diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8180015..795780e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,38 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 To see tags and releases, please go to [Tags](https://github.com/BioAnalyticResource/eFP-Seq_Browser/tags) on [GitHub](https://github.com/BioAnalyticResource/eFP-Seq_Browser).
 
+## [1.4.0] - 2024-08-08
+
+New feature:
+
+-   You can now run the eFP-Seq Browser locally on your machine (internet connection still required)\
+
+UI/UX:
+
+-   Added version number to citations
+-   Minor optimizations to improve readability
+
+Optimizations:
+
+-   Refactored and optimized code
+
+Security:
+
+-   Adjustments made to the Google Identity services for FedCM
+
+Update:
+
+-   Update packages
+-   Update service workers
+
+Bug fix:
+
+-   Fixed duplicate element IDs in generate data dialog
+-   Fixed generate data submit loading default data
+-   Fixed missing tissue input not highlighting correctly
+-   Fixed not being able to generate custom data under certain conditions
+-   Fixed styling issues
+
 ## [1.3.15] - 2024-01-15
 
 UI/UX:
diff --git a/cgi-bin/core/custom.js b/cgi-bin/core/custom.js
index 6b6daa9..71fdfd4 100644
--- a/cgi-bin/core/custom.js
+++ b/cgi-bin/core/custom.js
@@ -4,7 +4,7 @@
 //
 //=============================================================================
 /** Current version of eFP-Seq Browser with the following format: [v-version][version number: #.#.#][-][p-public OR d-dev][year - 4 digits][month - 2 digits][day - 2 digits] */
-const version = "v1.3.15-p20240710";
+const version = "v1.4.0-p20240808";
 
 // The following variables are purely meant for local development and testing purposes
 /** If the current environment is a developer environment */
diff --git a/cgi-bin/core/custom.min.js b/cgi-bin/core/custom.min.js
index d9c5f78..140cfc3 100644
--- a/cgi-bin/core/custom.min.js
+++ b/cgi-bin/core/custom.min.js
@@ -1 +1 @@
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data":"cgi-bin/data/bamdata_araport11.xml","Developmental transcriptome - Klepikova et al":"cgi-bin/data/bamdata_Developmental_transcriptome.xml"};let dataset_dictionary=base_dataset_dictionary,loadNewDataset=!1,count_bam_entries_in_xml=113;function count_bam_num(){const xhr=new XMLHttpRequest,url=base_src;xhr.responseType="document",xhr.onreadystatechange=()=>{if(xhr.readyState===XMLHttpRequest.DONE&&200===xhr.status){const response=xhr.responseXML;response&&response.getElementsByTagName("file")?count_bam_entries_in_xml=xhr.responseXML.getElementsByTagName("file").length:null==response&&console.log("failed at response"),document.getElementById("testing_count").innerHTML=count_bam_entries_in_xml}},xhr.open("GET",url),xhr.send()}function loadingScreen(terminate=!0){if(!1===terminate){document.getElementById("loading_screen").className="loading",document.getElementById("body_of").className="body_of_loading",document.getElementById("bodyContainer").classList.add("progressLoading"),document.getElementById("loading_screen").removeAttribute("hidden");const toDisableList=document.getElementsByClassName("disableOnLoading");for(const element of toDisableList)$("#"+element.id).prop("disabled",!0)}else{document.getElementById("loading_screen").className="loading done_loading",document.getElementById("body_of").className="body_of_loading body_of_loading_done",document.getElementById("bodyContainer").classList.remove("progressLoading"),document.getElementById("loading_screen").setAttribute("hidden",!0);const toDisableList=document.getElementsByClassName("disableOnLoading");for(const element of toDisableList)$("#"+element.id).prop("disabled",!1);addGFF(),uploadingData=!1}}count_bam_num();const 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round(x,digits){return parseFloat(x.toFixed(digits))}let colouring_part;function colour_part_by_id(id,part,fpkm,mode){colouring_part="all";for(const sra of sraList)id.replace("_svg","")==sra&&(colouring_part=sraDict[sra].svg_part);let paths1,paths2,fpkmUse=fpkm;fpkmUse=Array.isArray(fpkmUse)?fpkmUse[variantPosition]:parseFloat(fpkmUse),max_abs_scale=document.getElementById("rpkm_scale_input").value,(!max_abs_scale||max_abs_scale<=0)&&(max_abs_scale=1e3),document.getElementById(id)&&(paths1=document.getElementById(id).getElementsByTagName("path"),paths2=document.getElementById(id).getElementsByTagName("g"));let paths=null;if(paths1&&paths2&&(paths=Array.prototype.slice.call(paths1).concat(Array.prototype.slice.call(paths2))),null!=paths){if("abs"==mode){const r=255,g=255-parseInt(fpkmUse/max_abs_scale*255),b=0;if("all"==colouring_part)for(const path of paths)path.style.fill="rgb("+r+", "+g+", "+b+")";else for(const path of paths)if(path.id==colouring_part)if("g"==path.tagName){const 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data"==fpkmUse?fpkmUse:round(fpkmUse,2)}else console.log("Paths is null for id = "+id)}let rpkmAverage=1,rpkmMedian=1;function findRPKMValuesAcrossAll(){if(sraDict){const listOfSRA=Object.keys(sraDict),listOfRPKM=[];let rpkmTotal=0;for(const sra of listOfSRA)if(sraDict[sra].RPKM){const currentRPKM=sraDict[sra].RPKM[variantPosition];parseFloat(currentRPKM)&&(listOfRPKM.push(currentRPKM),rpkmTotal+=currentRPKM)}listOfRPKM.length>0&&(rpkmMedian=math.median(listOfRPKM)),rpkmAverage=rpkmTotal/listOfSRA.length}else displayError("ERROR IN RETRIEVING ALL DATA POINTS WITHIN DATASET")}function switchRPKMMode(selectedMode){let rel=!1;"rel_radio"===selectedMode&&(rel=!0),rel?(colouring_mode="rel",document.getElementById("abs_radio").classList.remove("active"),document.getElementById("rel_radio").classList.add("active"),$("#rpkm_scale_input").prop("disabled",!0)):(colouring_mode="abs",document.getElementById("rel_radio").classList.remove("active"),document.getElementById("abs_radio").classList.add("active"),$("#rpkm_scale_input").removeAttr("disabled")),rnaseq_calls&&rnaseq_calls.length>0&&whichAbsOrRel()}function colour_svgs_now(){const mode=colouring_mode;for(let i=0;i<count_bam_entries_in_xml;i++){if(exp_info[i]){const currentSRA=exp_info[i][0].slice(0,-4);let ctrl_fpkm_sum=0,ctrl_count=0,ctrl_avg_fpkm=0;for(let ii=0;ii<count_bam_entries_in_xml;ii++)-1!=exp_info[i][2].indexOf(exp_info[ii][0].slice(0,-4))&&(ctrl_count++,ctrl_fpkm_sum+=exp_info[ii][3][variantPosition]);0===ctrl_fpkm_sum&&sraDict[currentSRA].RPKM&&(ctrl_fpkm_sum=sraDict[currentSRA].RPKM[variantPosition]),ctrl_count>0?ctrl_avg_fpkm=ctrl_fpkm_sum/ctrl_count:(rpkmMedian&&1===rpkmMedian&&findRPKMValuesAcrossAll(),ctrl_avg_fpkm=rpkmMedian);let relativeRPKMValue=0;const relativeRPKM=[];let useRPKM="";useRPKM=sraDict[currentSRA].RPKM&&sraDict[currentSRA].RPKM[variantPosition]?sraDict[currentSRA].RPKM[variantPosition]:0,0==useRPKM&&0==ctrl_avg_fpkm?exp_info[i].splice(4,1,0):relativeRPKMValue=Math.log2(useRPKM/ctrl_avg_fpkm),relativeRPKM.push(relativeRPKMValue),sraDict[currentSRA].relativeRPKM=relativeRPKMValue,exp_info[i].splice(4,1,relativeRPKM),exp_info[i].splice(6,1,ctrl_avg_fpkm),useRPKM>=max_absolute_fpkm&&(max_absolute_fpkm=useRPKM),"Missing controls data"!=exp_info[i][4]&&Math.abs(exp_info[i][4])>=max_log_fpkm&&Math.abs(exp_info[i][4])<1e3&&(max_log_fpkm=Math.abs(exp_info[i][4])),"rel"===colouring_mode?exp_info[i][4]||0==exp_info[i][4]||(exp_info[i][4]=-999999):exp_info[i][3][variantPosition]||0==exp_info[i][3][variantPosition]||(exp_info[i][3][variantPosition]=-999999)}else logError("Issue retrieving exp_info for "+mode+" within BAM entry point "+i);whichAbsOrRel()}document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update"),change_rpkm_colour_scale(colouring_mode)}function get_input_values(){locus=document.getElementById("locus").value,locus=locus.trim().toUpperCase(),yscale_input=document.getElementById("yscale_input").value,("Auto"==yscale_input||parseInt(yscale_input)<1)&&(yscale_input=parseInt(-1)),max_abs_scale=document.getElementById("rpkm_scale_input").value}function update_all_images(status){null!=document.getElementById("locus")&&(new_locus=document.getElementById("locus").value,new_locus===old_locus?($.xhrPool.abortAll(),variants_radio_options(status)):new_locus!=old_locus&&(getGFF(new_locus),old_locus=new_locus,setTimeout((function(){$.xhrPool.abortAll(),variants_radio_options(status)}),1650)))}async function variants_radio_options(status){get_input_values(),fetch(`${BE_URL}/cgi-bin/get_gene_structures.cgi?locus=${locus}`).then((async response=>{const gene_res=await response.json();locus_start=gene_res.locus_start,locus_end=gene_res.locus_end,splice_variants=JSON.stringify(gene_res.splice_variants),populate_table(status),populate_efp_modal(status);const variants_div=document.getElementById("variants_div");if(variants_div?.firstChild)for(;variants_div.firstChild;)variants_div.removeChild(variants_div.firstChild);$("#variant_select").ddslick("destroy");let append_str='<select id="variant_select">';if(gene_res.variant_count&&parseInt(gene_res.variant_count)>0)for(let i=0;i<parseInt(gene_res.variant_count);i++)gene_res.splice_variants?.[i]?.gene_structure&&(append_str+='<option value="'+i+'"',append_str+=' data-imagesrc="data:image/png;base64,'+gene_res.splice_variants[i].gene_structure+'" style="max-width:none;"></option>');else append_str+='<option value="'+i+'"',append_str+=' data-imagesrc="'+img_gene_struct_error+'" style="max-width:none;"></option>';if(gene_res.splice_variants?.[0]?.gene_structure){img_gene_struct_1="data:image/png;base64,"+gene_res.splice_variants[0].gene_structure;const all_gene_structure_imgs=document.getElementsByClassName("gene_structure_img");for(const element of all_gene_structure_imgs)element.src="data:image/png;base64,"+gene_res.splice_variants[0].gene_structure}else{img_gene_struct_1=img_gene_struct_error;const all_gene_structure_imgs=document.getElementsByClassName("gene_structure_img");for(const element of all_gene_structure_imgs)element.src="data:image/png;base64,"+gene_res.splice_variants[0].gene_structure}$("input[type=radio][name=radio_group]").change((function(){gene_structure_radio_on_change()})),append_str+="</select></div>",$("#variants_div").append(append_str),document.getElementById("variant_select")&&$("#variant_select").ddslick({width:"100%",onSelected:function(){gene_structure_radio_on_change()}}),document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update")})).catch((error=>{displayError("ERROR processing and getting gene structures!"),generateToastNotification(`Error processing gene structures: ${error.message}`,"ERROR"),console.error(`Error processing gene structures: ${error.message}`)}))}function displayError(errorMessage){$("#displayError").empty();let append_str='<p class="warning_core" style="text-align:center;">'+errorMessage+" <br /><br /> PLEASE REFRESH PAGE, RELOAD OR RE-INPUT DATA OR TRY AGAIN AT A LATER TIME </p>";console.error("Error in logic:",errorMessage),$("#displayError").append(append_str),$("#locus_button").prop("disabled",!0),$("#abs_scale_button").prop("disabled",!0),progress_percent=100,$("div#progress").width(progress_percent+"%"),loadingScreen(!0),document.title=`eFP-Seq Browser: !ERROR! - ${locus} - ${datasetName}`}function logError(errorMessage){console.error("Error in logic:",errorMessage)}let variant_selected,variantPosition=0;function gene_structure_radio_on_change(){if(document.getElementsByClassName("dd-selected-value")&&document.getElementsByClassName("dd-selected-value")[0]&&document.getElementsByClassName("dd-selected-value")[0].value){variant_selected=document.getElementsByClassName("dd-selected-value")[0].value,variantPosition=variant_selected;let variant_img=document.getElementsByClassName("dd-selected-image")[0].src;document.getElementsByClassName("dd-selected-image")&&document.getElementsByClassName("dd-selected-image")[0]&&!document.getElementsByClassName("dd-selected-image")[0].alt&&(document.getElementsByClassName("dd-selected-image")[0].alt="RNA-Seq Coverage");let all_gene_structure_imgs=document.getElementsByClassName("gene_structure_img");for(let i=0;i<all_gene_structure_imgs.length;i++)all_gene_structure_imgs[i].src=variant_img;for(let i=0;i<exp_info.length;i++){let itLocus=exp_info[i][0].split("_")[0];document.getElementById(itLocus+"_gene_structure_img").src=variant_img;let rpkmValue,rpbValue=sraDict[itLocus].r[variant_selected].toFixed(2);document.getElementById(itLocus+"_rpb").innerHTML=rpbValue,sraDict[exp_info[i][0].split("_svg")[0]]||(sraDict[exp_info[i][0].split("_svg")[0]]={}),sraDict[exp_info[i][0].split("_svg")[0]].rpb=rpbValue,sraDict[itLocus].RPKM&&sraDict[itLocus].RPKM[variant_selected]?rpkmValue=sraDict[itLocus].RPKM[variant_selected].toFixed(2):sraDict[itLocus].RPKM?logError("Unable to retrieve RPKM values at: [variant_selected] for "+itLocus):sraDict[itLocus]?logError('Unable to retrieve RPKM values at: ["RPKM"] for '+itLocus):logError(sraDict?"Unable to retrieve RPKM values at: SRA within sraDict":"Unable to retrieve RPKM values at: sraDict unreachable"),document.getElementById(itLocus+"_rpkm").innerHTML=rpkmValue,whichAbsOrRel(!0,i)}}document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update")}function whichAbsOrRel(preIterate=!1,iteratePos=0){if(!0===preIterate)absOrRel(iteratePos);else if(exp_info.length>0)for(let i=0;i<exp_info.length;i++)absOrRel(i);change_rpkm_colour_scale(colouring_mode)}function absOrRel(expInfoPos=0){let expInfo=exp_info[expInfoPos],currentSRA=expInfo[0].slice(0,-4);if("rel"==colouring_mode&&sraDict[currentSRA].relativeRPKM){document.getElementById("compareGeneVariants").disabled=!0,expInfo&&!expInfo[4]&&0!=expInfo[4]&&(expInfo[4]=-999999);let rpkmValue=sraDict[currentSRA].relativeRPKM.toFixed(2);document.getElementById(expInfo[0].split("_svg")[0]+"_rpkm").innerHTML=rpkmValue,sraDict[expInfo[0].split("_svg")[0]].rpkm=rpkmValue,colour_part_by_id(currentSRA+"_svg",sraDict[currentSRA].svg_part,sraDict[currentSRA].relativeRPKM,colouring_mode)}else{allCheckedOptions.length>0&&(document.getElementById("compareGeneVariants").disabled=!1),expInfo[3]||0==expInfo[3]||(expInfo[3]=-999999);let useRPKM="";if(variant_selected&&sraDict[currentSRA].RPKM&&sraDict[currentSRA].RPKM[variant_selected]){let rpkmValue=sraDict[currentSRA].RPKM[variant_selected].toFixed(2);document.getElementById(expInfo[0].split("_svg")[0]+"_rpkm").innerHTML=rpkmValue,useRPKM=rpkmValue}else{let rpkmValue=0;document.getElementById(expInfo[0].split("_svg")[0]+"_rpkm").innerHTML=rpkmValue,useRPKM=rpkmValue}colour_part_by_id(currentSRA+"_svg",sraDict[currentSRA].svg_part,useRPKM,colouring_mode)}}function parseIntArray(arr){for(let i=0,len=arr.length;i<len;i++)arr[i]=parseInt(arr[i],10);return arr}let rnaseq_image_url=`${BE_URL}/cgi-bin/rnaSeqMapCoverage.cgi`,match_drive="",progress_percent=0,rnaseq_change=1,totalreadsMapped_dic={},dumpOutputs="",dumpMethod="simple",callDumpOutputs=!1,rpkmCount=1,listOfRecordsDisplayed=[];function rnaseq_images(status){changePublicData();if(dumpOutputs="",data={},rnaseq_success=1,rpkmCount=1,match_drive="",listOfRecordsDisplayed=[],get_input_values(),CreateFilteredeFPList(),rnaseq_calls.length===count_bam_entries_in_xml){rnaseq_change=1;for(let i=0;i<count_bam_entries_in_xml;i++){let tissueWebservice=rnaseq_calls[i][0]||"undefined",sraRecordNumber=rnaseq_calls[i][1]||"unknown";if("Google Drive"===sraDict[sraList[i]].bam_type){let linkString=sraDict[sraList[i]].drive_link,driveLinkSplit=linkString.split("?usp=sharing");driveLinkSplit=driveLinkSplit[0].split("drive.google.com/drive/folders/"),match_drive=driveLinkSplit.length>1?driveLinkSplit[1]:linkString}else if("Amazon AWS"===sraDict[sraList[i]].bam_type){let linkString=sraDict[sraList[i]].drive_link,driveLinkSplit=linkString.split("amazonaws.com/");1===driveLinkSplit.length&&(driveLinkSplit=linkString.split("araport.cyverse-cdn.tacc.cloud/")),match_drive=driveLinkSplit.length>1?driveLinkSplit[1]:linkString}data={status:status,numberofreads:sraDict[sraList[i]].numberofreads,hexcodecolour:sraDict[sraList[i]].hexColourCode,remoteDrive:match_drive,bamType:sraDict[sraList[i]].bam_type,filename:sraDict[sraList[i]].filenameIn,tissue:tissueWebservice,record:sraRecordNumber,locus:locus,variant:1,start:locus_start,end:locus_end,yscale:yscale_input,cachedDatapoints:publicData,struct:splice_variants,dumpMethod:dumpMethod},$.ajax({method:"POST",url:rnaseq_image_url,data:data,dataType:"json",failure:function(){$("#failure").show()},success:function(response_rnaseq){let stopLoadingScreen=99;count_bam_entries_in_xml>0&&(stopLoadingScreen=parseInt((count_bam_entries_in_xml-1)/count_bam_entries_in_xml*100)),rnaseq_success++;let date_obj3=new Date;if(rnaseq_success_current_time=date_obj3.getTime(),progress_percent=rnaseq_change/count_bam_entries_in_xml*100,$("div#progress").width(progress_percent+"%"),progress_percent>stopLoadingScreen&&loadingScreen(!0),document.getElementById("progress_tooltip").innerHTML="Current progress is at "+progress_percent+"% done",document.getElementById("progress").title=progress_percent.toFixed(2)+"% ("+rnaseq_change+"/"+count_bam_entries_in_xml+")",document.title="eFP-Seq Browser:",progress_percent<100&&(document.title+=` Loading ${progress_percent.toFixed(1)}% -`),document.title+=` ${locus} - ${datasetName}`,response_rnaseq.status&&"success"===response_rnaseq.status&&response_rnaseq.record){let responseRecord=response_rnaseq.record||"unknown";if(listOfRecordsDisplayed.includes(responseRecord)?(responseRecord=findUnusedRecordDisplayName(responseRecord,listOfRecordsDisplayed),listOfRecordsDisplayed.push(responseRecord)):listOfRecordsDisplayed.push(responseRecord),listOfRecordsDisplayed=[],sraDict[responseRecord].bp_length=parseFloat(response_rnaseq.end)-parseFloat(response_rnaseq.start),sraDict[responseRecord].bp_start=parseFloat(response_rnaseq.start),sraDict[responseRecord].bp_end=parseFloat(response_rnaseq.end),sraDict[responseRecord].MappedReads=response_rnaseq.reads_mapped_to_locus,totalreadsMapped_dic[responseRecord]=response_rnaseq.totalReadsMapped,sraDict[responseRecord].locusValue=response_rnaseq.locus,sraDict[responseRecord].r=response_rnaseq.r,sraDict[responseRecord].dataVisualization=response_rnaseq.rnaseqbase64,locus!=response_rnaseq.locus)throw new Error(`ERROR: ${locus}'s RNA-Seq API request returned with data for some other locus.`);let r=[];if(response_rnaseq.ss_y&&response_rnaseq.sum_y&&response_rnaseq.sum_xy&&response_rnaseq.sum_x&&response_rnaseq.ss_x&&response_rnaseq.end&&response_rnaseq.start){parseInt(response_rnaseq.ss_y);let sum_y=parseInt(response_rnaseq.sum_y),ssy=parseInt(response_rnaseq.ss_y),sum_xy=parseIntArray(response_rnaseq.sum_xy.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),sum_x=parseIntArray(response_rnaseq.sum_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),ssx=(parseIntArray(response_rnaseq.sum_xx.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),parseIntArray(response_rnaseq.ss_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),parseIntArray(response_rnaseq.ss_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(","))),n=parseInt(response_rnaseq.end)-parseInt(response_rnaseq.start),sp=[];for(let i=0;i<sum_xy.length;i++)sp.splice(i,0,sum_xy[i]-sum_x[i]*sum_y/n),r.splice(i,0,sp[i]/Math.sqrt(ssx[i]*ssy))}else r=response_rnaseq.r;if(document.getElementById(responseRecord+"_rnaseq_img")&&response_rnaseq.rnaseqbase64?"None"!