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@@ -1,14 +1,308 @@
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-$view = new view;
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-$view->name = 'est_search';
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-$view->description = 'EST Search';
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-$view->tag = '';
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-$view->view_php = '';
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-$view->base_table = 'feature_for_search';
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-$view->is_cacheable = FALSE;
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-$view->api_version = 2;
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-$view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
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-$handler = $view->new_display('default', 'Defaults', 'default');
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-$handler->override_option('fields', array(
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+<?php
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+
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+/*************************************************************************
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+ * tripal_search_unigene_views_data()
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+ */
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+
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+function tripal_search_unigene_views_data() {
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+ global $db_url;
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+ $data = array();
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+
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+ // if the chado database is not local to the drupal database
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+ // then we need to set the database name. This should always
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+ // be 'chado'.
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+ if(is_array($db_url) and array_key_exists('chado', $db_url)) {
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+ $database = 'chado';
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+ }
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+
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+ // Basic table definition
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+ $data['unigene_for_search']['table']['group'] = 'Tripal Search feature';
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+ $data['unigene_for_search']['table']['base'] = array(
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+ 'field' => 'unigene_for_search_id',
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+ 'title' => t('Chado Feature with searchable annotations'),
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+ 'help' => t('A materialized view for feature is generated to enable the search for different annotations'),
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+ );
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+ if ($database) {
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+ $data['unigene_for_search']['table']['base']['database'] = $database;
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+ }
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+
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+ // Table Field Definitions----------------------
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+ // Field: feature_id (integer)
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+ $data['unigene_for_search']['unigene_for_search_id'] = array(
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+ 'title' => t('unigene_for_search ID'),
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+ 'help' => t('The primary key of unigene_for_search'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field_numeric',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_numeric',
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+ ),
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+ );
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+
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+ // Field: feature_id (integer)
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+ $data['unigene_for_search']['feature_id'] = array(
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+ 'title' => t('feature ID'),
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+ 'help' => t('The primary key of a feature'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field_numeric',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_numeric',
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+ ),
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+ );
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+
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+ // Field: name (character varying(1024))
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+ $data['unigene_for_search']['feature_type'] = array(
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+ 'title' => t('feature_type'),
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+ 'help' => t('Type of the feature'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_feature_type_id',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ // Field: name (character varying(255),)
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+ $data['unigene_for_search']['feature_name'] = array(
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+ 'title' => t('feature_name'),
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+ 'help' => t('The optional human-readable common name for a feature, for display purposes.'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_string',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ // Field: uniquename (text)
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+ $data['unigene_for_search']['feature_uniquename'] = array(
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+ 'title' => t('feature_uniquename'),
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+ 'help' => t('The unique name for a feature; may not be necessarily be particularly human-readable, although this is preferred. This name must be unique for this type of feature within this organism.'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_string',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ // Field: is_obsolete (boolean)
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+ $data['unigene_for_search']['feature_is_obsolete'] = array(
