function information($paramOne = null)
{
$this->updateItem = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->breadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
if ($this->updateItem != null) {
$this->sqlDataArray = array('info_update_id' => $this->updateItem);
$this->updateData = $this->model->getUpdate($this->sqlDataArray);
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['updateData'] = $this->updateData[0];
$this->principalData['updateItem'] = true;
}
} else {
$this->updateData = $this->model->getUpdate();
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['updateData'] = $this->updateData;
$this->principalData['updateItem'] = false;
}
}
View::setHeaderVars('title', 'Update Information');
View::setHeaderVars('specificKeywords', '');
View::setHeaderVars('description', '');
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('update/index', $this->principalData);
View::render('footer');
}
function searchList($paramOne = null)
{
$this->actualPage = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->breadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['activeCachePirna'] = '';
$this->principalData['activeCacheAlignament'] = '';
$this->principalData['activeCacheCluster'] = '';
if ($this->actualPage === 'pirna') {
$this->sqlDataArray = array('cache_type' => 'pirna');
$this->principalData['activeCachePirna'] = 'class="active"';
$this->temporaryTitle = 'piRNA';
} elseif ($this->actualPage === 'alignament') {
$this->sqlDataArray = array('cache_type' => 'alignament');
$this->principalData['activeCacheAlignament'] = 'class="active"';
$this->temporaryTitle = 'Alignament';
} elseif ($this->actualPage === 'cluster') {
$this->sqlDataArray = array('cache_type' => 'cluster');
$this->principalData['activeCacheCluster'] = 'class="active"';
$this->temporaryTitle = 'Cluster';
}
$this->cacheData = $this->model->searchCache($this->sqlDataArray);
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['cacheData'] = $this->cacheData;
}
View::setHeaderVars('title', $this->temporaryTitle . ' Results Cache');
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', cache results, search pirna cache');
View::setHeaderVars('description', 'Stored piRNA search');
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('cache/index', $this->principalData);
View::render('footer');
}
function alignament($paramOne = null)
{
$this->actualPage = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->sqlDataArray = array('alignament_id' => $this->actualPage);
$this->resultInformation = $this->model->getInformation($this->sqlDataArray, 'alignament');
$this->resultPirna = $this->model->getPirna($this->sqlDataArray);
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['alignamentInfo'] = $this->resultInformation;
$this->principalData['quantityPirna'] = $this->resultPirna['quantityPirna'];
if ($this->principalData['quantityPirna'] > 0) {
$this->principalData['listPirnaTwo'] = $this->resultPirna['listPirnaTwo'];
$this->principalData['tabActive'] = $this->resultPirna['tabActive'];
$this->principalData['contentTabActive'] = $this->resultPirna['contentTabActive'];
}
}
View::setHeaderVars('title', 'Alignament Information');
View::setHeaderVars('specificKeywords', '');
View::setHeaderVars('description', '');
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'index, follow');
View::render('header');
View::render('information/alignament', $this->principalData);
View::render('footer-clean');
}
function cluster($paramOne = 1)
{
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->actualPage = FormElements::filterString($paramOne);
$this->principalData['resultPage'] = false;
if (isset($_POST['search']) || isset($_GET['cluster_chromosome']) && isset($_GET['cluster_start']) && isset($_GET['cluster_end'])) {
$this->principalData['resultPage'] = true;
$this->initialResult = ($this->actualPage - 1) * $this->resultsPerPage;
$this->sqlDataArray = array('initialItem' => $this->initialResult, 'maximumQuantity' => $this->resultsPerPage);
$this->searchResults = $this->model->searchCluster($this->sqlDataArray);
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['resultCount'] = $this->searchResults[0];
$this->principalData['totalPages'] = $this->searchResults[1];
$this->principalData['resultSearch'] = $this->searchResults[2];
$this->principalData['resultQuery'] = $this->searchResults[3];
$this->temporaryPagination = $this->model->pagination($this->actualPage, $this->searchResults[1]);