==response_rnaseq.rnaseqbase64&&response_rnaseq.rnaseqbase64.length>=3?(document.getElementById(responseRecord+"_rnaseq_img").src="data:image/png;base64,"+response_rnaseq.rnaseqbase64,rnaseq_change+=1):(document.getElementById(responseRecord+"_rnaseq_img").src="https://"+window.location.host+window.location.pathname+"cgi-bin/img/error.webp",console.error("Unable to create RNA-Seq map coverage data for: Locus - "+locus+", SRA - "+responseRecord+", dataset - "+base_src)):(document.getElementById(`${responseRecord}_rnaseq_img`)&&(document.getElementById(`${responseRecord}_rnaseq_img`).src=`https://${window.location.host}${window.location.pathname}/cgi-bin/img/error.webp`),console.error("Unable to create RNA-Seq map coverage data for: Locus - "+locus+", SRA - "+responseRecord+", dataset - "+base_src)),document.getElementById(responseRecord+"_rpb").innerHTML=parseFloat(r[0]).toFixed(2),sraDict[responseRecord].rpb=parseFloat(r[0]).toFixed(2),document.getElementById(responseRecord+"_rpkm").innerHTML=response_rnaseq["absolute-fpkm"],updateRPKMAbsoluteMax(response_rnaseq["absolute-fpkm"]),sraDict[responseRecord].RPKM=response_rnaseq["absolute-fpkm"],rpkmCount++,document.getElementById(responseRecord+"_totalReadsNum").innerHTML="Total reads = "+response_rnaseq.totalReadsMapped,callDumpOutputs)if(dumpOutputs+='\t\telif (record == "'+response_rnaseq.record+'"):\n',"complex"==dumpMethod){for(dumpOutputs+='\t\t\tdumpJSON(200, "'+response_rnaseq.locus+'", '+response_rnaseq.variant+", "+response_rnaseq.chromosome+", "+response_rnaseq.start+", "+response_rnaseq.end+', "'+response_rnaseq.record+'", "'+response_rnaseq.tissue+'", "'+response_rnaseq.rnaseqbase64+'", '+response_rnaseq.reads_mapped_to_locus+", "+response_rnaseq["absolute-fpkm"]+", ["+response_rnaseq.r+"], "+response_rnaseq.totalReadsMapped+", ["+response_rnaseq.exp_arr+"], [",r=0;r<response_rnaseq.ReadsMappedNucleotidePosition.length;r+=2)dumpOutputs+="["+response_rnaseq.ReadsMappedNucleotidePosition[r]+"]",r!=response_rnaseq.ReadsMappedNucleotidePosition.length-2&&(dumpOutputs+=", ");dumpOutputs+="], {";for(let e=0;e<response_rnaseq.expected_expr_in_variant.length;e++)dumpOutputs+='"'+GFF_List[e].replace(locus,"")+'": ',dumpOutputs+="["+response_rnaseq.expected_expr_in_variant[e]+"]",e!=response_rnaseq.expected_expr_in_variant.length-1&&(dumpOutputs+=", ");dumpOutputs+="})\n"}else dumpOutputs+='\t\t\tdumpJSON(200, "'+response_rnaseq.locus+'", '+response_rnaseq.variant+", "+response_rnaseq.chromosome+", "+response_rnaseq.start+", "+response_rnaseq.end+', "'+response_rnaseq.record+'", "'+response_rnaseq.tissue+'", "'+response_rnaseq.rnaseqbase64+'", '+response_rnaseq.reads_mapped_to_locus+", ["+response_rnaseq["absolute-fpkm"]+"], ["+response_rnaseq.r+"], "+response_rnaseq.totalReadsMapped+")\n";for(let ii=0;ii<count_bam_entries_in_xml;ii++)exp_info&&exp_info[ii]&&exp_info[ii][0]&&exp_info[ii][0]==responseRecord+"_svg"&&(exp_info[ii].splice(3,1,response_rnaseq["absolute-fpkm"]),exp_info[ii].splice(5,1,r));colour_part_by_id(responseRecord+"_svg","Shapes",response_rnaseq["absolute-fpkm"][variantPosition],colouring_mode)}else if(response_rnaseq.status&&"fail"===response_rnaseq.status){let responseRecord=response_rnaseq.record||"unknown";listOfRecordsDisplayed.includes(responseRecord)?(responseRecord=findUnusedRecordDisplayName(responseRecord,listOfRecordsDisplayed),listOfRecordsDisplayed.push(responseRecord)):listOfRecordsDisplayed.push(responseRecord),responseRecord&&document.getElementById(`${responseRecord}_rnaseq_img`)&&(document.getElementById(`${responseRecord}_rnaseq_img`).src=`https://${window.location.host}${window.location.pathname}/cgi-bin/img/error.webp`),rnaseq_change+=1,responseRecord&&document.getElementById(responseRecord+"_rpb")&&(document.getElementById(responseRecord+"_rpb").innerHTML=null,sraDict[responseRecord]||(sraDict[responseRecord]={}),sraDict[responseRecord].rpb=null),responseRecord&&document.getElementById(responseRecord+"_rpkm")&&(document.getElementById(responseRecord+"_rpkm").innerHTML=null,updateRPKMAbsoluteMax(null),sraDict[responseRecord].RPKM=null),rpkmCount++,responseRecord&&document.getElementById(responseRecord+"_totalReadsNum")&&response_rnaseq.totalReadsMapped&&(document.getElementById(responseRecord+"_totalReadsNum").innerHTML="Total reads = "+response_rnaseq.totalReadsMapped),responseRecord&&document.getElementById(responseRecord+"_row")&&document.getElementById(responseRecord+"_row").classList.add("mainEntriesError"),console.error("Unable to create RNA-Seq map coverage data for: Locus - "+locus+", SRA - "+responseRecord+", dataset - "+base_src)}else console.log("Error!",response_rnaseq,data);rpkmCount==count_bam_entries_in_xml&&(colour_svgs_now(),date_obj4=new Date,rnaseq_success_end_time=date_obj4.getTime(),document.getElementById("progress_tooltip").innerHTML=rnaseq_success+" / count_bam_entries_in_xml requests completed<br/>Load time ~= "+String(round(parseInt(rnaseq_success_end_time-rnaseq_success_start_time)/6e4))+" mins."),document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update"),responsiveRNAWidthResize(),toggleResponsiveTable()},error:function(xhr,status,error){generateToastNotification(`Error getting RNA-Seq map coverage for ${data.record} - ${error.message}`,"ERROR"),console.error("Error getting RNA-Seq map coverage!",xhr,status,error)}})}}}function findUnusedRecordDisplayName(recordID="unknown",listCheckAgainst=sraList,it=0){if(Array.isArray(listCheckAgainst)){let newName=recordID+"_"+it;if(listCheckAgainst.includes(newName))findUnusedRecordDisplayName(recordID,listCheckAgainst,it+1);else if(!listCheckAgainst.includes(newName))return newName}else findUnusedRecordDisplayName(recordID,listCheckAgainst=[])}function updateRPKMAbsoluteMax(RPKMCheckAgainst){let currentRPKMAbsMax=parseInt(document.getElementById("rpkm_scale_input").value);1e3===currentRPKMAbsMax&&(currentRPKMAbsMax=1);let newRPKMValue=parseInt(RPKMCheckAgainst);newRPKMValue>currentRPKMAbsMax&&(document.getElementById("rpkm_scale_input").value=newRPKMValue)}const svgAgainstData={"ath-10dayOldSeedling":{name:"10 Day Old Seedling",subunit:["all","root","shoot"]},"ath-15dayOldSeedling":{name:"15 Day Old Seedling",subunit:["all","root","shoot"]},"ath-etiolatedSeedling":{name:"Etiolated Seedling",subunit:["etiolatedseedling"]},"ath-Flower":{name:"Flower",subunit:["flower","receptacle"]},"ath-FlowerParts":{name:"Flower Parts",subunit:["all","petals","stamen","sepals","carpels"]},"ath-GerminatingSeed":{name:"Germinating Seed"},"ath-Internode":{name:"Internode"},"ath-leaf":{name:"Leaf",subunit:["leaf"]},"ath-LeafParts":{name:"Leaf Parts",subunit:["all","lamina","petiole","veins"]},"ath-Pollen":{name:"Pollen"},"ath-RootTip":{name:"Root Tip"},"ath-rosettePlusRoot":{name:"Rosette Plus Root",subunit:["all","shoot","root"]},"ath-Seed1-4":{name:"Seed 1-4"},"ath-Seed5-7":{name:"Seed 5-7"},"ath-Seed8+":{name:"Seed 8+"},"ath-SenescentLeaf":{name:"Senescent Leaf"},"ath-ShootApexInflorescense":{name:"Shoot Apex Inflorescense"},"ath-ShootApexVegetative-Transition":{name:"Shoot Apex Vegetative-Transition"},"ath-Silique1-5":{name:"Silique 1-5"},"ath-Silique6-10":{name:"Silique 6-10"},"ath-YoungLeaf1-4":{name:"Young Leaf 1-4"},"ath-EarlyBuddingFlower":{name:"Early Budding Flower",subunit:["all","shoot","buds"]},"ath-EarlyBuddingFlower":{name:"Early Budding Flower",subunit:["all","shoot","buds"]},"ath-FlowerBud":{name:"Flower Bud",subunit:["flowerBud"]},"ath-Stamen":{name:"Stamen",subunit:["all","anthers","filament"]},"ath-StigmaAndOvaries":{name:"Stigma And Ovaries",subunit:["all","Stigma_tissue","Ovary_tissue"]},"ath-WholeSilique":{name:"Whole Silique",subunit:["silique","all","seed"]},"ath-youngSeedling":{name:"Young Seedling",subunit:["all","root","hypocotyl","cotyledon"]},"ath-FlowerDevelopment1":{name:"Late Flower Development (1)",subunit:["flowerDevelopmentPart1"]},"ath-FlowerDevelopment2":{name:"Flower Development 2",subunit:["flowerDevelopmentPart2"]},"ath-FlowerDevelopment3":{name:"Flower Development 3",subunit:["flowerDevelopmentPart3"]},"ath-FlowerDevelopment4":{name:"Flower Development 4",subunit:["flowerDevelopmentPart4"]},"ath-FlowerDevelopment5":{name:"Flower Development 5",subunit:["flowerDevelopmentPart5"]},"ath-FlowerDevelopment6-8":{name:"Flower Development 6-8",subunit:["flowerDevelopmentPart6"]},"ath-FlowerDevelopment9-11":{name:"Flower Development 9-11",subunit:["flowerDevelopmentPart9"]},"ath-FlowerDevelopment12-14":{name:"Flower Development 12-14",subunit:["flowerDevelopmentPart12"]},"ath-FlowerDevelopment15-18":{name:"Flower Development 15-18",subunit:["flowerDevelopmentPart15"]},"ath-FlowerDevelopment19":{name:"Flower Development 19",subunit:["flowerDevelopmentPart19"]},"ath-Other":{name:"Other"}};function checkAgainstSVG(svg,subunit,returnName=!1){let svgName=svg.split(".")[0],toReturn=returnName?svgAgainstData[svgName].name:subunit;return svgAgainstData[svgName]&&!returnName&&(svgAgainstData[svgName].subunit?svgAgainstData[svgName].subunit.includes(subunit)||(svgAgainstData[svgName].subunit_name?toReturn=svgAgainstData[svgName].subunit_name:svgAgainstData[svgName].subunit[0]&&(toReturn=svgAgainstData[svgName].subunit[0])):"all"!==subunit&&(toReturn="all")),toReturn}let efp_table_column,variantdiv_str,sraList=[],sraDict={},sraCountDic={},tissueSRADic={},datasetName="data",iteration_num=1,moreDetails='Show More Details <i class="material-icons detailsIcon">arrow_drop_down</i>',lessDetails='Show Less Details <i class="material-icons detailsIcon">arrow_drop_up</i>';function populate_table(status){$("#theTable").empty(),$("#compareTable").empty(),rnaseq_calls=[],exp_info=[],rnaseq_success=0,date_obj5=new Date,rnaseq_success_start_time=date_obj5.getTime(),max_absolute_fpkm=-1,max_log_fpkm=-1,svg_colouring_element=null,gene_structure_colouring_element=null,sraList=[],sraDict={},sraCountDic={},tissueSRADic={},rpkmAverage=1,rpkmMedian=1;let img_created='<img loading="lazy" src="data:image/png;base64,'+exon_intron_scale+'" alt="RNA-Seq mapped image" style="float: right; margin-right: 10px;">',tableHeader='<thead><tr><th class="sortable colTitle" id="colTitle" onclick="ChangeColArrow(this.id)" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 250px;"><div class="row" id="colTitleRow"><div class="col-10">Title</div><div class="col-1"><img loading="lazy" class="sortingArrow" id="colTitleArrow" src="./cgi-bin/SVGs/arrowDefault.svg" alt="Sorting arrow"></div></div></th><th class="colRNA" id="colRNA" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; max-width: 576px;">RNA-Seq Coverage'+img_created+'</th><th class="sortable colrpb" id="colrpb" onclick="ChangeColArrow(this.id)" title="Point biserial correlation coefficient. Closer to 1 suggests a \'best\' match" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="colrpbRow"><div class="col-7" >r<sub>pb</sub></div><div class="col-1"><img loading="lazy" class="sortingArrow" id="colrpbArrow" src="./cgi-bin/SVGs/arrowDefault.svg" alt="Default sort arrow"></div></div></th><th class="coleFP" id="eFP_th" class="sortable" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 100px;">eFP (RPKM)</th><th class="sortable colRPKM" id="colRPKM" onclick="ChangeColArrow(this.id)" title="Reads Per Kilobase of transcript per Million mapped reads. Higher number suggest more mapped reads/expression" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="colRPKMRow"><div class="col-8">RPKM</div><div class="col-1"><img loading="lazy" class="sortingArrow" id="colRPKMArrow" src="./cgi-bin/SVGs/arrowDefault.svg" alt="Default sort arrow"></div></div></th><th class="sortable colDetails" id="colDetails" onclick="ChangeColArrow(this.id)" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 275px;"><div class="row" id="colDetailsRow"><div class="col-10">Details</div><div class="col-1"><img loading="lazy" class="sortingArrow" id="colDetailsArrow" src="./cgi-bin/SVGs/arrowDefault.svg" alt="Default sort arrow"></div></div></th><th class="sortable colCompare" id="colCompare" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; max-width: 30px;" hidden><div class="row" id="colCompareRow"></div></th></tr></thead><tbody id="data_table_body"></tbody>';$("#theTable").append(tableHeader);let compareHeader='<thead><tr><th id="compare_colTitle" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 250px;"><div class="row" id="compare_colTitleRow"><div class="col-xs-10">Title</div></div></th><th id="compare_colRNA" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; max-width: 576px;">RNA-Seq Coverage'+img_created+'</th><th id="compare_colrpb" title="Point biserial correlation coefficient. Closer to 1 suggests a \'best\' match" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="compare_colrpbRow"><div class="col-xs-6">r<sub>pb</sub></div></div></th><th id="compare_eFP_th" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 100px;">eFP (RPKM)</th><th id="compare_colRPKM" title="Reads Per Kilobase of transcript per Million mapped reads. Higher number suggest more mapped reads/expression" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="compare_colRPKMRow"><div class="col-xs-7">RPKM</div></div></th><th id="compare_colDetails" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 275px;"><div class="row" id="compare_colDetailsRow"><div class="col-xs-10">Details</div></div></th></tr></thead><tbody id="compare_table_body"></tbody>';$("#compareTable").append(compareHeader),$.ajax({url:base_src,dataType:"xml",success:function(xml_res){$(xml_res).find("files").each((function(){datasetName=$(this).attr("xmltitle")||"Uploaded dataset",datasetName=datasetName.trim(),0===datasetName.length&&(datasetName="Uploaded dataset"),document.getElementById("uploaded_dataset").innerHTML=datasetName})),document.title="eFP-Seq Browser:",progress_percent<100&&(document.title+=` Loading ${progress_percent.toFixed(1)}% -`),document.title+=` ${locus} - ${datasetName}`,iteration_num=1,$(xml_res).find("file").each((function(){let experimentno=$(this).attr("record_number")||"unknown";if(sraList.includes(experimentno)&&(experimentno=findUnusedRecordDisplayName(experimentno,sraList)),sraList.includes(experimentno)){if(sraCountDic[experimentno]){sraCountDic[experimentno]+=1;let tempExperimentNo=experimentno+"("+sraCountDic[experimentno]+")";sraList.push(tempExperimentNo),sraDict[tempExperimentNo]={}}}else sraCountDic[experimentno]=1,sraList.push(experimentno),sraDict[experimentno]={};let title=$(this).attr("description");sraDict[experimentno].title=title;let description=$(this).attr("info");sraDict[experimentno].description=description;let svg=$(this).attr("svgname");sraDict[experimentno].svg=svg;let svg_part=$(this).attr("svg_subunit");svg_part=checkAgainstSVG(svg,svg_part),sraDict[experimentno].svg_part=svg_part,tissueSRADic[checkAgainstSVG(svg,svg_part,!0)]?tissueSRADic[checkAgainstSVG(svg,svg_part,!0)].push(experimentno):tissueSRADic[checkAgainstSVG(svg,svg_part,!0)]=[experimentno];let url=$(this).attr("url");sraDict[experimentno].url=url;let publicationid=$(this).attr("publication_link");sraDict[experimentno].publicationid=publicationid;let hexColourCode,numberofreads=$(this).attr("total_reads_mapped");null!=numberofreads&&""!=numberofreads||(numberofreads="0"),sraDict[experimentno].numberofreads=numberofreads,hexColourCode=null==$(this).attr("hex_colour")||""==$(this).attr("hex_colour")?"0x64cc65":$(this).attr("hex_colour"),sraDict[experimentno].hexColourCode=hexColourCode;let filenameIn=$(this).attr("filename");null!=filenameIn&&""!=filenameIn&&null!=filenameIn||(filenameIn="accepted_hits.bam"),sraDict[experimentno].filenameIn=filenameIn;let species=$(this).attr("species");sraDict[experimentno].species=species;let controls=[];if(null==$(this).find("controls")[0].innerHTML)for(let i=1;i<$(this).find("controls")[0].childNodes.length;i+2)controls.push($(this).find("controls")[0].childNodes[i].firstChild.textContent);else null!=$(this).find("controls")[0].innerHTML&&(controls=$(this).find("controls")[0].innerHTML.replace(/<bam_exp>/g,"").replace(/<\/bam_exp>/g,",").replace(/\n/g," ").replace(/ /g,"").split(","));sraDict[experimentno].controls=controls;let links="";if(controls.length>0)for(let i=controls.length;i--;)"MEDIAN"!=controls[i]?links+='<a href="https://www.ncbi.nlm.nih.gov/Traces/sra/?run='+controls[i]+'"target="_blank" rel="noopener">'+controls[i]+"</a> ":links+=controls[i];sraDict[experimentno].links=links;let controlsString="";if(controls.length>0)for(let y=0;y<controls.length;y++)controlsString+=controls[y].toString(),y<controls.length-2&&(controlsString+=", ");sraDict[experimentno].controlsString=controlsString.trim();let name=$(this).attr("name");sraDict[experimentno].name=name;let tissue=$(this).attr("svgname");tissue&&("ath-"===tissue.trim().substr(0,4)&&(tissue=tissue.slice(4,tissue.length).trim()),".svg"===tissue.trim().substr(tissue.length-4,4)&&(tissue=tissue.slice(0,tissue.length-4).trim())),rnaseq_calls.push([tissue,experimentno]),sraDict[experimentno].tissue=tissue;let bam_type=$(this).attr("bam_type");sraDict[experimentno].bam_type=bam_type;let drive_link=$(this).attr("name");sraDict[experimentno].drive_link=drive_link;let read_map_method=$(this).attr("read_map_method");sraDict[experimentno].read_map_method=read_map_method;let igbView_link="https://bioviz.org/bar.html?";igbView_link+="version=A_thaliana_Jun_2009&",igbView_link+="gene_id="+locus+"&",igbView_link+="feature_url_0="+drive_link+"&",igbView_link+="genome=A_thaliana_Jun_2009&",igbView_link+="annotation_set=Araport11&",igbView_link+="query_url="+drive_link+"&",igbView_link+="server_url=bar";let append_str='<tr class="mainEntries" id="'+experimentno+'_row">',table_dl_str="<table id='table_dl'>\n\t<tbody>\n";table_dl_str+="\t\t<caption>"+document.getElementById("xmlDatabase").value+"</caption>\n",append_str+='<td class="colTitle" style="width: 250px; font-size: 12px;" id="'+experimentno+'_title">'+title+"</td>\n",append_str+=`\n\t\t\t\t\t<td class="colRNA" style="max-width: 576px;">\n\t\t\t\t\t\t<img\n\t\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\t\tid="${experimentno}_rnaseq_img"\n\t\t\t\t\t\t\talt="RNA-Seq mapped image for: ${experimentno}"\n\t\t\t\t\t\t\tstyle="min-width:420px; max-width:576px; width:95%; height: auto;"\n\t\t\t\t\t\t\tclass="rnaseq_img responsiveRNAWidth"\n\t\t\t\t\t\t\tsrc="${img_loading_base64}"\n\t\t\t\t\t\t/>\n\n\t\t\t\t\t\t<br/>\n\n\t\t\t\t\t\t<img\n\t\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\t\tid="${experimentno}_gene_structure_img"\n\t\t\t\t\t\t\tstyle="max-width: 576px; width:100%; height: auto;"\n\t\t\t\t\t\t\tclass="gene_structure_img"\n\t\t\t\t\t\t\tsrc="${img_gene_struct_1}"\n\t\t\t\t\t\t\talt="Gene variant image for: ${experimentno}"\n\t\t\t\t\t\t/>\n\t\t\t\t\t</td>\n\n\t\t\t\t`,append_str+='<td id="'+experimentno+'_rpb" class="rpb_value colrpb" style="font-size: 12px; width: 50px; ">'+"-9999</td>",append_str+='<td class="coleFP" tag="svg_name" style="width:  75px;"><div id="'+experimentno+'_svg" name="'+svg.substring(0,svg.length-4).slice(4)+'_tissue" tag='+svg_part+'_subtissue" width="75" height="75" style="width: 75px; height: 75px; max-width: 75px; max-height: 75px;">'+document.getElementById(svg.substring(4).replace(".svg","_svg")).innerHTML+'</div><div class="mdl-tooltip" for="'+experimentno+'_svg">'+svg.substring(4).replace(".svg","")+"</div></td>\n",append_str+='<td class="colRPKM" id="'+experimentno+'_rpkm" style="font-size: 12px; width: 50px; ">-9999</td>',append_str+='<td class="colDetails" id="'+experimentno+'_details" style="font-size: 12px;"><div id="'+experimentno+'_description" name="'+description.trim()+'">'+truncateDescription(description)+"</div>","Amazon AWS"===bam_type&&(append_str+='<div id="igbLink_'+experimentno+'">Show: <a href="'+igbView_link+'" target="_blank" rel="noopener">Alignments in IGB</a></div>'),experimentno.includes("unknown")&&!publicationid||(append_str+='<div id="extraLinks_'+experimentno+'">Go to: ',experimentno.includes("unknown")||(append_str+='<a href="'+url+'" target="_blank" rel="noopener">NCBI SRA</a>'),experimentno.includes("unknown")&&publicationid&&(append_str+=" or "),publicationid&&(append_str+='<a href="'+publicationid+'" target="_blank" rel="noopener">PubMed</a>'),append_str+="</div>"),append_str+='<a id="clickForMoreDetails_'+iteration_num+'" name="'+experimentno+'_description" onclick="clickDetailsTextChange(this.id)" href="javascript:(function(){$(\'#'+experimentno+"').toggle();})()\">"+moreDetails.trim()+"</a>",append_str+='<div id="'+experimentno+'" class="moreDetails" style="display:none">',links&&(append_str+="Controls: "+links+"<br/>"),append_str+="Species: "+species+"<br>",append_str+='<div id="'+experimentno+'_sra">SRA: '+experimentno+"</div>",append_str+='<div id="'+experimentno+'_totalReadsNum">Total reads = '+numberofreads+"</div>",null!