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+ 'title' => t('feature_is_obsolete'),
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+ 'help' => t('Boolean indicating whether this feature has been obsoleted. Some chado instances may choose to simply remove the feature altogether, others may choose to keep an obsolete row in the table.'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_boolean_operator_string',
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+ ),
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+ );
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+
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+ // Field: common name (varchar 255)
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+ $data['unigene_for_search']['organism_common_name'] = array(
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+ 'title' => 'organism_common_name',
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+ 'help' => 'The common name of the organism.',
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_organism_common_name',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ // Field: seqlen (integer)
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+ $data['unigene_for_search']['feature_seqlen'] = array(
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+ 'title' => t('feature_seqlen'),
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+ 'help' => t('The length of the residue feature. See column:residues. This column is partially redundant with the residues column, and also with featureloc. This column is required because the location may be unknown and the residue sequence may not be manifested, yet it may be desirable to store and query the length of the feature. The seqlen should always be manifested where the length of the sequence is known.'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field_numeric',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_numeric',
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+ ),
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+ );
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+
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+ // Field: name (character varying(1024))
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+ $data['unigene_for_search']['go_term'] = array(
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+ 'title' => t('go_term'),
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+ 'help' => t('GO Terms associated with a feature'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_string',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ // Field: name (character varying(255),)
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+ $data['unigene_for_search']['unigene'] = array(
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+ 'title' => t('unigene'),
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+ 'help' => t('Unigene analysis name.'),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_analysis_name',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ // Field: value (text,)
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+ $data['unigene_for_search']['blast_value'] = array(
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+ 'title' => t('value'),
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+ 'help' => t(''),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_string',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ // Field: value (text,)
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+ $data['unigene_for_search']['kegg_value'] = array(
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+ 'title' => t('value'),
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+ 'help' => t(''),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_string',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ // Field: value (text,)
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+ $data['unigene_for_search']['interpro_value'] = array(
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+ 'title' => t('value'),
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+ 'help' => t(''),
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+ 'field' => array(
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+ 'handler' => 'views_handler_field',
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+ 'click sortable' => TRUE,
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+ ),
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+ 'sort' => array(
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+ 'handler' => 'views_handler_sort',
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+ ),
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+ 'filter' => array(
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+ 'handler' => 'views_handler_filter_string',
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+ ),
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+ 'argument' => array(
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+ 'handler' => 'views_handler_argument_string',
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+ ),
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+ );
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+
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+ return $data;
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+}
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+
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+/*************************************************************************
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+ * tripal_search_unigene_views_handlers
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+ */
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+function tripal_search_unigene_views_handlers() {
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+ return array(
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+ 'info' => array(
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+ 'path' => drupal_get_path('module', 'tripal_search_unigene'),
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+ ),
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+ 'handlers' => array(
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+ 'views_handler_filter_organism_common_name' => array(
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+ 'parent' => 'views_handler_filter_string'
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+ ),
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+ 'views_handler_filter_analysis_name' => array(
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+ 'parent' => 'views_handler_filter_string'
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+ ),