$this->principalData['pagination'] = $this->temporaryPagination[0];
$this->principalData['activePagination'] = $this->temporaryPagination[1];
}
} else {
$this->principalData['formToken'] = FormElements::formToken();
}
$this->principalData['qttResultPage'] = $this->resultsPerPage;
$this->cannonicalUrl = URL . 'search/cluster';
$this->principalData['activeSearchPirna'] = '';
$this->principalData['activeSearchAlignament'] = '';
$this->principalData['activeSearchCluster'] = 'class="active"';
View::setHeaderVars('title', 'Search Cluster');
View::setHeaderVars('specificKeywords', '');
View::setHeaderVars('description', '');
View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl);
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('search/cluster', $this->principalData);
View::render('footer-clean');
}
function searchCluster($sqlDataArray = array())
{
if (isset($_POST['search'])) {
$this->dataArray = array('cluster_chromosome' => FormElements::getPostInteger('inputSearchChromosome', true), 'cluster_start' => FormElements::getPostInteger('inputSearchStart', true), 'cluster_end' => FormElements::getPostInteger('inputSearchEnd', true));
$this->formToken = FormElements::getPostString('token', true);
parent::checkFormRequired($this->dataArray);
parent::checkFormToken($this->formToken, 'search/cluster');
} elseif (isset($_GET['cluster_chromosome']) && isset($_GET['cluster_start']) && isset($_GET['cluster_end'])) {
$this->dataArray = array('cluster_chromosome' => FormElements::filterInteger($_GET['cluster_chromosome'], true), 'cluster_start' => FormElements::filterInteger($_GET['cluster_start'], true), 'cluster_end' => FormElements::filterInteger($_GET['cluster_end'], true));
}
if (!in_array('errorRequiredField', $this->dataArray) && (isset($_GET['cluster_chromosome']) || $this->formToken === Session::getSession('formToken')) && !FlashMessages::hasFlashMessage()) {
$cookieData = date('Y-m-d') . '|cluster|' . 'cluster_chromosome|' . $this->dataArray['cluster_chromosome'] . '|cluster_start|' . $this->dataArray['cluster_start'] . '|cluster_end|' . $this->dataArray['cluster_end'];
if (isset($_COOKIE['pirna_db_cache_search'])) {
$newData = $_COOKIE['pirna_db_cache_search'] . '@' . $cookieData;
} else {
$newData = $cookieData;
}
setcookie('pirna_db_cache_search', $newData, time() + 86400 * 30 * 30, '/');
Session::unsetSession('formToken');
$this->sqlAllResults = 'SELECT cluster_code,
cluster_chromosome,
cluster_start,
cluster_end
FROM cluster
WHERE cluster_chromosome = ' . $this->dataArray['cluster_chromosome'] . ' AND
cluster_start >= ' . $this->dataArray['cluster_start'] . ' AND
cluster_end <= ' . $this->dataArray['cluster_end'];
$this->allResults = $this->db->select($this->sqlAllResults);
$this->results[0] = count($this->allResults);
$this->results[1] = ceil($this->results[0] / $sqlDataArray['maximumQuantity']);
$this->sql = 'SELECT cluster_code,
cluster_chromosome,
cluster_start,
cluster_end
FROM cluster
WHERE cluster_chromosome = ' . $this->dataArray['cluster_chromosome'] . ' AND
cluster_start >= ' . $this->dataArray['cluster_start'] . ' AND
cluster_end <= ' . $this->dataArray['cluster_end'] . '
LIMIT :initialItem, :maximumQuantity';
$this->results[2] = $this->db->select($this->sql, $sqlDataArray);
$this->results[3] = '?cluster_chromosome=' . $this->dataArray['cluster_chromosome'] . '&' . 'cluster_start=' . $this->dataArray['cluster_start'] . '&' . 'cluster_end=' . $this->dataArray['cluster_end'];
if ($this->results[0] > 0) {
return $this->results;
} else {
FlashMessages::setFlashMessage('noresult', '<b>Not Found!</b><br />None cluster was found using your query..');
}
}
}
function createInfo($paramOne = null)
{
$this->model->checkLogged();
if ($paramOne === 'faq') {
if (isset($_POST['submit'])) {
$this->model->sendCreateInfo('faq');
}
$this->principalData['formToken'] = FormElements::formToken();
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
}
View::setHeaderVars('title', 'Admin');
View::render('sidebar-admin');
View::render('administration/createinfofaq', $this->principalData);
} elseif ($paramOne === 'article') {
if (isset($_POST['submit'])) {
$this->model->sendCreateInfo('article');
}
$this->principalData['formToken'] = FormElements::formToken();
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
}
View::setHeaderVars('title', 'Admin');
View::render('sidebar-admin');
View::render('administration/createinfoarticle', $this->principalData);
} elseif ($paramOne === 'informations') {
if (isset($_POST['submit'])) {
