<?php
/**
 * @file
 * .module file of TripalD3.
 */

use Drupal\Core\Url;

/**
 * Implements hook_theme().
 * Used by BLAST UI submission forms.
 *
 * @see templates in /templates
 */
function blast_ui_theme($existing, $type, $theme, $path) {  
  $context_links = [
    // blast/nucleotide.
    'link_Nucleotide' => \Drupal::l(t('Nucleotide'), Url::fromRoute('blast_ui.nucleotide')),
    // blast/protien.
    'link_Protien'    => \Drupal::l(t('Protein'), Url::fromRoute('blast_ui.protien')),
    
    // NUCLEOTIDE PROGRAM.
    // blast/nucleotide/nucleotide
    'link_blastn'     => \Drupal::l(t('blastn'), Url::fromRoute('blast_ui.nucleotide_nucleotide')),
    // blast/nucleotide/protien
    'link_blastx'     => \Drupal::l(t('blastx'), Url::fromRoute('blast_ui.nucleotide_protien')),
    
    // PROTIEN PROGRAM.
    // blast/protien/nucleotide.
    'link_tblastn'    => \Drupal::l(t('tblastn'), Url::fromRoute('blast_ui.protien_nucleotide')),
    // blast/protien/protien.
    'link_blastp'     => \Drupal::l(t('blastp'), Url::fromRoute('blast_ui.protien_protien')),
    
    // MISC/ADMIN. 
    'link_config'     => \Drupal::l(t('configuration'), Url::fromUri('admin/tripal/extension/tripal_blast/blast_ui')),
    'link_jobs'       => \Drupal::l(t('tripal jobs'), Url::fromUri('blast_ui.protien_nucleotide')), 
    'link_nodeadd'    => \Drupal::l(t('create BLAST database'), Url::fromUri('node/add/blastdb')),
    'link_dbadd'      => \Drupal::l(t('configuration'), Url::fromUri('admin/tripal/chado/tripal_db/add')),
    'link_dbfields'   => \Drupal::l(t('drupal field API'), Url::fromUri('admin/structure/types/manage/blastdb/fields'))
  ];

  $variables = [
    // BLAST UI Menupage.
    'theme-blast-ui-menupage' => [
      'variables' => ['context_links' => $context_links],
      'template'  => 'template-blast-ui-menupage',
    ],
    
    // BLAST Help page.
    'theme-blast-ui-help' => [
      'variables' => ['context_links' => $context_links],
      'template'  => 'template-blast-ui-help',
    ],
  ];

  return $variables;
}