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@@ -1,952 +0,0 @@
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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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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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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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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'counter_start' => '1',
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- 'exclude' => 0,
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- 'id' => 'counter',
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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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- 'feature_id' => array(
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- 'label' => 'feature ID',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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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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- 'empty' => '',
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- 'hide_empty' => 0,
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- 'empty_zero' => 0,
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- 'set_precision' => FALSE,
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- 'precision' => 0,
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- 'decimal' => '.',
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- 'separator' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'exclude' => 1,
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- 'id' => 'feature_id',
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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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- 'feature_name' => array(
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- 'label' => 'Sequence',
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- 'alter' => array(
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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 1,
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- 'path' => 'ID[feature_id]',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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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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- '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' => 'unigene_for_search',
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- 'field' => 'feature_name',
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- 'relationship' => 'none',
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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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- 'alter_text' => 0,
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- 'text' => '',
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- 'make_link' => 0,
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- 'path' => '',
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- 'link_class' => '',
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- 'alt' => '',
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- 'prefix' => '',
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- 'suffix' => '',
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- 'target' => '',
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- 'help' => '',
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- 'trim' => 0,
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- 'max_length' => '',
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- 'word_boundary' => 1,
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- 'ellipsis' => 1,
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- 'html' => 0,
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|
|
- 'strip_tags' => 0,
|
|
|
- ),
|
|
|
- 'empty' => '',
|
|
|
- 'hide_empty' => 0,
|
|
|
- 'empty_zero' => 0,
|
|
|
- 'exclude' => 0,
|
|
|