$this->model->sendCreateInfo('informations');
}
$this->principalData['formToken'] = FormElements::formToken();
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
}
View::setHeaderVars('title', 'Admin');
View::render('sidebar-admin');
View::render('administration/createinfoinformations', $this->principalData);
} elseif ($paramOne === 'update') {
if (isset($_POST['submit'])) {
$this->model->sendCreateInfo('update');
}
$this->principalData['formToken'] = FormElements::formToken();
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
}
View::setHeaderVars('title', 'Admin');
View::render('sidebar-admin');
View::render('administration/createinfoupdate', $this->principalData);
}
}
function cluster($paramOne = 1)
{
$this->model->quantityCacheSearch();
$this->model->breadCumbs();
$this->actualPage = FormElements::filterInteger($paramOne);
$this->initialResult = ($this->actualPage - 1) * $this->resultsPerPage;
$this->sqlDataArray = array('initialItem' => $this->initialResult, 'maximumQuantity' => 5);
$this->browseData = $this->model->getBrowseCluster($this->sqlDataArray);
if (FlashMessages::hasFlashMessage()) {
$this->principalData['FlashMessage'] = FlashMessages::displayFlashMessage();
} else {
$this->principalData['countResults'] = $this->browseData['quantityAllCluster'];
$this->principalData['browseData'] = $this->browseData['clusterList'];
$this->principalData['totalPages'] = $this->browseData['totalPages'];
$this->temporaryPagination = $this->model->pagination($this->actualPage, $this->browseData['totalPages']);
$this->principalData['pagination'] = $this->temporaryPagination[0];
$this->principalData['activePagination'] = $this->temporaryPagination[1];
}
if ($this->actualPage === 1) {
$this->cannonicalUrl = URL . 'browse/cluster';
} else {
$this->cannonicalUrl = '';
}
$this->principalData['qttResultPage'] = $this->resultsPerPage;
$this->principalData['activeBrowsePirna'] = '';
$this->principalData['activeBrowseDataset'] = '';
$this->principalData['activeBrowseCluster'] = 'class="active"';
View::setHeaderVars('title', 'Browse piRNA Clusters');
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', piRNA cluster List, piRNA cluster, browse piRNA cluster');
View::setHeaderVars('description', 'Browse all the piRNA clusters in the database');
View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl);
View::setHeaderVars('robots', 'index, follow');
View::render('header');
View::render('browse/cluster', $this->principalData);
View::render('footer-clean');
}
function sendCreateInfo($type = null)
{
if ($type === 'faq') {
$this->table = 'faq';
$this->dataArray = array('faq_title' => FormElements::getPostString('createFaqTitle', true), 'faq_content' => FormElements::getPostString('createFaqContent', true), 'faq_type' => FormElements::getPostString('createFaqType', true));
} elseif ($type === 'article') {
$this->table = 'system_article';
$this->dataArray = array('article_title' => FormElements::getPostString('createArticleTitle', true), 'article_author' => FormElements::getPostString('createArticleAuthor', true), 'article_journal' => FormElements::getPostString('createArticleJournal', true), 'article_date' => FormElements::getPostString('createArticleDate', true), 'article_reference' => FormElements::getPostString('createArticleReference', true));
} elseif ($type === 'informations') {
$this->table = 'general_text';
$this->dataArray = array('text_content' => FormElements::getPostString('createInformationsContent', true), 'text_type' => FormElements::getPostString('createInformationsType', true));
} elseif ($type === 'update') {
$this->table = 'info_update';
$this->dataArray = array('info_update_title' => FormElements::getPostString('createUpdateTitle', true), 'info_update_content' => FormElements::getPostString('createUpdateContent', true));
} else {
FlashMessages::setFlashMessage('error', '<b>Error!</b><br />This Section Does not Exists.');
}
$this->formToken = FormElements::getPostString('token', true);
parent::checkFormRequired($this->dataArray);
parent::checkFormToken($this->formToken, 'administration/createinfo/' . $type);
if (!FlashMessages::hasFlashMessage()) {
Session::unsetSession('formToken');
$this->resultsDelete = $this->db->insert($this->table, $this->dataArray);
if (count($this->resultsDelete) === 1) {
FlashMessages::setFlashMessage('success', '<b>Success!</b><br />Succesfully Created.');
} else {
FlashMessages::setFlashMessage('error', '<b>Error!</b><br />Unsuccesfully Created.');
}
}
}