=read_map_method&&read_map_method.length>0&&(append_str+='<div id="'+experimentno+'_readMappedMethod">Read map method = '+read_map_method.trim()+"</div>"),append_str+='<a id="clickForMoreDetails_'+iteration_num+'_less" name="'+experimentno+'_description" onclick="clickDetailsTextChange(this.id)" href="javascript:(function(){$(\'#'+experimentno+"').toggle();})()\">"+lessDetails+"</a></div></td>\n",append_str+='<td class="colCompare" style="font-size: 12px; max-width: 30px;"><div id="'+experimentno+'_compareVariant"><input type="checkbox" name="compareCheckbox" class="compareCheckbox" value="compareCheckbox" id="'+experimentno+'_compareCheckbox" onclick="tableCheckbox(this.id);"></div></td>',append_str+="</tr>",iteration_num++,$("#theTable").append(append_str);let compareColumn=document.getElementsByClassName("fltrow")[0].childNodes[6];(compareColumn&&void 0===compareColumn.classList[0]||"undefined"===compareColumn.classList[0])&&(compareColumn.classList=["colCompare"],compareColumn.innerHTML='<input type="checkbox" name="compareCheckbox" class="compareCheckbox" value="compareCheckbox" id="allCheckbox" onclick="disableAllComparison();">'),exp_info.push([experimentno+"_svg",svg_part,controls,0,0,0,0]),!0===loadNewDataset?(setTimeout((function(){count_bam_num()}),200),setTimeout((function(){rnaseq_images(status)}),10)):rnaseq_images(status)})),$.tablesorter.addParser({id:"rpb_sorter",is:function(s){return!1},format:function(s){return NaN==s?-99999:null==s?-999999:s==1/0?99999:s==-1/0?-99999:parseFloat(s)},type:"numeric"}),$.tablesorter.addParser({id:"rpkm_sorter",is:function(s){return!1},format:function(s){return NaN==s?-99999:null==s?-999999:s==1/0?99999:s==-1/0?-99999:"Missing controls data"==s?-9999999:parseFloat(s)},type:"numeric"}),$("#theTable").tablesorter({headers:{0:{},1:{sorter:!1},2:{sorter:"rpb_sorter"},3:{},4:{sorter:"rpkm_sorter"},5:{}}}),$("#theTable").trigger("update")},error:function(xhr,status,error){generateToastNotification(`Error getting data from data file: ${error.message}`,"ERROR"),console.log("Error getting data from data file: "+error.message)}});new TableFilter("theTable",{base_path:"cgi-bin/core/packages/tableFilter/",columns_exact_match:[!1,!1,!1,!1,!1,!1],watermark:["Filter","Filter","Filter","Filter","Filter","Filter"],highlight_keywords:!1,no_results_message:!0,auto_filter:!0,auto_filter_delay:500,col_1:"none",popup_filters:!1,filters_row_index:1,alternate_rows:!1,msg_filter:"Filtering..."}).init(),change_rpkm_colour_scale(colouring_mode);for(let j=0;j<colSortList.length;j++){CheckElementWidth(colSortList[j]+"Arrow",8)}createVariantDiv()}function createVariantDiv(){null==gene_structure_colouring_element&&document.getElementById("flt1_theTable")&&document.getElementById("flt1_theTable").parentElement&&(gene_structure_colouring_element=document.getElementById("flt1_theTable").parentElement),gene_structure_colouring_element.innerHTML="",$("#variant_select").ddslick("destroy"),document.getElementsByClassName("fltrow")[0].childNodes[1].innerHTML="",variantdiv_str='<div 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truncateDescription(stringInput){if(null!=stringInput||null!=stringInput)return stringInput.length>30?stringInput.substring(0,30)+"...":stringInput}let remainder_efp=0,efp_length=0,eFPSortedSRA=[],efp_RPKM_values=[];function populate_efp_modal(status){toggleResponsiveTable(2),$("#efpModalTable").empty(),efp_table_column="",eFPSortedSRA=[];const allSRASorted=document.getElementsByClassName("colTitle");for(let s=2;s<allSRASorted.length;s++){let SRASortedID=allSRASorted[s].id.substring(0,allSRASorted[s].id.length-6);"none"!=document.getElementById(SRASortedID+"_row").style.display&&eFPSortedSRA.push(SRASortedID)}remainder_efp=eFPSortedSRA.length%11,efp_length=eFPSortedSRA.length,efp_RPKM_values=[];for(let i=0;i<eFPSortedSRA.length;i++)isNaN(parseFloat(sraDict[eFPSortedSRA[i]].RPKM))||efp_RPKM_values.push(parseFloat(sraDict[eFPSortedSRA[i]].RPKM));$("#efpModalTable").append(`\n\t\t\t<p class="eFP_thead">\n\t\t\t\tAGI-ID:\n\t\t\t\t\t<a href="https://www.arabidopsis.org/servlets/TairObject?type=locus&name=${locus} target="_blank" rel="noopener">\n\t\t\t\t\t\t${locus}\n\t\t\t\t\t</a>\n\t\t\t</p>\n\t\t`),"abs"===colouring_mode?$("#efpModalTable").append(`\n\t\t\t\t<p class="eFP_thead">\n\t\t\t\t\teFP Colour Scale:\n\n\t\t\t\t\t<img\n\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\tsrc="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQD//wD//AD/+QD/9wD/9AD/8gD/7wD/7QD/6gD/6AD/5QD/4gD/4AD/3QD/2wD/2AD/1gD/ 0wD/0QD/zgD/zAD/yQD/xgD/xAD/wQD/vwD/vAD/ugD/twD/tQD/sgD/rwD/rQD/qgD/qAD/pQD/ owD/oAD/ngD/mwD/mQD/lgD/kwD/kQD/jgD/jAD/iQD/hwD/hAD/ggD/fwD/fAD/egD/dwD/dQD/ cgD/cAD/bQD/awD/aAD/ZgD/YwD/YAD/XgD/WwD/WQD/VgD/VAD/UQD/TwD/TAD/SQD/RwD/RAD/ QgD/PwD/PQD/OgD/OAD/NQD/MwD/MAD/LQD/KwD/KAD/JgD/IwD/IQD/HgD/HAD/GQD/FgD/FAD/ EQD/DwD/DAD/CgD/BwD/BQD/AgCkIVxRAAAAs0lEQVQ4jWNg5+Dk4ubh5eMXEBQSFhEVE5eQlJKW kZWTV1BUUlZRVVPX0NTS1tHV0zcwNDI2MTUzt7C0sraxtbN3cHRydnF1c/fw9PL28fXzDwgMCg4J DQuPiIyKjomNi09ITEpOSU1Lz8jMYhi1hERLGBmpbgljbBwjiiWMnFyMVLcECOhkCZBIZUzPYKSV JaDgYkxKZkxNY2SkmU8gljDCLaFdxDMmw4NrGOWTUUuItwQAG8496iMoCNwAAAAASUVORK5CYII="\n\t\t\t\t\t\tclass="colourScale"\n\t\t\t\t\t\talt="Absolute RPKM colour scale"\n\t\t\t\t\t/>\n\n\t\t\t\t\tMin: ${Math.min.apply(null,efp_RPKM_values).toFixed(1)} RPKM,\n\n\t\t\t\t\tMax: ${Math.max.apply(null,efp_RPKM_values).toFixed(1)} RPKM\n\t\t\t\t</p>\n\n\t\t\t\t<br />\n\n\t\t\t\t<table>\n\t\t\t\t\t<tbody class="eFP_tbody">\n\t\t\t\t</tbody>\n\t\t\t`):"rel"===colouring_mode&&$("#efpModalTable").append(`\n\t\t\t\t<p class="eFP_thead">\n\t\t\t\t\teFP Colour Scale:\n\n\t\t\t\t\t<img\n\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\tsrc="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQAAAP8FBfkKCvQPD+8UFOoZGeUeHuAjI9soKNYtLdEzM8w4OMY9PcFCQrxHR7dMTLJRUa1W VqhbW6NgYJ5mZplra5NwcI51dYl6eoR/f3+EhHqJiXWOjnCTk2uZmWaenmCjo1uoqFatrVGysky3 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i=0;i<11*~~(eFPSortedSRA.length/11);i+=11)if("null"!=document.getElementById(eFPSortedSRA[i+10]).outerHTML){efp_table_column="<tr>";for(let r=0;r<11;r++)efp_table_column+=generateEFPTableItem(eFPSortedSRA[i+r],sraDict[eFPSortedSRA[i+r]].title);efp_table_column+="</tr>",$("#eFPtable").append(efp_table_column)}for(let r=0;r<12;r++)if(remainder_efp===r){efp_table_column="<tr>";for(let c=remainder_efp;c>0;c--)efp_table_column+=generateEFPTableItem(eFPSortedSRA[efp_length-c],sraDict[eFPSortedSRA[efp_length-c]].title);efp_table_column+="</tr>",$("#eFPtable").append(efp_table_column)}toggleResponsiveTable()}function generateEFPTableItem(id,title){return id&&title?`\n\t\t\t<td>\n\t\t\t\t<div\n\t\t\t\t\tclass="efp_table_tooltip"\n\t\t\t\t\tid="${id}_rep"\n\t\t\t\t\tonclick="ScrollToRNARow('${id}_row')"\n\t\t\t\t>\n\t\t\t\t\t${document.getElementById(id+"_svg").outerHTML}\n\t\t\t\t\t<span class="efp_table_tooltip_text">\n\t\t\t\t\t${id} - ${title}\n\t\t\t\t\t</span>\n\t\t\t\t</div>\n\t\t\t</td>\n\t\t`:""}function change_rpkm_colour_scale(colouring_mode){if(null===svg_colouring_element&&document.getElementById("flt3_theTable")&&document.getElementById("flt3_theTable").parentElement&&(svg_colouring_element=document.getElementById("flt3_theTable").parentElement),svg_colouring_element&&svg_colouring_element.innerHTML&&(svg_colouring_element.innerHTML=""),"rel"==colouring_mode){const img_created=document.createElement("img");img_created.src="data:image/png;base64,"+relative_rpkm_scale,img_created.style="margin-top: 10px;",svg_colouring_element&&svg_colouring_element.appendChild(img_created)}else{const img_created=document.createElement("img");img_created.src="data:image/png;base64,"+absolute_rpkm_scale,img_created.style="margin-top: 10px;",img_created.alt="Absolute RPKM Scale",svg_colouring_element&&svg_colouring_element.appendChild(img_created)}const columnList=["colTitle","colRNA","colrpb","coleFP","colRPKM","colDetails"];let tds=[];document.getElementsByClassName("fltrow")&&document.getElementsByClassName("fltrow")[0]&&(tds=document.getElementsByClassName("fltrow")[0].getElementsByTagName("td"));for(let i=0;i<tds.length;i++)tds[i].style="border: 1px solid #D3D3D3",tds[i].classList.add(columnList[i])}function locus_validation(){const loc=document.getElementById("locus").value;9==loc.length&&("A"==loc[0]||"a"==loc[0])&&("T"==loc[1]||"t"==loc[1])&&(loc[2]>=1&&loc[2]<=5||"C"==loc[2]||"M"==loc[2]||"c"==loc[2]||"m"==loc[2])&&("G"==loc[3]||"g"==loc[3])&&loc[4]>=0&&loc[4]<=9&&loc[5]>=0&&loc[5]<=9&&loc[6]>=0&&loc[6]<=9&&loc[7]>=0&&loc[7]<=9&&loc[8]>=0&&loc[8]<=9?$("#locus_button").removeAttr("disabled"):$("#locus_button").prop("disabled",!0)}function yscale_validation(){const yscale=document.getElementById("yscale_input").value;parseInt(yscale)>0||"Auto"==yscale||""==yscale?$("#locus_button").removeAttr("disabled"):$("#locus_button").prop("disabled",!0)}function rpkm_validation(){parseInt(document.getElementById("rpkm_scale_input").value)>0?$("#abs_scale_button").removeAttr("disabled"):$("#abs_scale_button").prop("disabled",!0)}let databasesAdded=!1;function reset_database_options(){$(".userAdded").remove(),dataset_dictionary=base_dataset_dictionary,list_modified=!1,databasesAdded=!1}let xml_title,get_xml_list_output=[],user_exist=!1,list_modified=!1,check_for_change=0,match_title={},title_list=[];function get_user_XML_display(){const AuthUser=findAuthUser();""==users_email&&null==users_email&&null==users_email||users_email!==AuthUser?""!=users_email&&users_email!=AuthUser&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in")):$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/get_xml_list.php?user="+users_email,dataType:"json",failure:function(){console.log("ERROR! Something went wrong")},success:function(get_xml_list_return){xml_title=void 0,match_title={},title_list=[];let unnamed_title_num=1,private_version_num=1;if(get_xml_list_output=get_xml_list_return,"fail"==get_xml_list_output.status)console.log("Error code: "+get_xml_list_output.error),user_exist=!1;else if("success"==get_xml_list_output.status){if(user_exist=!0,check_for_change!=get_xml_list_output.files.length&&(reset_database_options(),list_modified=!1),check_for_change=get_xml_list_output.files.length,get_xml_list_output.files.length>0)for(let i=0;i<get_xml_list_output.files.length;i++){xml_title=void 0,xml_title=get_xml_list_output.files[i][1],xml_title&&0!==xml_title.trim()?.length&&"Uploaded dataset"!==xml_title?"Araport 11 RNA-seq data"==xml_title?(xml_title="Araport 11 RNA-seq data - Private version #"+private_version_num,private_version_num+=1):"Developmental transcriptome - Klepikova et al"==xml_title&&(xml_title="Developmental transcriptome - Klepikova et al - Private version #"+private_version_num,private_version_num+=1):(xml_title="Uploaded dataset - Unnamed dataset #"+unnamed_title_num,unnamed_title_num+=1),title_list.push(xml_title);const xml_fle_name=get_xml_list_output.files[i][0];match_title[xml_title]=xml_fle_name,i==get_xml_list_output.files.length-1&&create_data_list(get_xml_list_output.files.length)}setTimeout((function(){if(!list_modified)for(let c=0;c<get_xml_list_output.files.length;c++)dataset_dictionary[title_list[c]]=datalist_Title[title_list[c]],document.getElementById("xmlDatabase").innerHTML+=`\n\t\t\t\t\t\t\t\t\t<option\n\t\t\t\t\t\t\t\t\t\tclass="userAdded"\n\t\t\t\t\t\t\t\t\t\ttag="private"\n\t\t\t\t\t\t\t\t\t\tvalue="${title_list[c]}"\n\t\t\t\t\t\t\t\t\t\tid="${title_list[c]}"\n\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\t\t\t\t${title_list[c]}\n\t\t\t\t\t\t\t\t\t</option>\n\t\t\t\t\t\t\t\t`;list_modified=!0}),1e3)}databasesAdded=!0},error:function(xhr,status,error){generateToastNotification(`Error getting user data: ${error.message}`,"ERROR"),console.log(`Error getting user data: ${error.message}`)}})}let datalist=[],datalist_Title={};function create_data_list(size){if(datalist=[],datalist_Title={},size>0)for(let i=0;i<size;i++)$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/get_xml.php?file="+match_title[title_list[i]],dataType:"json",success:function(get_xml_return){const xml_file=get_xml_return;datalist.push(xml_file.data)},error:function(xhr,status,error){generateToastNotification(`Error getting user private datasets: ${error.message}`,"ERROR"),console.log(`Error getting user private datasets: ${error.message}`)}}),i===size-1&&setTimeout((function(){dlCallLength=size,DatalistXHRCall(datalist)}),200)}let testDoc,dlCallLength=0,dlCallPosition=0;function DatalistXHRCall(datalistData){if(dlCallPosition!=dlCallLength){const xhr=new XMLHttpRequest,url=datalistData[dlCallPosition];xhr.responseType="document",xhr.onreadystatechange=()=>{if(xhr.readyState===XMLHttpRequest.DONE&&200===xhr.status){let response=xhr.responseXML;if(response){let responseTitle=response.getElementsByTagName("files")[0].attributes.xmltitle.nodeValue;datalist_Title[responseTitle]=datalistData[dlCallPosition],dlCallPosition+=1,DatalistXHRCall(datalistData)}}},xhr.open("GET",url),xhr.send()}}function validateEmail(email){return/\S+@\S+\.\S+/.test(email)}function findAuthUser(){return global_user&&global_user.email?global_user.email:""}function check_if_Google_login(){const AuthUser=findAuthUser();users_email&&AuthUser&&users_email===AuthUser?!1===databasesAdded&&(document.getElementById("private_dataset_header").style.display="block",get_user_XML_display()):(signOut(),remove_private_database())}function add_user_xml_by_upload(){get_user_XML_display(),setTimeout((function(){const AuthUser=findAuthUser();user_exist?user_exist&&(dataset_dictionary[datasetName]?dataset_dictionary[datasetName]&&(users_email===AuthUser?(list_modified=!1,check_for_change=0,$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_xml.php?user="+users_email+"&file="+match_title[datasetName]}),$.ajax({method:"POST",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/upload.php",data:{user:users_email,xml:upload_src,title:datasetName}})):""!=users_email&&users_email!=AuthUser&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in"))):users_email===AuthUser?$.ajax({method:"POST",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/upload.php",data:{user:users_email,xml:upload_src,title:datasetName}}):""!=users_email&&users_email!=AuthUser&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in"))):users_email===AuthUser?$.ajax({method:"POST",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/upload.php",data:{user:users_email,xml:upload_src,title:datasetName}}):""!=users_email&&users_email!=AuthUser&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in")),get_user_XML_display()}),1e4)}let uploadingData=!1;function which_upload_option(){uploadingData=!0;const AuthUser=findAuthUser();""!=users_email&&users_email===AuthUser?document.getElementById("upload_modal").click():""!=users_email&&users_email!=AuthUser?(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in")):""==users_email&&document.getElementById("upload_logX").click()}let public_title_list=[],total_amount_of_datasets=0;function delete_fill(){$("#delete_fill").empty(),$("#publicDatabaseDownload").empty(),public_title_list=[];for(let public_title in base_dataset_dictionary)base_dataset_dictionary.hasOwnProperty(public_title)&&public_title_list.push(public_title);let deleteBoxNum=0;total_amount_of_datasets=public_title_list.length+title_list.length;for(let i=0;i<public_title_list.length;i++)$("#publicDatabaseDownload").append(`\n\t\t\t\t<input\n\t\t\t\t\ttype="checkbox"\n\t\t\t\t\ttag="publicDataCheckbox"\n\t\t\t\t\tclass="publicDataCheckbox"\n\t\t\t\t\tonchange="disableDeletePublic()"\n\t\t\t\t\tid="deleteBox_${deleteBoxNum}"\n\t\t\t\t\tvalue="${public_title_list[i]}"\n\t\t\t\t>\n\t\t\t\t\t${public_title_list[i]}\n\t\t\t\t</input>\n\t\t\t\t<br />\n\t\t\t`),deleteBoxNum+=1;for(let i=0;i<title_list.length;i++)$("#delete_fill").append(`\n\t\t\t\t<input\n\t\t\t\t\ttype="checkbox"\n\t\t\t\t\ttag="privateDataCheckbox"\n\t\t\t\t\tclass="privateDataCheckbox"\n\t\t\t\t\tonchange="disableDeletePublic()"\n\t\t\t\t\tid="deleteBox_${deleteBoxNum}"\n\t\t\t\t\tvalue="${title_list[i]}"\n\t\t\t\t>\n\t\t\t\t\t${title_list[i]}\n\t\t\t\t</input>\n\t\t\t\t<br />\n\t\t\t`),deleteBoxNum+=1}let isDeletePublicDisabled=!1;function disableDeletePublic(){for(let i=0;i<public_title_list.length;i++){if(document.getElementById("deleteBox_"+i).checked&&"publicDataCheckbox"==document.getElementById("deleteBox_"+i).className){isDeletePublicDisabled||(document.getElementById("deleteXML_button").classList.add("disabled"),isDeletePublicDisabled=!0);break}isDeletePublicDisabled&&(document.getElementById("deleteXML_button").classList.remove("disabled"),isDeletePublicDisabled=!1)}}function CheckIfSelectedXML(){const AuthUser=findAuthUser();for(let i=0;i<title_list.length;i++){const deleteBox_id="deleteBox_"+(i+2);if(document.getElementById(deleteBox_id).checked&&users_email===AuthUser)return!0}if(1)return!1}function delete_selectedXML(){const AuthUser=findAuthUser();for(let i=0;i<title_list.length;i++){const deleteBox_id="deleteBox_"+(i+2);document.getElementById(deleteBox_id)&&document.getElementById(deleteBox_id).checked&&users_email===AuthUser&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_xml.php?user="+users_email+"&file="+match_title[document.getElementById(deleteBox_id).value]})}databasesAdded=!1}function confirm_deleteUser(){const AuthUser=findAuthUser();""!=users_email&&users_email===AuthUser&&$("#logoutModal").is(":visible")&&delete_allXMLs(AuthUser)}function delete_allXMLs(verify){const AuthUser=findAuthUser();if(verify===AuthUser){for(let i=0;i<title_list.length;i++){const deleteBox_id="deleteBox_"+(i+2);users_email===AuthUser&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_xml.php?user="+users_email+"&file="+match_title[document.getElementById(deleteBox_id).value]})}delete_user(),databasesAdded=!1}}function delete_user(){const AuthUser=findAuthUser();""!