Add Related Peptides for Scan. Restore getPeptides() in Crosslink and…

… Looplink to fix created bug in Merged Image and Merged Structure view links
yeastrc · Nov 16, 2015 · 9846d3d · 9846d3d
1 parent 0a07412
commit 9846d3d
Show file tree

Hide file tree

Showing 41 changed files with 2,472 additions and 214 deletions.
diff --git a/WebRoot/WEB-INF/jsp-includes/viewPeptidesRelatedToPSMsByScanId.jsp b/WebRoot/WEB-INF/jsp-includes/viewPeptidesRelatedToPSMsByScanId.jsp
@@ -0,0 +1,89 @@
+
+<%--  viewPeptidesRelatedToPSMsByScanId.jsp  --%>
+
+
+		<script type="text/javascript" src="${ contextPath }/js/viewPeptidesRelatedToPSMsByScanId.js"></script>
+
+
+
+
+
+
+	<%--  View Peptides Related to PSM Info Overlay Div ,  Click on a line for a link and this div pops up --%>
+
+
+
+
+	<%--  View Peptides Related to PSM Info Overlay Background --%>
+
+
+
+	<div id="view_data_related_to_psm_data_modal_dialog_overlay_background" class="view-data-related-to-psm-data-modal-dialog-overlay-background" style="display: none;"  >
+
+	</div>
+
+
+	<%--  View Peptides Related to PSM Info Overlay Div --%>
+
+
+	<div id="view_data_related_to_psm_data_overlay_div" class=" view-data-related-to-psm-data-overlay-div " style="display: none; "  >
+
+
+		<div id="view-data-related-to-psm-data-overlay-header" class="view-data-related-to-psm-data-overlay-header" style="width:100%; " >
+			<h1 id="view-data-related-to-psm-data-overlay-X-for-exit-overlay" class="view-data-related-to-psm-data-overlay-X-for-exit-overlay" >X</h1>
+			<h1 id="view-data-related-to-psm-data-overlay-header-text" class="view-data-related-to-psm-data-overlay-header-text" >Peptides for Scan</h1>
+		</div>
+		<div id="view-data-related-to-psm-data-overlay-body" class="view-data-related-to-psm-data-overlay-body" >
+
+
+			<div id="view_data_related_to_psm_data_overlay_data_container"  >
+
+
+
+
+			</div>			
+
+		</div>
+	</div>
+
+
+
+
+	<%--  Peptides Related to PSM Table Template --%>
+
+
+	<script id="peptides_related_to_psm_block_template"  type="text/x-handlebars-template">
+
+			<%--  include the template text  --%>
+			<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_includes/viewPeptidesRelatedToPSMsByScanId.jsp_templates/peptides_related_to_psm_block_template.jsp" %>
+
+	</script>
+
+
+	<%--  Peptides Related to PSM Entry Template --%>
+
+	<script id="peptides_related_to_psm_row_entry_template"  type="text/x-handlebars-template">
+
+			<%--  include the template text  --%>
+			<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_includes/viewPeptidesRelatedToPSMsByScanId.jsp_templates/peptides_related_to_psm_row_entry_template.jsp" %>
+
+	</script>
+
+
+
+	<%--  Peptides Related to PSM Entry Template --%>
+
+	<script id="peptides_related_to_psm_child_row_template"  type="text/x-handlebars-template">
+
+			<%--  include the template text  --%>
+			<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_includes/viewPeptidesRelatedToPSMsByScanId.jsp_templates/peptides_related_to_psm_child_row_template.jsp" %>
+
+	</script>
+
+
+
+
+
+
+
+
diff --git a/WebRoot/WEB-INF/jsp-includes/viewPsmsLoadedFromWebServiceTemplateFragment.jsp b/WebRoot/WEB-INF/jsp-includes/viewPsmsLoadedFromWebServiceTemplateFragment.jsp
@@ -43,4 +43,8 @@
 
 	</script>
 
+
+	<%-- include the overlay for when click on the "N" for is PSM Unique --%>
+
+	<%@ include file="/WEB-INF/jsp-includes/viewPeptidesRelatedToPSMsByScanId.jsp" %>
 
diff --git a/WebRoot/WEB-INF/jsp-pages/viewMergedCrosslinkProtein.jsp b/WebRoot/WEB-INF/jsp-pages/viewMergedCrosslinkProtein.jsp
@@ -457,7 +457,7 @@
 				
 			</script>
 
-				<table style="" id="crosslink-table" class="tablesorter">
+				<table style="" id="crosslink-table" class="tablesorter top_data_table_jq ">
 