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+ 'views_handler_filter_feature_type_id' => array(
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+ 'parent' => 'views_handler_filter_numeric'
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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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+ * tripal_search_unigene_views_default_views
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+ */
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+function tripal_search_unigene_views_default_views () {
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+ $views = array();
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+ $view = new view;
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+ $view->name = 'unigene_search';
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+ $view->description = 'Unigene Search';
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+ $view->tag = '';
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+ $view->view_php = '';
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+ $view->base_table = 'unigene_for_search';
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+ $view->is_cacheable = FALSE;
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+ $view->api_version = 2;
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+ $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
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+ $handler = $view->new_display('default', 'Defaults', 'default');
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+ $handler->override_option('fields', array(
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'counter' => array(
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'label' => '#',
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'alter' => array(
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@@ -28,7 +322,7 @@ $handler->override_option('fields', array(
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'ellipsis' => 1,
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'html' => 0,
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'strip_tags' => 0,
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- ),
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+ ),
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'empty' => '',
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'hide_empty' => 0,
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'empty_zero' => 0,
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@@ -38,7 +332,7 @@ $handler->override_option('fields', array(
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'table' => 'views',
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'field' => 'counter',
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'relationship' => 'none',
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- ),
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+ ),
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'feature_id' => array(
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'label' => 'feature ID',
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'alter' => array(
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@@ -58,7 +352,7 @@ $handler->override_option('fields', array(
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'ellipsis' => 1,
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'html' => 0,
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'strip_tags' => 0,
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- ),
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+ ),
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'empty' => '',
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'hide_empty' => 0,
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'empty_zero' => 0,
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@@ -70,10 +364,10 @@ $handler->override_option('fields', array(
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'suffix' => '',
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'exclude' => 1,
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'id' => 'feature_id',
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- 'table' => 'feature_for_search',
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+ 'table' => 'unigene_for_search',
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'field' => 'feature_id',
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'relationship' => 'none',
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- ),
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+ ),
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'feature_name' => array(
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'label' => 'Sequence',
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'alter' => array(
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@@ -93,16 +387,16 @@ $handler->override_option('fields', array(
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'ellipsis' => 1,
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'html' => 0,
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'strip_tags' => 0,
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- ),
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+ ),
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'empty' => '',
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'hide_empty' => 0,
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'empty_zero' => 0,
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'exclude' => 0,
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'id' => 'feature_name',
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- 'table' => 'feature_for_search',
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+ 'table' => 'unigene_for_search',
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'field' => 'feature_name',
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'relationship' => 'none',
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- ),
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+ ),
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'organism_common_name' => array(
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'label' => 'Organism',
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'alter' => array(
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@@ -122,16 +416,16 @@ $handler->override_option('fields', array(
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'ellipsis' => 1,
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'html' => 0,
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'strip_tags' => 0,
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- ),