=users_email&&users_email===AuthUser&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_user.php?user="+users_email}),signOut()}let warningActive_index_XML="nope",warningActive_index_account="nope";function showWarning_index(whichWarning){1===whichWarning?isDeletePublicDisabled||("nope"==warningActive_index_XML?(document.getElementById("warning_index_xml").className="warning_index",warningActive_index_XML="yes"):"yes"==warningActive_index_XML&&hideWarning_index(whichWarning)):2===whichWarning&&("nope"==warningActive_index_account?(document.getElementById("warning_index_account").className="warning_index",warningActive_index_account="yes"):"yes"==warningActive_index_account&&hideWarning_index(whichWarning))}function hideWarning_index(whichWarning){1===whichWarning?(document.getElementById("warning_index_xml").className="warning_nope_index",warningActive_index_XML="nope"):2===whichWarning&&(document.getElementById("warning_index_account").className="warning_nope_index",warningActive_index_account="nope")}function manage_DownloadXML(){const numberOfOptions=title_list.length+2;for(let i=0;i<numberOfOptions;i++){const downloadBox_id="deleteBox_"+i;document.getElementById(downloadBox_id).checked&&($("#downloadXML").attr("href",dataset_dictionary[document.getElementById(downloadBox_id).value]).attr("download",document.getElementById(downloadBox_id).value+".xml"),document.getElementById("downloadXML_button").click())}}const table_base="\t\t<tr>\n\t\t\t<th>Title*</th>\n\t\t\t<th>Description*</th>\n\t\t\t<th>Record Number *</th>\n\t\t\t<th>RNA-Seq Data/BAM file repository link*</th>\n\t\t\t<th>Repository type*</th>\n\t\t\t<th>BAM Filename*</th>\n\t\t\t<th>Publication Link</th>\n\t\t\t<th>SRA/NCBI Link</th>\n\t\t\t<th>Total Reads Mapped*</th>\n\t\t\t<th>Read Map Method</th>\n\t\t\t<th>Species*</th>\n\t\t\t<th>Tissue*</th>\n\t\t\t<th>Tissue subunit*</th>\n\t\t\t<th>Controls</th>\n\t\t\t<th>Replicate Controls</th>\n\t\t</tr>\n";function fill_tableCSV(){$("#XMLtoCSVtable").empty();for(let i=0;i<total_amount_of_datasets;i++){const downloadBox_id="deleteBox_"+i;$.ajax({url:dataset_dictionary[document.getElementById(downloadBox_id).value],dataType:"xml",failure:function(){console.log("Failed at opening XML for conversion into a CSV file. Please contact an admin")},success:function(xml_data){let fileTitle;$(xml_data).find("files").each((function(){fileTitle=$(this).attr("xmltitle"),""!=fileTitle&&"Uploaded dataset"!=fileTitle||(fileTitle="Uploaded dataset"),fileTitle=fileTitle.split(" ").join("_")}));const $title=$(xml_data).find("file");let table_add="";table_add+="<table id='"+fileTitle+"'>\n\t<tbody>\n",table_add+="\t\t<caption>"+fileTitle+"</caption>\n",table_add+=table_base,$title.each((function(){table_add+="\t\t<tr>\n";const title=$(this).attr("description");table_add+="\t\t\t<td>"+title+"</td>\n";const desc=$(this).attr("info");table_add+="\t\t\t<td>"+desc+"</td>\n";const record_number=$(this).attr("record_number");table_add+="\t\t\t<td>"+record_number+"</td>\n";const bam_link=$(this).attr("name");table_add+="\t\t\t<td>"+bam_link+"</td>\n";const bam_type=$(this).attr("bam_type");table_add+="\t\t\t<td>"+bam_type+"</td>\n";let bam_filename=$(this).attr("filename");null!=bam_filename&&"undefined"!==bam_filename&&".bam"!==bam_filename||(bam_filename="accepted_hits.bam"),table_add+="\t\t\t<td>"+bam_filename+"</td>\n";const publication_link=$(this).attr("publication_link");table_add+="\t\t\t<td>"+publication_link+"</td>\n";const publication_url=$(this).attr("url");table_add+="\t\t\t<td>"+publication_url+"</td>\n";let total_reads_mapped=$(this).attr("total_reads_mapped");null!=total_reads_mapped&&""!=total_reads_mapped||(total_reads_mapped="0"),table_add+="\t\t\t<td>"+total_reads_mapped+"</td>\n";const read_map_method=$(this).attr("read_map_method");table_add+="\t\t\t<td>"+read_map_method+"</td>\n";let species=$(this).attr("species");null!=species&&""!=species||(species="Arabidopsis thaliana"),table_add+="\t\t\t<td>"+species+"</td>\n";const svgname=$(this).attr("svgname");table_add+="\t\t\t<td>"+svgname+"</td>\n";const svg_subunit=$(this).attr("svg_subunit");table_add+="\t\t\t<td>"+svg_subunit+"</td>\n";let controlsXMLString="";if($(this).find("controls")[0].innerHTML)for(let j=1;j<$(this).find("controls")[0].childNodes.length;j+=2)$(this).find("controls")[0].childNodes[j].firstChild&&(controlsXMLString+=$(this).find("controls")[0].childNodes[j].firstChild.textContent,j<$(this).find("controls")[0].childNodes.length-2&&(controlsXMLString+=", "));table_add+="\t\t\t<td>"+controlsXMLString+"</td>\n";let RcontrolsXMLString="";if($(this).find("groupwith")[0].innerHTML)for(let j=1;j<$(this).find("groupwith")[0].childNodes.length;j+=2)$(this).find("groupwith")[0].childNodes[j].firstChild&&(RcontrolsXMLString+=$(this).find("groupwith")[0].childNodes[j].firstChild.textContent,j<$(this).find("groupwith")[0].childNodes.length-2&&(RcontrolsXMLString+=", "));table_add+="\t\t\t<td>"+RcontrolsXMLString+"</td>\n",table_add+="\t\t</tr>\n"})),table_add+="\t</tbody>\n</table>",document.getElementById("XMLtoCSVtable").innerHTML+=table_add},error:function(xhr,status,error){generateToastNotification(`Error filling data table: ${error.message}`,"ERROR"),console.log(`Error filling data table: ${error.message}`)}})}}function download_XMLtableCSV(){for(let i=0;i<total_amount_of_datasets;i++){const downloadBox_id="deleteBox_"+i;if(document.getElementById(downloadBox_id).checked){const tableTitle=document.getElementById(downloadBox_id).value.split(" ").join("_");$("#"+tableTitle).tableToCSV()}}}const downloadIndexTable_base="\t\t<tr>\n\t\t\t<th>Title</th>\n\t\t\t<th>Record Number</th>\n\t\t\t<th>Tissue</th>\n\t\t\t<th>Tissue subunit</th>\n\t\t\t<th>Locus</th>\n\t\t\t<th>bp Length</th>\n\t\t\t<th>bp Start site</th>\n\t\t\t<th>bp End site</th>\n\t\t\t<th>Total number of reads</th>\n\t\t\t<th>Reads mapped to locus</th>\n\t\t\t<th>rpb</th>\n\t\t\t<th>RPKM</th>\n\t\t\t<th>Controls</th>\n\t\t</tr>\n";function download_mainTableCSV(){document.getElementById("download_icon").classList.add("progressLoading"),document.getElementById("bodyContainer").classList.add("progressLoading"),populate_efp_modal(1),$("#hiddenDownloadModal_table").empty();let downloadIndexTable_str="<table id='downloadIndexTable'>\n\t<tbody>\n";downloadIndexTable_str+="\t\t<caption>"+datasetName.split(" ").join("_")+"</caption>\n",downloadIndexTable_str+=downloadIndexTable_base;for(const sra of eFPSortedSRA)downloadIndexTable_str+="\t\t<tr>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].title+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sra+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].svg.substr(4,sraDict[sra].svg.length-8)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].svg_part+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].locusValue+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].bp_length)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].bp_start)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].bp_end)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].numberofreads+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].MappedReads)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].rpb+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].RPKM[variantPosition].toFixed(2))+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].controlsString)+"</td>\n",downloadIndexTable_str+="\t\t</tr>\n";downloadIndexTable_str+="\t</tbody>\n</table>",document.getElementById("hiddenDownloadModal_table").innerHTML+=downloadIndexTable_str,$("#hiddenDownloadModal_table").tableToCSV(),document.getElementById("download_icon").classList.remove("progressLoading"),document.getElementById("bodyContainer").classList.remove("progressLoading")}let publicData=!0;function changePublicData(forceFalse=!1){publicData=!forceFalse&&!uploadingData&&(1==document.getElementById("xmlDatabase").selectedIndex||2==document.getElementById("xmlDatabase").selectedIndex)}let isPrecache=!0;function checkPreload(){if(get_input_values(),verifyLoci(locus)){loadingScreen(!1),progress_percent=0,document.title=`eFP-Seq Browser: Loading 0% - ${locus}`,document.getElementById("progress").title="0%",$("div#progress").width(progress_percent+"%");for(const property in base_dataset_dictionary){if(base_src===base_dataset_dictionary[property]){publicData=!0;break}publicData=!1}publicData&&"AT2G24270"==locus&&"simple"==dumpMethod&&!callDumpOutputs?(variants_radio_options(1),isPrecache=!0):(update_all_images(0),isPrecache=!1)}else console.error(`The following locus is not valid: ${locus}`)}function verifyLoci(locusToVerify){if("string"==typeof locusToVerify){const regexPattern=new RegExp("^[A][T][MC0-9][G][0-9]{5}[.][0-9]{1,2}$|^[A][T][MC0-9][G][0-9]{5}$","i");return locusToVerify.trim().match(regexPattern)}return!1}let parse_output,GFF_List=[];function getGFF(locusID){GFF_List=[],$.ajax({url:`https://bar.utoronto.ca/webservices/bar_araport/gene_structure_by_locus.php?locus=${locusID}`,dataType:"json",crossDomain:!0,headers:{"Access-Control-Allow-Origin":"*"},failure:function(){console.log("Getting GFFs (getGFF) information failed to retrieve locus information from Araport11")},success:function(gene_res){if(parse_output=gene_res,parse_output.wasSuccessful){let parsed_features=parse_output.features[0].subfeatures;for(let i=0;i<parsed_features.length;i++)null!=parsed_features[i].uniqueID?GFF_List.push(parsed_features[i].uniqueID):GFF_List.push("Error retrieving unique ID/GFF")}else"fail"==parse_output.status?console.log("Error: Cannot find GFF ID's with parse output. Please contact admin"):"false"==parse_output.wasSuccessful&&(null!=parse_output.error?console.log("Error: Cannot find GFF ID's due to following error: "+parse_output.error+". Please contact admin"):console.log("Error: Cannot find GFF ID's with parse output. Please contact admin"))},error:function(xhr,status,error){generateToastNotification(`Error getting GFFs (getGFF) information failed to retrieve locus information from Araport11: ${error.message}`,"ERROR"),console.log(`Error getting GFFs (getGFF) information failed to retrieve locus information from Araport11: ${error.message}`)}})}function addGFF(){if(document.getElementsByClassName("dd-option").length>0)for(let i=0;i<GFF_List.length;i++)document.getElementsByClassName("dd-option")[i]&&document.getElementsByClassName("dd-option")[i].setAttribute("title",GFF_List[i])}function hiddenGoogleSignin(){const signInButtonList=document.getElementsByClassName("abcRioButtonLightBlue");for(let i=0;i<signInButtonList.length;i++)signInButtonList[i]&&signInButtonList[i].setAttribute("id","loginClick"+i)}function remove_private_database(){databasesAdded=!1,document.getElementById("private_dataset_header").style.display="none";const privateList=document.getElementsByClassName("userAdded");for(let i=0;i<privateList.length;i++)$("#xmlDatabase option:last").remove();check_for_change=0}function correctAGIIDInput(){if(document.getElementById("locus")&&document.getElementById("locus").value&&document.getElementById("locus").value.trim().length>0){const locusID=document.getElementById("locus").value.trim().split("/");locusID[0]?document.getElementById("locus").value=locusID[0].toUpperCase().trim():document.getElementById("locus").value=document.getElementById("locus").value.trim(),locus_validation()}}function returnBackToTop(){document.getElementById("main_content").scrollTop=0}function toggleOptionsTable(){"false"===document.getElementById("tableToggle").getAttribute("aria-expanded")?(document.getElementById("tableToggle").setAttribute("aria-expanded",!0),document.getElementById("filterDropdown").classList.add("show")):(document.getElementById("tableToggle").setAttribute("aria-expanded",!1),document.getElementById("filterDropdown").classList.remove("show"))}function toggleTableOptionsView(){document.getElementById("tableFilter-tab").classList.value.includes("active")?(document.getElementById("tableFilter-tab").classList.remove("active"),document.getElementById("eFPFilter-tab").classList.add("active"),document.getElementById("tableFilter").classList.remove("show","active"),document.getElementById("eFPFilter").classList.add("show","active")):(document.getElementById("tableFilter-tab").classList.add("active"),document.getElementById("eFPFilter-tab").classList.remove("active"),document.getElementById("tableFilter").classList.add("show","active"),document.getElementById("eFPFilter").classList.remove("show","active"))}let downloadDivNum=1;function downloadDiv(id){html2canvas(document.getElementById(id)).then((canvas=>{$("#appendCanvas").empty(),canvas.id="downloadDivNum_"+downloadDivNum,document.getElementById("appendCanvas").appendChild(canvas),document.getElementById("downloadDivNum_"+downloadDivNum).style.width="100%",$("#DownloadImageModal").modal("toggle"),downloadDivNum++}))}function displayNavBAR(hideNavbar=!1){const displayNav=$("#navbar_menu").is(":visible")||hideNavbar;document.getElementById("navbar_menu").style.display=displayNav?"none":"block",document.getElementById("main_content").className=displayNav?"col-sm-12":"col-sm-9",document.getElementById("openMenu").style.display=displayNav?"block":"none",document.getElementById("theTable")&&(displayNav?document.getElementById("theTable").classList.add("RNATable"):document.getElementById("theTable").classList.remove("RNATable"))}function adjustFooterSize(){const navbar=document.getElementById("navbar_menu");navbar&&(document.getElementById("nm_footer").style.width=navbar.offsetWidth+"px",navbar.scrollHeight==navbar.clientHeight?document.getElementById("nm_footer").classList.contains("navbar_menu_footer_overflow_abs")||(document.getElementById("nm_footer").classList.remove("navbar_menu_footer_overflow_sticky"),document.getElementById("nm_footer").classList.add("navbar_menu_footer_overflow_abs")):navbar.scrollHeight>navbar.clientHeight&&(document.getElementById("nm_footer").classList.contains("navbar_menu_footer_overflow_sticky")||(document.getElementById("nm_footer").classList.remove("navbar_menu_footer_overflow_abs"),document.getElementById("nm_footer").classList.add("navbar_menu_footer_overflow_sticky"))))}function adjustTableOptionsDropdownSize(){document.getElementById("filterDropdown").style.left=(document.body.offsetWidth-2*document.getElementById("tableToggle").offsetWidth-document.getElementById("filterDropdown").offsetWidth).toString()+"px"}function adjustSubmissionIFrameSize(){const iFrameSize=.7*window.innerHeight;document.getElementById("submissioniframe").height=iFrameSize+"px"}let usedToggle=!1;function toggleTableCol(colClass,enable){const column=document.getElementsByClassName(colClass);if(enable)for(const element of column)element&&element.removeAttribute("hidden");else if(!enable)for(const element of column)element&&element.setAttribute("hidden",!0)}let responsiveRNAWidthAdjusted=!1;function responsiveRNAWidthResize(){const responsive=document.getElementsByClassName("responsiveRNAWidth");if(window.innerWidth<=575){for(let i=0;i<responsive.length;i++)responsive[i].style.minWidth=.93*window.innerWidth+"px";responsiveRNAWidthAdjusted=!0}else if(window.innerWidth>575&&responsiveRNAWidthAdjusted)for(let i=0;i<responsive.length;i++)responsive[i].style.minWidth="420px"}function toggleResponsiveTableOptions(colTitleBool,colRNABool,colrpbBool,coleFPBool,colRPKMBool,colDetailsBool,colCompareBool){toggleTableCol("colTitle",colTitleBool),document.getElementById("toggleTitle").checked=colTitleBool,toggleTableCol("colRNA",colRNABool),document.getElementById("toggleRNA").checked=colRNABool,toggleTableCol("colrpb",colrpbBool),document.getElementById("togglerpb").checked=colrpbBool,toggleTableCol("coleFP",coleFPBool),document.getElementById("toggleeFP").checked=coleFPBool,toggleTableCol("colRPKM",colRPKMBool),document.getElementById("toggleRPKM").checked=colRPKMBool,toggleTableCol("colDetails",colDetailsBool),document.getElementById("toggleDetails").checked=colDetailsBool,toggleTableCol("colCompare",colCompareBool),document.getElementById("toggleCompare").checked=colCompareBool,RememberToggleOptions(colTitleBool,colRNABool,colrpbBool,coleFPBool,colRPKMBool,colDetailsBool,colCompareBool)}function determineResponsiveTable(){document.body.offsetWidth<=576?(toggleResponsiveTable(2),displayNavBAR(!0)):toggleResponsiveTable(0)}function toggleResponsiveTable(forceToggle=0){"none"!=document.getElementById("tableToggle").style.display&&(1==forceToggle||window.innerWidth<=575&&!usedToggle?toggleResponsiveTableOptions(!1,!0,!1,!1,!1,!1,!1):2==forceToggle||window.innerWidth>=1100&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!0,!0,!0,!1):3==forceToggle||window.innerWidth<830&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!1,!1,!1,!1,!1):4==forceToggle||window.innerWidth<900&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!1,!1,!1,!1):5==forceToggle||window.innerWidth<990&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!1,!0,!1,!1):(6==forceToggle||window.innerWidth<1100&&!usedToggle)&&toggleResponsiveTableOptions(!0,!0,!0,!0,!0,!1,!1))}let ToggledTable=[!0,!0,!0,!0,!0,!0,!1];function RememberToggleOptions(title=!0,rna=!0,rpb=!0,efp=!0,rpkm=!0,details=!0,compare=!1){ToggledTable=[title,rna,rpb,efp,rpkm,details,compare]}const colSortList=["colTitle","colrpb","colRPKM","colDetails"];function ResizeArrowRow(){for(const col of colSortList){const colRow=col+"Row";document.getElementById(colRow).style.width=document.getElementById(colRow).parentNode.offsetWidth-2+"px";CheckElementWidth(col+"Arrow",8)}}function CheckElementWidth(arrowID,widthCheckFor){document.getElementById(arrowID).offsetWidth<widthCheckFor&&(document.getElementById(arrowID).style.width=widthCheckFor+"px")}function ChangeColArrow(tableArrowID){setTimeout((function(){const arrowColID=tableArrowID+"Arrow";document.getElementById(tableArrowID).classList.contains("headerSortDown")?document.getElementById(arrowColID).src="./cgi-bin/SVGs/arrowSortDown.svg":document.getElementById(tableArrowID).classList.contains("headerSortUp")&&(document.getElementById(arrowColID).src="./cgi-bin/SVGs/arrowSortUp.svg");for(const col of colSortList){CheckElementWidth(col+"Arrow",8)}}),100)}function ScrollToRNARow(rowID){document.getElementById("closemodal_efPOverview").click(),$("#main_content").animate({scrollTop:$("#"+rowID).offset().top},"slow"),document.getElementById(rowID)&&(document.getElementById(rowID).className+=" scrollToRow",setTimeout((function(){document.getElementById(rowID).className+=" scrollToRowRemove"}),2e3),setTimeout((function(){document.getElementById(rowID).classList.remove("scrollToRow"),document.getElementById(rowID).classList.remove("scrollToRowRemove")}),4050))}function IfPressEnter(event,toClickButton){13!=event.which&&13!=event.keyCode||$("#"+toClickButton).click()}let shareLink,BrowserDetected=!1;function DetectBrowser(){if(!1===BrowserDetected){const userAgentParser={"Microsoft+Edge":{Contain:["Edge"]},Opera:{Contain:["OPR","Opera"]},Firefox:{Contain:["Firefox"],NContain:["Seamonkey"]},Seamonkey:{Contain:["Seamonkey"]},Chrome:{Contain:["Chrome"],NContain:["Chromium"]},Chromium:{Contain:["Chromium"]},"Internet+Explorer":{Contain:["MSIE"]},Safari:{Contain:["Safari"],NContain:["Chromium","Chrome"]}};let userAgentParserKeys,detectBrowser;userAgentParser?userAgentParserKeys=Object.keys(userAgentParser):logError("Unable retrieve userAgentParser");let notDetectedBrowser=!0;for(const userAgent of userAgentParserKeys)for(let c=0;c<userAgentParser[userAgent].Contain.length;c++)if(notDetectedBrowser&&-1!