- 'id' => 'organism_common_name',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'organism_common_name',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'feature_seqlen' => array(
|
|
|
- 'label' => 'Length',
|
|
|
- 'alter' => array(
|
|
|
- 'alter_text' => 1,
|
|
|
- 'text' => '[feature_seqlen] bp',
|
|
|
- 'make_link' => 0,
|
|
|
- 'path' => '',
|
|
|
- 'link_class' => '',
|
|
|
- 'alt' => '',
|
|
|
- 'prefix' => '',
|
|
|
- 'suffix' => '',
|
|
|
- 'target' => '',
|
|
|
- 'help' => '',
|
|
|
- 'trim' => 0,
|
|
|
- 'max_length' => '',
|
|
|
- 'word_boundary' => 1,
|
|
|
- 'ellipsis' => 1,
|
|
|
- 'html' => 0,
|
|
|
- 'strip_tags' => 0,
|
|
|
- ),
|
|
|
- 'empty' => '',
|
|
|
- 'hide_empty' => 0,
|
|
|
- 'empty_zero' => 0,
|
|
|
- 'set_precision' => FALSE,
|
|
|
- 'precision' => 0,
|
|
|
- 'decimal' => '.',
|
|
|
- 'separator' => ',',
|
|
|
- 'prefix' => '',
|
|
|
- 'suffix' => '',
|
|
|
- 'exclude' => 0,
|
|
|
- 'id' => 'feature_seqlen',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'feature_seqlen',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'feature_type' => array(
|
|
|
- 'label' => 'Type',
|
|
|
- 'alter' => array(
|
|
|
- 'alter_text' => 0,
|
|
|
- 'text' => '',
|
|
|
- 'make_link' => 0,
|
|
|
- 'path' => '',
|
|
|
- 'link_class' => '',
|
|
|
- 'alt' => '',
|
|
|
- 'prefix' => '',
|
|
|
- 'suffix' => '',
|
|
|
- 'target' => '',
|
|
|
- 'help' => '',
|
|
|
- 'trim' => 0,
|
|
|
- 'max_length' => '',
|
|
|
- 'word_boundary' => 1,
|
|
|
- 'ellipsis' => 1,
|
|
|
- 'html' => 0,
|
|
|
- 'strip_tags' => 0,
|
|
|
- ),
|
|
|
- 'empty' => '',
|
|
|
- 'hide_empty' => 0,
|
|
|
- 'empty_zero' => 0,
|
|
|
- 'exclude' => 0,
|
|
|
- 'id' => 'feature_type',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'feature_type',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'go_term' => array(
|
|
|
- 'label' => 'GO Term',
|
|
|
- 'alter' => array(
|
|
|
- 'alter_text' => 0,
|
|
|
- 'text' => '',
|
|
|
- 'make_link' => 0,
|
|
|
- 'path' => '',
|
|
|
- 'link_class' => '',
|
|
|
- 'alt' => '',
|
|
|
- 'prefix' => '',
|
|
|
- 'suffix' => '',
|
|
|
- 'target' => '',
|
|
|
- 'help' => '',
|
|
|
- 'trim' => 0,
|
|
|
- 'max_length' => '',
|
|
|
- 'word_boundary' => 1,
|
|
|
- 'ellipsis' => 1,
|
|
|
- 'html' => 0,
|
|
|
- 'strip_tags' => 0,
|
|
|
- ),
|
|
|
- 'empty' => '',
|
|
|
- 'hide_empty' => 0,
|
|
|
- 'empty_zero' => 0,
|
|
|
- 'exclude' => 0,
|
|
|
- 'id' => 'go_term',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'go_term',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'blast_value' => array(
|
|
|
- 'label' => 'Blast',
|
|
|
- 'alter' => array(
|
|
|
- 'alter_text' => 0,
|
|
|
- 'text' => '',
|
|
|
- 'make_link' => 0,
|
|
|
- 'path' => '',
|
|
|
- 'link_class' => '',
|
|
|
- 'alt' => '',
|
|
|
- 'prefix' => '',
|
|
|
- 'suffix' => '',
|
|
|
- 'target' => '',
|
|
|
- 'help' => '',
|
|
|
- 'trim' => 1,
|
|
|
- 'max_length' => '200',
|
|
|
- 'word_boundary' => 0,
|
|
|
- 'ellipsis' => 1,
|
|
|
- 'html' => 0,
|
|
|
- 'strip_tags' => 0,
|
|
|
- ),
|
|
|
- 'empty' => '',
|
|
|
- 'hide_empty' => 0,
|
|
|
- 'empty_zero' => 0,
|
|
|
- 'exclude' => 0,
|
|
|
- 'id' => 'blast_value',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'blast_value',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'kegg_value' => array(
|
|
|
- 'label' => 'KEGG',
|
|
|
- 'alter' => array(
|
|
|
- 'alter_text' => 0,
|
|
|
- 'text' => '',
|
|
|
- 'make_link' => 0,
|
|
|
- 'path' => '',
|
|
|
- 'link_class' => '',
|
|
|
- 'alt' => '',
|
|
|
- 'prefix' => '',
|
|
|
- 'suffix' => '',
|
|
|
- 'target' => '',
|
|
|
- 'help' => '',
|
|
|
- 'trim' => 1,
|
|
|
- 'max_length' => '200',
|
|
|
- 'word_boundary' => 0,
|
|
|
- 'ellipsis' => 1,
|
|
|
- 'html' => 0,
|
|
|
- 'strip_tags' => 0,
|
|
|
- ),
|
|
|
- 'empty' => '',
|
|
|
- 'hide_empty' => 0,
|
|
|
- 'empty_zero' => 0,
|
|
|
- 'exclude' => 0,
|
|
|
- 'id' => 'kegg_value',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'kegg_value',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'interpro_value' => array(
|
|
|
- 'label' => 'Interpro',
|
|
|
- 'alter' => array(
|
|
|
- 'alter_text' => 0,
|
|
|
- 'text' => '',
|
|
|
- 'make_link' => 0,
|
|
|
- 'path' => '',
|
|
|
- 'link_class' => '',
|
|
|
