/**
* File with actions of the website
*
* @author Wendel Hime Lino Castro
*/
var idForm = "";
var pageSize = 10;
var offset = 1;
var totalValues = 10;
/**
* method used to verify paged responses
* @param acientID ancient id
* @param actualID id of actual form
* @returns status
*/
function verifyPagedResponse(acientID, actualID, values) {
var status = false;
var numberOfPages = 0;
$("#totalResults").show();
$("#totalResults").text("Found " + totalValues + " results");
if (totalValues <= 10) {
numberOfPages = 1;
} else {
var number = (values / pageSize);
if (Math.round(number) - number > 0) {
numberOfPages = Math.round(number);
} else {
numberOfPages = Math.round(number + 1);
}
// var number = (values + pageSize - 1) / pageSize;
// if(Math.round(number) - number > 0) {
// numberOfPages = Math.round(number);
// } else {
// numberOfPages = Math.trunc(number);
// }
}
$("#numberPage").attr("max", numberOfPages);
$("#totalNumberPages").text(numberOfPages);
if (parseInt($("#numberPage").val()) > parseInt($("#totalNumberPages").text())) {
$("#numberPage").val(1);
}
if (acientID == actualID) {
if ((totalValues - offset) <= pageSize && ($("#numberPage").val() == $("#totalNumberPages").text())) {
$("#more").attr("disabled", "disabled");
$("#last").attr("disabled", "disabled");
} else {
$("#more").removeAttr("disabled");
$("#last").removeAttr("disabled");
}
if (offset <= 1) {
offset = 1;
$("#less").attr("disabled", "disabled");
$("#begin").attr("disabled", "disabled");
} else {
$("#less").removeAttr("disabled");
$("#begin").removeAttr("disabled");
}
if (offset < 10 && $("#numberPage").val() > $("#totalNumberPages").text()) {
$("#numberPage").val(1);
$("#more").attr("disabled", "disabled");
$("#last").attr("disabled", "disabled");
}
status = true;
} else {
offset = 1;
if ((totalValues - offset) <= pageSize && ($("#numberPage").val() == $("#totalNumberPages").text())) {
$("#more").attr("disabled", "disabled");
$("#last").attr("disabled", "disabled");
} else {
$("#more").removeAttr("disabled");
$("#last").removeAttr("disabled");
}
$("#less").attr("disabled", "disabled");
$("#begin").attr("disabled", "disabled");
$("#numberPage").val(1);
}
return status;
}
/**
* Hide button back
*/
$("#back").toggle();
$("#totalResults").toggle();
$("#more").attr("disabled", "disabled");
$("#last").attr("disabled", "disabled");
$("#less").attr("disabled", "disabled");
$("#begin").attr("disabled", "disabled");
$(".pagination-section").toggle();
$("#test").hide();
$(".result").remove();
/**
* Button back on click
*/
$("#back").click(function() {
pageSize = 10;
offset = 1;
totalValues = 10;
$("#searchPanel").show();
$("#back").hide();
$("#totalResults").hide();
$(".pagination-section").hide();
$(".result").remove();
});
$("#begin").click(function() {
offset = 1;
$("#numberPage").val("1");
$(".result").remove();
$(idForm).submit();
});
$("#more").click(function() {
if (offset == 1) {
offset = 10;
} else {
offset += 10;
}
$("#numberPage").val(parseInt($("#numberPage").val()) + 1);
$(".result").remove();
$(idForm).submit();
});
$("#less").click(function() {
offset -= 10;
if (offset < 1) {
offset = 1
}
$("#numberPage").val(parseInt($("#numberPage").val()) - 1);
$(".result").remove();
$(idForm).submit();
});
$("#last").click(function() {
offset = (totalValues - 10);
$("#numberPage").val($("#totalNumberPages").text());
$(".result").remove();
$(idForm).submit();
});
$(function() {
$("#skipPagination").submit(
function() {
var numberPage = $("#numberPage").val();
if (numberPage <= 1)
offset = 1;
else
offset = parseInt("" + (numberPage - 1) * 10);
$(".result").remove();
$(idForm).submit();
return false;
}
);
});
function submitGeneIdentifier() {
}
/**
* Add function to submit form
*/
$(function() {
$("#formGeneIdentifier").submit(
function() {
$(".errors").remove();
var pagedResponse = searchGene($(this).serialize(), pageSize, offset).responseJSON;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#formGeneIdentifier", totalValues))
idForm = "#formGeneIdentifier";
var gene = pagedResponse.response;
if (gene.length > 0) {
contentGeneData(gene);
} else {
$("#formGeneIdentifier").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
$(function autommaticId() {
if($("#id").val() != "") {
$("input[name=geneID]").val($("#id").val());
$(".errors").remove();
var pagedResponse = searchGene($("#formGeneIdentifier").serialize(), pageSize, offset).responseJSON;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#formGeneIdentifier", totalValues))
idForm = "#formGeneIdentifier";
var gene = pagedResponse.response;
if (gene.length > 0) {
contentGeneData(gene);
} else {
$("#formGeneIdentifier").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
}
})
/**
* Add function to submit form
*/
$(function() {
$("#formGeneDescription").submit(
function() {
$(".errors").remove();
var pagedResponse = searchGene($(this).serialize(), pageSize, offset).responseJSON;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#formGeneDescription", totalValues))
idForm = "#formGeneDescription";
var gene = pagedResponse.response;
if (gene.length > 0) {
contentGeneData(gene);
} else {
$("#formGeneDescription").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
/**
* Add function to submit form
*/
$(function() {
$("#formAnalysesProteinCodingGenes").submit(
function() {
$(".errors").remove();
if(
($.inArray("Interpro", $('#components').val()) == 0 && $('input[name=noIP]').prop("checked")) ||
($.inArray("GO", $('#components').val()) == 0 && $('input[name=noGO]').prop("checked")) ||
($.inArray("TCDB", $('#components').val()) == 0 && $('input[name=noTC]').prop("checked")) ||
($.inArray("eggNOG", $('#components').val()) == 0 && $('input[name=noOrth]').prop("checked")) ||
($.inArray("KEGG", $('#components').val()) == 0 && $('input[name=noKEGG]').prop("checked")) ||
($.inArray("RPS-BLAST", $('#components').val()) == 0 && $('input[name=noRps]').prop("checked")) ||
($.inArray("BLAST", $('#components').val()) == 0 && $('input[name=noBlast]').prop("checked"))
) {
$("#formAnalysesProteinCodingGenes").append("<div class='alert alert-danger errors'>Wrong query: positive and negative results required simultaneously</div>");
return false;
}
$("input[name=blastID]").val($("input[name=blastID]").val().replace(/\s/g, ""));
$("input[name=rpsID]").val($("input[name=rpsID]").val().replace(/\s/g, ""));
$("input[name=koID]").val($("input[name=koID]").val().replace(/\s/g, ""));
$("input[name=orthID]").val($("input[name=orthID]").val().replace(/\s/g, ""));
$("input[name=tcdbID]").val($("input[name=tcdbID]").val().replace(/\s/g, ""));
$("input[name=goID]").val($("input[name=goID]").val().replace(/\s/g, ""));
$("input[name=interproID]").val($("input[name=interproID]").val().replace(/\s/g, ""));
var pagedResponse = analysesCDS($(this).serialize(), pageSize, offset).responseJSON;
try {
var ids = pagedResponse.response;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#formAnalysesProteinCodingGenes", totalValues))
idForm = "#formAnalysesProteinCodingGenes";
if (ids.length > 0) {
var featuresIDs = ids.join(" ");
var data = searchGeneByID(featuresIDs).responseJSON.response;
if (data.length > 0) {
contentGeneData(data);
} else {
$("#formAnalysesProteinCodingGenes").append("<div class='alert alert-danger errors'>Ooops, no gene found</div>");
$("#totalResults").hide();
}
} else {
$("#formAnalysesProteinCodingGenes").append("<div class='alert alert-danger errors'>Ooops, no gene found</div>");
$("#totalResults").hide();
}
} catch(exception) {
$("#formAnalysesProteinCodingGenes").append("<div class='alert alert-danger errors'>Ooops, no gene found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
/**
* Add function to submit form
*/
$(function() {
$("#trna-form").submit(
function() {
$(".errors").remove();
