clean up theme files for tripal_search_unigene

theme_tripal/views-exposed-form--unigene_search.tpl.php

@@ -1,195 +0,0 @@
-<?php
-// $Id: views-exposed-form.tpl.php,v 1.4.4.1 2009/11/18 20:37:58 merlinofchaos Exp $
-/**
- * @file views-exposed-form.tpl.php
- *
- * This template handles the layout of the views exposed filter form.
- *
- * Variables available:
- * - $widgets: An array of exposed form widgets. Each widget contains:
- * - $widget->label: The visible label to print. May be optional.
- * - $widget->operator: The operator for the widget. May be optional.
- * - $widget->widget: The widget itself.
- * - $button: The submit button for the form.
- *
- * @ingroup views_templates
- */
-?>
-<?php if (!empty($q)): ?>
-  <?php
-    // This ensures that, if clean URLs are off, the 'q' is added first so that
-    // it shows up first in the URL.
-    print $q;
-
-  ?>
-<?php endif;     //dsm($widgets);?>
-<div class="tripal_search_unigene-views-exposed-form views-exposed-form">
-  <div class="views-exposed-widgets clear-block">
-    
-    <?php 
-    	$feature_type_id =  $widgets['filter-feature_type']; 
-    	$orgnism_common_name =  $widgets['filter-organism_common_name'];
-    	$analysis_name =  $widgets['filter-unigene'];
-    	$feature_name =  $widgets['filter-feature_name'];
-    	$feature_seqlen =  $widgets['filter-feature_seqlen'];
-    	$cvterm_name =  $widgets['filter-go_term'];
-    	$blast_value =  $widgets['filter-blast_value'];
-    	$interpro_value =  $widgets['filter-interpro_value'];
-    	$kegg_value =  $widgets['filter-kegg_value'];
-    ?>
-    
-    <div id="tripal-search-unigene-exposed-widgets">
-    <div> Search ESTs or unigene contigs by name, assembly, sequence type, length, or their putative function. <br><br></div>
-			<fieldset class="tripal-search-unigene-exposed-widgets-fields">
-				<legend>Search by Name</legend>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $orgnism_common_name->id; ?>"><?php print $orgnism_common_name->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($orgnism_common_name->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $orgnism_common_name->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-					<?php print $orgnism_common_name->widget; ?>
-					</div>
-				</div>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $feature_name->id; ?>"><?php print $feature_name->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($feature_name->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $feature_name->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $feature_name->widget; ?>
-					</div>
-				</div>
-			</fieldset>
-
-			<fieldset class="tripal-search-unigene-exposed-widgets-fields">
-				<legend>Search by Assembly</legend>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $feature_type_id->id; ?>"><?php print $feature_type_id->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($feature_type_id->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $feature_type_id->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-					<?php print $feature_type_id->widget; ?>
-					</div>
-				</div>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $analysis_name->id; ?>"><?php print $analysis_name->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($analysis_name->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $analysis_name->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $analysis_name->widget; ?>
-					</div>
-				</div>
-			</fieldset>
-
-			<fieldset class="tripal-search-unigene-exposed-widgets-fields">
-				<legend>Search by Sequence</legend>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $feature_seqlen->id; ?>"><?php print $feature_seqlen->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($feature_seqlen->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $feature_seqlen->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-					<?php print $feature_seqlen->widget; ?>