==navigator.userAgent.indexOf(userAgentParser[element].Contain[c])){if(!userAgentParser[element].NContain){detectBrowser=element,notDetectedBrowser=!1;break}{const failLength=userAgentParser[element].NContain.length;let passLength=0;if(userAgentParser[element].NContain.forEach((agent=>{-1!==navigator.userAgent.indexOf(agent)&&passLength++})),passLength!=failLength){detectBrowser=element,notDetectedBrowser=!1;break}}}if(detectBrowser){$("#notChrome").empty();const append_str=' or through the following <a href="https://www.google.com/search?q=manage+cookies+in+'+detectBrowser+'" target="_blank" rel="noopener">Google search results</a>';$("#notChrome").append(append_str)}BrowserDetected=!0}}function CreateFilteredeFPList(){if($("#filtereFPList").empty(),tissueSRADic){const allTissuesDisplayed=Object.keys(tissueSRADic);for(const tissue of allTissuesDisplayed){let append_str='<li class="form-check">';append_str+='<input class="form-check-input" type="checkbox" id="'+tissue.replace(" ","_")+'" onclick="ToggleFilteredeFP(this.id, this.checked);" style="margin: 6px 5px 0;" value="toggleeFP" checked>',append_str+='<p class="form-check-label" for="toggleTitle" style="padding-left: 20px; font-weight: 10;">'+tissue+"</p>",append_str+="</li>",$("#filtereFPList").append(append_str)}}else logError("Unable to use tissueSRADic")}function ToggleFilteredeFP(whichToToggle,OnOrOff){const whichSVG=whichToToggle.replace("_"," "),whichSRA=tissueSRADic[whichSVG];if(!0===OnOrOff)for(let i=0;i<whichSRA.length;i++)document.getElementById(whichSRA[i]+"_row")&&document.getElementById(whichSRA[i]+"_row").removeAttribute("hidden");else if(!1===OnOrOff)for(let i=0;i<whichSRA.length;i++)document.getElementById(whichSRA[i]+"_row")&&document.getElementById(whichSRA[i]+"_row").setAttribute("hidden",!0)}function LoadSubmittedData(){emptyLanding(),progress_percent=0,document.title=`eFP-Seq Browser: Loading 0% - ${locus}`,loadingScreen(!1),setTimeout((function(){count_bam_num(),disableAllComparison()}),200),update_all_images(0)}function generateShareLink(changeURL=!1){let url="https://"+window.location.host+window.location.pathname;url+="?locus="+locus+"&dataset="+base_src,shareLink=url,changeURL&&window.history.pushState&&window.history.pushState({},"Title",window.location.pathname+"?locus="+locus+"&dataset="+base_src),document.getElementById("shareLinkTextArea").textContent=shareLink}const shareLinkInputs={};function readShareLink(){const query=window.location.search.substr(1);let locusInput=!1,datasetInput=!1;if(""!=query){const inputs=query.split("&");for(const input of inputs){const queryInputs=input.split("=");if(queryInputs.length>1)if("locus"===queryInputs[0].split("%20").join(" ").trim()){const qIValue=input.substring(6).split("%20").join(" ").trim();shareLinkInputs.locus=qIValue,document.getElementById("locus").value=qIValue,locusInput=!0}else if("dataset"===queryInputs[0].split("%20").join(" ").trim()){const qIValue=input.substring(8).split("%20").join(" ").trim();shareLinkInputs.dataset=qIValue,base_src=qIValue,datasetInput=!0}}locusInput&&datasetInput?(emptyLanding(),progress_percent=0,document.title=`eFP-Seq Browser: Loading 0% - ${locus}`,sraDict={},sraCountDic={},loadNewDataset=!1,setTimeout((function(){count_bam_num(),disableAllComparison(),checkPreload()}),200),toggleResponsiveTable(0)):displayError(locusInput&&!1===datasetInput?"ERROR IN SHARE LINK! Missing dataset":!1===locusInput&&datasetInput?"ERROR IN SHARE LINK! Missing locus":"ERROR IN SHARE LINK! Missing locus and dataset")}}function copyToClipboard(){""!==document.getElementById("shareLinkTextArea").trim()&&(document.getElementById("shareLinkTextArea").select(),document.execCommand("copy"))}let allCheckedOptions=[];function tableCheckbox(whatID,disableAll=!1){const whatSRA=whatID.split("_")[0];if(disableAll)disableAllComparison();else if(!1===disableAll&&document.getElementById(whatID)&&document.getElementById(whatID).checked){allCheckedOptions.push(whatSRA);const iterationProcess={};for(let i=0;i<GFF_List.length;i++){let append_str='<tr class="compareDataRow" id="'+whatSRA+"_compareRow"+i+'">';parseInt(i)===parseInt(variantPosition)?append_str+='<td style="width: 250px; font-size: 12px;" id="'+whatSRA+"_compareTitle"+i+'">'+document.getElementById(whatSRA+"_title").innerHTML+" ... ("+GFF_List[i]+")</td>\n":append_str+='<td style="width: 250px; font-size: 12px;" id="'+whatSRA+"_compareTitle"+i+'">^^^ ... ('+GFF_List[i]+")</td>\n",append_str+='<td style="max-width: 576px;"><img loading="lazy" id="'+whatSRA+"_rnaseq_img"+i+'" alt="RNA-Seq mapped image for:'+whatSRA+'" style="min-width:420px; max-width:576px; width:95%; height: auto;" src="" /><br/><img loading="lazy" id="'+whatSRA+"_gene_structure_img"+i+'" style="max-width: 576px; width:100%; height: auto;" src="" alt="Gene variant image for:'+whatSRA+'"/></td>\n',append_str+='<td id="'+whatSRA+"_rpb"+i+'" style="font-size: 12px; width: 50px; ">'+sraDict[whatSRA].r[i].toFixed(2)+"</td>",append_str+='<td tag="svg_name" style="width:  75px;"><div id="'+whatSRA+"_svg"+i+'" name="'+sraDict[whatSRA].svg.substr(4).replace(".","_")+'_tissue" tag='+sraDict[whatSRA].svg_part+'_subtissue" width="75" height="75" style="width: 75px; height: 75px; max-width: 75px; max-height: 75px;">'+document.getElementById(sraDict[whatSRA].svg.substr(4).replace(".svg","_svg")).innerHTML+'</div><div class="mdl-tooltip" for="'+whatSRA+"_svg"+i+'">'+sraDict[whatSRA].svg.substring(4).replace(".svg","")+"</div></td>\n",append_str+='<td id="'+whatSRA+"_rpkm"+i+'" style="font-size: 12px; width: 50px; ">'+sraDict[whatSRA].RPKM[i].toFixed(2)+"</td>",parseInt(i)===parseInt(variantPosition)?append_str+='<td style="width: 250px; font-size: 12px;" id="'+whatSRA+"_compareTitle"+i+'"><div id="'+whatSRA+'_descriptionCompare" name="'+document.getElementById(whatSRA+"_description").getAttribute("name")+'">'+document.getElementById(whatSRA+"_description").innerHTML+'</div><div id="igbLinkCompare_'+whatSRA+'">'+document.getElementById("igbLink_"+whatSRA).innerHTML+'</div><div id="extraLinksCompare_'+whatSRA+'">'+document.getElementById("extraLinks_"+whatSRA).innerHTML+"</div></td>\n":append_str+='<td style="width: 250px; font-size: 12px;" id="'+whatSRA+"_compareTitle"+i+'">^^^</td>\n',append_str+="</tr>",iterationProcess[i]=whatSRA+"_compareRow"+i,document.getElementById("compareTable").innerHTML+=append_str,document.getElementById(whatSRA+"_rnaseq_img"+i)&&document.getElementById(whatSRA+"_rnaseq_img"+i).setAttribute("src",document.getElementById(whatSRA+"_rnaseq_img").src),document.getElementById(whatSRA+"_gene_structure_img"+i)&&document.getElementById(whatSRA+"_gene_structure_img"+i).setAttribute("src",document.getElementsByClassName("dd-option-image")[i].src),sraDict[whatSRA].RPKM&&sraDict[whatSRA].RPKM[i]&&colour_part_by_id(whatSRA+"_svg"+i,sraDict[whatSRA].svg_part,sraDict[whatSRA].RPKM[i],colouring_mode)}document.getElementById(whatID).checked=!0,document.getElementById("allCheckbox").checked=!0,"rel"!=colouring_mode&&(document.getElementById("compareGeneVariants").disabled=!1)}else!1===disableAll?(disableCompare(whatSRA),allCheckedOptions.splice(allCheckedOptions.indexOf(whatSRA),1),document.getElementById(whatID).checked=!1):!0===disableAll&&disableAllComparison(),0===allCheckedOptions.length&&(document.getElementById("compareGeneVariants").disabled=!0)}function disableCompare(whatSRA){for(let i=0;i<GFF_List.length;i++)null!=document.getElementById(whatSRA+"_compareRow"+i)&&document.getElementById(whatSRA+"_compareRow"+i).remove()}function disableAllComparison(){if(document.getElementById("allCheckbox")){let compareDataRows=document.getElementsByClassName("compareDataRow");for(let c=compareDataRows.length-1;c>=0;c--)document.getElementsByClassName("compareDataRow")[c].remove();allCheckedOptions=[],compareDataRows=document.getElementsByClassName("compareCheckbox");for(let c=0;c<compareDataRows.length;c++)document.getElementsByClassName("compareCheckbox")[c].checked=!1;document.getElementById("allCheckbox").checked=!1;const listOfEntries=[],mainEntries=document.getElementsByClassName("mainEntries");for(let m=0;m<mainEntries.length;m++){const mainID=mainEntries[m].id;!1===listOfEntries.includes(mainID)?listOfEntries.push(mainID):document.getElementsByClassName("mainEntries")[m].remove()}document.getElementById("compareGeneVariants").disabled=!0}}function PnCDisappear(){document.getElementById("PrivacyAndCookies").setAttribute("hidden",!0),document.cookie="eSBAcceptedCookies=1; expires=Friday, December 31, 9999 at 7:00:00 AM; SameSite=Lax; Secure",document.cookie="eSBVersion="+version+"; expires=Friday, December 31, 9999 at 7:00:00 AM; SameSite=Lax; Secure"}function setUpCookies(){const cookies=document.cookie.split(";");let cookieAccept,cookieVersion;for(const cookie of cookies){const whichCookie=cookie.split("=");if(whichCookie[0]&&"eSBAcceptedCookies"===whichCookie[0].trim()&&(cookieAccept=whichCookie[1].trim()),whichCookie[0]&&"eSBVersion"===whichCookie[0].trim()&&(cookieVersion=whichCookie[1].trim()),cookieAccept&&cookieVersion)break}cookieAccept&&"1"===cookieAccept?document.getElementById("PrivacyAndCookies").setAttribute("hidden",!1):document.getElementById("PrivacyAndCookies").removeAttribute("hidden"),cookieVersion&&cookieVersion!==version&&(document.getElementById("PrivacyAndCookies").removeAttribute("hidden"),document.cookie="eSBAcceptedCookies=0; SameSite=Lax; Secure")}function appendVersionNumber(elementId){const versionText=`<br><br>The eFP-Seq Browser's current version number is: ${version}`;document.getElementById(elementId).innerHTML+=versionText}function displayVersionNumber(){appendVersionNumber("citationText"),appendVersionNumber("feedbackText")}let toastCounter=0;function generateToastNotification(message,header="Notification"){if(message){let dataAttributeValue=`toast-${toastCounter}`;const toast=`\n\t\t<div class="toast" role="alert" aria-live="assertive" aria-atomic="true" data-toast="${dataAttributeValue}" style="background-color: rgba(255, 255, 255, 1);">\n\t\t\t<div class="toast-header">\n\t\t\t\t<img\n\t\t\t\t\tsrc="cgi-bin/img/BAR-logo.svg"\n\t\t\t\t\tclass="rounded me-2"\n\t\t\t\t\talt="BAR notification"\n\t\t\t\t\tstyle="width: 20px; 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\ No newline at end of file
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round(x,digits){return parseFloat(x.toFixed(digits))}let colouring_part;function colour_part_by_id(id,part,fpkm,mode){colouring_part="all";for(const sra of sraList)id.replace("_svg","")==sra&&(colouring_part=sraDict[sra].svg_part);let paths1,paths2,fpkmUse=fpkm;fpkmUse=Array.isArray(fpkmUse)?fpkmUse[variantPosition]:parseFloat(fpkmUse),max_abs_scale=document.getElementById("rpkm_scale_input").value,(!max_abs_scale||max_abs_scale<=0)&&(max_abs_scale=1e3),document.getElementById(id)&&(paths1=document.getElementById(id).getElementsByTagName("path"),paths2=document.getElementById(id).getElementsByTagName("g"));let paths=null;if(paths1&&paths2&&(paths=Array.prototype.slice.call(paths1).concat(Array.prototype.slice.call(paths2))),null!=paths){if("abs"==mode){const r=255,g=255-parseInt(fpkmUse/max_abs_scale*255),b=0;if("all"==colouring_part)for(const path of paths)path.style.fill="rgb("+r+", "+g+", "+b+")";else for(const path of paths)if(path.id==colouring_part)if("g"==path.tagName){const child_paths=path.getElementsByTagName("path");for(const child of child_paths)child.style.fill="rgb("+r+", "+g+", "+b+")"}else path.style.fill="rgb("+r+", "+g+", "+b+")"}else if("rel"==mode){let hex="";const log_scale_max=3;let log_scaling=0;if("Missing controls data"!=fpkmUse&&Math.abs(fpkmUse)>log_scale_max?log_scaling=log_scale_max:"Missing controls data"!=fpkmUse&&(log_scaling=Math.abs(fpkmUse)),log_scaling/=log_scale_max,"Missing controls data"==fpkmUse?hex="#D9D9D9":fpkmUse>0?hex=generate_colour("FFFF00","FF0000",log_scaling):0==fpkmUse?hex="FFFF00":fpkmUse<0&&(hex=generate_colour("FFFF00","0000FF",log_scaling)),"all"==colouring_part)for(const path of paths)path.style.fill=hex;else for(const path of paths)if(path.id==colouring_part)if("g"==path.tagName){const child_paths=path.getElementsByTagName("path");for(const child of child_paths)child.style.fill=hex}else path.style.fill=hex}document.getElementById(id.replace("_svg","_rpkm")).innerHTML="Missing controls data"==fpkmUse?fpkmUse:round(fpkmUse,2)}else console.log("Paths is null for id = "+id)}let rpkmAverage=1,rpkmMedian=1;function findRPKMValuesAcrossAll(){if(sraDict){const listOfSRA=Object.keys(sraDict),listOfRPKM=[];let rpkmTotal=0;for(const sra of listOfSRA)if(sraDict[sra].RPKM){const currentRPKM=sraDict[sra].RPKM[variantPosition];parseFloat(currentRPKM)&&(listOfRPKM.push(currentRPKM),rpkmTotal+=currentRPKM)}listOfRPKM.length>0&&(rpkmMedian=math.median(listOfRPKM)),rpkmAverage=rpkmTotal/listOfSRA.length}else displayError("ERROR IN RETRIEVING ALL DATA POINTS WITHIN DATASET")}function switchRPKMMode(selectedMode){let rel=!1;"rel_radio"===selectedMode&&(rel=!0),rel?(colouring_mode="rel",document.getElementById("abs_radio").classList.remove("active"),document.getElementById("rel_radio").classList.add("active"),$("#rpkm_scale_input").prop("disabled",!0)):(colouring_mode="abs",document.getElementById("rel_radio").classList.remove("active"),document.getElementById("abs_radio").classList.add("active"),$("#rpkm_scale_input").removeAttr("disabled")),rnaseq_calls&&rnaseq_calls.length>0&&whichAbsOrRel()}function colour_svgs_now(){const mode=colouring_mode;for(let i=0;i<count_bam_entries_in_xml;i++){if(exp_info[i]){const currentSRA=exp_info[i][0].slice(0,-4);let ctrl_fpkm_sum=0,ctrl_count=0,ctrl_avg_fpkm=0;for(let ii=0;ii<count_bam_entries_in_xml;ii++)-1!=exp_info[i][2].indexOf(exp_info[ii][0].slice(0,-4))&&(ctrl_count++,ctrl_fpkm_sum+=exp_info[ii][3][variantPosition]);0===ctrl_fpkm_sum&&sraDict[currentSRA].RPKM&&(ctrl_fpkm_sum=sraDict[currentSRA].RPKM[variantPosition]),ctrl_count>0?ctrl_avg_fpkm=ctrl_fpkm_sum/ctrl_count:(rpkmMedian&&1===rpkmMedian&&findRPKMValuesAcrossAll(),ctrl_avg_fpkm=rpkmMedian);let relativeRPKMValue=0;const relativeRPKM=[];let useRPKM="";useRPKM=sraDict[currentSRA].RPKM&&sraDict[currentSRA].RPKM[variantPosition]?sraDict[currentSRA].RPKM[variantPosition]:0,0==useRPKM&&0==ctrl_avg_fpkm?exp_info[i].splice(4,1,0):relativeRPKMValue=Math.log2(useRPKM/ctrl_avg_fpkm),relativeRPKM.push(relativeRPKMValue),sraDict[currentSRA].relativeRPKM=relativeRPKMValue,exp_info[i].splice(4,1,relativeRPKM),exp_info[i].splice(6,1,ctrl_avg_fpkm),useRPKM>=max_absolute_fpkm&&(max_absolute_fpkm=useRPKM),"Missing controls data"!=exp_info[i][4]&&Math.abs(exp_info[i][4])>=max_log_fpkm&&Math.abs(exp_info[i][4])<1e3&&(max_log_fpkm=Math.abs(exp_info[i][4])),"rel"===colouring_mode?exp_info[i][4]||0==exp_info[i][4]||(exp_info[i][4]=-999999):exp_info[i][3][variantPosition]||0==exp_info[i][3][variantPosition]||(exp_info[i][3][variantPosition]=-999999)}else logError("Issue retrieving exp_info for "+mode+" within BAM entry point "+i);whichAbsOrRel()}document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update"),change_rpkm_colour_scale(colouring_mode)}function get_input_values(){locus=document.getElementById("locus").value,locus=locus.trim().toUpperCase(),yscale_input=document.getElementById("yscale_input").value,("Auto"==yscale_input||parseInt(yscale_input)<1)&&(yscale_input=parseInt(-1)),max_abs_scale=document.getElementById("rpkm_scale_input").value}function update_all_images(status){null!=document.getElementById("locus")&&(new_locus=document.getElementById("locus").value,new_locus===old_locus?($.xhrPool.abortAll(),variants_radio_options(status)):new_locus!=old_locus&&(getGFF(new_locus),old_locus=new_locus,setTimeout((function(){$.xhrPool.abortAll(),variants_radio_options(status)}),1650)))}async function variants_radio_options(status){get_input_values(),fetch(`${BE_URL}/cgi-bin/get_gene_structures.cgi?locus=${locus}`).then((async response=>{const gene_res=await response.json();locus_start=gene_res.locus_start,locus_end=gene_res.locus_end,splice_variants=JSON.stringify(gene_res.splice_variants),populate_table(status),populate_efp_modal(status);const variants_div=document.getElementById("variants_div");if(variants_div?.firstChild)for(;variants_div.firstChild;)variants_div.removeChild(variants_div.firstChild);$("#variant_select").ddslick("destroy");let append_str='<select id="variant_select">';if(gene_res.variant_count&&parseInt(gene_res.variant_count)>0)for(let i=0;i<parseInt(gene_res.variant_count);i++)gene_res.splice_variants?.[i]?.gene_structure&&(append_str+='<option value="'+i+'"',append_str+=' data-imagesrc="data:image/png;base64,'+gene_res.splice_variants[i].gene_structure+'" style="max-width:none;"></option>');else append_str+='<option value="'+i+'"',append_str+=' data-imagesrc="'+img_gene_struct_error+'" style="max-width:none;"></option>';if(gene_res.splice_variants?.[0]?.gene_structure){img_gene_struct_1="data:image/png;base64,"+gene_res.splice_variants[0].gene_structure;const all_gene_structure_imgs=document.getElementsByClassName("gene_structure_img");for(const element of all_gene_structure_imgs)element.src="data:image/png;base64,"+gene_res.splice_variants[0].gene_structure}else{img_gene_struct_1=img_gene_struct_error;const all_gene_structure_imgs=document.getElementsByClassName("gene_structure_img");for(const element of all_gene_structure_imgs)element.src="data:image/png;base64,"+gene_res.splice_variants[0].gene_structure}$("input[type=radio][name=radio_group]").change((function(){gene_structure_radio_on_change()})),append_str+="</select></div>",$("#variants_div").append(append_str),document.getElementById("variant_select")&&$("#variant_select").ddslick({width:"100%",onSelected:function(){gene_structure_radio_on_change()}}),document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update")})).catch((error=>{displayError("ERROR processing and getting gene structures!"),generateToastNotification(`Error processing gene structures: ${error.message}`,"ERROR"),console.error(`Error processing gene structures: ${error.message}`)}))}function displayError(errorMessage){$("#displayError").empty();let append_str='<p class="warning_core" style="text-align:center;">'+errorMessage+" <br /><br /> PLEASE REFRESH PAGE, RELOAD OR RE-INPUT DATA OR TRY AGAIN AT A LATER TIME </p>";console.error("Error in logic:",errorMessage),$("#displayError").append(append_str),$("#locus_button").prop("disabled",!0),$("#abs_scale_button").prop("disabled",!0),progress_percent=100,$("div#progress").width(progress_percent+"%"),loadingScreen(!0),document.title=`eFP-Seq Browser: !ERROR! - ${locus} - ${datasetName}`}function logError(errorMessage){console.error("Error in logic:",errorMessage)}let variant_selected,variantPosition=0;function gene_structure_radio_on_change(){if(document.getElementsByClassName("dd-selected-value")&&document.getElementsByClassName("dd-selected-value")[0]&&document.getElementsByClassName("dd-selected-value")[0].value){variant_selected=document.getElementsByClassName("dd-selected-value")[0].value,variantPosition=variant_selected;let variant_img=document.getElementsByClassName("dd-selected-image")[0].src;document.getElementsByClassName("dd-selected-image")&&document.getElementsByClassName("dd-selected-image")[0]&&!document.getElementsByClassName("dd-selected-image")[0].alt&&(document.getElementsByClassName("dd-selected-image")[0].alt="RNA-Seq Coverage");let all_gene_structure_imgs=document.getElementsByClassName("gene_structure_img");for(let i=0;i<all_gene_structure_imgs.length;i++)all_gene_structure_imgs[i].src=variant_img;for(let i=0;i<exp_info.length;i++){let itLocus=exp_info[i][0].split("_")[0];document.getElementById(itLocus+"_gene_structure_img").src=variant_img;let rpkmValue,rpbValue=sraDict[itLocus].r[variant_selected].toFixed(2);document.getElementById(itLocus+"_rpb").innerHTML=rpbValue,sraDict[exp_info[i][0].split("_svg")[0]]||(sraDict[exp_info[i][0].split("_svg")[0]]={}),sraDict[exp_info[i][0].split("_svg")[0]].rpb=rpbValue,sraDict[itLocus].RPKM&&sraDict[itLocus].RPKM[variant_selected]?rpkmValue=sraDict[itLocus].RPKM[variant_selected].toFixed(2):sraDict[itLocus].RPKM?logError("Unable to retrieve RPKM values at: [variant_selected] for "+itLocus):sraDict[itLocus]?logError('Unable to retrieve RPKM values at: ["RPKM"] for '+itLocus):logError(sraDict?"Unable to retrieve RPKM values at: SRA within sraDict":"Unable to retrieve RPKM values at: sraDict unreachable"),document.getElementById(itLocus+"_rpkm").innerHTML=rpkmValue,whichAbsOrRel(!0,i)}}document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update")}function whichAbsOrRel(preIterate=!1,iteratePos=0){if(!0===preIterate)absOrRel(iteratePos);else if(exp_info.length>0)for(let i=0;i<exp_info.length;i++)absOrRel(i);change_rpkm_colour_scale(colouring_mode)}function absOrRel(expInfoPos=0){let expInfo=exp_info[expInfoPos],currentSRA=expInfo[0].slice(0,-4);if("rel"==colouring_mode&&sraDict[currentSRA].relativeRPKM){document.getElementById("compareGeneVariants").disabled=!0,expInfo&&!expInfo[4]&&0!