var pagedResponse = trnaSearch($(this).serialize(), pageSize, offset).responseJSON;
var tRNAList = pagedResponse.response;
totalValues = pagedResponse.total;
if (tRNAList.length > 0) {
if (!verifyPagedResponse(idForm, "#trna-form", totalValues))
idForm = "#trna-form";
var featuresIDs = "";
for (i = 0; i < tRNAList.length; i++) {
featuresIDs += tRNAList[i].id + " ";
}
var data = searchGeneByID(featuresIDs).responseJSON.response;
if (data.length > 0) {
contentGeneData(data);
} else {
$("#trna-form").append("<div class='alert alert-danger errors'>Ooops, no gene found</div>");
$("#totalResults").hide();
}
} else {
$("#trna-form").append("<div class='alert alert-danger errors'>Ooops, no gene found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
$(function() {
$("#rRNA-form").submit(function() {
$(".errors").remove();
var pagedResponse = searchrRNA($(this).serialize(), pageSize, offset).responseJSON;
var rRNAList = pagedResponse.response;
totalValues = pagedResponse.total;
if(rRNAList.length > 0) {
if (!verifyPagedResponse(idForm, "#rRNA-form", totalValues))
idForm = "#rRNA-form";
var featuresIDs = "";
for (i = 0; i < rRNAList.length; i++) {
featuresIDs += rRNAList[i] + " ";
}
var data = searchGeneByID(featuresIDs).responseJSON.response;
if (data.length > 0) {
contentGeneData(data);
} else {
$("#rRNA-form").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
} else {
$("#rRNA-form").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
});
});
/**
* Add function to submit form
*/
$(function() {
$("#tandemRepeats-form").submit(
function() {
$(".errors").remove();
var pagedResponse = tandemRepeatsSearch($(this).serialize(), pageSize, offset).responseJSON;
var tandemRepeatsList = pagedResponse.response;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#tandemRepeats-form", totalValues))
idForm = "#tandemRepeats-form";
if (tandemRepeatsList.length > 0) {
$("#searchPanel").hide();
$("#back").show();
var html = "<table class='table table-striped table-bordered table-hover result'>" +
" <thead>" +
" <tr>" +
" <th>Contig</th>" +
" <th>Start coordinate</th>" +
" <th>End coordinate</th>" +
" <th>Repeat length</th>" +
" <th>Copy number</th>" +
" <th>Repeat sequence</th>" +
" </tr>" +
" </thead>" +
" <tbody>";
for (i = 0; i < tandemRepeatsList.length; i++) {
html += " <tr>" +
" <td>"+tandemRepeatsList[i].contig+" (<a href='"+window.location.pathname.replace("/SearchDatabase", "")+"/DownloadFileByContigAndType?contig=" + tandemRepeatsList[i].contig + "&type=trf' target='_blank'>result</a>)</td>" +
" <td>" + tandemRepeatsList[i].start + "</td>" +
" <td>" + tandemRepeatsList[i].end + "</td>" +
" <td>" + tandemRepeatsList[i].length + "</td>" +
" <td>" + tandemRepeatsList[i].copy_number + "</td>" +
" <td>" + tandemRepeatsList[i].sequence + "</td>" +
" </tr>";
}
html += " </tbody>" +
"</table>";
$("#searchPanel").parent().append(html);
$(".pagination-section").show();
} else {
$("#tandemRepeats-form").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
$(function() {
$('select[name=type]').focus(
function() {
if ($('select[name=type] option').length <= 1) {
ribosomal_rnas = getRibosomalRNAs().responseJSON.response;
for (i = 0; i < ribosomal_rnas.length; i++) {
$('select[name=type]').append($('<option>', {
value: ribosomal_rnas[i],
text: ribosomal_rnas[i]
}));
}
}
return false
}
);
});
$(function() {
$('select[name=ncRNAtargetClass]').focus(
function() {
if ($('select[name=ncRNAtargetClass] option').length <= 1) {
target_classes = getTargetClass().responseJSON.response;
for (i = 0; i < target_classes.length; i++) {
$('select[name=ncRNAtargetClass]').append($('<option>', {
value: target_classes[i],
text: target_classes[i]
}));
}
}
return false
}
);
});
/**
* Add function to submit form
*/
$(function() {
$("#otherNonCodingRNAs-form").submit(
function() {
$(".errors").remove();
var pagedResponse = ncRNASearch($(this).serialize(), pageSize, offset).responseJSON;
var nonCodingRNAList = pagedResponse.response;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#otherNonCodingRNAs-form", totalValues))
idForm = "#otherNonCodingRNAs-form";
if (nonCodingRNAList.length > 0) {
var featuresIDs = "";
for (i = 0; i < nonCodingRNAList.length; i++) {
featuresIDs += nonCodingRNAList[i].id + " ";
}
var data = searchGeneByID(featuresIDs).responseJSON.response;
if (data.length > 0) {
contentGeneData(data);
} else {
$("#otherNonCodingRNAs-form").append("<div class='alert alert-danger errors'>Ooops, no gene found</div>");
$("#totalResults").hide();
}
} else {
$("#otherNonCodingRNAs-form").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
;
return false;
}
);
});
/**
* Add function to submit form
*/
$(function() {
$("#transcriptionalTerminators-form").submit(
function() {
$(".errors").remove();
var pagedResponse = transcriptionalTerminatorSearch($(this).serialize(), pageSize, offset).responseJSON;
var transcriptionalTerminatorList = pagedResponse.response;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#transcriptionalTerminators-form", totalValues))
idForm = "#transcriptionalTerminators-form";
if (transcriptionalTerminatorList.length > 0) {
$("#searchPanel").hide();
$("#back").show();
var html = "<table class='table table-striped table-bordered table-hover result'>" +
" <thead>" +
" <tr>" +
" <th>Contig</th>" +
" <th>Start coordinate</th>" +
" <th>End coordinate</th>" +
" <th>Confidence</th>" +
" <th>Hairpin score</th>" +
" <th>Tail score</th>" +
" </tr>" +
" </thead>" +
" <tbody>";
for (i = 0; i < transcriptionalTerminatorList.length; i++) {
html += " <tr>" +
" <td>" + transcriptionalTerminatorList[i].contig + " (<a href='"+window.location.pathname.replace("/SearchDatabase", "")+"/DownloadFileByContigAndType?contig=" + transcriptionalTerminatorList[i].contig + "&type=transterm' target='_blank'>result</a>)</td>" +
" <td>" + transcriptionalTerminatorList[i].start + "</td>" +
" <td>" + transcriptionalTerminatorList[i].end + "</td>" +
" <td>" + transcriptionalTerminatorList[i].confidence + "</td>" +
" <td>" + transcriptionalTerminatorList[i].hairpin_score + "</td>" +
" <td>" + transcriptionalTerminatorList[i].tail_score + "</td>" +
" </tr>";
}
html += " </tbody>" +
"</table>";
$("#searchPanel").parent().append(html);
$(".pagination-section").show();
} else {
$("#transcriptionalTerminators-form").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
/**
* Add function to submit form
*/
$(function() {
$("#ribosomalBindingSites-form").submit(
function() {
$(".errors").remove();
var pagedResponse = rbsSearch($(this).serialize(), pageSize, offset).responseJSON;
var rbsList = pagedResponse.response;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#ribosomalBindingSites-form", totalValues))
idForm = "#ribosomalBindingSites-form";
if (rbsList.length > 0) {
$("#searchPanel").hide();
$("#back").show();
var html = "<table class='table table-striped table-bordered table-hover result'>" +
" <thead>" +
" <tr>"+
" <th></th>"+
" <th colspan='2'>Ribosomal binding sites</th>"+
" <th colspan='2'>Old start</th>"+
" </tr>"+
" <tr>" +
" <th>Contig</th>" +
" <th>Site position</th>" +
" <th>Site pattern</th>" +
" <th>Codon</th>" +
" <th>Start Position</th>" +
" <th>New start codon</th>" +
" <th>Position shift</th>" +
" </tr>" +
" </thead>" +
" <tbody>";
for (i = 0; i < rbsList.length; i++) {
html += "<tr>" +
" <td>" + rbsList[i].contig + " (<a href='"+window.location.pathname.replace("/SearchDatabase", "")+"/DownloadFileByContigAndType?contig=" + rbsList[i].contig + "&type=rbsfinder' target='_blank'>result</a>)</td>" +
" <td>" + rbsList[i].end + "</td>" +
" <td>" + rbsList[i].site_pattern + "</td>" +
" <td>" + rbsList[i].old_start + "</td>" +
" <td>" + rbsList[i].old_position + "</td> " +
" <td>" + rbsList[i].new_start + "</td>";