 					<thead>
 					<tr>

diff --git a/WebRoot/WEB-INF/jsp-pages/viewMergedImage.jsp b/WebRoot/WEB-INF/jsp-pages/viewMergedImage.jsp
@@ -606,7 +606,7 @@
 				  </div>			
 
 
-				<table id="link_info_table" class="link-info-table  " >
+				<table id="link_info_table" class="link-info-table  top_data_table_jq " >
 					<thead>
 					<tr>
 						<th style="text-align:left;width:60%;font-weight:bold;">Name</th>
@@ -731,6 +731,7 @@
 			reported_peptide_id="{{ reportedPeptide.id }}"
 			search_id="{{ searchId }}"
 			project_id="${ project_id }"
+			peptide_q_value_cutoff="{{ peptideQValueCutoff }}"			
 			psm_q_value_cutoff="{{ psmQValueCutoff }}"
 		>
 
@@ -823,6 +824,7 @@
 			reported_peptide_id="{{ reportedPeptide.id }}"
 			search_id="{{ searchId }}"
 			project_id="${ project_id }"
+			peptide_q_value_cutoff="{{ peptideQValueCutoff }}"			
 			psm_q_value_cutoff="{{ psmQValueCutoff }}"			
 		>
 			<td>{{reportedPeptide.sequence}}</td>
@@ -914,6 +916,7 @@
 			reported_peptide_id="{{ reportedPeptide.id }}"
 			search_id="{{ searchId }}"
 			project_id="${ project_id }"
+			peptide_q_value_cutoff="{{ peptideQValueCutoff }}"			
 			psm_q_value_cutoff="{{ psmQValueCutoff }}"
 		>
 			<td>{{reportedPeptide.sequence}}</td>

diff --git a/WebRoot/WEB-INF/jsp-pages/viewMergedLooplinkProtein.jsp b/WebRoot/WEB-INF/jsp-pages/viewMergedLooplinkProtein.jsp
@@ -479,7 +479,7 @@
 			</script>
 
 
-				<table style="" id="crosslink-table" class="tablesorter">
+				<table style="" id="crosslink-table" class="tablesorter top_data_table_jq ">
 
 				  <thead>
 					<tr>

diff --git a/WebRoot/WEB-INF/jsp-pages/viewMergedPeptide.jsp b/WebRoot/WEB-INF/jsp-pages/viewMergedPeptide.jsp
@@ -406,7 +406,7 @@
 			</script>
 
 
-				<table style="" id="crosslink-table" class="tablesorter">
+				<table style="" id="crosslink-table" class="tablesorter top_data_table_jq ">
 
 					<thead>
 					<tr>

diff --git a/WebRoot/WEB-INF/jsp-pages/viewMergedStructure.jsp b/WebRoot/WEB-INF/jsp-pages/viewMergedStructure.jsp
@@ -77,6 +77,8 @@
 
 		<link type="text/css" rel="stylesheet" href="${ contextPath }/css/jquery.qtip.min.css" />
 
+		<link rel="stylesheet" href="${ contextPath }/css/tablesorter.css" type="text/css" media="print, projection, screen" />
+
 
 		<link REL="stylesheet" TYPE="text/css" HREF="${contextPath}/css/lorikeet.css">
 
@@ -507,7 +509,7 @@
 				  </div>			
 
 
-				<table id="link_info_table" class="link-info-table tablesorter " >
+				<table id="link_info_table" class="link-info-table tablesorter top_data_table_jq " >
 					<thead>
 					<tr>
 						<th style="text-align:left;width:60%;font-weight:bold;">Search Name</th>
@@ -631,6 +633,7 @@
 			reported_peptide_id="{{ reportedPeptide.id }}"
 			search_id="{{ searchId }}"
 			project_id="${ project_id }"
+			peptide_q_value_cutoff="{{ peptideQValueCutoff }}"			
 			psm_q_value_cutoff="{{ psmQValueCutoff }}"
 		>
 			<td>{{reportedPeptide.sequence}}</td>
@@ -724,6 +727,7 @@
 			reported_peptide_id="{{ reportedPeptide.id }}"
 			search_id="{{ searchId }}"
 			project_id="${ project_id }"
+			peptide_q_value_cutoff="{{ peptideQValueCutoff }}"			
 			psm_q_value_cutoff="{{ psmQValueCutoff }}"		
 		>
 			<td>{{reportedPeptide.sequence}}</td>
@@ -815,6 +819,7 @@
 			reported_peptide_id="{{ reportedPeptide.id }}"
 			search_id="{{ searchId }}"
 			project_id="${ project_id }"
+			peptide_q_value_cutoff="{{ peptideQValueCutoff }}"			
 			psm_q_value_cutoff="{{ psmQValueCutoff }}"
 		>
 			<td>{{reportedPeptide.sequence}}</td>

diff --git a/WebRoot/WEB-INF/jsp-pages/viewSearchCrosslinkProtein.jsp b/WebRoot/WEB-INF/jsp-pages/viewSearchCrosslinkProtein.jsp
@@ -379,7 +379,7 @@
 