=expInfo[4]&&(expInfo[4]=-999999);let rpkmValue=sraDict[currentSRA].relativeRPKM.toFixed(2);document.getElementById(expInfo[0].split("_svg")[0]+"_rpkm").innerHTML=rpkmValue,sraDict[expInfo[0].split("_svg")[0]].rpkm=rpkmValue,colour_part_by_id(currentSRA+"_svg",sraDict[currentSRA].svg_part,sraDict[currentSRA].relativeRPKM,colouring_mode)}else{allCheckedOptions.length>0&&(document.getElementById("compareGeneVariants").disabled=!1),expInfo[3]||0==expInfo[3]||(expInfo[3]=-999999);let useRPKM="";if(variant_selected&&sraDict[currentSRA].RPKM&&sraDict[currentSRA].RPKM[variant_selected]){let rpkmValue=sraDict[currentSRA].RPKM[variant_selected].toFixed(2);document.getElementById(expInfo[0].split("_svg")[0]+"_rpkm").innerHTML=rpkmValue,useRPKM=rpkmValue}else{let rpkmValue=0;document.getElementById(expInfo[0].split("_svg")[0]+"_rpkm").innerHTML=rpkmValue,useRPKM=rpkmValue}colour_part_by_id(currentSRA+"_svg",sraDict[currentSRA].svg_part,useRPKM,colouring_mode)}}function parseIntArray(arr){for(let i=0,len=arr.length;i<len;i++)arr[i]=parseInt(arr[i],10);return arr}let rnaseq_image_url=`${BE_URL}/cgi-bin/rnaSeqMapCoverage.cgi`,match_drive="",progress_percent=0,rnaseq_change=1,totalreadsMapped_dic={},dumpOutputs="",dumpMethod="simple",callDumpOutputs=!1,rpkmCount=1,listOfRecordsDisplayed=[];function rnaseq_images(status){changePublicData();if(dumpOutputs="",data={},rnaseq_success=1,rpkmCount=1,match_drive="",listOfRecordsDisplayed=[],get_input_values(),CreateFilteredeFPList(),rnaseq_calls.length===count_bam_entries_in_xml){rnaseq_change=1;for(let i=0;i<count_bam_entries_in_xml;i++){let tissueWebservice=rnaseq_calls[i][0]||"undefined",sraRecordNumber=rnaseq_calls[i][1]||"unknown";if("Google Drive"===sraDict[sraList[i]].bam_type){let linkString=sraDict[sraList[i]].drive_link,driveLinkSplit=linkString.split("?usp=sharing");driveLinkSplit=driveLinkSplit[0].split("drive.google.com/drive/folders/"),match_drive=driveLinkSplit.length>1?driveLinkSplit[1]:linkString}else if("Amazon AWS"===sraDict[sraList[i]].bam_type){let linkString=sraDict[sraList[i]].drive_link,driveLinkSplit=linkString.split("amazonaws.com/");1===driveLinkSplit.length&&(driveLinkSplit=linkString.split("araport.cyverse-cdn.tacc.cloud/")),match_drive=driveLinkSplit.length>1?driveLinkSplit[1]:linkString}data={status:status,numberofreads:sraDict[sraList[i]].numberofreads,hexcodecolour:sraDict[sraList[i]].hexColourCode,remoteDrive:match_drive,bamType:sraDict[sraList[i]].bam_type,filename:sraDict[sraList[i]].filenameIn,tissue:tissueWebservice,record:sraRecordNumber,locus:locus,variant:1,start:locus_start,end:locus_end,yscale:yscale_input,cachedDatapoints:publicData,struct:splice_variants,dumpMethod:dumpMethod},$.ajax({method:"POST",url:rnaseq_image_url,data:data,dataType:"json",failure:function(){$("#failure").show()},success:function(response_rnaseq){let stopLoadingScreen=99;count_bam_entries_in_xml>0&&(stopLoadingScreen=parseInt((count_bam_entries_in_xml-1)/count_bam_entries_in_xml*100)),rnaseq_success++;let date_obj3=new Date;if(rnaseq_success_current_time=date_obj3.getTime(),progress_percent=rnaseq_change/count_bam_entries_in_xml*100,$("div#progress").width(progress_percent+"%"),progress_percent>stopLoadingScreen&&loadingScreen(!0),document.getElementById("progress_tooltip").innerHTML="Current progress is at "+progress_percent+"% done",document.getElementById("progress").title=progress_percent.toFixed(2)+"% ("+rnaseq_change+"/"+count_bam_entries_in_xml+")",document.title="eFP-Seq Browser:",progress_percent<100&&(document.title+=` Loading ${progress_percent.toFixed(1)}% -`),document.title+=` ${locus} - ${datasetName}`,response_rnaseq.status&&"success"===response_rnaseq.status&&response_rnaseq.record){let responseRecord=response_rnaseq.record||"unknown";if(listOfRecordsDisplayed.includes(responseRecord)?(responseRecord=findUnusedRecordDisplayName(responseRecord,listOfRecordsDisplayed),listOfRecordsDisplayed.push(responseRecord)):listOfRecordsDisplayed.push(responseRecord),listOfRecordsDisplayed=[],sraDict[responseRecord].bp_length=parseFloat(response_rnaseq.end)-parseFloat(response_rnaseq.start),sraDict[responseRecord].bp_start=parseFloat(response_rnaseq.start),sraDict[responseRecord].bp_end=parseFloat(response_rnaseq.end),sraDict[responseRecord].MappedReads=response_rnaseq.reads_mapped_to_locus,totalreadsMapped_dic[responseRecord]=response_rnaseq.totalReadsMapped,sraDict[responseRecord].locusValue=response_rnaseq.locus,sraDict[responseRecord].r=response_rnaseq.r,sraDict[responseRecord].dataVisualization=response_rnaseq.rnaseqbase64,locus!=response_rnaseq.locus)throw new Error(`ERROR: ${locus}'s RNA-Seq API request returned with data for some other locus.`);let r=[];if(response_rnaseq.ss_y&&response_rnaseq.sum_y&&response_rnaseq.sum_xy&&response_rnaseq.sum_x&&response_rnaseq.ss_x&&response_rnaseq.end&&response_rnaseq.start){parseInt(response_rnaseq.ss_y);let sum_y=parseInt(response_rnaseq.sum_y),ssy=parseInt(response_rnaseq.ss_y),sum_xy=parseIntArray(response_rnaseq.sum_xy.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),sum_x=parseIntArray(response_rnaseq.sum_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),ssx=(parseIntArray(response_rnaseq.sum_xx.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),parseIntArray(response_rnaseq.ss_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),parseIntArray(response_rnaseq.ss_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(","))),n=parseInt(response_rnaseq.end)-parseInt(response_rnaseq.start),sp=[];for(let i=0;i<sum_xy.length;i++)sp.splice(i,0,sum_xy[i]-sum_x[i]*sum_y/n),r.splice(i,0,sp[i]/Math.sqrt(ssx[i]*ssy))}else r=response_rnaseq.r;if(document.getElementById(responseRecord+"_rnaseq_img")&&response_rnaseq.rnaseqbase64?"None"!==response_rnaseq.rnaseqbase64&&response_rnaseq.rnaseqbase64.length>=3?(document.getElementById(responseRecord+"_rnaseq_img").src="data:image/png;base64,"+response_rnaseq.rnaseqbase64,rnaseq_change+=1):(document.getElementById(responseRecord+"_rnaseq_img").src="https://"+window.location.host+window.location.pathname+"cgi-bin/img/error.webp",console.error("Unable to create RNA-Seq map coverage data for: Locus - "+locus+", SRA - "+responseRecord+", dataset - "+base_src)):(document.getElementById(`${responseRecord}_rnaseq_img`)&&(document.getElementById(`${responseRecord}_rnaseq_img`).src=`https://${window.location.host}${window.location.pathname}/cgi-bin/img/error.webp`),console.error("Unable to create RNA-Seq map coverage data for: Locus - "+locus+", SRA - "+responseRecord+", dataset - "+base_src)),document.getElementById(responseRecord+"_rpb").innerHTML=parseFloat(r[0]).toFixed(2),sraDict[responseRecord].rpb=parseFloat(r[0]).toFixed(2),document.getElementById(responseRecord+"_rpkm").innerHTML=response_rnaseq["absolute-fpkm"],updateRPKMAbsoluteMax(response_rnaseq["absolute-fpkm"]),sraDict[responseRecord].RPKM=response_rnaseq["absolute-fpkm"],rpkmCount++,document.getElementById(responseRecord+"_totalReadsNum").innerHTML="Total reads = "+response_rnaseq.totalReadsMapped,callDumpOutputs)if(dumpOutputs+='\t\telif (record == "'+response_rnaseq.record+'"):\n',"complex"==dumpMethod){for(dumpOutputs+='\t\t\tdumpJSON(200, "'+response_rnaseq.locus+'", '+response_rnaseq.variant+", "+response_rnaseq.chromosome+", "+response_rnaseq.start+", "+response_rnaseq.end+', "'+response_rnaseq.record+'", "'+response_rnaseq.tissue+'", "'+response_rnaseq.rnaseqbase64+'", '+response_rnaseq.reads_mapped_to_locus+", "+response_rnaseq["absolute-fpkm"]+", ["+response_rnaseq.r+"], "+response_rnaseq.totalReadsMapped+", ["+response_rnaseq.exp_arr+"], [",r=0;r<response_rnaseq.ReadsMappedNucleotidePosition.length;r+=2)dumpOutputs+="["+response_rnaseq.ReadsMappedNucleotidePosition[r]+"]",r!=response_rnaseq.ReadsMappedNucleotidePosition.length-2&&(dumpOutputs+=", ");dumpOutputs+="], {";for(let e=0;e<response_rnaseq.expected_expr_in_variant.length;e++)dumpOutputs+='"'+GFF_List[e].replace(locus,"")+'": ',dumpOutputs+="["+response_rnaseq.expected_expr_in_variant[e]+"]",e!=response_rnaseq.expected_expr_in_variant.length-1&&(dumpOutputs+=", ");dumpOutputs+="})\n"}else dumpOutputs+='\t\t\tdumpJSON(200, "'+response_rnaseq.locus+'", '+response_rnaseq.variant+", "+response_rnaseq.chromosome+", "+response_rnaseq.start+", "+response_rnaseq.end+', "'+response_rnaseq.record+'", "'+response_rnaseq.tissue+'", "'+response_rnaseq.rnaseqbase64+'", '+response_rnaseq.reads_mapped_to_locus+", ["+response_rnaseq["absolute-fpkm"]+"], ["+response_rnaseq.r+"], "+response_rnaseq.totalReadsMapped+")\n";for(let ii=0;ii<count_bam_entries_in_xml;ii++)exp_info&&exp_info[ii]&&exp_info[ii][0]&&exp_info[ii][0]==responseRecord+"_svg"&&(exp_info[ii].splice(3,1,response_rnaseq["absolute-fpkm"]),exp_info[ii].splice(5,1,r));colour_part_by_id(responseRecord+"_svg","Shapes",response_rnaseq["absolute-fpkm"][variantPosition],colouring_mode)}else if(response_rnaseq.status&&"fail"===response_rnaseq.status){let responseRecord=response_rnaseq.record||"unknown";listOfRecordsDisplayed.includes(responseRecord)?(responseRecord=findUnusedRecordDisplayName(responseRecord,listOfRecordsDisplayed),listOfRecordsDisplayed.push(responseRecord)):listOfRecordsDisplayed.push(responseRecord),responseRecord&&document.getElementById(`${responseRecord}_rnaseq_img`)&&(document.getElementById(`${responseRecord}_rnaseq_img`).src=`https://${window.location.host}${window.location.pathname}/cgi-bin/img/error.webp`),rnaseq_change+=1,responseRecord&&document.getElementById(responseRecord+"_rpb")&&(document.getElementById(responseRecord+"_rpb").innerHTML=null,sraDict[responseRecord]||(sraDict[responseRecord]={}),sraDict[responseRecord].rpb=null),responseRecord&&document.getElementById(responseRecord+"_rpkm")&&(document.getElementById(responseRecord+"_rpkm").innerHTML=null,updateRPKMAbsoluteMax(null),sraDict[responseRecord].RPKM=null),rpkmCount++,responseRecord&&document.getElementById(responseRecord+"_totalReadsNum")&&response_rnaseq.totalReadsMapped&&(document.getElementById(responseRecord+"_totalReadsNum").innerHTML="Total reads = "+response_rnaseq.totalReadsMapped),responseRecord&&document.getElementById(responseRecord+"_row")&&document.getElementById(responseRecord+"_row").classList.add("mainEntriesError"),console.error("Unable to create RNA-Seq map coverage data for: Locus - "+locus+", SRA - "+responseRecord+", dataset - "+base_src)}else console.log("Error!",response_rnaseq,data);rpkmCount==count_bam_entries_in_xml&&(colour_svgs_now(),date_obj4=new Date,rnaseq_success_end_time=date_obj4.getTime(),document.getElementById("progress_tooltip").innerHTML=rnaseq_success+" / count_bam_entries_in_xml requests completed<br/>Load time ~= "+String(round(parseInt(rnaseq_success_end_time-rnaseq_success_start_time)/6e4))+" mins."),document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update"),responsiveRNAWidthResize(),toggleResponsiveTable()},error:function(xhr,status,error){generateToastNotification(`Error getting RNA-Seq map coverage for ${data.record} - ${error.message}`,"ERROR"),console.error("Error getting RNA-Seq map coverage!",xhr,status,error)}})}}}function findUnusedRecordDisplayName(recordID="unknown",listCheckAgainst=sraList,it=0){if(Array.isArray(listCheckAgainst)){let newName=recordID+"_"+it;if(listCheckAgainst.includes(newName))findUnusedRecordDisplayName(recordID,listCheckAgainst,it+1);else if(!listCheckAgainst.includes(newName))return newName}else findUnusedRecordDisplayName(recordID,listCheckAgainst=[])}function updateRPKMAbsoluteMax(RPKMCheckAgainst){let currentRPKMAbsMax=parseInt(document.getElementById("rpkm_scale_input").value);1e3===currentRPKMAbsMax&&(currentRPKMAbsMax=1);let newRPKMValue=parseInt(RPKMCheckAgainst);newRPKMValue>currentRPKMAbsMax&&(document.getElementById("rpkm_scale_input").value=newRPKMValue)}const svgAgainstData={"ath-10dayOldSeedling":{name:"10 Day Old Seedling",subunit:["all","root","shoot"]},"ath-15dayOldSeedling":{name:"15 Day Old Seedling",subunit:["all","root","shoot"]},"ath-etiolatedSeedling":{name:"Etiolated Seedling",subunit:["etiolatedseedling"]},"ath-Flower":{name:"Flower",subunit:["flower","receptacle"]},"ath-FlowerParts":{name:"Flower Parts",subunit:["all","petals","stamen","sepals","carpels"]},"ath-GerminatingSeed":{name:"Germinating Seed"},"ath-Internode":{name:"Internode"},"ath-leaf":{name:"Leaf",subunit:["leaf"]},"ath-LeafParts":{name:"Leaf Parts",subunit:["all","lamina","petiole","veins"]},"ath-Pollen":{name:"Pollen"},"ath-RootTip":{name:"Root Tip"},"ath-rosettePlusRoot":{name:"Rosette Plus Root",subunit:["all","shoot","root"]},"ath-Seed1-4":{name:"Seed 1-4"},"ath-Seed5-7":{name:"Seed 5-7"},"ath-Seed8+":{name:"Seed 8+"},"ath-SenescentLeaf":{name:"Senescent Leaf"},"ath-ShootApexInflorescense":{name:"Shoot Apex Inflorescense"},"ath-ShootApexVegetative-Transition":{name:"Shoot Apex Vegetative-Transition"},"ath-Silique1-5":{name:"Silique 1-5"},"ath-Silique6-10":{name:"Silique 6-10"},"ath-YoungLeaf1-4":{name:"Young Leaf 1-4"},"ath-EarlyBuddingFlower":{name:"Early Budding Flower",subunit:["all","shoot","buds"]},"ath-EarlyBuddingFlower":{name:"Early Budding Flower",subunit:["all","shoot","buds"]},"ath-FlowerBud":{name:"Flower Bud",subunit:["flowerBud"]},"ath-Stamen":{name:"Stamen",subunit:["all","anthers","filament"]},"ath-StigmaAndOvaries":{name:"Stigma And Ovaries",subunit:["all","Stigma_tissue","Ovary_tissue"]},"ath-WholeSilique":{name:"Whole Silique",subunit:["silique","all","seed"]},"ath-youngSeedling":{name:"Young Seedling",subunit:["all","root","hypocotyl","cotyledon"]},"ath-FlowerDevelopment1":{name:"Late Flower Development (1)",subunit:["flowerDevelopmentPart1"]},"ath-FlowerDevelopment2":{name:"Flower Development 2",subunit:["flowerDevelopmentPart2"]},"ath-FlowerDevelopment3":{name:"Flower Development 3",subunit:["flowerDevelopmentPart3"]},"ath-FlowerDevelopment4":{name:"Flower Development 4",subunit:["flowerDevelopmentPart4"]},"ath-FlowerDevelopment5":{name:"Flower Development 5",subunit:["flowerDevelopmentPart5"]},"ath-FlowerDevelopment6-8":{name:"Flower Development 6-8",subunit:["flowerDevelopmentPart6"]},"ath-FlowerDevelopment9-11":{name:"Flower Development 9-11",subunit:["flowerDevelopmentPart9"]},"ath-FlowerDevelopment12-14":{name:"Flower Development 12-14",subunit:["flowerDevelopmentPart12"]},"ath-FlowerDevelopment15-18":{name:"Flower Development 15-18",subunit:["flowerDevelopmentPart15"]},"ath-FlowerDevelopment19":{name:"Flower Development 19",subunit:["flowerDevelopmentPart19"]},"ath-Other":{name:"Other"}};function checkAgainstSVG(svg,subunit,returnName=!1){let svgName=svg.split(".")[0],toReturn=returnName?svgAgainstData[svgName].name:subunit;return svgAgainstData[svgName]&&!returnName&&(svgAgainstData[svgName].subunit?svgAgainstData[svgName].subunit.includes(subunit)||(svgAgainstData[svgName].subunit_name?toReturn=svgAgainstData[svgName].subunit_name:svgAgainstData[svgName].subunit[0]&&(toReturn=svgAgainstData[svgName].subunit[0])):"all"!