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Updates to Merged Protein pages, AJAX load per Search data.
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danjasuw committed Nov 2, 2015
1 parent 8dad5ee commit 37d9629
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Showing 24 changed files with 2,104 additions and 103 deletions.
90 changes: 77 additions & 13 deletions WebRoot/WEB-INF/jsp-pages/viewMergedCrosslinkProtein.jsp
100644 → 100755
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Expand Up @@ -58,6 +58,9 @@

<script type="text/javascript" src="${ contextPath }/js/toggleVisibility.js"></script>


<script type="text/javascript" src="${ contextPath }/js/viewCrosslinkProteinsLoadedFromWebServiceTemplate.js"></script>

<script type="text/javascript" src="${ contextPath }/js/viewPsmsLoadedFromWebServiceTemplate.js"></script>
<script type="text/javascript" src="${ contextPath }/js/viewCrosslinkReportedPeptidesLoadedFromWebServiceTemplate.js"></script>

Expand Down Expand Up @@ -225,6 +228,48 @@
<%@ include file="/WEB-INF/jsp-includes/viewPsmsLoadedFromWebServiceTemplateFragment.jsp" %>
<%@ include file="/WEB-INF/jsp-includes/viewCrosslinkReportedPeptidesLoadedFromWebServiceTemplateFragment.jsp" %>



<%-- Crosslink Protein Template --%>



<script id="crosslink_protein_block_template" type="text/x-handlebars-template">

<%-- include the template text --%>
<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_pages/viewMergedCrosslinkProtein.jsp_templates/crosslink_protein_block_template.jsp" %>

</script>


<%-- Crosslink Protein Entry Template --%>



<%-- !!! Handlebars template: Crosslink Protein Entry Template !!!!!!!!! --%>


<script id="crosslink_protein_data_row_entry_template" type="text/x-handlebars-template">

<%-- include the template text --%>
<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_pages/viewMergedCrosslinkProtein.jsp_templates/crosslink_protein_data_row_entry_template.jsp" %>

</script>



<%-- Crosslink Protein Child row Entry Template --%>


<script id="crosslink_protein_child_row_entry_template" type="text/x-handlebars-template">

<%-- include the template text --%>
<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_pages/viewMergedCrosslinkProtein.jsp_templates/crosslink_protein_child_row_entry_template.jsp" %>

</script>



<div class="overall-enclosing-block">

<h2 style="margin-bottom:5px;">List merged search proteins:</h2>
Expand Down Expand Up @@ -304,15 +349,6 @@
</td>
</tr>

<%--
<tr>
<td>Filter out xlinks with no unique peptides:</td>
<td>
<html:checkbox property="filterNonUniquePeptides" styleId="filterNonUniquePeptides" onchange="searchFormChanged()" ></html:checkbox>
</td>
</tr>
--%>

<tr>
<td>Exclude organisms:</td>
<td>
Expand Down Expand Up @@ -468,12 +504,30 @@
<logic:iterate id="crosslink" name="crosslinks">
<%--
<tr id="<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein1.nrProtein.nrseqId" />-<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein1Position" />-<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein2.nrProtein.nrseqId" />-<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein2Position" />"
style="cursor: pointer; "
onclick="toggleVisibility(this)"
toggle_visibility_associated_element_id="<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein1.nrProtein.nrseqId" />-<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein1Position" />-<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein2.nrProtein.nrseqId" />-<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein2Position" />"
>

--%>
<tr
style="cursor: pointer; "
onclick="viewCrosslinkProteinsLoadedFromWebServiceTemplate.showHideCrosslinkProteins( { clickedElement : this })"
project_id="${ projectId }"
search_ids="<c:forEach var="searchEntryForThisRow" items="${ crosslink.mergedSearchProteinCrosslink.searches }">,${ searchEntryForThisRow.id }</c:forEach>"
peptide_q_value_cutoff="${ peptideQValueCutoff }"
psm_q_value_cutoff="${ psmQValueCutoff }"
protein_1_id="<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein1.nrProtein.nrseqId" />"
protein_2_id="<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein2.nrProtein.nrseqId" />"
protein_1_position="<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein1Position" />"
protein_2_position="<bean:write name="crosslink" property="mergedSearchProteinCrosslink.protein2Position" />"
>


<c:forEach items="${ crosslink.searchContainsCrosslink }" var="isMarked" varStatus="searchVarStatus">

Expand Down Expand Up @@ -536,7 +590,14 @@


<%-- colspan set to the number of searches plus the number of other columns --%>
<td colspan="<c:out value="${ fn:length( searches ) + 9 + colspanPeptidesAdded }"></c:out>" align="center">
<td colspan="<c:out value="${ fn:length( searches ) + 9 + colspanPeptidesAdded }"></c:out>" align="center" class=" child_data_container_jq ">


<div style="color: green; font-size: 16px; padding-top: 10px; padding-bottom: 10px;" >
Loading...
</div>