 
 
-				<table style="" id="crosslink-table" class="tablesorter">
+				<table style="" id="crosslink-table" class="tablesorter top_data_table_jq ">
 
 					<thead>
 					<tr>

diff --git a/WebRoot/WEB-INF/jsp-pages/viewSearchLooplinkProtein.jsp b/WebRoot/WEB-INF/jsp-pages/viewSearchLooplinkProtein.jsp
@@ -381,7 +381,7 @@
 			</script>
 
 
-				<table style="" id="crosslink-table" class="tablesorter">
+				<table style="" id="crosslink-table" class="tablesorter  top_data_table_jq ">
 
 					<thead>
 					<tr>

diff --git a/WebRoot/WEB-INF/jsp-pages/viewSearchPeptide.jsp b/WebRoot/WEB-INF/jsp-pages/viewSearchPeptide.jsp
@@ -378,7 +378,7 @@
 
 
 
-				<table style="" id="crosslink-table" class="tablesorter">
+				<table style="" id="crosslink-table" class="tablesorter  top_data_table_jq ">
 
 					<thead>
 					<tr>
@@ -399,7 +399,12 @@
 							</th>
 						</c:if>
 
-						<th data-tooltip="Number of PSMs matched to this peptide (or linked pair)" class="tool_tip_attached_jq integer-number-column-header" style="width:10%;font-weight:bold;">#&nbsp;PSMs</th>
+						<th data-tooltip="Number of PSMs matched to this peptide (or linked pair)" class="tool_tip_attached_jq integer-number-column-header" style="width:10%;font-weight:bold; white-space: nowrap;"># PSMs</th>
+
+						<c:if test="${ showNumberUniquePSMs }">
+							<th data-tooltip="Number of scans that uniquely matched to this reported peptide" class="tool_tip_attached_jq integer-number-column-header" style="width:10%;font-weight:bold; white-space: nowrap;"># Unique</th>
+						</c:if>
+
 						<th data-tooltip="Best q-value among PSMs that matched this peptide (or linked pair)" class="tool_tip_attached_jq" style="width:10%;font-weight:bold;">Best&nbsp;PSM <span style="white-space: nowrap">Q-value</span></th>
 					</tr>
 					</thead>
@@ -412,6 +417,7 @@
 								reported_peptide_id="${ peptideEntry.reportedPeptide.id }"
 								search_id="${ search.id }"
 								project_id="${ projectId }"
+								peptide_q_value_cutoff="${ peptideQValueCutoff }"  <%-- JSP EL value --%>
 								psm_q_value_cutoff="${ psmQValueCutoff }"
 								>
 
@@ -485,12 +491,34 @@
 															></span>
 									</a>
 								</td>
+
+								<c:if test="${ showNumberUniquePSMs }">
+
+									<td class="integer-number-column" 
+										><bean:write name="peptideEntry" property="numUniquePsms" />
+									</td>
+								</c:if>					
+
+
 								<td><c:out  value="${ peptideEntry.bestPsmQValue }" /></td>
 							</tr>
 
 							<tr class="expand-child" style="display:none;">
 
-							 <td colspan="11" align="center" class=" child_data_container_jq ">
+								<%--  Adjust colspan for number of columns in current table --%>
+
+
+								<%--  Init to zero --%>
+								<c:set var="colspanPeptidesAdded" value="${ 0 }" />
+
+								<%--   Now add 1 for each column being displayed --%>
+								<c:if test="${ showTopLevelPeptideQValue }">
+									<c:set var="colspanPeptidesAdded" value="${ colspanPeptidesAdded + 1 }" />
+								</c:if>
+
+
+
+							 <td colspan="<c:out value="${ 11 + colspanPeptidesAdded }"></c:out>" align="center" class=" child_data_container_jq ">
 
 									<div style="color: green; font-size: 16px; padding-top: 10px; padding-bottom: 10px;" >
 										Loading...

