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', $this->principalData);
View::render('footer');
}
function archive($paramOne = 'pirna', $paramTwo = null, $paramThree = null)
{
$this->actualPage = FormElements::filterString($paramOne);
$this->dataType = FormElements::filterString($paramTwo);
$this->archiveExtension = FormElements::filterString($paramThree);
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['downloadPage'] = false;
if (!empty($this->dataType) && !empty($this->archiveExtension)) {
$this->principalData['downloadPage'] = true;
}
$this->principalData['activeDownloadPirna'] = '';
$this->principalData['activeDownloadDataset'] = '';
$this->principalData['activeDownloadAlignament'] = '';
$this->principalData['activeDownloadCluster'] = '';
if ($this->actualPage === 'pirna') {
$this->model->generateLog('download pirna', 'download', '400');
$this->principalData['activeDownloadPirna'] = 'class="active"';
$this->temporaryTitle = 'piRNA';
$this->principalData['sizeHsaFile'] = Files::getFileSize('downloads/pirna/hsa-pirna-list.txt');
$this->principalData['downloadType'] = 'pirna/hsa-pirna-list';
$this->cannonicalUrl = URL . 'download/archive/pirna';
} elseif ($this->actualPage === 'dataset') {
$this->model->generateLog('download dataset', 'download', '420');
$this->principalData['activeDownloadDataset'] = 'class="active"';
$this->temporaryTitle = 'Dataset';
$this->principalData['sizeHsaFile'] = Files::getFileSize('downloads/dataset/hsa-dataset-list.txt');
$this->principalData['downloadType'] = 'dataset/hsa-dataset-list';
$this->cannonicalUrl = '';
} elseif ($this->actualPage === 'alignament') {
$this->model->generateLog('download alignament', 'download', '440');
$this->principalData['activeDownloadAlignament'] = 'class="active"';
$this->temporaryTitle = 'Alignament';
$this->principalData['sizeHsaFile'] = Files::getFileSize('downloads/alignament/hsa-alignament-list.txt');
$this->principalData['downloadType'] = 'alignament/hsa-alignament-list';
$this->cannonicalUrl = '';
} elseif ($this->actualPage === 'cluster') {
$this->model->generateLog('download cluster', 'download', '430');
$this->principalData['activeDownloadCluster'] = 'class="active"';
$this->temporaryTitle = 'Cluster';
$this->principalData['sizeHsaFile'] = Files::getFileSize('downloads/cluster/hsa-cluster-list.txt');
$this->principalData['downloadType'] = 'cluster/hsa-cluster-list';
$this->cannonicalUrl = '';
}
$this->principalData['downloadTitle'] = $this->temporaryTitle;
View::setHeaderVars('title', 'Download ' . $this->temporaryTitle);
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', piRNA download, dataset download, alignament download');
View::setHeaderVars('description', 'Download piRNA sequences, alignaments or full datasets');
View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl);
View::setHeaderVars('robots', 'index, follow');
View::render('header');
View::render('download/index', $this->principalData);
View::render('footer');
}
function informations($paramOne = 'pirna')
{
$this->actualPage = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->breadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['activeAboutPirna'] = '';
$this->principalData['activeAboutDatabase'] = '';
$this->principalData['activeAboutDataset'] = '';
$this->principalData['activeAboutReference'] = '';
$this->principalData['activeAboutStatistics'] = '';
if ($this->actualPage === 'database') {
$this->sqlDataArray = array('text_type' => 'database');
$this->temporaryTitle = 'Database';
$this->principalData['activeAboutDatabase'] = 'class="active"';
} elseif ($this->actualPage === 'dataset') {
$this->sqlDataArray = array('text_type' => 'dataset');
$this->temporaryTitle = 'Dataset';
$this->principalData['activeAboutDataset'] = 'class="active"';
} elseif ($this->actualPage === 'reference') {
$this->sqlDataArray = array('text_type' => 'reference');
$this->temporaryTitle = 'Reference';
$this->principalData['activeAboutReference'] = 'class="active"';
} elseif ($this->actualPage === 'statistics') {
$this->temporaryTitle = 'Statistics';
$this->principalData['activeAboutStatistics'] = 'class="active"';
} else {
$this->sqlDataArray = array('text_type' => 'pirna');
$this->temporaryTitle = 'piRNA';
$this->principalData['activeAboutPirna'] = 'class="active"';
}
if ($this->actualPage === 'statistics') {
$this->aboutData = $this->model->getAboutStatistics();
$this->principalData['aboutDataTitle'] = $this->temporaryTitle;
$this->principalData['aboutData'] = $this->aboutData;
} else {
$this->aboutData = $this->model->getAboutInformation($this->sqlDataArray);
$this->principalData['aboutDataTitle'] = $this->temporaryTitle;
$this->principalData['aboutData'] = $this->aboutData['text_content'];
}
View::setHeaderVars('title', 'About ' . $this->temporaryTitle);
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ' ,about pirna, about database, about dataset, about');
View::setHeaderVars('description', 'Informations about piRNAs, origin, functions, database and datasets');
