<commit_before>

<%--   !!!!!!!!!   UNUSED   !!!!!!!!!!!!!!!!!!!!!! --%>


<%--    psmPeptideCutoffBlock_inDataEntryForm.jsp --%>

<%--    This file will be included inside the data entry form the user sees  --%>

<%--  The section at the top of the page with the cutoffs --%>

<%@ include file="/WEB-INF/jsp-includes/strutsTaglibImport.jsp" %>
<%@ include file="/WEB-INF/jsp-includes/jstlTaglibImport.jsp" %>


<%--  TODO:  TEMP --%>

	<%--  use <c:set> since cannot have in page <style> inside a table --%>

	<c:set var="cutoff_input_psm_peptide_label" >padding-left: 10px; font-weight: bold;</c:set>
	<c:set var="cutoff_input_annotation_name">padding-left: 20px;</c:set>


<c:forEach var="cutoffPageDisplayRootPerSearchDataListEntry" items="${ cutoffPageDisplayRootRequestEntry.perSearchDataList  }">
		
	<%-- Spacer --%>  
	<tr>
		<td style="height: 6px;"></td>
	</tr>

	
	<tr>
		<td style="white-space: nowrap; padding-right: 5px;" valign="top">
			For Search ID: <c:out value="${ cutoffPageDisplayRootPerSearchDataListEntry.searchId }"></c:out> 
		</td>
	</tr>
	
	
	<tr>
	  <td class="  ">
	
	
		<div >
			PSM Filters:  display of entered filters here
		</div>
		
		<div >
			Peptide Filters:  display of entered filters here
		</div>
		
		<br>
		
		<div style="padding: 3px; border-style: solid; border-width: 2px; border-color: grey; ">
	
			<div style="padding: 3px; text-align: center;" >
				Displayed in an overlay
			</div>
			
			 <br>
			 
			 
			<table >
				<c:if test="${ not empty cutoffPageDisplayRootPerSearchDataListEntry.psmAnnotationCutoffData }" >
					<tr>
						<td style=" ${ cutoff_input_psm_peptide_label } ">
							PSM Filters:
						</td>
					</tr>
				</c:if>
				
				<c:forEach var="psmAnnotationCutoffDataEntry" items="${ cutoffPageDisplayRootPerSearchDataListEntry.psmAnnotationCutoffData  }">
				
					<c:set var="class_string_tool_tip_attached_jq"></c:set>
				
					<c:if test="${ not empty psmAnnotationCutoffDataEntry.annotationDescription }">
						<c:set var="class_string_tool_tip_attached_jq"> tool_tip_attached_jq </c:set>
					</c:if>
					
					<%--  TODO: consider adding searchProgramDisplayName to tooltip --%>
											
					<tr class= " annotation_entry_root_tr_jq " style="">
						<td>
							<span style="white-space: nowrap;  ${ cutoff_input_annotation_name } "
								class="   ${ class_string_tool_tip_attached_jq }  "
								<c:if test="${ not empty psmAnnotationCutoffDataEntry.annotationDescription }">
									data-tooltip="Annotation Description: <c:out value="${ psmAnnotationCutoffDataEntry.annotationDescription }"></c:out>"
								</c:if>
							><c:out value="${ psmAnnotationCutoffDataEntry.annotationName }"
							></c:out> (<c:out value="${ psmAnnotationCutoffDataEntry.searchProgramDisplayName }"
							></c:out>)</span></td>
							
						<td style="padding-right: 5px;">
							<input type="text" 
								id="annotation_cutoff_input_field_ann_id_${ psmAnnotationCutoffDataEntry.annotationTypeId }"
								class=" psm_annotation_cutoff_input_field_jq  annotation_cutoff_input_field_jq  ${ class_string_tool_tip_attached_jq }" 
								data-type_id="${ psmAnnotationCutoffDataEntry.annotationTypeId }"
								data-search_id="${ cutoffPageDisplayRootPerSearchDataListEntry.searchId }"
								<c:if test="${ not empty psmAnnotationCutoffDataEntry.annotationDescription }">
									data-tooltip="Annotation Description: <c:out value="${ psmAnnotationCutoffDataEntry.annotationDescription }"></c:out>"
								</c:if> 
								value="<%--- <c:out value="${ psmAnnotationCutoffDataEntry.annotationValue }"></c:out> --%>" />
						<%-- 
						<html:text property="psmQValueCutoff" styleId="psmQValueCutoff" onchange="searchFormChanged_ForNag(); searchFormChanged_ForDefaultPageView();" ></html:text></td>
						--%> 
							