==subunit&&(toReturn="all")),toReturn}let efp_table_column,variantdiv_str,sraList=[],sraDict={},sraCountDic={},tissueSRADic={},datasetName="data",iteration_num=1,moreDetails='Show More Details <i class="material-icons detailsIcon">arrow_drop_down</i>',lessDetails='Show Less Details <i class="material-icons detailsIcon">arrow_drop_up</i>';function populate_table(status){$("#theTable").empty(),$("#compareTable").empty(),rnaseq_calls=[],exp_info=[],rnaseq_success=0,date_obj5=new Date,rnaseq_success_start_time=date_obj5.getTime(),max_absolute_fpkm=-1,max_log_fpkm=-1,svg_colouring_element=null,gene_structure_colouring_element=null,sraList=[],sraDict={},sraCountDic={},tissueSRADic={},rpkmAverage=1,rpkmMedian=1;let img_created='<img loading="lazy" src="data:image/png;base64,'+exon_intron_scale+'" alt="RNA-Seq mapped image" style="float: right; margin-right: 10px;">',tableHeader='<thead><tr><th class="sortable colTitle" id="colTitle" onclick="ChangeColArrow(this.id)" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 250px;"><div class="row" id="colTitleRow"><div class="col-10">Title</div><div class="col-1"><img loading="lazy" class="sortingArrow" id="colTitleArrow" src="./cgi-bin/SVGs/arrowDefault.svg" alt="Sorting arrow"></div></div></th><th class="colRNA" id="colRNA" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; max-width: 576px;">RNA-Seq Coverage'+img_created+'</th><th class="sortable colrpb" id="colrpb" onclick="ChangeColArrow(this.id)" title="Point biserial correlation coefficient. Closer to 1 suggests a \'best\' match" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="colrpbRow"><div class="col-7" >r<sub>pb</sub></div><div class="col-1"><img loading="lazy" class="sortingArrow" id="colrpbArrow" src="./cgi-bin/SVGs/arrowDefault.svg" alt="Default sort arrow"></div></div></th><th class="coleFP" id="eFP_th" class="sortable" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 100px;">eFP (RPKM)</th><th class="sortable colRPKM" id="colRPKM" onclick="ChangeColArrow(this.id)" title="Reads Per Kilobase of transcript per Million mapped reads. Higher number suggest more mapped reads/expression" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="colRPKMRow"><div class="col-8">RPKM</div><div class="col-1"><img loading="lazy" class="sortingArrow" id="colRPKMArrow" src="./cgi-bin/SVGs/arrowDefault.svg" alt="Default sort arrow"></div></div></th><th class="sortable colDetails" id="colDetails" onclick="ChangeColArrow(this.id)" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 275px;"><div class="row" id="colDetailsRow"><div class="col-10">Details</div><div class="col-1"><img loading="lazy" class="sortingArrow" id="colDetailsArrow" src="./cgi-bin/SVGs/arrowDefault.svg" alt="Default sort arrow"></div></div></th><th class="sortable colCompare" id="colCompare" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; max-width: 30px;" hidden><div class="row" id="colCompareRow"></div></th></tr></thead><tbody id="data_table_body"></tbody>';$("#theTable").append(tableHeader);let compareHeader='<thead><tr><th id="compare_colTitle" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 250px;"><div class="row" id="compare_colTitleRow"><div class="col-xs-10">Title</div></div></th><th id="compare_colRNA" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; max-width: 576px;">RNA-Seq Coverage'+img_created+'</th><th id="compare_colrpb" title="Point biserial correlation coefficient. Closer to 1 suggests a \'best\' match" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="compare_colrpbRow"><div class="col-xs-6">r<sub>pb</sub></div></div></th><th id="compare_eFP_th" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 100px;">eFP (RPKM)</th><th id="compare_colRPKM" title="Reads Per Kilobase of transcript per Million mapped reads. Higher number suggest more mapped reads/expression" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 75px;"><div class="row" id="compare_colRPKMRow"><div class="col-xs-7">RPKM</div></div></th><th id="compare_colDetails" style="border: 1px solid #D3D3D3; background-color: #F0F0F0; width: 275px;"><div class="row" id="compare_colDetailsRow"><div class="col-xs-10">Details</div></div></th></tr></thead><tbody id="compare_table_body"></tbody>';$("#compareTable").append(compareHeader),$.ajax({url:base_src,dataType:"xml",success:function(xml_res){$(xml_res).find("files").each((function(){datasetName=$(this).attr("xmltitle")||"Uploaded dataset",datasetName=datasetName.trim(),0===datasetName.length&&(datasetName="Uploaded dataset"),document.getElementById("uploaded_dataset").innerHTML=datasetName})),document.title="eFP-Seq Browser:",progress_percent<100&&(document.title+=` Loading ${progress_percent.toFixed(1)}% -`),document.title+=` ${locus} - ${datasetName}`,iteration_num=1,$(xml_res).find("file").each((function(){let experimentno=$(this).attr("record_number")||"unknown";if(sraList.includes(experimentno)&&(experimentno=findUnusedRecordDisplayName(experimentno,sraList)),sraList.includes(experimentno)){if(sraCountDic[experimentno]){sraCountDic[experimentno]+=1;let tempExperimentNo=experimentno+"("+sraCountDic[experimentno]+")";sraList.push(tempExperimentNo),sraDict[tempExperimentNo]={}}}else sraCountDic[experimentno]=1,sraList.push(experimentno),sraDict[experimentno]={};let title=$(this).attr("description");sraDict[experimentno].title=title;let description=$(this).attr("info");sraDict[experimentno].description=description;let svg=$(this).attr("svgname");sraDict[experimentno].svg=svg;let svg_part=$(this).attr("svg_subunit");svg_part=checkAgainstSVG(svg,svg_part),sraDict[experimentno].svg_part=svg_part,tissueSRADic[checkAgainstSVG(svg,svg_part,!0)]?tissueSRADic[checkAgainstSVG(svg,svg_part,!0)].push(experimentno):tissueSRADic[checkAgainstSVG(svg,svg_part,!0)]=[experimentno];let url=$(this).attr("url");sraDict[experimentno].url=url;let publicationid=$(this).attr("publication_link");sraDict[experimentno].publicationid=publicationid;let hexColourCode,numberofreads=$(this).attr("total_reads_mapped");null!=numberofreads&&""!=numberofreads||(numberofreads="0"),sraDict[experimentno].numberofreads=numberofreads,hexColourCode=null==$(this).attr("hex_colour")||""==$(this).attr("hex_colour")?"0x64cc65":$(this).attr("hex_colour"),sraDict[experimentno].hexColourCode=hexColourCode;let filenameIn=$(this).attr("filename");null!=filenameIn&&""!=filenameIn&&null!=filenameIn||(filenameIn="accepted_hits.bam"),sraDict[experimentno].filenameIn=filenameIn;let species=$(this).attr("species");sraDict[experimentno].species=species;let controls=[];if(null==$(this).find("controls")[0].innerHTML)for(let i=1;i<$(this).find("controls")[0].childNodes.length;i+2)controls.push($(this).find("controls")[0].childNodes[i].firstChild.textContent);else null!=$(this).find("controls")[0].innerHTML&&(controls=$(this).find("controls")[0].innerHTML.replace(/<bam_exp>/g,"").replace(/<\/bam_exp>/g,",").replace(/\n/g," ").replace(/ /g,"").split(","));sraDict[experimentno].controls=controls;let links="";if(controls.length>0)for(let i=controls.length;i--;)"MEDIAN"!=controls[i]?links+='<a href="https://www.ncbi.nlm.nih.gov/Traces/sra/?run='+controls[i]+'"target="_blank" rel="noopener">'+controls[i]+"</a> ":links+=controls[i];sraDict[experimentno].links=links;let controlsString="";if(controls.length>0)for(let y=0;y<controls.length;y++)controlsString+=controls[y].toString(),y<controls.length-2&&(controlsString+=", ");sraDict[experimentno].controlsString=controlsString.trim();let name=$(this).attr("name");sraDict[experimentno].name=name;let tissue=$(this).attr("svgname");tissue&&("ath-"===tissue.trim().substr(0,4)&&(tissue=tissue.slice(4,tissue.length).trim()),".svg"===tissue.trim().substr(tissue.length-4,4)&&(tissue=tissue.slice(0,tissue.length-4).trim())),rnaseq_calls.push([tissue,experimentno]),sraDict[experimentno].tissue=tissue;let bam_type=$(this).attr("bam_type");sraDict[experimentno].bam_type=bam_type;let drive_link=$(this).attr("name");sraDict[experimentno].drive_link=drive_link;let read_map_method=$(this).attr("read_map_method");sraDict[experimentno].read_map_method=read_map_method;let igbView_link="https://bioviz.org/bar.html?";igbView_link+="version=A_thaliana_Jun_2009&",igbView_link+="gene_id="+locus+"&",igbView_link+="feature_url_0="+drive_link+"&",igbView_link+="genome=A_thaliana_Jun_2009&",igbView_link+="annotation_set=Araport11&",igbView_link+="query_url="+drive_link+"&",igbView_link+="server_url=bar";let append_str='<tr class="mainEntries" id="'+experimentno+'_row">',table_dl_str="<table id='table_dl'>\n\t<tbody>\n";table_dl_str+="\t\t<caption>"+document.getElementById("xmlDatabase").value+"</caption>\n",append_str+='<td class="colTitle" style="width: 250px; font-size: 12px;" id="'+experimentno+'_title">'+title+"</td>\n",append_str+=`\n\t\t\t\t\t<td class="colRNA" style="max-width: 576px;">\n\t\t\t\t\t\t<img\n\t\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\t\tid="${experimentno}_rnaseq_img"\n\t\t\t\t\t\t\talt="RNA-Seq mapped image for: ${experimentno}"\n\t\t\t\t\t\t\tstyle="min-width:420px; max-width:576px; width:95%; height: auto;"\n\t\t\t\t\t\t\tclass="rnaseq_img responsiveRNAWidth"\n\t\t\t\t\t\t\tsrc="${img_loading_base64}"\n\t\t\t\t\t\t/>\n\n\t\t\t\t\t\t<br/>\n\n\t\t\t\t\t\t<img\n\t\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\t\tid="${experimentno}_gene_structure_img"\n\t\t\t\t\t\t\tstyle="max-width: 576px; width:100%; height: auto;"\n\t\t\t\t\t\t\tclass="gene_structure_img"\n\t\t\t\t\t\t\tsrc="${img_gene_struct_1}"\n\t\t\t\t\t\t\talt="Gene variant image for: ${experimentno}"\n\t\t\t\t\t\t/>\n\t\t\t\t\t</td>\n\n\t\t\t\t`,append_str+='<td id="'+experimentno+'_rpb" class="rpb_value colrpb" style="font-size: 12px; width: 50px; ">'+"-9999</td>",append_str+='<td class="coleFP" tag="svg_name" style="width:  75px;"><div id="'+experimentno+'_svg" name="'+svg.substring(0,svg.length-4).slice(4)+'_tissue" tag='+svg_part+'_subtissue" width="75" height="75" style="width: 75px; height: 75px; max-width: 75px; max-height: 75px;">'+document.getElementById(svg.substring(4).replace(".svg","_svg")).innerHTML+'</div><div class="mdl-tooltip" for="'+experimentno+'_svg">'+svg.substring(4).replace(".svg","")+"</div></td>\n",append_str+='<td class="colRPKM" id="'+experimentno+'_rpkm" style="font-size: 12px; width: 50px; ">-9999</td>',append_str+='<td class="colDetails" id="'+experimentno+'_details" style="font-size: 12px;"><div id="'+experimentno+'_description" name="'+description.trim()+'">'+truncateDescription(description)+"</div>","Amazon AWS"===bam_type&&(append_str+='<div id="igbLink_'+experimentno+'">Show: <a href="'+igbView_link+'" target="_blank" rel="noopener">Alignments in IGB</a></div>'),experimentno.includes("unknown")&&!publicationid||(append_str+='<div id="extraLinks_'+experimentno+'">Go to: ',experimentno.includes("unknown")||(append_str+='<a href="'+url+'" target="_blank" rel="noopener">NCBI SRA</a>'),experimentno.includes("unknown")&&publicationid&&(append_str+=" or "),publicationid&&(append_str+='<a href="'+publicationid+'" target="_blank" rel="noopener">PubMed</a>'),append_str+="</div>"),append_str+='<a id="clickForMoreDetails_'+iteration_num+'" name="'+experimentno+'_description" onclick="clickDetailsTextChange(this.id)" href="javascript:(function(){$(\'#'+experimentno+"').toggle();})()\">"+moreDetails.trim()+"</a>",append_str+='<div id="'+experimentno+'" class="moreDetails" style="display:none">',links&&(append_str+="Controls: "+links+"<br/>"),append_str+="Species: "+species+"<br>",append_str+='<div id="'+experimentno+'_sra">SRA: '+experimentno+"</div>",append_str+='<div id="'+experimentno+'_totalReadsNum">Total reads = '+numberofreads+"</div>",null!=read_map_method&&read_map_method.length>0&&(append_str+='<div id="'+experimentno+'_readMappedMethod">Read map method = '+read_map_method.trim()+"</div>"),append_str+='<a id="clickForMoreDetails_'+iteration_num+'_less" name="'+experimentno+'_description" onclick="clickDetailsTextChange(this.id)" href="javascript:(function(){$(\'#'+experimentno+"').toggle();})()\">"+lessDetails+"</a></div></td>\n",append_str+='<td class="colCompare" style="font-size: 12px; max-width: 30px;"><div id="'+experimentno+'_compareVariant"><input type="checkbox" name="compareCheckbox" class="compareCheckbox" value="compareCheckbox" id="'+experimentno+'_compareCheckbox" onclick="tableCheckbox(this.id);"></div></td>',append_str+="</tr>",iteration_num++,$("#theTable").append(append_str);let compareColumn=document.getElementsByClassName("fltrow")[0].childNodes[6];(compareColumn&&void 0===compareColumn.classList[0]||"undefined"===compareColumn.classList[0])&&(compareColumn.classList=["colCompare"],compareColumn.innerHTML='<input type="checkbox" name="compareCheckbox" class="compareCheckbox" value="compareCheckbox" id="allCheckbox" onclick="disableAllComparison();">'),exp_info.push([experimentno+"_svg",svg_part,controls,0,0,0,0]),!0===loadNewDataset?(setTimeout((function(){count_bam_num()}),200),setTimeout((function(){rnaseq_images(status)}),10)):rnaseq_images(status)})),$.tablesorter.addParser({id:"rpb_sorter",is:function(s){return!1},format:function(s){return NaN==s?-99999:null==s?-999999:s==1/0?99999:s==-1/0?-99999:parseFloat(s)},type:"numeric"}),$.tablesorter.addParser({id:"rpkm_sorter",is:function(s){return!1},format:function(s){return NaN==s?-99999:null==s?-999999:s==1/0?99999:s==-1/0?-99999:"Missing controls data"==s?-9999999:parseFloat(s)},type:"numeric"}),$("#theTable").tablesorter({headers:{0:{},1:{sorter:!1},2:{sorter:"rpb_sorter"},3:{},4:{sorter:"rpkm_sorter"},5:{}}}),$("#theTable").trigger("update")},error:function(xhr,status,error){generateToastNotification(`Error getting data from data file: ${error.message}`,"ERROR"),console.log("Error getting data from data file: "+error.message)}});new TableFilter("theTable",{base_path:"cgi-bin/core/packages/tableFilter/",columns_exact_match:[!1,!1,!1,!1,!1,!1],watermark:["Filter","Filter","Filter","Filter","Filter","Filter"],highlight_keywords:!1,no_results_message:!0,auto_filter:!0,auto_filter_delay:500,col_1:"none",popup_filters:!1,filters_row_index:1,alternate_rows:!1,msg_filter:"Filtering..."}).init(),change_rpkm_colour_scale(colouring_mode);for(let j=0;j<colSortList.length;j++){CheckElementWidth(colSortList[j]+"Arrow",8)}createVariantDiv()}function createVariantDiv(){null==gene_structure_colouring_element&&document.getElementById("flt1_theTable")&&document.getElementById("flt1_theTable").parentElement&&(gene_structure_colouring_element=document.getElementById("flt1_theTable").parentElement),gene_structure_colouring_element.innerHTML="",$("#variant_select").ddslick("destroy"),document.getElementsByClassName("fltrow")[0].childNodes[1].innerHTML="",variantdiv_str='<div id="variants_div">',variantdiv_str+="</div>",document.getElementsByClassName("fltrow")[0].childNodes[1].innerHTML=variantdiv_str,$("#variant_select").ddslick({width:"100%",onSelected:function(){gene_structure_radio_on_change()}})}function clickDetailsTextChange(details_id){if(null!=document.getElementById(details_id))if(document.getElementById(details_id).innerHTML==moreDetails){document.getElementById(details_id).setAttribute("hidden",!0);const innerDescription=document.getElementById(document.getElementById(details_id).name);innerDescription.textContent=innerDescription.getAttribute("name")}else if(document.getElementById(details_id).innerHTML==lessDetails){const ogID=details_id.substring(0,details_id.length-5);document.getElementById(ogID).removeAttribute("hidden");const innerDescription=document.getElementById(document.getElementById(details_id).name);innerDescription.textContent=truncateDescription(innerDescription.getAttribute("name"))}}function truncateDescription(stringInput){if(null!=stringInput||null!=stringInput)return stringInput.length>30?stringInput.substring(0,30)+"...":stringInput}let remainder_efp=0,efp_length=0,eFPSortedSRA=[],efp_RPKM_values=[];function populate_efp_modal(status){toggleResponsiveTable(2),$("#efpModalTable").empty(),efp_table_column="",eFPSortedSRA=[];const allSRASorted=document.getElementsByClassName("colTitle");for(let s=2;s<allSRASorted.length;s++){let SRASortedID=allSRASorted[s].id.substring(0,allSRASorted[s].id.length-6);"none"!=document.getElementById(SRASortedID+"_row").style.display&&eFPSortedSRA.push(SRASortedID)}remainder_efp=eFPSortedSRA.length%11,efp_length=eFPSortedSRA.length,efp_RPKM_values=[];for(let i=0;i<eFPSortedSRA.length;i++)isNaN(parseFloat(sraDict[eFPSortedSRA[i]].RPKM))||efp_RPKM_values.push(parseFloat(sraDict[eFPSortedSRA[i]].RPKM));$("#efpModalTable").append(`\n\t\t\t<p class="eFP_thead">\n\t\t\t\tAGI-ID:\n\t\t\t\t\t<a href="https://www.arabidopsis.org/servlets/TairObject?type=locus&name=${locus} target="_blank" rel="noopener">\n\t\t\t\t\t\t${locus}\n\t\t\t\t\t</a>\n\t\t\t</p>\n\t\t`),"abs"===colouring_mode?$("#efpModalTable").append(`\n\t\t\t\t<p class="eFP_thead">\n\t\t\t\t\teFP Colour Scale:\n\n\t\t\t\t\t<img\n\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\tsrc="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQD//wD//AD/+QD/9wD/9AD/8gD/7wD/7QD/6gD/6AD/5QD/4gD/4AD/3QD/2wD/2AD/1gD/ 0wD/0QD/zgD/zAD/yQD/xgD/xAD/wQD/vwD/vAD/ugD/twD/tQD/sgD/rwD/rQD/qgD/qAD/pQD/ owD/oAD/ngD/mwD/mQD/lgD/kwD/kQD/jgD/jAD/iQD/hwD/hAD/ggD/fwD/fAD/egD/dwD/dQD/ cgD/cAD/bQD/awD/aAD/ZgD/YwD/YAD/XgD/WwD/WQD/VgD/VAD/UQD/TwD/TAD/SQD/RwD/RAD/ QgD/PwD/PQD/OgD/OAD/NQD/MwD/MAD/LQD/KwD/KAD/JgD/IwD/IQD/HgD/HAD/GQD/FgD/FAD/ EQD/DwD/DAD/CgD/BwD/BQD/AgCkIVxRAAAAs0lEQVQ4jWNg5+Dk4ubh5eMXEBQSFhEVE5eQlJKW kZWTV1BUUlZRVVPX0NTS1tHV0zcwNDI2MTUzt7C0sraxtbN3cHRydnF1c/fw9PL28fXzDwgMCg4J 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i=0;i<11*~~(eFPSortedSRA.length/11);i+=11)if("null"!=document.getElementById(eFPSortedSRA[i+10]).outerHTML){efp_table_column="<tr>";for(let r=0;r<11;r++)efp_table_column+=generateEFPTableItem(eFPSortedSRA[i+r],sraDict[eFPSortedSRA[i+r]].title);efp_table_column+="</tr>",$("#eFPtable").append(efp_table_column)}for(let r=0;r<12;r++)if(remainder_efp===r){efp_table_column="<tr>";for(let c=remainder_efp;c>0;c--)efp_table_column+=generateEFPTableItem(eFPSortedSRA[efp_length-c],sraDict[eFPSortedSRA[efp_length-c]].title);efp_table_column+="</tr>",$("#eFPtable").append(efp_table_column)}toggleResponsiveTable()}function generateEFPTableItem(id,title){return id&&title?`\n\t\t\t<td>\n\t\t\t\t<div\n\t\t\t\t\tclass="efp_table_tooltip"\n\t\t\t\t\tid="${id}_rep"\n\t\t\t\t\tonclick="ScrollToRNARow('${id}_row')"\n\t\t\t\t>\n\t\t\t\t\t${document.getElementById(id+"_svg").outerHTML}\n\t\t\t\t\t<span class="efp_table_tooltip_text">\n\t\t\t\t\t${id} - ${title}\n\t\t\t\t\t</span>\n\t\t\t\t</div>\n\t\t\t</td>\n\t\t`:""}function change_rpkm_colour_scale(colouring_mode){if(null===svg_colouring_element&&document.getElementById("flt3_theTable")&&document.getElementById("flt3_theTable").parentElement&&(svg_colouring_element=document.getElementById("flt3_theTable").parentElement),svg_colouring_element&&svg_colouring_element.innerHTML&&(svg_colouring_element.innerHTML=""),"rel"==colouring_mode){const img_created=document.createElement("img");img_created.src="data:image/png;base64,"+relative_rpkm_scale,img_created.style="margin-top: 10px;",svg_colouring_element&&svg_colouring_element.appendChild(img_created)}else{const img_created=document.createElement("img");img_created.src="data:image/png;base64,"+absolute_rpkm_scale,img_created.style="margin-top: 10px;",img_created.alt="Absolute RPKM Scale",svg_colouring_element&&svg_colouring_element.appendChild(img_created)}const columnList=["colTitle","colRNA","colrpb","coleFP","colRPKM","colDetails"];let tds=[];document.getElementsByClassName("fltrow")&&document.getElementsByClassName("fltrow")[0]&&(tds=document.getElementsByClassName("fltrow")[0].getElementsByTagName("td"));for(let i=0;i<tds.length;i++)tds[i].style="border: 1px solid #D3D3D3",tds[i].classList.add(columnList[i])}function locus_validation(){const loc=document.getElementById("locus").value;9==loc.length&&("A"==loc[0]||"a"==loc[0])&&("T"==loc[1]||"t"==loc[1])&&(loc[2]>=1&&loc[2]<=5||"C"==loc[2]||"M"==loc[2]||"c"==loc[2]||"m"==loc[2])&&("G"==loc[3]||"g"==loc[3])&&loc[4]>=0&&loc[4]<=9&&loc[5]>=0&&loc[5]<=9&&loc[6]>=0&&loc[6]<=9&&loc[7]>=0&&loc[7]<=9&&loc[8]>=0&&loc[8]<=9?$("#locus_button").removeAttr("disabled"):$("#locus_button").prop("disabled",!0)}function yscale_validation(){const yscale=document.getElementById("yscale_input").value;parseInt(yscale)>0||"Auto"==yscale||""==yscale?$("#locus_button").removeAttr("disabled"):$("#locus_button").prop("disabled",!0)}function rpkm_validation(){parseInt(document.getElementById("rpkm_scale_input").value)>0?$("#abs_scale_button").removeAttr("disabled"):$("#abs_scale_button").prop("disabled",!0)}let databasesAdded=!1;function reset_database_options(){$(".userAdded").remove(),dataset_dictionary=base_dataset_dictionary,list_modified=!1,databasesAdded=!1}let xml_title,get_xml_list_output=[],user_exist=!1,list_modified=!1,check_for_change=0,match_title={},title_list=[];function get_user_XML_display(){const AuthUser=findAuthUser();""==users_email&&null==users_email&&null==users_email||users_email!==AuthUser?""!=users_email&&users_email!=AuthUser&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in")):$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/get_xml_list.php?user="+users_email,dataType:"json",failure:function(){console.log("ERROR! Something went wrong")},success:function(get_xml_list_return){xml_title=void 0,match_title={},title_list=[];let unnamed_title_num=1,private_version_num=1;if(get_xml_list_output=get_xml_list_return,"fail"==get_xml_list_output.status)console.log("Error code: "+get_xml_list_output.error),user_exist=!1;else if("success"==get_xml_list_output.status){if(user_exist=!0,check_for_change!