-					</div>
-				</div>
-			</fieldset>
-
-			<fieldset class="tripal-search-unigene-exposed-widgets-fields">
-				<legend>Search by Putative Function</legend>
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $cvterm_name->id; ?>"><?php print $cvterm_name->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($cvterm_name->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $cvterm_name->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-					<?php print $cvterm_name->widget; ?>
-					</div>
-				</div>
-
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $blast_value->id; ?>"><?php print $blast_value->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($blast_value->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $blast_value->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $blast_value->widget; ?>
-					</div>
-				</div>
-				
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $kegg_value->id; ?>"><?php print $kegg_value->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($kegg_value->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $kegg_value->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $kegg_value->widget; ?>
-					</div>
-				</div>
-				
-				<div class="tripal-search-unigene-exposed-widget">
-					<div class="tripal-search-unigene-form-labels">
-						<label for="<?php print $interpro_value->id; ?>"><?php print $interpro_value->label; ?>
-						</label>
-					</div>
-					<?php if (!empty($interpro_value->operator)): ?>
-					<div class="tripal_search_unigene-views-operator">
-					<?php print $interpro_value->operator; ?>
-					</div>
-					<?php endif; ?>
-					<div class="tripal_search_unigene-views-widget">
-						<?php print $interpro_value->widget; ?>
-					</div>
-				</div>
-			</fieldset>
-
-		</div>
-    
-    <div class="tripal-search-unigene-exposed-widget">
-    	<input TYPE="Button" value="Reset" onClick="window.location = '<?php global $base_url; print "$base_url/est_search"?>';">
-      <?php $button = preg_replace("'Apply'", "Search", $button); print $button ?>
-    </div>
-  </div>
-</div>

theme_tripal/views-view-table--unigene_search.tpl.php

@@ -1,221 +0,0 @@
-<?php
-// $Id: views-view-table.tpl.php,v 1.8 2009/01/28 00:43:43 merlinofchaos Exp $
-/**
- * @file views-view-table.tpl.php
- * Template to display a view as a table.
- *
- * - $title : The title of this group of rows.  May be empty.
- * - $header: An array of header labels keyed by field id.
- * - $fields: An array of CSS IDs to use for each field id.
- * - $class: A class or classes to apply to the table, based on settings.
- * - $row_classes: An array of classes to apply to each row, indexed by row
- *   number. This matches the index in $rows.
- * - $rows: An array of row items. Each row is an array of content.
- *   $rows are keyed by row number, fields within rows are keyed by field ID.
- * @ingroup views_templates
- */
-?>
-
-<?php
-$total = $view->total_rows;
-$query = $view->build_info['query'];
-$pager = $view->pager;
-$limit = $pager ['items_per_page'];
-$offset = $pager ['current_page'] * $limit;
-$args = $view->build_info['query_args'];
-global $base_url;
-?>
-
-<a id="tripal_search_unigene-result-top" name="search_results">
-&nbsp;&nbsp;&nbsp;Your search produced <b><?php print $total ?></b> results<br>
-<i>&nbsp;&nbsp;&nbsp;Note: To get complete annotation for a sequence, click on the sequence name.</i>
-</a>
-<table class="tripal_search_unigene-table <?php print $class; ?> tripal-table-horz">
-  <?php if (!empty($title)) : ?>
-    <caption><?php print $title; ?></caption>
-  <?php endif; ?>
-  <thead>
-    <tr class="tripal_search_unigene-table-header tripal-table-header">
-      <?php foreach ($header as $field => $label): ?>
-        <th class="views-field views-field-<?php print $fields[$field]; ?>">
-          <?php print $label; ?>
-        </th>
-      <?php endforeach; ?>