if(rbsList[i].position_shift === undefined) {
html += " <td>0</td>";
} else {
html += " <td>" + rbsList[i].position_shift + "</td>";
}
html += " </tr>";
}
html += " </tbody>" +
"</table>";
$("#searchPanel").parent().append(html);
$(".pagination-section").show();
} else {
$("#ribosomalBindingSites-form").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
$(function() {
$("#geneByPosition").submit(
function() {
$(".errors").remove();
if(idForm != "#geneByPosition") {
offset = 1;
}
var pagedResponse = getGeneByPosition($(this).serialize(), pageSize, offset).responseJSON;
var list = pagedResponse.response;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#geneByPosition", totalValues))
idForm = "#geneByPosition";
if(list.length > 0) {
$("#searchPanel").hide();
$("#back").show();
contentGeneData(list);
} else {
$("#back").click();
$("#horizontalGeneTransfers-form").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
/**
* Add function to submit form
*/
$(function() {
$("#horizontalGeneTransfers-form").submit(
function() {
$(".errors").remove();
var pagedResponse = alienhunterSearch($(this).serialize(), pageSize, offset).responseJSON;
var alienhunterList = pagedResponse.response;
totalValues = pagedResponse.total;
if (!verifyPagedResponse(idForm, "#horizontalGeneTransfers-form", totalValues))
idForm = "#horizontalGeneTransfers-form";
if (alienhunterList.length > 0) {
$("#searchPanel").hide();
$("#back").show();
var html = "<table class='table table-striped table-bordered table-hover result'>" +
" <thead>" +
" <tr>" +
" <th>Genes</th>" +
" <th>Contig</th>" +
" <th>Start coordinate</th>" +
" <th>End coordinate</th>" +
" <th>Score</th>" +
" <th>Length</th>" +
" <th>Threshold</th>" +
" </tr>" +
" </thead>" +
" <tbody>";
for (var i = 0; i < alienhunterList.length; i++) {
html += " <tr>" +
" <td><button id='horizontal-transference-" + alienhunterList[i].id+"' type='button' class='btn btn-info btn-md'>Genes</button></td>" +
" <td>" + alienhunterList[i].contig + " (<a href='"+window.location.pathname.replace("/SearchDatabase", "")+"/DownloadFileByContigAndType?contig=" + alienhunterList[i].contig + "&type=alienhunter' target='_blank'>result</a>)</td>" +
" <td>" + alienhunterList[i].start + "</td>" +
" <td>" + alienhunterList[i].end + "</td>" +
" <td>" + alienhunterList[i].score + "</td>" +
" <td>" + alienhunterList[i].length + "</td>" +
" <td>" + alienhunterList[i].threshold + "</td>" +
" </tr>";
}
html += " </tbody>" +
"</table>";
$("#searchPanel").parent().append(html);
$(".pagination-section").show();
var contig = "";
var start = 0;
var end = 0;
for (var i = 0; i < alienhunterList.length; i++) {
contig = alienhunterList[i].contig;
start = alienhunterList[i].start;
end = alienhunterList[i].end;
$("#horizontal-transference-" + alienhunterList[i].id).click((function(contig, start, end) {
return function() {
$(".result").remove();
$("#contigGenePosition").val(contig);
$("#start").val(start);
$("#end").val(end);
$(".result").remove();
$("#geneByPosition").submit();
return false;
}
})(contig, start, end));
}
contig = "";
start = 0;
end = 0;
} else {
$("#horizontalGeneTransfers-form").append("<div class='alert alert-danger errors'>No results found</div>");
$("#totalResults").hide();
}
return false;
}
);
});
/**
* Method used to deal with content of gene
*
* @param data
* @returns
*/
function contentGeneData(data) {
for (var i = 0; i < data.length; i++) {
var feature = data[i];
var htmlContent = getHTMLContent("search-database/gene.tt").responseJSON.response;
htmlContent = htmlContent.replace(/(\[\% result.feature_id \%\])+/gim, feature.feature_id);
htmlContent = htmlContent.replace(/(\[\% result.name \%\])/gim, feature.name);
htmlContent = htmlContent.replace(/(\[\% result.uniquename \%\])/gim, feature.uniquename);
$("#searchPanel").hide();
$("#back").show();
$(".pagination-section").show();
$("#searchPanel").parent().append(htmlContent);
$("#result-panel-title-" + feature.feature_id).on("click", function() {
var href = $(this).attr('href');
var name = $(this).text().substring(0, $(this).text().indexOf("-") - 1);
var product = $(this).text().substring($(this).text().indexOf("-") + 1, $(this).text().length);
var data = getGeneBasics(href.replace("#", "")).responseJSON.response;
dealDataResults(href, name, data, product);
return false;
});
}
}
/**
* Method used to deal with data results and standard visualization, need to
* modularize
*
* @param href
* panel of results
* @param featureName
* @param data
* @returns
*/
function dealDataResults(href, featureName, data, product) {
if ($(href).is(":hidden")) {
data = data[0];
var htmlContent = getHTMLContent("search-database/geneBasics.tt").responseJSON.response;
htmlContent = htmlContent.replace("[% result.type %]", data.predictor);
htmlContent = htmlContent.replace("[% result.uniquename %]", data.uniquename);
htmlContent = htmlContent.replace("[% result.fstart %]", data.fstart);
htmlContent = htmlContent.replace("[% result.fend %]", data.fend);
htmlContent = htmlContent.replace("[% result.length %]", (data.fend - data.fstart + 1));
var type = data.type;
var name = data.uniquename;
var subsequence = getSubsequence(type, featureName, name, data.fstart, data.fend).responseJSON.response;
var htmlSequence = getHTMLContent("search-database/sequence.tt").responseJSON.response;
htmlSequence = htmlSequence.replace("[% result.pathname %]", window.location.pathname.replace("/SearchDatabase", ""));
htmlSequence = htmlSequence.replace("[% result.contig %]", data.uniquename);
htmlSequence = htmlSequence.replace("[% result.start %]", data.fstart );
htmlSequence = htmlSequence.replace("[% result.end %]", data.fend );
htmlSequence = htmlSequence.replace("[% result.reverseComplement %]", 0);
htmlSequence = htmlSequence.replace("[% result.feature_id %]", href.replace("#", ""));
htmlSequence = htmlSequence.replace("[% result.feature_id %]", href.replace("#", ""));
htmlSequence = htmlSequence.replace("[% result.sequence %]", subsequence.sequence);
if (type == "CDS") {
htmlContent += htmlSequence;
var subevidences = new Array();
subevidences = getSubEvidences(href.replace("#", ""), featureName).responseJSON.response;
//subevidences = subevidences.sort(function(a,b){
// var x = a.type.toLowerCase();
// var y = b.type.toLowerCase();
// return x > y ? -1 : x < y ? 1 : 0;
//});
subevidences = subevidences.sort(function(a,b){
var x = a.program_description.toLowerCase();
var y = b.program_description.toLowerCase();
return x < y ? -1 : x > y ? 1 : 0;
});
var components = new Object();
var componentsEvidences = new Array();
var counterComponentsEvidences = 0;
for (var i = 0; i < subevidences.length; i++) {
var componentName = subevidences[i].program.replace(".pl", "");
if ($.inArray(componentName, componentsEvidences) == -1) {
var htmlEvidence = getHTMLContent("search-database/evidences.tt").responseJSON.response;
htmlEvidence = htmlEvidence.replace("[% result.componentName %]", componentName);
htmlEvidence = htmlEvidence.replace("[% result.id %]", href.replace("#", ""));
if (subevidences[i].type == 'intervals') {
if(subevidences[i].program == "annotation_go.pl") {
var fuckingTitle = subevidences[i].program_description;
if(subevidences[i].is_obsolete[0] == undefined)
fuckingTitle = "<a>" + fuckingTitle + " - No results found</a>";
else
fuckingTitle = "<a href='#evidence-annotation_go-"+href.replace("#", "")+"' data-toggle='collapse' data-parent='#accordion' >" + fuckingTitle + "</a>";
htmlEvidence = "<div class='panel panel-default'>"+
"<div class='panel-heading'>"+
" <div class='panel-title'>" +
" <div class='row'><div class='col-md-12'>" + fuckingTitle + "</div></div>"+
" </div>"+
"</div>"+
"<div id='evidence-annotation_go-"+href.replace("#", "")+"' class='panel-body collapse'>";
