $featureloc) {
|
|
|
+ // if type is a 'match' then ignore it. We will handle those below
|
|
|
+ if (preg_match('/(^match$|^.*?_match|match_part)$/', $featureloc->feature_id->type_id->name)) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ $alignments[] = array(
|
|
|
+ 'name' => $featureloc->srcfeature_id->name,
|
|
|
+ 'type' => $featureloc->srcfeature_id->type_id->name,
|
|
|
+ 'fmin' => $featureloc->fmin,
|
|
|
+ 'is_fmin_partial' => $featureloc->is_fmin_partial,
|
|
|
+ 'fmax' => $featureloc->fmax,
|
|
|
+ 'is_fmax_partial' => $featureloc->is_fmax_partial,
|
|
|
+ 'phase' => $featureloc->phase,
|
|
|
+ 'strand' => $featureloc->strand,
|
|
|
+ );
|
|
|
}
|
|
|
- }
|
|
|
- // in matching features, the left feature is always the feature
|
|
|
- // provided to this function.
|
|
|
- foreach ($mfeaturelocs as $featureloc) {
|
|
|
- // get more information about the right feature
|
|
|
- $select = array('feature_id' => $featureloc->right_srcfeature_id);
|
|
|
- $rfeature = chado_generate_var('feature', $select);
|
|
|
- // now add to the list
|
|
|
- $alignment = new stdClass();
|
|
|
- $alignment->record = $featureloc;
|
|
|
- $alignment->right_feature = $rfeature;
|
|
|
- $alignment->name = $rfeature->name;
|
|
|
- $alignment->type = $rfeature->type_id->name;
|
|
|
- $alignment->fmin = $featureloc->left_fmin;
|
|
|
- $alignment->is_fmin_partial = $featureloc->left_is_fmin_partial;
|
|
|
- $alignment->fmax = $featureloc->left_fmax;
|
|
|
- $alignment->is_fmax_partial = $featureloc->left_is_fmax_partial;
|
|
|
- $alignment->phase = $featureloc->left_phase;
|
|
|
- $alignment->strand = $featureloc->left_strand;
|
|
|
- $alignment->right_fmin = $featureloc->right_fmin;
|
|
|
- $alignment->right_is_fmin_partial = $featureloc->right_is_fmin_partial;
|
|
|
- $alignment->right_fmax = $featureloc->right_fmax;
|
|
|
- $alignment->right_is_fmax_partial = $featureloc->right_is_fmax_partial;
|
|
|
- $alignment->right_phase = $featureloc->right_phase;
|
|
|
- $alignment->right_strand = $featureloc->right_strand;
|
|
|
- $alignments[] = $alignment;
|
|
|
- if (property_exists($rfeature, 'nid')) {
|
|
|
- $alignment->nid = $rfeature->nid;
|
|
|
+ // in matching features, the left feature is always the feature
|
|
|
+ // provided to this function.
|
|
|
+ foreach ($mfeaturelocs as $featureloc) {
|
|
|
+ // get more information about the right feature
|
|
|
+ $select = array('feature_id' => $featureloc->right_srcfeature_id);
|
|
|
+ $rfeature = chado_generate_var('feature', $select);
|
|
|
+ // now add to the list
|
|
|
+ $alignments[] = array(
|
|
|
+ 'name' => $rfeature->name,
|
|
|
+ 'type' => $rfeature->type_id->name,
|
|
|
+ 'fmin' => $featureloc->left_fmin,
|
|
|
+ 'is_fmin_partial' => $featureloc->left_is_fmin_partial,
|
|
|
+ 'fmax' => $featureloc->left_fmax,
|
|
|
+ 'is_fmax_partial' => $featureloc->left_is_fmax_partial,
|
|
|
+ 'phase' => $featureloc->left_phase,
|
|
|
+ 'strand' => $featureloc->left_strand,
|
|
|
+ 'right_fmin' => $featureloc->right_fmin,
|
|
|
+ 'right_is_fmin_partial' => $featureloc->right_is_fmin_partial,
|
|
|
+ 'right_fmax' => $featureloc->right_fmax,
|
|
|
+ 'right_is_fmax_partial' => $featureloc->right_is_fmax_partial,
|
|
|
+ 'right_phase' => $featureloc->right_phase,
|
|
|
+ 'right_strand' => $featureloc->right_strand,
|
|
|
+ );
|
|
|
+ }
|
|
|
+ $i = 0;
|
|
|
+ foreach ($alignments as $alignment) {
|
|
|
+ $entity->{$field_name}['und'][$i]['value'] = $alignment;
|
|
|
+ $i++;
|
|
|
}
|
|
|
}
|
|
|
- $entity->{$field_name}['und'][0]['featurelocs'] = $alignments;
|
|
|
-}
|
|
|
-/**
|
|
|
- * This function is for features that align through an intermediate such
|
|
|
- * as 'EST_match' or 'match'. This occurs in the case where two sequences
|
|
|
- * align but where one does not align perfectly. Some ESTs may be in a contig
|
|
|
- * but not all of the EST. Portions may overhang and not be included in the
|
|
|
- * consensus if quality is bad.