-    </tr>
-  </thead>
-  <tbody>
-    <?php foreach ($rows as $count => $row): 
-    			$rowclass = "";
-    			if ($count % 2 != 0) {
-    				$rowclass = "tripal_search_unigene-table-even-row tripal-table-even-row";
-    			} else {
-    				$rowclass = "tripal_search_unigene-table-odd-row tripal-table-odd-row";
-    			}
-    ?>
-      <tr class="<?php print $rowclass?> <?php print implode(' ', $row_classes[$count]); ?>">
-        <?php foreach ($row as $field => $content): ?>
-          <td class="views-field views-field-<?php print $fields[$field]; ?>">
-            <?php print $content; ?>
-          </td>
-        <?php endforeach; ?>
-      </tr>
-    <?php endforeach; ?>
-  </tbody>
-</table>
-
-<?php /* if ($count != 0) {
-	// Generate Excel files
-	// set parameters for excel file
-	$param_excel= array();
-	global $user;
-	$dir = file_directory_path().'/tripal/tripal_search_unigene/'.session_id();
-	if (!file_exists($dir)) {
-		mkdir ($dir, 0777);
-	}
-	$file =session_id().'/unigene_search_result.xls';
-	
-	$param_excel['sheet_name']		= 'unigene_search';
-	$path = "/tripal/tripal_search_unigene/$file";
-	$param_excel['filename']		= file_directory_path().$path;
-	$path_url =url("sites/default/files/tripal/tripal_search_unigene/$file");
-	# set SQL
-	$sql = "$query LIMIT $limit OFFSET $offset";
-	# create heades
-	$col_chr = 'A';
-	$headers = array();
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'hyperlink', 'field' => 'unigene_for_search_feature_name', 'heading' => 'Feature name');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 10, 'type' => 'text', 'field' => 'unigene_for_search_organism_common_name', 'heading' => 'Organism');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 10, 'type' => 'text', 'field' => 'unigene_for_search_feature_seqlen', 'heading' => 'Length');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 10, 'type' => 'text', 'field' => 'unigene_for_search_feature_type', 'heading' => 'Type');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'text', 'field' => 'unigene_for_search_go_term', 'heading' => 'GO term');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'text', 'field' => 'unigene_for_search_blast_value', 'heading' => 'Blast');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'text', 'field' => 'unigene_for_search_kegg_value', 'heading' => 'KEGG');
-	$headers[$col_chr++] = array('align' => 'left', 'width' => 20, 'type' => 'text', 'field' => 'unigene_for_search_interpro_value', 'heading' => 'Interpro');
-	
-	# populate data
-	$result = chado_query($sql, $args);
-	$data = array();
-	while ($row = db_fetch_array($result)) {
-		$data[] = array ('unigene_for_search_feature_name' => $row['unigene_for_search_feature_name'],
-									 'hyperlink_unigene_for_search_feature_name' => "$base_url/ID".$row['unigene_for_search_feature_id'],
-									 'unigene_for_search_organism_common_name' => $row['unigene_for_search_organism_common_name'],
-									 'unigene_for_search_feature_seqlen' => $row['unigene_for_search_feature_seqlen'],
-									 'unigene_for_search_feature_type' => $row['unigene_for_search_feature_type'],
-									 'unigene_for_search_go_term' => $row['unigene_for_search_go_term'],
-									 'unigene_for_search_blast_value' => $row['unigene_for_search_blast_value'],
-									 'unigene_for_search_kegg_value' => $row['unigene_for_search_kegg_value'],
-									 'unigene_for_search_interpro_value' => $row['unigene_for_search_interpro_value']
-									 );
-	}
-	# add headers and data
-	$param_excel['contents']['sheet']['headers']= $headers;
-	$param_excel['contents']['sheet']['data']= $data;
-	# generate excel
-	ml_generate_excel($param_excel);
-	print "&nbsp;&nbsp;&nbsp;<a href=\"$path_url\">Download as Excel file</a>";
-	
-}
-*/?>
-
-<?php 
-# ----------------------------------------- #
-# [UD] ml_generate_excel
-# ----------------------------------------- #