							<input type="hidden" class=" annotation_cutoff_default_value_field_jq " 
								value="<c:out value="${ psmAnnotationCutoffDataEntry.annotationDefaultValue }"></c:out>" >
								
								
						</td>
					</tr>
				
				</c:forEach>
		
				<%-- Spacer --%>  
				<tr>
					<td style="height: 6px;"></td>
				</tr>
						
				<c:if test="${ not empty cutoffPageDisplayRootPerSearchDataListEntry.peptideAnnotationCutoffData }" >
					<tr>
						<td style=" ${ cutoff_input_psm_peptide_label } ">
							Peptide Filters: 
						</td>
					</tr>
				</c:if>

				<c:forEach var="peptideAnnotationCutoffDataEntry" items="${ cutoffPageDisplayRootPerSearchDataListEntry.peptideAnnotationCutoffData  }">
			
					<c:set var="class_string_tool_tip_attached_jq"></c:set>
			
					<c:if test="${ not empty peptideAnnotationCutoffDataEntry.annotationDescription }">
						<c:set var="class_string_tool_tip_attached_jq"> tool_tip_attached_jq </c:set>
					</c:if>
						
				
					<tr class= " annotation_entry_root_tr_jq " style=""> <%-- REMOVED hidden initially, displayed via Javascript --%>
						<td>
							<span style="white-space: nowrap;  ${ cutoff_input_annotation_name } "
								class="   ${ class_string_tool_tip_attached_jq } "
								<c:if test="${ not empty peptideAnnotationCutoffDataEntry.annotationDescription }">
									data-tooltip="Annotation Description: <c:out value="${ peptideAnnotationCutoffDataEntry.annotationDescription }"></c:out>"
								</c:if>
								><c:out value="${ peptideAnnotationCutoffDataEntry.annotationName }"
								></c:out> (<c:out value="${ peptideAnnotationCutoffDataEntry.searchProgramDisplayName }"
							></c:out>)</span>
						</td>
						<td>
							<input type="text" 
								id="annotation_cutoff_input_field_ann_id_${ peptideAnnotationCutoffDataEntry.annotationTypeId }"
								class=" peptide_annotation_cutoff_input_field_jq  annotation_cutoff_input_field_jq  ${ class_string_tool_tip_attached_jq } " 
								data-type_id="${ peptideAnnotationCutoffDataEntry.annotationTypeId }"  
								data-search_id="${ cutoffPageDisplayRootPerSearchDataListEntry.searchId }"  
								<c:if test="${ not empty peptideAnnotationCutoffDataEntry.annotationDescription }">
									data-tooltip="Annotation Description: <c:out value="${ peptideAnnotationCutoffDataEntry.annotationDescription }"></c:out>"
								</c:if>
								value="<%--- <c:out value="${ peptideAnnotationCutoffDataEntry.annotationValue }"></c:out> --%>" />
								
									<input type="hidden" class=" annotation_cutoff_default_value_field_jq " 
										value="<c:out value="${ peptideAnnotationCutoffDataEntry.annotationDefaultValue }"></c:out>" >
								
						</td>
					</tr>
					
				</c:forEach>

			</table>
			<br>
			Add "Save", "Cancel", and "Set to Defaults" buttons here
					
			
				
		</div>
	
		</td>
	</tr>
				
</c:forEach>				

<tr>
  <td>
	<div style="position: relative; ">
  		<div style="width: 400px;" class="error-message-container error_message_container_jq" id="error_message_cutoff_value_invalid">
  			<div class="error-message-inner-container" >
  				<div class="error-message-close-x error_message_close_x_jq">X</div>
	  			<div class="error-message-text" >Cutoff value is not valid</div>
  			</div>
	  	</div>
	</div>
		