- 'alt' => '',
|
|
|
- 'prefix' => '',
|
|
|
- 'suffix' => '',
|
|
|
- 'target' => '',
|
|
|
- 'help' => '',
|
|
|
- 'trim' => 1,
|
|
|
- 'max_length' => '200',
|
|
|
- 'word_boundary' => 0,
|
|
|
- 'ellipsis' => 1,
|
|
|
- 'html' => 0,
|
|
|
- 'strip_tags' => 0,
|
|
|
- ),
|
|
|
- 'empty' => '',
|
|
|
- 'hide_empty' => 0,
|
|
|
- 'empty_zero' => 0,
|
|
|
- 'exclude' => 0,
|
|
|
- 'id' => 'interpro_value',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'interpro_value',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- ));
|
|
|
- $handler->override_option('arguments', array(
|
|
|
- 'null' => array(
|
|
|
- 'default_action' => 'default',
|
|
|
- 'style_plugin' => 'default_summary',
|
|
|
- 'style_options' => array(),
|
|
|
- 'wildcard' => 'all',
|
|
|
- 'wildcard_substitution' => 'All',
|
|
|
- 'title' => '',
|
|
|
- 'breadcrumb' => '',
|
|
|
- 'default_argument_type' => 'fixed',
|
|
|
- 'default_argument' => '',
|
|
|
- 'validate_type' => 'php',
|
|
|
- 'validate_fail' => 'empty',
|
|
|
- 'must_not_be' => 0,
|
|
|
- 'id' => 'null',
|
|
|
- 'table' => 'views',
|
|
|
- 'field' => 'null',
|
|
|
- 'validate_user_argument_type' => 'uid',
|
|
|
- 'validate_user_roles' => array(
|
|
|
- '2' => 0,
|
|
|
- '3' => 0,
|
|
|
- '5' => 0,
|
|
|
- '4' => 0,
|
|
|
- ),
|
|
|
- 'relationship' => 'none',
|
|
|
- 'default_options_div_prefix' => '',
|
|
|
- 'default_argument_fixed' => '',
|
|
|
- 'default_argument_user' => 0,
|
|
|
- 'default_argument_php' => '',
|
|
|
- 'validate_argument_node_type' => array(
|
|
|
- 'iframe' => 0,
|
|
|
- 'news' => 0,
|
|
|
- 'chado_analysis' => 0,
|
|
|
- 'chado_analysis_blast' => 0,
|
|
|
- 'chado_analysis_interpro' => 0,
|
|
|
- 'chado_analysis_kegg' => 0,
|
|
|
- 'chado_analysis_unigene' => 0,
|
|
|
- 'chado_feature' => 0,
|
|
|
- 'chado_library' => 0,
|
|
|
- 'chado_organism' => 0,
|
|
|
- 'calendar_event' => 0,
|
|
|
- 'page' => 0,
|
|
|
- 'story' => 0,
|
|
|
- ),
|
|
|
- 'validate_argument_node_access' => 0,
|
|
|
- 'validate_argument_nid_type' => 'nid',
|
|
|
- 'validate_argument_vocabulary' => array(
|
|
|
- '17' => 0,
|
|
|
- '13' => 0,
|
|
|
- '14' => 0,
|
|
|
- '15' => 0,
|
|
|
- '16' => 0,
|
|
|
- '9' => 0,
|
|
|
- '10' => 0,
|
|
|
- '11' => 0,
|
|
|
- '12' => 0,
|
|
|
- '5' => 0,
|
|
|
- '6' => 0,
|
|
|
- '7' => 0,
|
|
|
- '8' => 0,
|
|
|
- ),
|
|
|
- 'validate_argument_type' => 'tid',
|
|
|
- 'validate_argument_transform' => 0,
|
|
|
- 'validate_user_restrict_roles' => 0,
|
|
|
- 'validate_argument_php' => 'if (count($view->exposed_input)) {
|
|
|
-return TRUE;
|
|
|
-}',
|
|
|
- ),
|
|
|
- ));
|
|
|
- $handler->override_option('filters', array(
|
|
|
- 'feature_name' => array(
|
|
|
- 'operator' => 'contains',
|
|
|
- 'value' => '',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 1,
|
|
|
- 'operator' => 'feature_name_op',
|
|
|
- 'identifier' => 'feature_name',
|
|
|
- 'label' => 'sequence name',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'case' => 0,
|
|
|
- 'id' => 'feature_name',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'feature_name',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'feature_seqlen' => array(
|
|
|
- 'operator' => '>=',
|
|
|
- 'value' => array(
|
|
|
- 'value' => '',
|
|
|
- 'min' => '',
|
|
|
- 'max' => '',
|
|
|
- ),
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 1,
|
|
|
- 'operator' => 'feature_seqlen_op',
|
|
|
- 'identifier' => 'feature_seqlen',
|
|
|
- 'label' => 'sequence length (bp)',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'id' => 'feature_seqlen',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'feature_seqlen',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'feature_type' => array(
|
|
|
- 'operator' => '=',
|
|
|
- 'value' => '260',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 0,
|
|
|
- 'operator' => 'feature_type_op',
|
|
|
- 'identifier' => 'feature_type',
|
|
|
- 'label' => 'type of sequence',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'case' => 0,
|
|
|
- 'id' => 'feature_type',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'feature_type',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'go_term' => array(
|
|
|