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+ ),
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'empty' => '',
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'hide_empty' => 0,
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'empty_zero' => 0,
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'exclude' => 0,
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'id' => 'organism_common_name',
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- 'table' => 'feature_for_search',
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+ 'table' => 'unigene_for_search',
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'field' => 'organism_common_name',
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'relationship' => 'none',
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- ),
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+ ),
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'feature_seqlen' => array(
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'label' => 'Length',
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'alter' => array(
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@@ -151,7 +445,7 @@ $handler->override_option('fields', array(
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'ellipsis' => 1,
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'html' => 0,
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'strip_tags' => 0,
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- ),
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+ ),
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'empty' => '',
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'hide_empty' => 0,
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'empty_zero' => 0,
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@@ -163,10 +457,10 @@ $handler->override_option('fields', array(
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'suffix' => '',
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'exclude' => 0,
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'id' => 'feature_seqlen',
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- 'table' => 'feature_for_search',
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|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'feature_seqlen',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'feature_type' => array(
|
|
|
'label' => 'Type',
|
|
|
'alter' => array(
|
|
|
@@ -186,16 +480,16 @@ $handler->override_option('fields', array(
|
|
|
'ellipsis' => 1,
|
|
|
'html' => 0,
|
|
|
'strip_tags' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'empty' => '',
|
|
|
'hide_empty' => 0,
|
|
|
'empty_zero' => 0,
|
|
|
'exclude' => 0,
|
|
|
'id' => 'feature_type',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'feature_type',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'go_term' => array(
|
|
|
'label' => 'GO Term',
|
|
|
'alter' => array(
|
|
|
@@ -215,16 +509,16 @@ $handler->override_option('fields', array(
|
|
|
'ellipsis' => 1,
|
|
|
'html' => 0,
|
|
|
'strip_tags' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'empty' => '',
|
|
|
'hide_empty' => 0,
|
|
|
'empty_zero' => 0,
|
|
|
'exclude' => 0,
|
|
|
'id' => 'go_term',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'go_term',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'blast_value' => array(
|
|
|
'label' => 'Blast',
|
|
|
'alter' => array(
|
|
|
@@ -244,16 +538,16 @@ $handler->override_option('fields', array(
|
|
|
'ellipsis' => 1,
|
|
|
'html' => 0,
|
|
|
'strip_tags' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'empty' => '',
|
|
|
'hide_empty' => 0,
|
|
|
'empty_zero' => 0,
|
|
|
'exclude' => 0,
|
|
|
'id' => 'blast_value',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'blast_value',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'kegg_value' => array(
|
|
|
'label' => 'KEGG',
|
|
|
'alter' => array(
|
|
|
@@ -273,16 +567,16 @@ $handler->override_option('fields', array(
|
|
|
'ellipsis' => 1,
|
|
|
'html' => 0,
|
|
|
'strip_tags' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'empty' => '',
|
|
|
'hide_empty' => 0,
|
|
|
'empty_zero' => 0,
|
|
|
'exclude' => 0,
|
|
|
'id' => 'kegg_value',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'kegg_value',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'interpro_value' => array(
|
|
|
'label' => 'Interpro',
|
|
|
'alter' => array(
|
|
|
@@ -302,18 +596,18 @@ $handler->override_option('fields', array(
|
|
|
'ellipsis' => 1,
|
|
|
'html' => 0,
|
|
|
'strip_tags' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'empty' => '',
|
|
|
'hide_empty' => 0,
|
|
|
'empty_zero' => 0,
|
|
|
'exclude' => 0,
|
|
|
'id' => 'interpro_value',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'interpro_value',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
-));
|
|
|
-$handler->override_option('arguments', array(
|
|
|
+ ),
|
|
|
+ ));
|
|
|
+ $handler->override_option('arguments', array(
|
|
|
'null' => array(
|
|
|
'default_action' => 'default',
|
|
|
'style_plugin' => 'default_summary',
|
|
|
@@ -336,7 +630,7 @@ $handler->override_option('arguments', array(
|
|
|
'3' => 0,
|
|
|
'5' => 0,
|
|
|
'4' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'relationship' => 'none',
|
|
|
'default_options_div_prefix' => '',
|
|
|
'default_argument_fixed' => '',
|
|
|
@@ -356,7 +650,7 @@ $handler->override_option('arguments', array(
|
|
|
'calendar_event' => 0,
|
|
|
'page' => 0,
|
|
|
'story' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'validate_argument_node_access' => 0,
|
|
|
'validate_argument_nid_type' => 'nid',
|
|
|
'validate_argument_vocabulary' => array(
|
|
|
@@ -373,16 +667,16 @@ $handler->override_option('arguments', array(
|
|
|
'6' => 0,
|
|
|
'7' => 0,
|
|
|
'8' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'validate_argument_type' => 'tid',
|
|
|
'validate_argument_transform' => 0,
|
|
|
'validate_user_restrict_roles' => 0,
|
|
|
'validate_argument_php' => 'if (count($view->exposed_input)) {
|
|
|
return TRUE;
|
|
|
}',
|
|
|
- ),
|
|
|
-));
|
|
|
-$handler->override_option('filters', array(
|
|
|
+ ),
|
|
|
+ ));
|
|
|
+ $handler->override_option('filters', array(
|
|
|
'feature_name' => array(
|
|
|
'operator' => 'contains',
|
|
|
'value' => '',
|
|
|
@@ -395,20 +689,20 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'sequence name',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'case' => 0,
|
|
|
'id' => 'feature_name',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'feature_name',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'feature_seqlen' => array(
|
|
|
'operator' => '>=',
|
|
|
'value' => array(
|
|
|
'value' => '',
|
|
|
'min' => '',