var biologicalProcess = "<div class='panel panel-default'><div class='panel-heading'><div class='panel-title'>Biological process</div></div><div class='panel-body'><div class='notice-board'><ul>";
var molecularFunction = "<div class='panel panel-default'><div class='panel-heading'><div class='panel-title'>Molecular function</div></div><div class='panel-body'><div class='notice-board'><ul>";
var celularComponent = "<div class='panel panel-default'><div class='panel-heading'><div class='panel-title'>Celular component</div></div><div class='panel-body'><div class='notice-board'><ul>";
for (var j = 0; j < subevidences[i].is_obsolete.length; j++) {
for (var k = 0; k < subevidences[i].is_obsolete[j].length; k++) {
var evidences = "";
if(subevidences[i].is_obsolete[j][k].includes('Biological Process')) {
evidences = subevidences[i].is_obsolete[j][k].split("Biological Process: ");
} else if(subevidences[i].is_obsolete[j][k].includes('Molecular Function')) {
evidences = subevidences[i].is_obsolete[j][k].split("Molecular Function: ");
} else if(subevidences[i].is_obsolete[j][k].includes('Cellular Component')) {
evidences = subevidences[i].is_obsolete[j][k].split("Cellular Component: ");
}
for(var l = 0; l < evidences.length; l++) {
if(evidences[l] != "") {
var regexGO = /(GO:\d+)/g;
var evidence = evidences[l];
var process = regexGO.exec(evidence);
if(process != null) {
evidence = evidence.replace(process[0], "<a style='color: rgb(35, 82, 124);' target='_blank' href='http://www.ebi.ac.uk/QuickGO/GTerm?id="+process[0]+"'>"+process[0]+"</a>");
}
if(subevidences[i].is_obsolete[j][k].includes('Biological Process') && !biologicalProcess.includes(process[0]) ) {
biologicalProcess+= "<li>" + evidence + "</li>";
} else if(subevidences[i].is_obsolete[j][k].includes('Molecular Function') && !molecularFunction.includes(process[0])) {
molecularFunction+= "<li>" + evidence + "</li>";
} else if(subevidences[i].is_obsolete[j][k].includes('Cellular Component') && !celularComponent.includes(process[0])) {
celularComponent+= "<li>" + evidence + "</li>";
}
}
}
}
}
var caralho = /li/g;
if (caralho.exec(biologicalProcess) == undefined || caralho.exec(biologicalProcess) == null ) {
biologicalProcess += "<li>No terms found</li>";
}
caralho = /li/g;
if (caralho.exec(molecularFunction) == undefined || caralho.exec(molecularFunction) == null) {
molecularFunction += "<li>No terms found</li>";
}
caralho = /li/g;
if (caralho.exec(celularComponent) == undefined || caralho.exec(celularComponent) == null) {
celularComponent += "<li>No terms found</li>";
}
biologicalProcess += "</ul></div></div></div>";
molecularFunction += "</ul></div></div></div>";
celularComponent += "</ul></div></div></div>";
htmlEvidence += biologicalProcess + molecularFunction + celularComponent+ "</div></div></div>";
} else {
htmlEvidence = htmlEvidence.replace("[% result.descriptionComponent %]", "<div class='row'><div class='col-md-11'><a style='color: inherit;' id='anchor-evidence-" + componentName + "-" + href.replace("#", "") + "' data-toggle='collapse' data-parent='#accordion' href='#evidence-" + componentName + "-" + href.replace("#", "") + "'>" + subevidences[i].program_description + "</a></div><div class='col-md-1'><a href='" + window.location.pathname.replace("/SearchDatabase", "") + "/ViewResultByComponentID?locus_tag=" + featureName + "&name="+componentName+"' target='_blank'>View</a></div></div>");
}
} else if(subevidences[i].type == 'similarity') {
htmlEvidence = htmlEvidence.replace("[% result.descriptionComponent %]", "<a id='anchor-evidence-" + componentName + "-" + href.replace("#", "") + "' data-toggle='collapse' data-parent='#accordion' href='#evidence-" + componentName + "-" + href.replace("#", "") + "'>" + subevidences[i].program_description + "</a>");
} else {
if(componentName == 'annotation_tcdb') {
htmlEvidence = htmlEvidence.replace("[% result.descriptionComponent %]", "<div class='row'><div class='col-md-11'>" + subevidences[i].program_description + " - No results found</div></div>");
} else {
htmlEvidence = htmlEvidence.replace("[% result.descriptionComponent %]", "<div class='row'><div class='col-md-11'>" + subevidences[i].program_description + " - No results found</div><div class='col-md-1'><a href='" + window.location.pathname.replace("/SearchDatabase", "") + "/ViewResultByComponentID?locus_tag=" + featureName + "&name="+componentName+"' target='_blank'>View</a></div></div>");
}
}
htmlContent += htmlEvidence;
componentsEvidences[counterComponentsEvidences] = componentName;
counterComponentsEvidences++;
}
if (typeof components[componentName] == 'undefined') {
components[componentName] = new Array();
}
var arrayEvidences = components[componentName];
if(componentName == "annotation_tmhmm") {
arrayEvidences[components[componentName].length] = {
"id" : subevidences[i].id,
"type" : subevidences[i].type,
"start" : subevidences[i].start,
"end" : subevidences[i].end
};
} else {
arrayEvidences[components[componentName].length] = {
"id" : subevidences[i].id,
"type" : subevidences[i].type
};
}
components[componentName] = arrayEvidences;
}
addPanelResult(href, htmlContent);
for (var component in components) {
console.log(component);
if(components[component].id != "") {
$("#anchor-evidence-" + component + "-" + href.replace("#", "")).click(function clickEvidences() {
var componentTemp = this.id.replace("anchor-evidence-", "");
componentTemp = componentTemp.replace("-" + href.replace("#", ""), "");
console.log(componentTemp);
if ($("#evidence-" + componentTemp + "-" + href.replace("#", "")).is(":hidden")) {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
for (i = 0; i < components[componentTemp].length; i++) {
var response = undefined;
if (componentTemp != "annotation_phobius" && componentTemp != "annotation_tmhmm" && componentTemp != 'annotation_orthology' && componentTemp != 'annotation_pathways'
&& componentTemp != 'annotation_interpro' && componentTemp != 'annotation_predgpi' && componentTemp != 'annotation_dgpi' && componentTemp != "annotation_tcdb" && componentTemp != "annotation_signalP") {
response = getSimilarityEvidenceProperties(components[componentTemp][i].id, componentTemp).responseJSON.response;
var htmlSubevidence = getHTMLContent("search-database/subEvidences.tt").responseJSON.response;
htmlSubevidence = htmlSubevidence.replace("[% result.feature_id %]", components[componentTemp][i].id);
htmlSubevidence = htmlSubevidence.replace("[% result.feature_id %]", "<div class='row'><div class='col-md-11'>" + response.identifier + " - " + response.description + "</div><div class='col-md-1'><a href='"+ window.location.pathname.replace("/SearchDatabase", "") +"/ViewResultByComponentID?locus_tag=" + featureName + "&name=" + componentTemp + "' target='_blank'>View</a></div></div>");
htmlSubevidence = htmlSubevidence.replace("[% result.feature_id %]", components[componentTemp][i].id);
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), htmlSubevidence);
}
if (components[componentTemp][i].type == "similarity") {
var html = "";
// if(componentTemp == "annotation_blast" || componentTemp == "annotation_rpsblast") {
html = getHTMLContent("search-database/similarityBasicResult.tt").responseJSON.response;
if (componentTemp == "annotation_blast") {
html = html.replace("[% result.identifier %]", "<a href='http://www.ncbi.nlm.nih.gov/protein/" + response.identifier + "' target='_blank' >" + response.identifier + "</a>");
} else if (componentTemp == "annotation_rpsblast") {
html = html.replace("[% result.identifier %]", "<a href='http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=" + response.identifier + "' target='_blank' >" + response.identifier + "</a>");
} else if (componentTemp == "annotation_hmmer") {