<%--
<table class="tablesorter" style="width:80%">
Expand Down Expand Up @@ -597,13 +658,15 @@
<tr class="expand-child" style="display:none;">

--%>
<%-- Adjust colspan for number of columns in current table --%>

<%-- Init to zero --%>
<%--
<c:set var="colspanPSMsAdded" value="${ 0 }" />

--%>
<%-- Now add 1 for each column being displayed --%>
<%--
<c:if test="${ crosslink.mergedSearchProteinCrosslink.anyLinksHaveBestPeptideQValue }">
<c:set var="colspanPSMsAdded" value="${ colspanPSMsAdded + 1 }" />
</c:if>
Expand All @@ -619,6 +682,7 @@
</logic:iterate>
</table>
--%>
</td>
</tr>

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71 changes: 68 additions & 3 deletions WebRoot/WEB-INF/jsp-pages/viewMergedLooplinkProtein.jsp
100644 → 100755
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Expand Up @@ -61,6 +61,7 @@

<script type="text/javascript" src="${ contextPath }/js/toggleVisibility.js"></script>

<script type="text/javascript" src="${ contextPath }/js/viewLooplinkProteinsLoadedFromWebServiceTemplate.js"></script>
<script type="text/javascript" src="${ contextPath }/js/viewPsmsLoadedFromWebServiceTemplate.js"></script>
<script type="text/javascript" src="${ contextPath }/js/viewLooplinkReportedPeptidesLoadedFromWebServiceTemplate.js"></script>

Expand Down Expand Up @@ -231,6 +232,49 @@
<%@ include file="/WEB-INF/jsp-includes/viewPsmsLoadedFromWebServiceTemplateFragment.jsp" %>

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




<%-- Looplink Protein Template --%>



<script id="looplink_protein_block_template" type="text/x-handlebars-template">

<%-- include the template text --%>
<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_pages/viewMergedLooplinkProtein.jsp_templates/looplink_protein_block_template.jsp" %>

</script>


<%-- Looplink Protein Entry Template --%>



<%-- !!! Handlebars template: Looplink Protein Entry Template !!!!!!!!! --%>


<script id="looplink_protein_data_row_entry_template" type="text/x-handlebars-template">

<%-- include the template text --%>
<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_pages/viewMergedLooplinkProtein.jsp_templates/looplink_protein_data_row_entry_template.jsp" %>

</script>



<%-- Looplink Protein Child row Entry Template --%>


<script id="looplink_protein_child_row_entry_template" type="text/x-handlebars-template">

<%-- include the template text --%>
<%@ include file="/WEB-INF/jsp_template_fragments/For_jsp_pages/viewMergedLooplinkProtein.jsp_templates/looplink_protein_child_row_entry_template.jsp" %>

</script>



<div class="overall-enclosing-block">

Expand Down Expand Up @@ -483,12 +527,29 @@

<logic:iterate id="looplink" name="looplinks">

<%--
<tr id="<bean:write name="looplink" property="mergedSearchProteinLooplink.protein.nrProtein.nrseqId" />-<bean:write name="looplink" property="mergedSearchProteinLooplink.proteinPosition1" />-<bean:write name="looplink" property="mergedSearchProteinLooplink.protein.nrProtein.nrseqId" />-<bean:write name="looplink" property="mergedSearchProteinLooplink.proteinPosition2" />"
style="cursor: pointer; "
onclick="toggleVisibility(this)"
toggle_visibility_associated_element_id="<bean:write name="looplink" property="mergedSearchProteinLooplink.protein.nrProtein.nrseqId" />-<bean:write name="looplink" property="mergedSearchProteinLooplink.proteinPosition1" />-<bean:write name="looplink" property="mergedSearchProteinLooplink.protein.nrProtein.nrseqId" />-<bean:write name="looplink" property="mergedSearchProteinLooplink.proteinPosition2" />"
>
--%>



<tr
style="cursor: pointer; "

onclick="viewLooplinkProteinsLoadedFromWebServiceTemplate.showHideLooplinkProteins( { clickedElement : this })"
project_id="${ projectId }"
search_ids="<c:forEach var="searchEntryForThisRow" items="${ looplink.mergedSearchProteinLooplink.searches }">,${ searchEntryForThisRow.id }</c:forEach>"
peptide_q_value_cutoff="${ peptideQValueCutoff }"
psm_q_value_cutoff="${ psmQValueCutoff }"
protein_id="<bean:write name="looplink" property="mergedSearchProteinLooplink.protein.nrProtein.nrseqId" />"
protein_position_1="<bean:write name="looplink" property="mergedSearchProteinLooplink.proteinPosition1" />"
protein_position_2="<bean:write name="looplink" property="mergedSearchProteinLooplink.proteinPosition2" />"
>

<c:forEach items="${ looplink.searchContainsLooplink }" var="isMarked" varStatus="searchVarStatus">