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('about/index', $this->principalData);
View::render('footer');
}
function index()
{
$this->model->quantityCacheSearch();
$this->model->breadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
View::setHeaderVars('title', 'Contact');
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', contact, message');
View::setHeaderVars('description', 'Contact informations page');
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('contact/index', $this->principalData);
View::render('footer');
}
function informations($paramOne = 'pirna')
{
$this->actualPage = FormElements::filterString($paramOne);
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['activeFaqPirna'] = '';
$this->principalData['activeFaqDatabase'] = '';
$this->principalData['activeFaqDataset'] = '';
$this->principalData['activeFaqLogs'] = '';
if ($this->actualPage === 'pirna') {
$this->principalData['activeFaqPirna'] = 'class="active"';
$this->sqlDataArray = array('faq_type' => '1');
$this->temporaryTitle = 'piRNA';
$this->cannonicalUrl = URL . 'faq/informations/pirna';
} elseif ($this->actualPage === 'database') {
$this->principalData['activeFaqDatabase'] = 'class="active"';
$this->sqlDataArray = array('faq_type' => '2');
$this->temporaryTitle = 'Database';
$this->cannonicalUrl = '';
} elseif ($this->actualPage === 'dataset') {
$this->principalData['activeFaqDataset'] = 'class="active"';
$this->sqlDataArray = array('faq_type' => '3');
$this->temporaryTitle = 'Dataset';
$this->cannonicalUrl = '';
} elseif ($this->actualPage === 'logs') {
$this->principalData['activeFaqLogs'] = 'class="active"';
$this->sqlDataArray = array('faq_type' => '4');
$this->temporaryTitle = 'Logs';
$this->cannonicalUrl = '';
}
$this->faqData = $this->model->getFaqData($this->sqlDataArray);
$this->principalData['faqTitle'] = $this->temporaryTitle;
$this->principalData['faqData'] = $this->faqData;
$this->principalData['faqType'] = $this->actualPage;
View::setHeaderVars('title', 'FAQ/Help ' . $this->temporaryTitle);
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', faq pirna, help pirna, faq, help');
View::setHeaderVars('description', 'Questions and step-by-step about functions of database');
View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl);
View::setHeaderVars('robots', 'index, follow');
View::render('header');
View::render('faq/index', $this->principalData);
View::render('footer');
}
function index()
{
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->principalData['formToken'] = FormElements::formToken();
$this->aboutPirnaData = $this->model->getAboutInformation();
$this->principalData['systemArticle'] = $this->aboutPirnaData['articleData'][0];
$this->cannonicalUrl = URL;
View::setHeaderVars('title', 'Home');
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', home');
View::setHeaderVars('description', 'piRNA database home page');
View::setHeaderVars('cannonicalUrl', $this->cannonicalUrl);
View::setHeaderVars('robots', 'index, follow');
View::render('header');
View::render('index/index', $this->principalData);
View::render('footer');
}
function informations($paramOne = null)
{
$this->model->quantityCacheSearch();
$this->model->BreadCumbs();
$this->model->footerFaq();
$this->model->footerSystemUpdate();
$this->errorInformation = array();
if ($paramOne === '400') {
$this->model->generateLog('error 400: ' . $_SERVER['REQUEST_URI'], 'error', '500');
$this->errorInformation['errorTitle'] = 'Erro 400';
$this->errorInformation['errorMessage'] = "Request Error.";
} elseif ($paramOne === '401') {
$this->model->generateLog('error 401: ' . $_SERVER['REQUEST_URI'], 'error', '510');
$this->errorInformation['errorTitle'] = 'Erro 401';
$this->errorInformation['errorMessage'] = "Authorization Required.";
} elseif ($paramOne === '403') {
$this->model->generateLog('error 403: ' . $_SERVER['REQUEST_URI'], 'error', '520');
$this->errorInformation['errorTitle'] = 'Erro 403';
$this->errorInformation['errorMessage'] = "Access Denied.";
} elseif ($paramOne === '500') {
$this->model->generateLog('error 500: ' . $_SERVER['REQUEST_URI'], 'error', '540');
$this->errorInformation['errorTitle'] = 'Error 500';
$this->errorInformation['errorMessage'] = "Server Internal Error.";
} else {
$this->model->generateLog('error 404: ' . $_SERVER['REQUEST_URI'], 'error', '530');
$this->errorInformation['errorTitle'] = 'Error 404';
$this->errorInformation['errorMessage'] = "Page Not Found.";
}
$this->principalData = $this->errorInformation;
View::setHeaderVars('title', $this->principalData['errorTitle']);
View::setHeaderVars('specificKeywords', DEFAULT_KEYWORDS . ', error');
View::setHeaderVars('description', $this->principalData['errorMessage']);
View::setHeaderVars('cannonicalUrl', '');
View::setHeaderVars('robots', 'noindex, nofollow');
View::render('header');
View::render('error/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', $this->principalData);
View::render('footer-clean');
}
function createInfo($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');
}