html = html.replace("[% result.identifier %]", response.identifier);
}
html = html.replace("[% result.description %]", response.description);
html = html.replace("[% result.evalue %]", response.evalue);
html = html.replace("[% result.percent_id %]", response.percent_id);
html = html.replace("[% result.similarity %]", response.similarity);
html = html.replace("[% result.score %]", response.score);
html = html.replace("[% result.block_size %]", response.block_size);
// }
addPanelResult("#subevidence-" + response.id, html);
console.log(response);
} else if (components[componentTemp][i].type == "intervals") {
var responseIntervals = getIntervalEvidenceProperties(components[componentTemp][i].id, componentTemp).responseJSON.response;
var listHTMLs = new Array();
var counterHTMLs = 0;
var idTable = "";
var architecture = "";
var counterTMHMM = 0;
if ($("#counterTMHMM").val() >= components[componentTemp].length) {
counterTMHMM = 0;
} else if ($("#counterTMHMM").val() != undefined) {
counterTMHMM = $("#counterTMHMM").val();
}
// ||
// $("#counterTMHMM").val() >= components[componentTemp].length
if ($("#tableArchitectureTMHMM-"+href.replace("#", "")) == undefined ||
$("#counterTMHMM").val() == undefined) {
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), "<table class='table table-striped table-hover'>" +
" <thead><tr><th>Direction</th><th>Start</th><th>End</th></tr></thead>" +
" <tbody id='tableArchitectureTMHMM-"+href.replace("#", "")+"' class='architecture-tmhmm' class='collapsed'>" +
" </tbody>" +
"</table>");
} else {
architecture = $("#tableArchitectureTMHMM-"+href.replace("#", "")).html();
}
if (componentTemp == 'annotation_interpro') {
for (var j = 0; j < responseIntervals.properties.length; j++) {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
html = getHTMLContent("search-database/interproBasicResult.tt").responseJSON.response;
html = html.replace("[% result.componentName %]", componentTemp);
html = html.replace("[% result.componentName %]", componentTemp);
html = html.replace("[% result.feature_id %]", href.replace("#", ""));
html = html.replace("[% result.feature_id %]", href.replace("#", ""));
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.counter %]", responseIntervals.properties[j].interpro_id + ' - ' + responseIntervals.properties[j].description_interpro);
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.interpro_id %]", responseIntervals.properties[j].interpro_id);
html = html.replace("[% result.interpro_id %]", responseIntervals.properties[j].interpro_id);
html = html.replace("[% result.interpro_id %]", responseIntervals.properties[j].interpro_id);
html = html.replace("[% result.description_interpro %]", responseIntervals.properties[j].description_interpro);
html = html.replace("[% result.description_interpro %]", responseIntervals.properties[j].description_interpro);
html = html.replace("[% result.DB_id %]", responseIntervals.properties[j].DB_id);
html = html.replace("[% result.DB_id %]", responseIntervals.properties[j].DB_id);
html = html.replace("[% result.DB_name %]", responseIntervals.properties[j].DB_name);
html = html.replace("[% result.description %]", responseIntervals.properties[j].description);
var regexGO = /(GO:\d+)/g;
if (responseIntervals.properties[j].evidence_process != undefined) {
var evidenceProcess = responseIntervals.properties[j].evidence_process;
var process = regexGO.exec(evidenceProcess);
evidenceProcess = evidenceProcess.replace(process[0], "<a href='http://www.ebi.ac.uk/QuickGO/GTerm?id="+process[0]+"'>"+process[0]+"</a>");
html = html.replace("[% result.evidence_process %]", evidenceProcess);
} else {
html = html.replace("[% result.evidence_process %]", responseIntervals.properties[j].evidence_process);
}
var regexGO = /(GO:\d+)/g;
if (responseIntervals.properties[j].evidence_function != undefined) {
var evidence = responseIntervals.properties[j].evidence_function;
var process2 = regexGO.exec(responseIntervals.properties[j].evidence_function);
evidence= evidence.replace(process2[0], "<a href='http://www.ebi.ac.uk/QuickGO/GTerm?id="+process2[0]+"'>"+process2[0]+"</a>");
html = html.replace("[% result.evidence_function %]", evidence);
} else {
html = html.replace("[% result.evidence_function %]", responseIntervals.properties[j].evidence_function);
}
var regexGO = /(GO:\d+)/g;
if (responseIntervals.properties[j].evidence_component != undefined) {
var evidence= responseIntervals.properties[j].evidence_component;
var process = regexGO.exec(evidence);
evidence= evidence.replace(process[0], "<a href='http://www.ebi.ac.uk/QuickGO/GTerm?id="+process[0]+"'>"+process[0]+"</a>");
html = html.replace("[% result.evidence_component %]", evidence);
} else {
html = html.replace("[% result.evidence_component %]", responseIntervals.properties[j].evidence_component);
}
html = html.replace("[% result.score %]", responseIntervals.properties[j].score);
listHTMLs[counterHTMLs] = html;
counterHTMLs++;
}
idTable = "#evidence-" + componentTemp + "-" + href.replace("#", "");
} else if (componentTemp == 'annotation_tmhmm') {
idTable = "#evidence-" + componentTemp + "-" + href.replace("#", "");
for (var j = 0; j < responseIntervals.properties.length; j++) {
// $("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
counterTMHMM++;
if($("#predicted-"+href.replace("#", "")).text() == "") {
listHTMLs[counterHTMLs] = "<div id='predicted-"+href.replace("#", "")+"' class='row architecture-tmhmm'><div class='col-md-3'><p>Predicted Transmembrane domains</p></div><div class='col-md-9'>" + responseIntervals.properties[j].predicted_TMHs + "</div></div>";
counterHTMLs++;
}
if (responseIntervals.properties[j].direction == "inside") {
$("#tableArchitectureTMHMM-"+href.replace("#", "")).append("<tr><td>Inside the cytoplasm</td><td>"+components[componentTemp][i].start+"</td><td>"+components[componentTemp][i].end+"</td></tr>");
} else if (responseIntervals.properties[j].direction == "outside") {
$("#tableArchitectureTMHMM-"+href.replace("#", "")).append("<tr><td>Outside the cytoplasm</td><td>"+components[componentTemp][i].start+"</td><td>"+components[componentTemp][i].end+"</td></tr>");
} else if (responseIntervals.properties[j].direction == "TMhelix") {
$("#tableArchitectureTMHMM-"+href.replace("#", "")).append("<tr><td>Transmembrane helix</td><td>"+components[componentTemp][i].start+"</td><td>"+components[componentTemp][i].end+"</td></tr>");
}
// if($("#architecture-tmhmm").text() == "" ||
// $("#architecture-tmhmm").text() == undefined ||
// $("#counterTMHMM").val() >= components[componentTemp].length) {
// architecture += " </tbody>" +
// "</table>";
// }
// listHTMLs[counterHTMLs] = "<div class='row architecture-tmhmm'><div class='col-md-3'><p>Architecture:</p></div><div class='col-md-9'><p id='architecture-tmhmm'>" + architecture + "</p></div></div>";
//listHTMLs[counterHTMLs] = "<div class='row architecture-tmhmm'><div class='col-md-12'>"+architecture+"</div></div>";
//counterHTMLs++;
listHTMLs[counterHTMLs] = "<input type='hidden' class='architecture-tmhmm' id='counterTMHMM' value='" + counterTMHMM + "' \>";
counterHTMLs++;
}
} else if (componentTemp == 'annotation_tcdb') {
for (var j = 0; j < responseIntervals.properties.length; j++) {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
html = getHTMLContent("search-database/tcdbBasicResult.tt").responseJSON.response;
html = html.replace("[% result.componentName %]", componentTemp);
html = html.replace("[% result.componentName %]", componentTemp);
html = html.replace("[% result.feature_id %]", href.replace("#", ""));
html = html.replace("[% result.feature_id %]", href.replace("#", ""));
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.counter %]", responseIntervals.properties[j].hit_description);