<%-- Include file is dependent on containing loop having varStatus="searchVarStatus" --%>
Expand Down Expand Up @@ -547,8 +608,9 @@
</c:if>

<%-- colspan set to the number of searches plus the number of other columns --%>
<td colspan="<c:out value="${ fn:length( searches ) + 8 + colspanPeptidesAdded }"></c:out>" align="center">
<td colspan="<c:out value="${ fn:length( searches ) + 8 + colspanPeptidesAdded }"></c:out>" align="center" class=" child_data_container_jq ">

<%--
<table class="tablesorter" style="width:80%">
<thead>
Expand Down Expand Up @@ -606,13 +668,15 @@
</tr>
<tr class="expand-child" style="display:none;">

--%>
<%-- Adjust colspan for number of columns in current table --%>

<%-- Init to zero --%>
<%--
<c:set var="colspanPSMsAdded" value="${ 0 }" />

--%>
<%-- Now add 1 for each column being displayed --%>
<%--
<c:if test="${ crosslink.mergedSearchProteinCrosslink.anyLinksHaveBestPeptideQValue }">
<c:set var="colspanPSMsAdded" value="${ colspanPSMsAdded + 1 }" />
</c:if>
Expand All @@ -628,6 +692,7 @@
</logic:iterate>
</table>
--%>
</td>
</tr>

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@@ -0,0 +1,35 @@



<%-- !!! Handlebars template !!!!!!!!! --%>



<%-- Protein Data Per Search Template --%>

<div >
<table class="tablesorter crosslink_protein_table_jq " style="width:80%">

<thead>
<tr>
<%--
<th style="text-align:left;width:{{ pageFormatting.nameWidthPercent }}%;font-weight:bold;">Name</th>
--%>
<th style="text-align:left;width:60%;font-weight:bold;">Name</th>

<th class="integer-number-column-header" style="width:10%;font-weight:bold;">Peptides</th>
<th class="integer-number-column-header" style="width:10%;font-weight:bold;">Unique peptides</th>
<th class="integer-number-column-header" style="width:10%;font-weight:bold;">Psms</th>

{{#if bestPeptideQValueSetAnyRows }}
<th style="text-align:left;width:10%;font-weight:bold;"><span style="white-space: nowrap">Best Peptide</span> <span style="white-space: nowrap">Q-value</span></th>
{{/if}}

<th style="text-align:left;width:10%;font-weight:bold;"><span style="white-space: nowrap">Best PSM</span> <span style="white-space: nowrap">Q-value</span></th>

</tr>
</thead>

</table>

</div>
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@@ -0,0 +1,20 @@



<%-- !!! Handlebars template !!!!!!!!! --%>



<%-- Protein Data Per Search Template --%>



<tr class="expand-child" style="display:none;">

<td colspan="{{ colSpan }}" align="center" class=" child_data_container_jq ">

<div style="color: green; font-size: 16px; padding-top: 10px; padding-bottom: 10px;" >
Loading...
</div>
</td>
</tr>
Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@


<%-- !!! Handlebars template !!!!!!!!! --%>



<%-- Protein Data Per Search Template --%>



<tr id=""
style="cursor: pointer; "

onclick="viewCrosslinkReportedPeptidesLoadedFromWebServiceTemplate.showHideCrosslinkReportedPeptides( { clickedElement : this })"
search_id="{{ data.searchId }}"
project_id="${ projectId }"
peptide_q_value_cutoff="{{ data.peptideQValueCutoff }}"
psm_q_value_cutoff="{{ data.psmQValueCutoff }}"
protein_1_id="{{ data.proteinId_1 }}"
protein_2_id="{{ data.proteinId_2 }}"
protein_1_position="{{ data.protein1Position }}"
protein_2_position="{{ data.protein2Position }}"
>
<td>{{ data.searchName }}</td>

<td class="integer-number-column-header"
><a class="show-child-data-link "
href="javascript:"
>{{ data.searchProteinCrosslink.numLinkedPeptides }}<span class="toggle_visibility_expansion_span_jq"
><img src="${contextPath}/images/icon-expand-small.png"
class=" icon-expand-contract-in-data-table "
></span><span class="toggle_visibility_contraction_span_jq"
style="display: none;"
><img src="${contextPath}/images/icon-collapse-small.png"
class=" icon-expand-contract-in-data-table "
></span>
</a>
</td>

<td class="integer-number-column-header">{{ data.searchProteinCrosslink.numUniqueLinkedPeptides }}</td>
<td class="integer-number-column-header">{{ data.searchProteinCrosslink.numPsms }}</td>
{{#if bestPeptideQValueSetAnyRows }}
<td style="white-space: nowrap">{{ data.searchProteinCrosslink.bestPeptideQValue }}</td>
{{/if}}
<td style="white-space: nowrap">{{ data.searchProteinCrosslink.bestPSMQValue }}</td>
</tr>


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