- 'operator' => 'contains',
|
|
|
- 'value' => '',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 1,
|
|
|
- 'operator' => 'go_term_op',
|
|
|
- 'identifier' => 'go_term',
|
|
|
- 'label' => 'GO term',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'case' => 0,
|
|
|
- 'id' => 'go_term',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'go_term',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'organism_common_name' => array(
|
|
|
- 'operator' => '=',
|
|
|
- 'value' => 'chickpea',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 0,
|
|
|
- 'operator' => 'organism_common_name_op',
|
|
|
- 'identifier' => 'organism_common_name',
|
|
|
- 'label' => 'organism',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'case' => 0,
|
|
|
- 'id' => 'organism_common_name',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'organism_common_name',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'unigene' => array(
|
|
|
- 'operator' => '=',
|
|
|
- 'value' => 'Cicer arietinum unigene v1',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 0,
|
|
|
- 'operator' => 'unigene_op',
|
|
|
- 'identifier' => 'unigene',
|
|
|
- 'label' => 'belongs to unigene',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'case' => 0,
|
|
|
- 'id' => 'unigene',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'unigene',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'interpro_value' => array(
|
|
|
- 'operator' => 'contains',
|
|
|
- 'value' => '',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 1,
|
|
|
- 'operator' => 'interpro_value_op',
|
|
|
- 'identifier' => 'interpro_value',
|
|
|
- 'label' => 'interpro description',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'case' => 0,
|
|
|
- 'id' => 'interpro_value',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'interpro_value',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'blast_value' => array(
|
|
|
- 'operator' => 'contains',
|
|
|
- 'value' => '',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 1,
|
|
|
- 'operator' => 'blast_value_op',
|
|
|
- 'identifier' => 'blast_value',
|
|
|
- 'label' => 'blast description',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'case' => 0,
|
|
|
- 'id' => 'blast_value',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'blast_value',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- 'kegg_value' => array(
|
|
|
- 'operator' => 'contains',
|
|
|
- 'value' => '',
|
|
|
- 'group' => '0',
|
|
|
- 'exposed' => TRUE,
|
|
|
- 'expose' => array(
|
|
|
- 'use_operator' => 1,
|
|
|
- 'operator' => 'kegg_value_op',
|
|
|
- 'identifier' => 'kegg_value',
|
|
|
- 'label' => 'kegg description',
|
|
|
- 'optional' => 1,
|
|
|
- 'remember' => 0,
|
|
|
- ),
|
|
|
- 'case' => 0,
|
|
|
- 'id' => 'kegg_value',
|
|
|
- 'table' => 'unigene_for_search',
|
|
|
- 'field' => 'kegg_value',
|
|
|
- 'relationship' => 'none',
|
|
|
- ),
|
|
|
- ));
|
|
|
- $handler->override_option('access', array(
|
|
|
- 'type' => 'none',
|
|
|
- ));
|
|
|
- $handler->override_option('cache', array(
|
|
|
- 'type' => 'none',
|
|
|
- ));
|
|
|
- $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(
|
|
|
- 'grouping' => '',
|
|
|
- 'override' => 1,
|
|
|
- 'sticky' => 0,
|
|
|
- 'order' => 'asc',
|
|
|
- 'columns' => array(
|
|
|
- 'feature_id' => 'feature_id',
|
|
|
- 'feature_name' => 'feature_name',
|
|
|
- 'feature_seqlen' => 'feature_seqlen',
|
|
|
- 'feature_type' => 'feature_type',
|
|
|
- 'go_term' => 'go_term',
|
|
|
- 'organism_common_name' => 'organism_common_name',
|
|
|
- 'unigene' => 'unigene',
|
|
|
- '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', 'unigene_search');
|
|
|
- $handler->override_option('menu', array(
|
|
|
- 'type' => 'normal',
|
|
|
- 'title' => 'Unigene Search',
|
|
|
- 'description' => 'Advanced Search for unigenes',
|
|
|
- 'weight' => '0',
|
|
|
- 'name' => 'primary-links',
|
|
|
- ));
|
|
|
- $handler->override_option('tab_options', array(
|
|
|
- 'type' => 'none',
|
|
|
- 'title' => '',
|
|
|
- 'description' => '',
|
|
|
- 'weight' => 0,
|
|
|
- 'name' => 'navigation',
|
|
|
- ));
|
|
|
- $views[$view->name] = $view;
|
|
|
-
|
|
|
- return $views;
|
|
|
-}
|
spficklin