  </td>
</tr><commit_msg>Move Filter Annotation cutoffs to inside Search Details Block<commit_after>
<%--    psmPeptideCutoffBlock_inCutoffOverlay.jsp --%>

<%--    This file will be included twice, once for "PSM" and once for "Peptide" cutoffs  --%>

<%--  The section at the top of the page with the cutoffs --%>

<%@ include file="/WEB-INF/jsp-includes/strutsTaglibImport.jsp" %>
<%@ include file="/WEB-INF/jsp-includes/jstlTaglibImport.jsp" %>


 	<%--   PSM or Peptide Block --%>
 
<c:if test="${ not empty annotationCutoffDataList }" >
	<tr style=" vertical-align: top; ">
		<td style="  line-height: 1.3em; <c:if test="${ not singleSearch }" > <%-- padding-top: 3px; padding-bottom: 3px; --%> width: 125px;</c:if> ">
			${ filterTypeDisplay } Filters:
			<a href="javascript:" >
				<img src="/proxl_generic/images/icon-edit-small.png" 
					onclick="cutoffProcessingCommonCode.openCutoffOverlay( { clickedThis : this } )"
					data-associated_overlay_container_id="${ filterTypeHTML_Id }_cutoffs_overlay_container__search_id_<bean:write name="search" property="id" />"
					class="tool_tip_attached_jq" data-tooltip="Edit filter values" 
					>
			</a>
			
		</td>
		<td style=" line-height: 1.3em; <c:if test="${ not singleSearch }" > <%-- padding-top: 3px; padding-bottom: 3px; --%> </c:if>">
			<%--  div updated with values from overlay --%>
			<div id="${ filterTypeHTML_Id }_cutoffs_search_id_<bean:write name="search" property="id" />" class=" ${ filterTypeHTML_Id }_cutoffs_jq "></div>
		</td>
	</tr>
	
	
	<tr class="table-no-border-no-cell-spacing-no-cell-padding">
		<td class="table-no-border-no-cell-spacing-no-cell-padding">  <%--  Cutoffs Overlay Holder --%>

			<%--  div that contains the overlay --%>
			<div id="${ filterTypeHTML_Id }_cutoffs_overlay_container__search_id_<bean:write name="search" property="id" />" 
				class=" cutoffs_overlay_container_jq  ${ filterTypeHTML_Id }_cutoffs_overlay_container_jq "
				style="position: relative; ">

			
				<%--  Cutoffs Overlay Background --%>
				
				<div class="filter-cutoffs-modal-dialog-overlay-background  filter_cutoffs_modal_dialog_overlay_background_jq " style="display: none;"  >
				</div>
				
				<%--  Cutoffs Overlay Div --%>
				
				<div class=" filter-cutoffs-modal-dialog-overlay-div overlay-outer-div  filter_cutoffs_modal_dialog_overlay_div_jq " style="display: none; "  >
				
				
					<div class="filter-cutoffs-modal-dialog-overlay-header" style="width:100%; " >
						
						<h1 class="filter-cutoffs-modal-dialog-overlay-X-for-exit-overlay " 
							onclick="cutoffProcessingCommonCode.cancel_RestoreUserValues( { clickedThis : this } )"
							>X</h1>
						
						<h1 class="filter-cutoffs-modal-dialog-overlay-header-text" ><c:out value="${ filterTypeDisplay }"></c:out> Filters</h1>
					</div>
					<div class="filter-cutoffs-modal-dialog-overlay-body" >
				
						
						<%--  This div encloses the fields and the buttons and marks what is part of this overlay --%>
						<div 
							class=" cutoff_overlay_enclosing_block_jq "  <%--  filterTypeHTML_Id == 'psm' or 'peptide' --%>
							 data-associated_cutoffs_display_block_id="${ filterTypeHTML_Id }_cutoffs_search_id_<bean:write name="search" property="id" />">
									 
						<table >
			<%-- 
								<tr>
									<td style="">
										${ filterTypeDisplay } Filters:
									</td>
								</tr>
			--%>				
							<c:forEach var="annotationCutoffDataEntry" items="${ annotationCutoffDataList  }">
							