-function ml_generate_excel ($param_excel) {
-	# get and update parameters
-	$writer		= ($param_excel['version'] == '2007') ? 'Excel2007' : 'Excel5';
-	$link_clr	= (empty($param_excel['link_clr'])) ? '0000FF' : $param_excel['link_clr'];
-	$filename	= $param_excel['filename'];
-	if (!preg_match("/(xls|xlsx)$/", $filename)) {
-		$filename = ($param_excel['version'] == '2007') ? $filename.'.xlsx' : $filename.'.xls';
-	}
-	/*********************************************/
-	# create an excel file
-	/*********************************************/
-	# create new PHPExcel object
-	$excel = new PHPExcel();
-	# Set properties
-	$excel->getProperties()->setCreator("Main Lab");
-	$excel->getProperties()->setLastModifiedBy("Main Lab");
-	$excel->getProperties()->setTitle("Office 2007 XLSX Document");
-	$excel->getProperties()->setSubject("");
-	$excel->getProperties()->setKeywords("");
-	$excel->getProperties()->setCategory("");
-	$excel->getProperties()->setDescription("");
-	# set default styles
-	$excel->getDefaultStyle()->getFont()->setName('Times New Roman');
-	$excel->getDefaultStyle()->getFont()->setSize(11);
-	# create worksheets
-	$sheet_no= 0;
-	foreach ($param_excel['contents'] as $sheet_name => $sheet) {
-		if ($sheet_no != 0) {
-			# add a new worksheet
-			$excel->createSheet();
-		}	
-		# set active sheet
-		$excel->setActiveSheetIndex($sheet_no);		
-		# get current worksheet
-		$worksheet = $excel->getActiveSheet();	
-		# set title for this sheet
-		$worksheet->setTitle($sheet_name);
-		# get headers
-		$headers= $param_excel['contents'][$sheet_name]['headers'];
-		# set style and headings for headers
-		foreach ($headers as $col_chr => $prop) {
-			# set alignment for column
-			$align= PHPExcel_Style_Alignment::HORIZONTAL_LEFT;
-			if ($prop['align'] == 'right') {
-				$align= PHPExcel_Style_Alignment::HORIZONTAL_RIGHT;
-			}
-			else if ($prop['align'] == 'center') {
-				$align= PHPExcel_Style_Alignment::HORIZONTAL_CENTER;
-			}
-			$worksheet->getStyle($col_chr.'1')->getAlignment()->setHorizontal($align);		
-			# set width
-			$worksheet->getColumnDimension($col_chr)->setWidth($prop['width']);
-			$worksheet->getStyle($col_chr.'1')->getFont()->setBold(true);
-			$worksheet->getStyle($col_chr.'1')->getFill()->setFillType(PHPExcel_Style_Fill::FILL_SOLID);
-			$worksheet->getStyle($col_chr.'1')->getFill()->getStartColor()->setARGB('FFCDCDCD');
-			$worksheet->setCellValue($col_chr.'1', $prop['heading']);
-		}		
-		# add data to current worksheet
-		foreach ($param_excel['contents'][$sheet_name]['data'] as $idx => $row) {
-			foreach ($headers as $col_chr => $prop) {
-				$loc= $col_chr.($idx+2);
-				# set alignment for cell
-				$align= PHPExcel_Style_Alignment::HORIZONTAL_LEFT;
-				if ($prop['align'] == 'right') {
-					$align= PHPExcel_Style_Alignment::HORIZONTAL_RIGHT;
-				}
-				else if ($prop['align'] == 'center') {
-					$align= PHPExcel_Style_Alignment::HORIZONTAL_CENTER;
-				}
-				$worksheet->getStyle($loc)->getAlignment()->setHorizontal($align);
-				
-				if (!empty($row[$prop['field']])) {
-					# set cell value
-					if ($prop['type'] == 'text') {
-						$worksheet->setCellValue($loc, $row[$prop['field']]);
-					}
-					else if ($prop['type'] == 'hyperlink') {
-						$worksheet->setCellValue($loc, $row[$prop['field']]);
-						if ($row['hyperlink_'.$prop['field']]) {
-							# add underline
-							$worksheet->getStyle($loc)->getFont()->setUnderline(PHPExcel_Style_Font::UNDERLINE_SINGLE);
-							# set link color
-							$worksheet->getStyle($loc)->getFont()->getColor()->setRGB($link_clr);		
-							# set URL
-							$worksheet->getCell($loc)->getHyperlink()->setUrl($row['hyperlink_'.$prop['field']]);
-						}
-					}
-				}
-			}
-		}
-		$sheet_no++;
-	}	
-		# create excel file
- 		$excel->setActiveSheetIndex(0);
- 		$objWriter = PHPExcel_IOFactory::createWriter($excel, $writer);
- 		$objWriter->save($filename);
-}
-?>