diff --git a/...esLoadedFromWebServiceTemplateFragment.jsp_templates/crosslink_peptide_block_template.jsp b/...esLoadedFromWebServiceTemplateFragment.jsp_templates/crosslink_peptide_block_template.jsp
@@ -13,10 +13,15 @@
 						<th class="integer-number-column-header" style=" font-weight:bold;">Pos</th>
 						<th style="text-align:left; font-weight:bold;">Peptide 2</th>
 						<th class="integer-number-column-header" style=" font-weight:bold;">Pos</th>
+
 						{{#if qvalueSetAnyRows}} <%-- Only show peptide q value column if any peptide q value are not null --%>
-						<th style="text-align:left; font-weight:bold;"><span style="white-space: nowrap">Q-value</span></th>
+							<th style="text-align:left; font-weight:bold;"><span style="white-space: nowrap">Q-value</span></th>
 						{{/if}}
 						<th class="integer-number-column-right-most-column-no-ts-header" style="font-weight:bold;">#&nbsp;PSMs</th>
+
+						{{#if showNumberUniquePSMs}} <%-- Only show column if any values are not null --%>
+							<th class=" integer-number-column-right-most-column-no-ts-header " style="font-weight:bold; white-space: nowrap;"># Unique</th>
+						{{/if}}
 				</tr>
 				</thead>
 				<tbody></tbody>

diff --git a/...romWebServiceTemplateFragment.jsp_templates/crosslink_peptide_data_row_entry_template.jsp b/...romWebServiceTemplateFragment.jsp_templates/crosslink_peptide_data_row_entry_template.jsp
@@ -12,6 +12,7 @@
 			reported_peptide_id="{{ data.reportedPeptide.id }}"
 			search_id="{{ searchId }}"
 			project_id="${ projectId }"  <%-- JSP EL value --%>
+			peptide_q_value_cutoff="${ peptideQValueCutoff }"  <%-- JSP EL value --%>
 			psm_q_value_cutoff="${ psmQValueCutoff }"  <%-- JSP EL value --%>
 		>
 
@@ -39,8 +40,10 @@
 										></span>
 				</a>
 			</td>												
-
-			<%-- 
-			<td class="integer-number-column-right-most-column-no-ts" style="" >{{data.numPsms}}</td>
-			--%>
+
+			{{#if showNumberUniquePSMs}} <%-- Only show column if any values are not null --%>
+				<td class="integer-number-column" 
+					>{{ data.numUniquePsms }}
+				</td>
+			{{/if}}	
 		</tr>
diff --git a/...desLoadedFromWebServiceTemplateFragment.jsp_templates/looplink_peptide_block_template.jsp b/...desLoadedFromWebServiceTemplateFragment.jsp_templates/looplink_peptide_block_template.jsp
@@ -21,6 +21,10 @@
 						{{/if}}
 
 						<th class="integer-number-column-right-most-column-no-ts-header" style="font-weight:bold;">#&nbsp;PSMs</th>
+
+						{{#if showNumberUniquePSMs}} <%-- Only show column if any values are not null --%>
+							<th class=" integer-number-column-right-most-column-no-ts-header " style="font-weight:bold; white-space: nowrap;"># Unique</th>
+						{{/if}}	
 				</tr>
 				</thead>
 				<tbody></tbody>

diff --git a/...FromWebServiceTemplateFragment.jsp_templates/looplink_peptide_data_row_entry_template.jsp b/...FromWebServiceTemplateFragment.jsp_templates/looplink_peptide_data_row_entry_template.jsp
@@ -11,6 +11,7 @@
 			reported_peptide_id="{{ data.reportedPeptide.id }}"
 			search_id="{{ searchId }}"
 			project_id="${ projectId }"  <%-- JSP EL value --%>
+			peptide_q_value_cutoff="${ peptideQValueCutoff }"  <%-- JSP EL value --%>
 			psm_q_value_cutoff="${ psmQValueCutoff }"  <%-- JSP EL value --%>
 		>
 
@@ -37,8 +38,11 @@
 										></span>
 				</a>
 			</td>												
-
-			<%-- 
-			<td class="integer-number-column-right-most-column-no-ts" style="" >{{ data.numPsms }}</td>
-			--%>
+
+
+			{{#if showNumberUniquePSMs}} <%-- Only show column if any values are not null --%>
+				<td class="integer-number-column" 
+					>{{ data.numUniquePsms }}
+				</td>
+			{{/if}}	
 		</tr>