|
|
|
'max' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'group' => '0',
|
|
|
'exposed' => TRUE,
|
|
|
'expose' => array(
|
|
|
@@ -418,12 +712,12 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'sequence length (bp)',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'id' => 'feature_seqlen',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'feature_seqlen',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'feature_type' => array(
|
|
|
'operator' => '=',
|
|
|
'value' => '260',
|
|
|
@@ -436,13 +730,13 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'type of sequence',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'case' => 0,
|
|
|
'id' => 'feature_type',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'feature_type',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'go_term' => array(
|
|
|
'operator' => 'contains',
|
|
|
'value' => '',
|
|
|
@@ -455,13 +749,13 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'GO term',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'case' => 0,
|
|
|
'id' => 'go_term',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'go_term',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'organism_common_name' => array(
|
|
|
'operator' => '=',
|
|
|
'value' => 'chickpea',
|
|
|
@@ -474,13 +768,13 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'organism',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'case' => 0,
|
|
|
'id' => 'organism_common_name',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'organism_common_name',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'unigene' => array(
|
|
|
'operator' => '=',
|
|
|
'value' => 'Cicer arietinum unigene v1',
|
|
|
@@ -493,13 +787,13 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'belongs to unigene',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'case' => 0,
|
|
|
'id' => 'unigene',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'unigene',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'interpro_value' => array(
|
|
|
'operator' => 'contains',
|
|
|
'value' => '',
|
|
|
@@ -512,13 +806,13 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'interpro description',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'case' => 0,
|
|
|
'id' => 'interpro_value',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'interpro_value',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'blast_value' => array(
|
|
|
'operator' => 'contains',
|
|
|
'value' => '',
|
|
|
@@ -531,13 +825,13 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'blast description',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'case' => 0,
|
|
|
'id' => 'blast_value',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'blast_value',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'kegg_value' => array(
|
|
|
'operator' => 'contains',
|
|
|
'value' => '',
|
|
|
@@ -550,32 +844,32 @@ $handler->override_option('filters', array(
|
|
|
'label' => 'kegg description',
|
|
|
'optional' => 1,
|
|
|
'remember' => 0,
|
|
|
- ),
|
|
|
+ ),
|
|
|
'case' => 0,
|
|
|
'id' => 'kegg_value',
|
|
|
- 'table' => 'feature_for_search',
|
|
|
+ 'table' => 'unigene_for_search',
|
|
|
'field' => 'kegg_value',
|
|
|
'relationship' => 'none',
|
|
|
- ),
|
|
|
-));
|
|
|
-$handler->override_option('access', array(
|
|
|
+ ),
|
|
|
+ ));
|
|
|
+ $handler->override_option('access', array(
|
|
|
'type' => 'none',
|
|
|
-));
|
|
|
-$handler->override_option('cache', array(
|
|
|
+ ));
|
|
|
+ $handler->override_option('cache', array(
|
|
|
'type' => 'none',
|
|
|
-));
|
|
|
-$handler->override_option('title', 'EST Unigene Search');
|
|
|
-$handler->override_option('css_class', 'tripal-search-feature');
|
|
|
-$handler->override_option('empty', '<?php
|
|
|
+ ));
|
|
|
+ $handler->override_option('title', 'Unigene Search');
|
|
|
+ $handler->override_option('css_class', 'tripal-search-feature');
|
|
|
+ $handler->override_option('empty', '<?php
|
|
|
$view = views_get_current_view();
|
|
|
if (count($view->exposed_input)) {
|
|
|
drupal_set_message("Your search returns no results. Please adjust your search criteria and try again.");
|
|
|
}
|
|
|
?>');
|
|
|
-$handler->override_option('empty_format', '3');
|
|
|
-$handler->override_option('use_pager', '1');
|
|
|
-$handler->override_option('style_plugin', 'table');
|
|
|
-$handler->override_option('style_options', array(
|
|
|
+ $handler->override_option('empty_format', '3');
|
|
|
+ $handler->override_option('use_pager', '1');
|
|
|
+ $handler->override_option('style_plugin', 'table');
|
|
|
+ $handler->override_option('style_options', array(
|
|
|
'grouping' => '',
|
|
|
'override' => 1,
|
|
|
'sticky' => 0,
|
|
|
@@ -591,64 +885,68 @@ $handler->override_option('style_options', array(
|
|
|
'blast_value' => 'blast_value',
|
|
|
'kegg_value' => 'kegg_value',
|
|
|
'interpro_value' => 'interpro_value',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'info' => array(
|
|
|
'feature_id' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'feature_name' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'feature_seqlen' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'feature_type' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'go_term' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'organism_common_name' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'unigene' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'blast_value' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'kegg_value' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
+ ),
|
|
|
'interpro_value' => array(
|
|
|
'sortable' => 1,
|
|
|
'separator' => '',
|
|
|
- ),
|
|
|
- ),
|
|
|
+ ),
|
|
|
+ ),
|
|
|
'default' => '-1',
|
|
|
-));
|
|
|
-$handler = $view->new_display('page', 'Page', 'page_1');
|
|
|
-$handler->override_option('path', 'est_search');
|
|
|
-$handler->override_option('menu', array(
|
|
|
+ ));
|
|
|
+ $handler = $view->new_display('page', 'Page', 'page_1');
|
|
|
+ $handler->override_option('path', 'unigene_search');
|
|
|
+ $handler->override_option('menu', array(
|
|
|
'type' => 'normal',
|
|
|
- 'title' => 'EST Unigene Search',
|
|
|
- 'description' => 'Advanced Search for EST and unigenes',
|
|
|
+ 'title' => 'Unigene Search',
|
|
|
+ 'description' => 'Advanced Search for unigenes',
|
|
|
'weight' => '0',
|
|
|
'name' => 'primary-links',
|
|
|
-));
|
|
|
-$handler->override_option('tab_options', array(
|
|
|
+ ));
|
|
|
+ $handler->override_option('tab_options', array(
|
|
|
'type' => 'none',
|
|
|
'title' => '',
|
|
|
'description' => '',
|
|
|
'weight' => 0,
|
|
|
'name' => 'navigation',
|
|
|
-));
|
|
|
+ ));
|
|
|
+ $views[$view->name] = $view;
|
|
|
+
|
|
|
+ return $views;
|
|
|
+}
|
ccheng