|
|
|
- * For example:
|
|
|
- * Feature 1: Contig --------------------
|
|
|
- * Feature 2: EST_match -------
|
|
|
- * Feature 3: EST ---------
|
|
|
- *
|
|
|
- * The feature provided to the function will always be the feature 1. The
|
|
|
- * featureloc columns prefixed with 'right' (e.g. right_fmin) belong to the
|
|
|
- * alignment of feature 3 with feature 2
|
|
|
- *
|
|
|
- * Features may align to more than one feature and are not matches. We do
|
|
|
- * not want to include these, so we have to filter on the SO terms:
|
|
|
- * match, or %_match
|
|
|
+ /**
|
|
|
+ * This function is for features that align through an intermediate such
|
|
|
+ * as 'EST_match' or 'match'. This occurs in the case where two sequences
|
|
|
+ * align but where one does not align perfectly. Some ESTs may be in a contig
|
|
|
+ * but not all of the EST. Portions may overhang and not be included in the
|
|
|
+ * consensus if quality is bad.
|
|
|
+ * For example:
|
|
|
+ * Feature 1: Contig --------------------
|
|
|
+ * Feature 2: EST_match -------
|
|
|
+ * Feature 3: EST ---------
|
|
|
*
|
|
|
- * @ingroup tripal_feature
|
|
|
- */
|
|
|
- function chado_linker__featureloc_get_matched_alignments($feature) {
|
|
|
-
|
|
|
- $sql = "
|
|
|
- SELECT
|
|
|
- FL1.featureloc_id as left_featureloc_id,
|
|
|
- FL1.srcfeature_id as left_srcfeature_id,
|
|
|
- FL1.feature_id as left_feature_id,
|
|
|
- FL1.fmin as left_fmin,
|
|
|
- FL1.is_fmin_partial as left_is_fmin_partial,
|
|
|
- FL1.fmax as left_fmax,
|
|
|
- FL1.is_fmax_partial as left_is_fmax_partial,
|
|
|
- FL1.strand as left_strand,
|
|
|
- FL1.phase as left_phase,
|
|
|
- FL1.locgroup as left_locgroup,
|
|
|
- FL1.rank as left_rank,
|
|
|
- FL2.featureloc_id as right_featureloc_id,
|
|
|
- FL2.srcfeature_id as right_srcfeature_id,
|
|
|
- FL2.feature_id as right_feature_id,
|
|
|
- FL2.fmin as right_fmin,
|
|
|
- FL2.is_fmin_partial as right_is_fmin_partial,
|
|
|
- FL2.fmax as right_fmax,
|
|
|
- FL2.is_fmax_partial as right_is_fmax_partial,
|
|
|
- FL2.strand as right_strand,
|
|
|
- FL2.phase as right_phase,
|
|
|
- FL2.locgroup as right_locgroup,
|
|
|
- FL2.rank as right_rank
|
|
|
- FROM {feature} F1
|
|
|
- INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id
|
|
|
- INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id
|
|
|
- INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id
|
|
|
- INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id
|
|
|
- WHERE
|
|
|
- F1.feature_id = :feature_id AND
|
|
|
- (CVT2.name = 'match' or CVT2.name like '%_match')
|
|
|
- ORDER BY FL1.fmin
|
|
|
- ";
|
|
|
-
|
|
|
- $results = chado_query($sql, array(':feature_id' => $feature->feature_id));
|
|
|
-
|
|
|
- // iterate through the results and add them to our featurelocs array
|
|
|
- $featurelocs = array();
|
|
|
- while ($fl = $results->fetchObject()) {
|
|
|
- // ignore featurelocs where the left and right srcfeature is the same
|
|
|
- if (strcmp($fl->left_srcfeature_id, $fl->right_srcfeature_id) == 0) {
|
|
|
- continue;
|
|
|
+ * The feature provided to the function will always be the feature 1. The
|
|
|
+ * featureloc columns prefixed with 'right' (e.g. right_fmin) belong to the
|
|
|
+ * alignment of feature 3 with feature 2
|
|
|
+ *
|
|
|
+ * Features may align to more than one feature and are not matches. We do
|
|
|
+ * not want to include these, so we have to filter on the SO terms:
|
|
|
+ * match, or %_match
|
|
|
+ *
|
|
|
+ * @ingroup tripal_feature
|
|
|
+ */
|
|
|
+ private function get_matched_alignments($feature) {
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT
|
|
|
+ FL1.featureloc_id as left_featureloc_id,
|
|
|
+ FL1.srcfeature_id as left_srcfeature_id,
|
|
|
+ FL1.feature_id as left_feature_id,
|
|
|
+ FL1.fmin as left_fmin,
|
|
|
+ FL1.is_fmin_partial as left_is_fmin_partial,
|
|
|
+ FL1.fmax as left_fmax,
|
|
|
+ FL1.is_fmax_partial as left_is_fmax_partial,
|
|
|
+ FL1.strand as left_strand,
|
|
|
+ FL1.phase as left_phase,
|
|
|
+ FL1.locgroup as left_locgroup,
|
|
|
+ FL1.rank as left_rank,
|
|
|
+ FL2.featureloc_id as right_featureloc_id,
|
|
|
+ FL2.srcfeature_id as right_srcfeature_id,
|
|
|
+ FL2.feature_id as right_feature_id,
|
|
|
+ FL2.fmin as right_fmin,
|
|
|
+ FL2.is_fmin_partial as right_is_fmin_partial,
|
|
|
+ FL2.fmax as right_fmax,
|
|
|
+ FL2.is_fmax_partial as right_is_fmax_partial,
|
|
|
+ FL2.strand as right_strand,
|
|
|
+ FL2.phase as right_phase,
|
|
|
+ FL2.locgroup as right_locgroup,
|
|
|
+ FL2.rank as right_rank
|
|
|
+ FROM {feature} F1
|
|
|
+ INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id
|
|
|
+ INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id
|
|
|
+ INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id
|
|
|
+ INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id
|
|
|
+ WHERE
|
|
|
+ F1.feature_id = :feature_id AND
|
|
|
+ (CVT2.name = 'match' or CVT2.name like '%_match')
|
|
|
+ ORDER BY FL1.fmin
|
|
|
+ ";
|
|
|
+
|
|
|
+ $results = chado_query($sql, array(':feature_id' => $feature->feature_id));
|
|
|
+
|
|
|
+ // iterate through the results and add them to our featurelocs array
|
|
|
+ $featurelocs = array();
|
|
|
+ while ($fl = $results->fetchObject()) {
|
|
|
+ // ignore featurelocs where the left and right srcfeature is the same
|
|
|
+ if (strcmp($fl->left_srcfeature_id, $fl->right_srcfeature_id) == 0) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ $featurelocs[] = $fl ;
|
|
|
}
|
|
|
- $featurelocs[] = $fl ;
|
|
|
+ return $featurelocs;
|
|
|
}
|
|
|
- return $featurelocs;
|
|
|
- }
|
|
|
|
|
|
-/**
|
|
|
- * Implements hook_ws_formatter().
|
|
|
- */
|
|
|
-function chado_linker__featureloc_ws_formatter(&$element, $entity_type, $entity,
|
|
|
- $field, $instance, $items) {
|
|
|
+ /**
|
|
|
+ * @see TripalField::widget_form()
|
|
|
+ */
|
|
|
+ function widget_form(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
|
|
|
|
|
|
-}
|
|
|
+ }
|
|
|
|
|
|
+}
|
|
|
/**
|
|
|
- * Implements hook_widget().
|
|
|
+ * Callback function for validating the chado_linker_featureloc_widget.
|
|
|
*/
|
|
|
-function chado_linker__featureloc_widget(&$widget, $form, $form_state, $field, $instance, $langcode, $items, $delta, $element) {
|
|
|
+function chado_linker__featureloc_widget_validate($element, &$form_state) {
|
|
|
|
|
|
}
|
|
|
/**
|
|
|
- * Callback function for validating the chado_linker_featureloc_widget.
|
|
|
+ * Validation function for the chado_linker_featureloc_formatter_settings_form.
|
|
|
*/
|
|
|
-function chado_linker__featureloc_widget_validate($element, &$form_state) {
|
|
|
+function chado_linker__featureloc_formatter_settings_form_validate(&$form, &$form_state) {
|
|
|
+
|
|
|
+ // Place here as an example for validating the settings form.
|
|
|
+}
|
|
|
|
|
|
-}
|
Stephen Ficklin