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.TCDB_ID %]", responseIntervals.properties[j].TCDB_ID);
html = html.replace("[% result.TCDB_ID %]", responseIntervals.properties[j].TCDB_ID);
html = html.replace("[% result.hit_description %]", responseIntervals.properties[j].hit_description);
html = html.replace("[% result.TCDB_class %]", responseIntervals.properties[j].TCDB_class);
html = html.replace("[% result.TCDB_subclass %]", responseIntervals.properties[j].TCDB_subclass);
html = html.replace("[% result.TCDB_family %]", responseIntervals.properties[j].TCDB_family);
html = html.replace("[% result.hit_name %]", responseIntervals.properties[j].hit_name);
html = html.replace("[% result.hit_name %]", responseIntervals.properties[j].hit_name);
html = html.replace("[% result.evalue %]", responseIntervals.properties[j].evalue);
html = html.replace("[% result.percent_id %]", responseIntervals.properties[j].percent_id);
html = html.replace("[% result.similarity %]", responseIntervals.properties[j].similarity);
listHTMLs[counterHTMLs] = html;
counterHTMLs++;
}
idTable = "#evidence-" + componentTemp + "-" + href.replace("#", "");
} else if (componentTemp == 'annotation_pathways') {
for (var j = 0; j < responseIntervals.properties.length; j++) {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
html = getHTMLContent("search-database/pathwaysBasicResult.tt").responseJSON.response;
html = html.replace("[% result.orthologous_group_id %]", responseIntervals.properties[j].orthologous_group_id);
html = html.replace("[% result.orthologous_group_id %]", responseIntervals.properties[j].orthologous_group_id);
html = html.replace("[% result.orthologous_group_id %]", responseIntervals.properties[j].orthologous_group_id);
html = html.replace("[% result.orthologous_group_description %]", responseIntervals.properties[j].orthologous_group_description);
if(responseIntervals.pathways.length > 0) {
html += "<div class='row'>"+
"<div class='col-md-12'>"+
" <div class='table-responsive'>"+
" <table class='table table-striped table-hover'>"+
" <thead>"+
" <tr>"+
" <th>Pathways:</th>"+
" <th>View map:</th>"+
" </tr>"+
" </thead>"+
" <tbody id='pathways-[% result.orthologous_group_id %]'>"+
" </tbody>"+
" </table>"+
" </div>"+
"</div>"+
"</div>";
html = html.replace("[% result.orthologous_group_id %]", responseIntervals.properties[j].orthologous_group_id);
}
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), html);
if(responseIntervals.pathways.length > 0) {
for (var pathway in responseIntervals.pathways) {
var htmlPathway = getHTMLContent("search-database/pathways.tt").responseJSON.response;
htmlPathway = htmlPathway.replace("[% result.metabolic_pathway_id %]", responseIntervals.pathways[pathway].id);
htmlPathway = htmlPathway.replace("[% result.metabolic_pathway_id %]", responseIntervals.pathways[pathway].id);
htmlPathway = htmlPathway.replace("[% result.metabolic_pathway_description %]", responseIntervals.pathways[pathway].description);
htmlPathway = htmlPathway.replace("[% result.viewmap %]", "<a href='reports/"+$("#report_pathways").val() + "/pathway_figures/" + responseIntervals.properties[j].orthologous_group_id +"-"+responseIntervals.pathways[pathway].id+".html' target='_blank'>Link</a>");
listHTMLs[counterHTMLs] = htmlPathway;
counterHTMLs++;
}
} idTable = "#pathways-" + responseIntervals.properties[j].orthologous_group_id;
}
} else if (componentTemp == 'annotation_orthology') {
for (var j = 0; j < responseIntervals.properties.length; j++) {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
html = getHTMLContent("search-database/orthologyBasicResult.tt").responseJSON.response;
html = html.replace("[% result.orthologous_hit %]", responseIntervals.properties[j].orthologous_hit);
html = html.replace("[% result.id %]", responseIntervals.id);
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), html);
for (var orthology in responseIntervals.orthologous_groups) {
var htmlOrthology = getHTMLContent("search-database/orthologies.tt").responseJSON.response;
htmlOrthology = htmlOrthology.replace("[% result.orthologous_group %]", responseIntervals.orthologous_groups[orthology].group);
htmlOrthology = htmlOrthology.replace("[% result.orthologous_group %]", responseIntervals.orthologous_groups[orthology].group);
htmlOrthology = htmlOrthology.replace("[% result.orthologous_group_description %]", responseIntervals.orthologous_groups[orthology].description);
listHTMLs[counterHTMLs] = htmlOrthology;
counterHTMLs++;
}
idTable = "#orthology-" + responseIntervals.id;
}
} else if (componentTemp == 'annotation_predgpi') {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
if (typeof (responseIntervals.properties[0].result) === 'undefined') {
for (var j = 0; j < responseIntervals.properties.length; j++) {
html = getHTMLContent("search-database/predgpiBasicResult.tt").responseJSON.response;
html = html.replace("[% result.componentName %]", componentTemp);
html = html.replace("[% result.componentName %]", componentTemp);
html = html.replace("[% result.feature_id %]", href.replace("#", ""));
html = html.replace("[% result.feature_id %]", href.replace("#", ""));
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.counter %]", responseIntervals.properties[j].name);
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.name %]", responseIntervals.properties[j].name);
html = html.replace("[% result.position %]", responseIntervals.properties[j].position);
html = html.replace("[% result.specificity %]", responseIntervals.properties[j].specificity);
html = html.replace("[% result.sequence %]", responseIntervals.properties[j].sequence);
html = html.replace("[% result.start %]", responseIntervals.properties[j].fstart);
html = html.replace("[% result.end %]", responseIntervals.properties[j].fend);
html = html.replace("[% result.strand %]", (responseIntervals.properties[j].fstart >responseIntervals.properties[j].fend ) ? -1 : 1);
listHTMLs[counterHTMLs] = html;
counterHTMLs++;
}
idTable = "#evidence-" + componentTemp + "-" + href.replace("#", "");
} else {
html = getHTMLContent("search-database/dgpiNoResult.tt").responseJSON.response;
html = html.replace("[% result.result %]", responseIntervals.properties[0].result);
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), html);
}
} else if (componentTemp == 'annotation_dgpi') {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
if (typeof (responseIntervals.properties[0].result) === 'undefined') {
for (var j = 0; j < responseIntervals.properties.length; j++) {
html = getHTMLContent("search-database/dgpiBasicResult.tt").responseJSON.response;
html = html.replace("[% result.componentName %]", componentTemp);
html = html.replace("[% result.componentName %]", componentTemp);
html = html.replace("[% result.feature_id %]", href.replace("#", ""));
html = html.replace("[% result.feature_id %]", href.replace("#", ""));
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.cleavage_site %]", responseIntervals.properties[j].cleavage_site);
html = html.replace("[% result.score %]", responseIntervals.properties[j].score);
html = html.replace("[% result.start %]", responseIntervals.properties[j].start);
html = html.replace("[% result.end %]", responseIntervals.properties[j].end);
html = html.replace("[% result.strand %]", responseIntervals.properties[j].strand);
listHTMLs[counterHTMLs] = html;
counterHTMLs++;
}
idTable = "#evidence-" + componentTemp + "-" + href.replace("#", "");
} else {
html = getHTMLContent("search-database/dgpiNoResult.tt").responseJSON.response;
html = html.replace("[% result.result %]", responseIntervals.properties[0].result);
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), html);
}
} else if (componentTemp == 'annotation_bigpi') {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