								<c:set var="class_string_tool_tip_attached_jq"></c:set>
							
								<c:if test="${ not empty annotationCutoffDataEntry.annotationDescription }">
									<c:set var="class_string_tool_tip_attached_jq"> tool_tip_attached_jq </c:set>
								</c:if>
								
								<%--  TODO: consider adding searchProgramDisplayName to tooltip --%>
														
								<tr class= " annotation_entry_root_tr_jq " style="">
									<td>
										<span style="white-space: nowrap;   "
											class="   ${ class_string_tool_tip_attached_jq }  "
											<c:if test="${ not empty annotationCutoffDataEntry.annotationDescription }">
												data-tooltip="<c:out value="${ annotationCutoffDataEntry.annotationDescription }"></c:out>"
											</c:if>
										><c:out value="${ annotationCutoffDataEntry.annotationName }"
										></c:out> (<c:out value="${ annotationCutoffDataEntry.searchProgramDisplayName }"
										></c:out>)</span></td>
										
									<td style="padding-right: 5px;" >
									
									  <div class=" cutoff_input_field_block_jq ">
									  
										<input type="text" 
											id="annotation_cutoff_input_field_ann_id_${ annotationCutoffDataEntry.annotationTypeId }"
											class=" ${ filterTypeHTML_Id }_annotation_cutoff_input_field_jq  annotation_cutoff_input_field_jq <%--  ${ class_string_tool_tip_attached_jq } --%> " 
											data-type_id="${ annotationCutoffDataEntry.annotationTypeId }"
											data-search_id="${ cutoffPageDisplayRootPerSearchDataListEntry.searchId }"
<%-- 											
											<c:if test="${ not empty annotationCutoffDataEntry.annotationDescription }">
												data-tooltip="<c:out value="${ annotationCutoffDataEntry.annotationDescription }"></c:out>"
											</c:if>
--%>
											value="<%--- <c:out value="${ annotationCutoffDataEntry.annotationValue }"></c:out> --%>" />						
									
										<input type="hidden" class=" annotation_cutoff_default_value_field_jq " 
											value="<c:out value="${ annotationCutoffDataEntry.annotationDefaultValue }"></c:out>" >
			
												<input type="hidden" class=" annotation_display_name_field_jq "
													value="<c:out value="${ annotationCutoffDataEntry.annotationName }"
															></c:out> (<c:out value="${ annotationCutoffDataEntry.searchProgramDisplayName }"
														></c:out>)" > 
												
												<input type="hidden" class=" annotation_description_field_jq "
													value="<c:out value="${ annotationCutoffDataEntry.annotationDescription }"></c:out>" > 								
									  </div>
									  	
									</td>
								</tr>
							
							</c:forEach>
							
							</table>
							
							<div style="position: relative; ">
						  		<div style="width: 400px;" class="error-message-container error_message_container_jq  error_message_cutoff_value_invalid_jq" >
						  			<div class="error-message-inner-container" >
						  				<div class="error-message-close-x error_message_close_x_jq">X</div>
							  			<div class="error-message-text" >Cutoff value is not valid</div>
						  			</div>
							  	</div>
							</div>
		
							
				
							<input type="button" value="Save" onclick="cutoffProcessingCommonCode.saveUserValues( { clickedThis : this } )" >
							<input type="button" value="Cancel" onclick="cutoffProcessingCommonCode.cancel_RestoreUserValues( { clickedThis : this } )" >
							<input type="button" value="Reset to Defaults" onclick="cutoffProcessingCommonCode.setToDefaultValues( { clickedThis : this } )" >
			
							
							</div>
					
						</div>
					</div>
						
				</div>


	</td>
</tr>
		
</c:if>
	
{'fraction_non_alphanumeric': 0.1480673097232979, 'fraction_numerical': 0.0025346757727240724, 'mean_word_length': 3.1362842166569598, 'pattern_counts': {'":': 0, '<': 280, '<?xml version=': 0, '>': 280, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5397097', 'n_tokens_mistral': 6203, 'n_tokens_neox': 4448, 'n_words': 779}