if (typeof (responseIntervals.properties[0].result) === 'undefined') {
for (var j = 0; j < responseIntervals.properties.length; j++) {
html = getHTMLContent("search-database/bigpiBasicResult.tt").responseJSON.response;
html = html.replace("[% result.counter %]", responseIntervals.properties[j].p_value);
html = html.replace("[% result.counter %]", counterHTMLs);
html = html.replace("[% result.pvalue %]", responseIntervals.properties[j].p_value);
html = html.replace("[% result.position %]", responseIntervals.properties[j].position);
html = html.replace("[% result.start %]", responseIntervals.properties[j].fstart);
html = html.replace("[% result.end %]", responseIntervals.properties[j].fend);
html = html.replace("[% result.strand %]", (responseIntervals.properties[j].fstart >responseIntervals.properties[j].fend ) ? -1 : 1);
html = html.replace("[% result.score %]", responseIntervals.properties[j].score);
listHTMLs[counterHTMLs] = html;
counterHTMLs++;
}
idTable = "#evidence-" + componentTemp + "-" + href.replace("#", "");
} else {
html = getHTMLContent("search-database/dgpiNoResult.tt").responseJSON.response;
html = html.replace("[% result.result %]", responseIntervals.properties[0].result);
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), html);
}
} else if (componentTemp == 'annotation_signalP') {
for (var j = 0; j < responseIntervals.properties.length; j++) {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
html = getHTMLContent("search-database/signalPBasicResult.tt").responseJSON.response;
html = html.replace("[% result.start_residue %]", responseIntervals.properties[j].start_residue);
html = html.replace("[% result.end_residue %]", responseIntervals.properties[j].end_residue);
html = html.replace("[% result.pep_sig %]", responseIntervals.properties[j].pep_sig);
html = html.replace("[% result.cutoff %]", responseIntervals.properties[j].cutoff);
html = html.replace("[% result.score %]", responseIntervals.properties[j].score);
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), html);
}
} else if (componentTemp == 'annotation_phobius') {
$("#evidence-" + componentTemp + "-" + href.replace("#", "")).empty();
$(".architecture-phobius").remove();
var signal = false;
var cleavage = "";
architecture = "";
var TMs = 0;
addPanelResult("#evidence-" + componentTemp + "-" + href.replace("#", ""), "<table class='table table-striped table-hover'><thead><tr><th>Direction</th><th>Start</th><th>End</th></tr></thead><tbody id='tableArchitecturePhobius-"+href.replace("#", "")+"' class='architecture-phobius' class='collapsed'></tbody></table>");
for (var j = 0; j < responseIntervals.properties.length; j++) {
if (responseIntervals.properties[j].classification == 'SIGNAL') {
signal = true;
}
if (responseIntervals.properties[j].hasOwnProperty("cleavage_position1")) {
cleavage += responseIntervals.properties[j].cleavage_position1;
}
if (responseIntervals.properties[j].hasOwnProperty("cleavage_position2")) {
cleavage += " - " + responseIntervals.properties[j].cleavage_position2;
}
if (responseIntervals.properties[j].hasOwnProperty("predicted_TMHs")) {
TMs = responseIntervals.properties[j].predicted_TMHs;
}
if (responseIntervals.properties[j].hasOwnProperty("region")) {
if (responseIntervals.properties[j].region == "NON CYTOPLASMIC") {
$("#tableArchitecturePhobius-"+href.replace("#", "")).append("<tr><td>Outside the cytoplasm</td><td>"+responseIntervals.properties[j].fstart+"</td><td>"+responseIntervals.properties[j].fend+"</td></tr>");
architecture += "O";
} else if (responseIntervals.properties[j].region == "TRANSMEM") {
$("#tableArchitecturePhobius-"+href.replace("#", "")).append("<tr><td>Transmembrane helix</td><td>"+responseIntervals.properties[j].fstart+"</td><td>"+responseIntervals.properties[j].fend+"</td></tr>");
architecture += "T";
} else if (responseIntervals.properties[j].region == "CYTOPLASMIC") {
$("#tableArchitecturePhobius-"+href.replace("#", "")).append("<tr><td>Inside the cytoplasm</td><td>"+responseIntervals.properties[j].fstart+"</td><td>"+responseIntervals.properties[j].fend+"</td></tr>");
architecture += "I";
}
if (!(j == responseIntervals.properties.length - 1)) {
architecture += "-";
}
}
}
if (signal) {
listHTMLs[counterHTMLs] = "<div class='row architecture-phobius'><div class='col-md-3'><p>Signal peptide:</p></div><div class='col-md-9'><p>Yes</p></div></div>";
counterHTMLs++;
}
if (cleavage != "") {
listHTMLs[counterHTMLs] = "<div class='row architecture-phobius'><div class='col-md-3'><p>Cleavage positions:</p></div><div class='col-md-9'><p>" + cleavage + "</p></div></div>";
counterHTMLs++;
}
if (TMs != 0) {
listHTMLs[counterHTMLs] = "<div class='row architecture-phobius'><div class='col-md-3'><p>Transmembrane domains:</p></div><div class='col-md-9'><p>" + TMs + "</p></div></div>";
counterHTMLs++;
}
// if (architecture != "") {
// listHTMLs[counterHTMLs] = "<div class='row architecture-phobius'><div class='col-md-3'><p>Architecture:</p></div><div class='col-md-9'><p>" + architecture + "</p></div></div>";
// counterHTMLs++;
// listHTMLs[counterHTMLs] = "<div class='row architecture-phobius'><div class='col-md-12'><div class='alert alert-info'><p>Architecture legend: O, outside the cytoplasm; T, transmembrane domain; I, inside the cytoplasm</p></div></div></div>";
// counterHTMLs++;
// }
idTable = "#evidence-" + componentTemp + "-" + href.replace("#", "");
}
// addPanelResult("#subevidence-"+data.id, html);
for (var index in listHTMLs) {
addPanelResult(idTable, listHTMLs[index]);
}
console.log(responseIntervals);
}
}
}
});
}
}
}
if (data.type == "tRNAscan") {
var data = getIntervalEvidenceProperties(href.replace("#", ""), data.type).responseJSON.response;
var htmlBasic = getHTMLContent("search-database/tRNABasicResult.tt").responseJSON.response;
htmlBasic = htmlBasic.replace("[% result.type %]", product);
htmlBasic = htmlBasic.replace("[% result.aminoacid %]", data.properties[0].aminoacid);
htmlBasic = htmlBasic.replace("[% result.anticodon %]", data.properties[0].anticodon);
htmlBasic = htmlBasic.replace("[% result.anticodon_start %]", data.properties[0].anticodon_start);
htmlBasic = htmlBasic.replace("[% result.anticodon_end %]", data.properties[0].anticodon_end);
htmlBasic = htmlBasic.replace("[% result.codon %]", data.properties[0].codon);
htmlBasic = htmlBasic.replace("[% result.score %]", data.properties[0].score);
htmlBasic = htmlBasic.replace("[% result.pseudogene %]", data.properties[0].pseudogene);
htmlBasic = htmlBasic.replace("[% result.download %]", "<a href='"+window.location.pathname.replace("/SearchDatabase", "")+"/DownloadFileByContigAndType?contig=" + name + "&type=" + type.replace("_scan", "").toLowerCase() + "' target='_blank'>Link</a>");
htmlContent += htmlBasic;
if (data.properties[0].hasOwnProperty("intron")) {
if (data.properties[0].intron == "yes") {
htmlBasic = getHTMLContent("search-database/tRNABasicResultHasIntron.tt").responseJSON.response;
htmlBasic = htmlBasic.replace("[% result.intron %]", data.properties[0].intron);
htmlBasic = htmlBasic.replace("[% result.coordinatesGene %]", data.properties[0].intron_start);
htmlBasic = htmlBasic.replace("[% result.coordinatesGenome %]", data.properties[0].intron_start_seq);
htmlContent += htmlBasic;
}
}
htmlContent += htmlSequence;
addPanelResult(href, htmlContent);
} else if (data.type == "RNA_scan") {
var data = getIntervalEvidenceProperties(href.replace("#", ""), data.type).responseJSON.response;
htmlBasic = getHTMLContent("search-database/rnaScanBasicResult.tt").responseJSON.response;
htmlBasic = htmlBasic.replace("[% result.target_description %]", data.properties[0].target_description);
htmlBasic = htmlBasic.replace("[% result.score %]", data.properties[0].score);
htmlBasic = htmlBasic.replace("[% result.evalue %]", data.properties[0].evalue);
htmlBasic = htmlBasic.replace("[% result.target_identifier %]", data.properties[0].target_identifier);
htmlBasic = htmlBasic.replace("[% result.target_name %]", data.properties[0].target_name);
htmlBasic = htmlBasic.replace("[% result.target_class %]", data.properties[0].target_class);
htmlBasic = htmlBasic.replace("[% result.bias %]", data.properties[0].bias);
htmlBasic = htmlBasic.replace("[% result.truncated %]", data.properties[0].truncated);
htmlBasic = htmlBasic.replace("[% result.download %]", "<a href='"+window.location.pathname.replace("/SearchDatabase", "")+"/DownloadFileByContigAndType?contig=" + name + "&type=" + type.replace("_scan", "").toLowerCase() + "' target='_blank'>Link</a>");
htmlContent += htmlBasic;
htmlContent += htmlSequence;
addPanelResult(href, htmlContent);
} else if (data.type == "rRNA_prediction") {
var data = getIntervalEvidenceProperties(href.replace("#", ""), data.type).responseJSON.response;
var htmlBasic = getHTMLContent("search-database/rRNAPredictionBasicResult.tt").responseJSON.response;
htmlBasic = htmlBasic.replace("[% result.molecule_type %]", data.properties[0].molecule_type);
htmlBasic = htmlBasic.replace("[% result.score %]", data.properties[0].score);
htmlBasic = htmlBasic.replace("[% result.download %]", "<a href='"+window.location.pathname.replace("/SearchDatabase", "")+"/DownloadFileByContigAndType?contig=" + name + "&type=" + type.replace("_scan", "").toLowerCase() + "' target='_blank'>Link</a>");
htmlContent += htmlBasic;
htmlContent += htmlSequence;
addPanelResult(href, htmlContent);
}
} else {
$(href).removeClass("collapsed");
$(href).addClass("collapse");
$(href + " .row").remove();
$(href + " .sequences").remove();
$(href + " .panel").remove();
$(href).hide();
}
}
/**
* Method used to add a panel of results in default panel
*
* @param href
* of the panel
* @param htmlContent
* to be added
* @returns
*/
function addPanelResult(href, htmlContent) {
$(href).append(htmlContent);
$(href).removeClass("collapse");
$(href).addClass("collapsed");
$(href).show();
}
/**
* Method used to change view and show data from the contig search
*/
$(function() {
$("#formSearchContig").submit(
function() {
$(".errors").remove();
var data = searchContig($(this).serialize()).responseJSON.response;
var htmlContent = getHTMLContent("search-database/contigs.tt").responseJSON.response;
htmlContent = htmlContent.replace(/(\[\% sequence.path \%\])+/gim, window.location.pathname.replace("/SearchDatabase", ""));
htmlContent = htmlContent.replace(/(\[\% sequence.id \%\])+/gim, data.geneID);
htmlContent = htmlContent.replace(/(\[\% sequence.name \%\])+/gim, data.gene);
htmlContent = htmlContent.replace(/(\[\% start \%\])+/gim, $("input[name=contigStart]").val());
htmlContent = htmlContent.replace(/(\[\% end \%\])/gim, $("input[name=contigEnd]").val());
htmlContent = htmlContent.replace(/(\[\% hadReverseComplement \%\])/gim, data.reverseComplement);
htmlContent = htmlContent.replace(/(\[\% sequence.id \%\])+/gim, data.geneID);
var sequence = ">"+data.gene;
if($("input[name=contigStart]").val() != "" && $("input[name=contigEnd]").val() != "") {
sequence += "_("+$("input[name=contigStart]").val() + "-"+$("input[name=contigEnd]").val()+")";
}
if(data.reverseComplement == 1) {
sequence += "_reverse_complemented";
}
sequence += "<br />"+ data.contig;
htmlContent = htmlContent.replace(/(\[\% contig \%\])+/gim, sequence);
$("#searchPanel").hide();
$("#back").show();
$("#searchPanel").parent().append(htmlContent);
// var titlePanel = "Contig search results";
// if ($("input[name=contigStart]").val() != "" &&
// $("input[name=contigEnd]").val() != "") {
// titlePanel += "from "
// + $("input[name=contigStart]").val()
// + " to "
// + $("input[name=contigEnd]").val() + " of ";
// }
// titlePanel += data.gene;
// if ($("input[name=revCompContig]").is(":checked")) {
// titlePanel += ", reverse complemented";
// }
// titlePanel += ")";
// $("#title-panel").text(titlePanel);
return false;
}
);
});
$("input[name=tmhmmQuant]").change(function() {
if($("input[name=tmhmmQuant]:checked").val() == "none")
$("input[name=TMHMMdom]").prop("disabled", true);
else
$("input[name=TMHMMdom]").prop("disabled", false);
});
$("input[name=tmQuant]").change(function() {
if($("input[name=tmQuant]:checked").val() == "none")
$("input[name=TMdom]").prop("disabled", true);
else
$("input[name=TMdom]").prop("disabled", false);
});
$("input[name=cleavageQuant]").change(function() {
if($("input[name=cleavageQuant]:checked").val() == "none")
$("input[name=cleavageSiteDGPI]").prop("disabled", true);
else
$("input[name=cleavageSiteDGPI]").prop("disabled", false);
});
$("input[name=scoreQuant]").change(function() {
if($("input[name=scoreQuant]:checked").val() == "none")
$("input[name=scoreDGPI]").prop("disabled", true);
else
$("input[name=scoreDGPI]").prop("disabled", false);
});
$("input[name=positionQuantPreDGPI]").change(function() {
if($("input[name=positionQuantPreDGPI]:checked").val() == "none")
$("input[name=positionPreDGPI]").prop("disabled", true);
else
$("input[name=positionPreDGPI]").prop("disabled", false);
});
$("input[name=specificityQuantPreDGPI]").change(function() {
if($("input[name=specificityQuantPreDGPI]:checked").val() == "none")
$("input[name=specificityPreDGPI]").prop("disabled", true);
else
$("input[name=specificityPreDGPI]").prop("disabled", false);
});
$("input[name=pvalueQuantBigpi]").change(function() {
if($("input[name=pvalueQuantBigpi]:checked").val() == "none")
$("input[name=pvalueBigpi]").prop("disabled", true);
else
$("input[name=pvalueBigpi]").prop("disabled", false);
});
$("input[name=positionQuantBigpi]").change(function() {
if($("input[name=positionQuantBigpi]:checked").val() == "none")
$("input[name=positionBigpi]").prop("disabled", true);
else
$("input[name=positionBigpi]").prop("disabled", false);
});
$("input[name=ncRNAevM]").change(function() {
if($("input[name=ncRNAevM]:checked").val() == "none")
$("input[name=ncRNAevalue]").prop("disabled", true);
else
$("input[name=ncRNAevalue]").prop("disabled", false);
});
$("input[name=TRFsize]").change(function() {
if($("input[name=TRFsize]:checked").val() == "none")
$("input[name=TRFrepSize]").prop("disabled", true);
else
$("input[name=TRFrepSize]").prop("disabled", false);
});
$("input[name=TTconfM]").change(function() {
if($("input[name=TTconfM]:checked").val() == "none")
$("input[name=TTconf]").prop("disabled", true);
else
$("input[name=TTconf]").prop("disabled", false);
});
$("input[name=TThpM]").change(function() {
if($("input[name=TThpM]:checked").val() == "none")
$("input[name=TThp]").prop("disabled", true);
else
$("input[name=TThp]").prop("disabled", false);
});
$("input[name=TTtailM]").change(function() {
if($("input[name=TTtailM]:checked").val() == "none")
$("input[name=TTtail]").prop("disabled", true);
else
$("input[name=TTtail]").prop("disabled", false);
});
$("input[name=AHlenM]").change(function() {
if($("input[name=AHlenM]:checked").val() == "none")
$("input[name=AHlen]").prop("disabled", true);
else
$("input[name=AHlen]").prop("disabled", false);
});
$("input[name=AHscM]").change(function() {
if($("input[name=AHscM]:checked").val() == "none")
$("input[name=AHscore]").prop("disabled", true);
else
$("input[name=AHscore]").prop("disabled", false);
});
$("input[name=AHthrM]").change(function() {
if($("input[name=AHthrM]:checked").val() == "none")
$("input[name=AHthr]").prop("disabled", true);
else
$("input[name=AHthr]").prop("disabled", false);
});
$("input[name=scoreQuantBigpi]").change(function() {
if($("input[name=scoreQuantBigpi]:checked").val() == "none")
$("input[name=scoreBigpi]").prop("disabled", true);
else
$("input[name=scoreBigpi]").prop("disabled", false);
});