=get_xml_list_output.files.length&&(reset_database_options(),list_modified=!1),check_for_change=get_xml_list_output.files.length,get_xml_list_output.files.length>0)for(let i=0;i<get_xml_list_output.files.length;i++){xml_title=void 0,xml_title=get_xml_list_output.files[i][1],xml_title&&0!==xml_title.trim()?.length&&"Uploaded dataset"!==xml_title?"Araport 11 RNA-seq data"==xml_title?(xml_title="Araport 11 RNA-seq data - Private version #"+private_version_num,private_version_num+=1):"Developmental transcriptome - Klepikova et al"==xml_title&&(xml_title="Developmental transcriptome - Klepikova et al - Private version #"+private_version_num,private_version_num+=1):(xml_title="Uploaded dataset - Unnamed dataset #"+unnamed_title_num,unnamed_title_num+=1),title_list.push(xml_title);const xml_fle_name=get_xml_list_output.files[i][0];match_title[xml_title]=xml_fle_name,i==get_xml_list_output.files.length-1&&create_data_list(get_xml_list_output.files.length)}setTimeout((function(){if(!list_modified)for(let c=0;c<get_xml_list_output.files.length;c++)dataset_dictionary[title_list[c]]=datalist_Title[title_list[c]],document.getElementById("xmlDatabase").innerHTML+=`\n\t\t\t\t\t\t\t\t\t<option\n\t\t\t\t\t\t\t\t\t\tclass="userAdded"\n\t\t\t\t\t\t\t\t\t\ttag="private"\n\t\t\t\t\t\t\t\t\t\tvalue="${title_list[c]}"\n\t\t\t\t\t\t\t\t\t\tid="${title_list[c]}"\n\t\t\t\t\t\t\t\t\t>\n\t\t\t\t\t\t\t\t\t\t${title_list[c]}\n\t\t\t\t\t\t\t\t\t</option>\n\t\t\t\t\t\t\t\t`;list_modified=!0}),1e3)}databasesAdded=!0},error:function(xhr,status,error){generateToastNotification(`Error getting user data: ${error.message}`,"ERROR"),console.log(`Error getting user data: ${error.message}`)}})}let datalist=[],datalist_Title={};function create_data_list(size){if(datalist=[],datalist_Title={},size>0)for(let i=0;i<size;i++)$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/get_xml.php?file="+match_title[title_list[i]],dataType:"json",success:function(get_xml_return){const xml_file=get_xml_return;datalist.push(xml_file.data)},error:function(xhr,status,error){generateToastNotification(`Error getting user private datasets: ${error.message}`,"ERROR"),console.log(`Error getting user private datasets: ${error.message}`)}}),i===size-1&&setTimeout((function(){dlCallLength=size,DatalistXHRCall(datalist)}),200)}let testDoc,dlCallLength=0,dlCallPosition=0;function DatalistXHRCall(datalistData){if(dlCallPosition!=dlCallLength){const xhr=new XMLHttpRequest,url=datalistData[dlCallPosition];xhr.responseType="document",xhr.onreadystatechange=()=>{if(xhr.readyState===XMLHttpRequest.DONE&&200===xhr.status){let response=xhr.responseXML;if(response){let responseTitle=response.getElementsByTagName("files")[0].attributes.xmltitle.nodeValue;datalist_Title[responseTitle]=datalistData[dlCallPosition],dlCallPosition+=1,DatalistXHRCall(datalistData)}}},xhr.open("GET",url),xhr.send()}}function validateEmail(email){return/\S+@\S+\.\S+/.test(email)}function findAuthUser(){return global_user&&global_user.email?global_user.email:""}function check_if_Google_login(){const AuthUser=findAuthUser();users_email&&AuthUser&&users_email===AuthUser?!1===databasesAdded&&(document.getElementById("private_dataset_header").style.display="block",get_user_XML_display()):(signOut(),remove_private_database())}function add_user_xml_by_upload(){get_user_XML_display(),setTimeout((function(){const AuthUser=findAuthUser();user_exist?user_exist&&(dataset_dictionary[datasetName]?dataset_dictionary[datasetName]&&(users_email===AuthUser?(list_modified=!1,check_for_change=0,$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_xml.php?user="+users_email+"&file="+match_title[datasetName]}),$.ajax({method:"POST",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/upload.php",data:{user:users_email,xml:upload_src,title:datasetName}})):""!=users_email&&users_email!=AuthUser&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in"))):users_email===AuthUser?$.ajax({method:"POST",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/upload.php",data:{user:users_email,xml:upload_src,title:datasetName}}):""!=users_email&&users_email!=AuthUser&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in"))):users_email===AuthUser?$.ajax({method:"POST",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/upload.php",data:{user:users_email,xml:upload_src,title:datasetName}}):""!=users_email&&users_email!=AuthUser&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in")),get_user_XML_display()}),1e4)}let uploadingData=!1;function which_upload_option(){uploadingData=!0;const AuthUser=findAuthUser();""!=users_email&&users_email===AuthUser?document.getElementById("upload_modal").click():""!=users_email&&users_email!=AuthUser?(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in")):""==users_email&&document.getElementById("upload_logX").click()}let public_title_list=[],total_amount_of_datasets=0;function delete_fill(){$("#delete_fill").empty(),$("#publicDatabaseDownload").empty(),public_title_list=[];for(let public_title in base_dataset_dictionary)base_dataset_dictionary.hasOwnProperty(public_title)&&public_title_list.push(public_title);let deleteBoxNum=0;total_amount_of_datasets=public_title_list.length+title_list.length;for(let i=0;i<public_title_list.length;i++)$("#publicDatabaseDownload").append(`\n\t\t\t\t<input\n\t\t\t\t\ttype="checkbox"\n\t\t\t\t\ttag="publicDataCheckbox"\n\t\t\t\t\tclass="publicDataCheckbox"\n\t\t\t\t\tonchange="disableDeletePublic()"\n\t\t\t\t\tid="deleteBox_${deleteBoxNum}"\n\t\t\t\t\tvalue="${public_title_list[i]}"\n\t\t\t\t>\n\t\t\t\t\t${public_title_list[i]}\n\t\t\t\t</input>\n\t\t\t\t<br />\n\t\t\t`),deleteBoxNum+=1;for(let i=0;i<title_list.length;i++)$("#delete_fill").append(`\n\t\t\t\t<input\n\t\t\t\t\ttype="checkbox"\n\t\t\t\t\ttag="privateDataCheckbox"\n\t\t\t\t\tclass="privateDataCheckbox"\n\t\t\t\t\tonchange="disableDeletePublic()"\n\t\t\t\t\tid="deleteBox_${deleteBoxNum}"\n\t\t\t\t\tvalue="${title_list[i]}"\n\t\t\t\t>\n\t\t\t\t\t${title_list[i]}\n\t\t\t\t</input>\n\t\t\t\t<br />\n\t\t\t`),deleteBoxNum+=1}let isDeletePublicDisabled=!1;function disableDeletePublic(){for(let i=0;i<public_title_list.length;i++){if(document.getElementById("deleteBox_"+i).checked&&"publicDataCheckbox"==document.getElementById("deleteBox_"+i).className){isDeletePublicDisabled||(document.getElementById("deleteXML_button").classList.add("disabled"),isDeletePublicDisabled=!0);break}isDeletePublicDisabled&&(document.getElementById("deleteXML_button").classList.remove("disabled"),isDeletePublicDisabled=!1)}}function CheckIfSelectedXML(){const AuthUser=findAuthUser();for(let i=0;i<title_list.length;i++){const deleteBox_id="deleteBox_"+(i+2);if(document.getElementById(deleteBox_id).checked&&users_email===AuthUser)return!0}if(1)return!1}function delete_selectedXML(){const AuthUser=findAuthUser();for(let i=0;i<title_list.length;i++){const deleteBox_id="deleteBox_"+(i+2);document.getElementById(deleteBox_id)&&document.getElementById(deleteBox_id).checked&&users_email===AuthUser&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_xml.php?user="+users_email+"&file="+match_title[document.getElementById(deleteBox_id).value]})}databasesAdded=!1}function confirm_deleteUser(){const AuthUser=findAuthUser();""!=users_email&&users_email===AuthUser&&$("#logoutModal").is(":visible")&&delete_allXMLs(AuthUser)}function delete_allXMLs(verify){const AuthUser=findAuthUser();if(verify===AuthUser){for(let i=0;i<title_list.length;i++){const deleteBox_id="deleteBox_"+(i+2);users_email===AuthUser&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_xml.php?user="+users_email+"&file="+match_title[document.getElementById(deleteBox_id).value]})}delete_user(),databasesAdded=!1}}function delete_user(){const AuthUser=findAuthUser();""!=users_email&&users_email===AuthUser&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_user.php?user="+users_email}),signOut()}let warningActive_index_XML="nope",warningActive_index_account="nope";function showWarning_index(whichWarning){1===whichWarning?isDeletePublicDisabled||("nope"==warningActive_index_XML?(document.getElementById("warning_index_xml").className="warning_index",warningActive_index_XML="yes"):"yes"==warningActive_index_XML&&hideWarning_index(whichWarning)):2===whichWarning&&("nope"==warningActive_index_account?(document.getElementById("warning_index_account").className="warning_index",warningActive_index_account="yes"):"yes"==warningActive_index_account&&hideWarning_index(whichWarning))}function hideWarning_index(whichWarning){1===whichWarning?(document.getElementById("warning_index_xml").className="warning_nope_index",warningActive_index_XML="nope"):2===whichWarning&&(document.getElementById("warning_index_account").className="warning_nope_index",warningActive_index_account="nope")}function manage_DownloadXML(){const numberOfOptions=title_list.length+2;for(let i=0;i<numberOfOptions;i++){const downloadBox_id="deleteBox_"+i;document.getElementById(downloadBox_id).checked&&($("#downloadXML").attr("href",dataset_dictionary[document.getElementById(downloadBox_id).value]).attr("download",document.getElementById(downloadBox_id).value+".xml"),document.getElementById("downloadXML_button").click())}}const table_base="\t\t<tr>\n\t\t\t<th>Title*</th>\n\t\t\t<th>Description*</th>\n\t\t\t<th>Record Number *</th>\n\t\t\t<th>RNA-Seq Data/BAM file repository link*</th>\n\t\t\t<th>Repository type*</th>\n\t\t\t<th>BAM Filename*</th>\n\t\t\t<th>Publication Link</th>\n\t\t\t<th>SRA/NCBI Link</th>\n\t\t\t<th>Total Reads Mapped*</th>\n\t\t\t<th>Read Map Method</th>\n\t\t\t<th>Species*</th>\n\t\t\t<th>Tissue*</th>\n\t\t\t<th>Tissue subunit*</th>\n\t\t\t<th>Controls</th>\n\t\t\t<th>Replicate Controls</th>\n\t\t</tr>\n";function fill_tableCSV(){$("#XMLtoCSVtable").empty();for(let i=0;i<total_amount_of_datasets;i++){const downloadBox_id="deleteBox_"+i;$.ajax({url:dataset_dictionary[document.getElementById(downloadBox_id).value],dataType:"xml",failure:function(){console.log("Failed at opening XML for conversion into a CSV file. Please contact an admin")},success:function(xml_data){let fileTitle;$(xml_data).find("files").each((function(){fileTitle=$(this).attr("xmltitle"),""!=fileTitle&&"Uploaded dataset"!=fileTitle||(fileTitle="Uploaded dataset"),fileTitle=fileTitle.split(" ").join("_")}));const $title=$(xml_data).find("file");let table_add="";table_add+="<table id='"+fileTitle+"'>\n\t<tbody>\n",table_add+="\t\t<caption>"+fileTitle+"</caption>\n",table_add+=table_base,$title.each((function(){table_add+="\t\t<tr>\n";const title=$(this).attr("description");table_add+="\t\t\t<td>"+title+"</td>\n";const desc=$(this).attr("info");table_add+="\t\t\t<td>"+desc+"</td>\n";const record_number=$(this).attr("record_number");table_add+="\t\t\t<td>"+record_number+"</td>\n";const bam_link=$(this).attr("name");table_add+="\t\t\t<td>"+bam_link+"</td>\n";const bam_type=$(this).attr("bam_type");table_add+="\t\t\t<td>"+bam_type+"</td>\n";let bam_filename=$(this).attr("filename");null!=bam_filename&&"undefined"!==bam_filename&&".bam"!==bam_filename||(bam_filename="accepted_hits.bam"),table_add+="\t\t\t<td>"+bam_filename+"</td>\n";const publication_link=$(this).attr("publication_link");table_add+="\t\t\t<td>"+publication_link+"</td>\n";const publication_url=$(this).attr("url");table_add+="\t\t\t<td>"+publication_url+"</td>\n";let total_reads_mapped=$(this).attr("total_reads_mapped");null!=total_reads_mapped&&""!=total_reads_mapped||(total_reads_mapped="0"),table_add+="\t\t\t<td>"+total_reads_mapped+"</td>\n";const read_map_method=$(this).attr("read_map_method");table_add+="\t\t\t<td>"+read_map_method+"</td>\n";let species=$(this).attr("species");null!=species&&""!=species||(species="Arabidopsis thaliana"),table_add+="\t\t\t<td>"+species+"</td>\n";const svgname=$(this).attr("svgname");table_add+="\t\t\t<td>"+svgname+"</td>\n";const svg_subunit=$(this).attr("svg_subunit");table_add+="\t\t\t<td>"+svg_subunit+"</td>\n";let controlsXMLString="";if($(this).find("controls")[0].innerHTML)for(let j=1;j<$(this).find("controls")[0].childNodes.length;j+=2)$(this).find("controls")[0].childNodes[j].firstChild&&(controlsXMLString+=$(this).find("controls")[0].childNodes[j].firstChild.textContent,j<$(this).find("controls")[0].childNodes.length-2&&(controlsXMLString+=", "));table_add+="\t\t\t<td>"+controlsXMLString+"</td>\n";let RcontrolsXMLString="";if($(this).find("groupwith")[0].innerHTML)for(let j=1;j<$(this).find("groupwith")[0].childNodes.length;j+=2)$(this).find("groupwith")[0].childNodes[j].firstChild&&(RcontrolsXMLString+=$(this).find("groupwith")[0].childNodes[j].firstChild.textContent,j<$(this).find("groupwith")[0].childNodes.length-2&&(RcontrolsXMLString+=", "));table_add+="\t\t\t<td>"+RcontrolsXMLString+"</td>\n",table_add+="\t\t</tr>\n"})),table_add+="\t</tbody>\n</table>",document.getElementById("XMLtoCSVtable").innerHTML+=table_add},error:function(xhr,status,error){generateToastNotification(`Error filling data table: ${error.message}`,"ERROR"),console.log(`Error filling data table: ${error.message}`)}})}}function download_XMLtableCSV(){for(let i=0;i<total_amount_of_datasets;i++){const downloadBox_id="deleteBox_"+i;if(document.getElementById(downloadBox_id).checked){const tableTitle=document.getElementById(downloadBox_id).value.split(" ").join("_");$("#"+tableTitle).tableToCSV()}}}const downloadIndexTable_base="\t\t<tr>\n\t\t\t<th>Title</th>\n\t\t\t<th>Record Number</th>\n\t\t\t<th>Tissue</th>\n\t\t\t<th>Tissue subunit</th>\n\t\t\t<th>Locus</th>\n\t\t\t<th>bp Length</th>\n\t\t\t<th>bp Start site</th>\n\t\t\t<th>bp End site</th>\n\t\t\t<th>Total number of reads</th>\n\t\t\t<th>Reads mapped to locus</th>\n\t\t\t<th>rpb</th>\n\t\t\t<th>RPKM</th>\n\t\t\t<th>Controls</th>\n\t\t</tr>\n";function download_mainTableCSV(){document.getElementById("download_icon").classList.add("progressLoading"),document.getElementById("bodyContainer").classList.add("progressLoading"),populate_efp_modal(1),$("#hiddenDownloadModal_table").empty();let downloadIndexTable_str="<table id='downloadIndexTable'>\n\t<tbody>\n";downloadIndexTable_str+="\t\t<caption>"+datasetName.split(" ").join("_")+"</caption>\n",downloadIndexTable_str+=downloadIndexTable_base;for(const sra of eFPSortedSRA)downloadIndexTable_str+="\t\t<tr>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].title+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sra+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].svg.substr(4,sraDict[sra].svg.length-8)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].svg_part+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].locusValue+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].bp_length)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].bp_start)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].bp_end)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].numberofreads+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].MappedReads)+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+sraDict[sra].rpb+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].RPKM[variantPosition].toFixed(2))+"</td>\n",downloadIndexTable_str+="\t\t\t<td>"+String(sraDict[sra].controlsString)+"</td>\n",downloadIndexTable_str+="\t\t</tr>\n";downloadIndexTable_str+="\t</tbody>\n</table>",document.getElementById("hiddenDownloadModal_table").innerHTML+=downloadIndexTable_str,$("#hiddenDownloadModal_table").tableToCSV(),document.getElementById("download_icon").classList.remove("progressLoading"),document.getElementById("bodyContainer").classList.remove("progressLoading")}let publicData=!0;function changePublicData(forceFalse=!1){publicData=!forceFalse&&!uploadingData&&(1==document.getElementById("xmlDatabase").selectedIndex||2==document.getElementById("xmlDatabase").selectedIndex)}let isPrecache=!0;function checkPreload(){if(get_input_values(),verifyLoci(locus)){loadingScreen(!1),progress_percent=0,document.title=`eFP-Seq Browser: Loading 0% - ${locus}`,document.getElementById("progress").title="0%",$("div#progress").width(progress_percent+"%");for(const property in base_dataset_dictionary){if(base_src===base_dataset_dictionary[property]){publicData=!0;break}publicData=!1}publicData&&"AT2G24270"==locus&&"simple"==dumpMethod&&!callDumpOutputs?(variants_radio_options(1),isPrecache=!0):(update_all_images(0),isPrecache=!1)}else console.error(`The following locus is not valid: ${locus}`)}function verifyLoci(locusToVerify){if("string"==typeof locusToVerify){const regexPattern=new RegExp("^[A][T][MC0-9][G][0-9]{5}[.][0-9]{1,2}$|^[A][T][MC0-9][G][0-9]{5}$","i");return locusToVerify.trim().match(regexPattern)}return!1}let parse_output,GFF_List=[];function getGFF(locusID){GFF_List=[],$.ajax({url:`https://bar.utoronto.ca/webservices/bar_araport/gene_structure_by_locus.php?locus=${locusID}`,dataType:"json",crossDomain:!0,headers:{"Access-Control-Allow-Origin":"*"},failure:function(){console.log("Getting GFFs (getGFF) information failed to retrieve locus information from Araport11")},success:function(gene_res){if(parse_output=gene_res,parse_output.wasSuccessful){let parsed_features=parse_output.features[0].subfeatures;for(let i=0;i<parsed_features.length;i++)null!=parsed_features[i].uniqueID?GFF_List.push(parsed_features[i].uniqueID):GFF_List.push("Error retrieving unique ID/GFF")}else"fail"==parse_output.status?console.log("Error: Cannot find GFF ID's with parse output. Please contact admin"):"false"==parse_output.wasSuccessful&&(null!=parse_output.error?console.log("Error: Cannot find GFF ID's due to following error: "+parse_output.error+". Please contact admin"):console.log("Error: Cannot find GFF ID's with parse output. Please contact admin"))},error:function(xhr,status,error){generateToastNotification(`Error getting GFFs (getGFF) information failed to retrieve locus information from Araport11: ${error.message}`,"ERROR"),console.log(`Error getting GFFs (getGFF) information failed to retrieve locus information from Araport11: ${error.message}`)}})}function addGFF(){if(document.getElementsByClassName("dd-option").length>0)for(let i=0;i<GFF_List.length;i++)document.getElementsByClassName("dd-option")[i]&&document.getElementsByClassName("dd-option")[i].setAttribute("title",GFF_List[i])}function hiddenGoogleSignin(){const signInButtonList=document.getElementsByClassName("abcRioButtonLightBlue");for(let i=0;i<signInButtonList.length;i++)signInButtonList[i]&&signInButtonList[i].setAttribute("id","loginClick"+i)}function remove_private_database(){databasesAdded=!1,document.getElementById("private_dataset_header").style.display="none";const privateList=document.getElementsByClassName("userAdded");for(let i=0;i<privateList.length;i++)$("#xmlDatabase option:last").remove();check_for_change=0}function correctAGIIDInput(){if(document.getElementById("locus")&&document.getElementById("locus").value&&document.getElementById("locus").value.trim().length>0){const locusID=document.getElementById("locus").value.trim().split("/");locusID[0]?document.getElementById("locus").value=locusID[0].toUpperCase().trim():document.getElementById("locus").value=document.getElementById("locus").value.trim(),locus_validation()}}function returnBackToTop(){document.getElementById("main_content").scrollTop=0}function toggleOptionsTable(){"false"===document.getElementById("tableToggle").getAttribute("aria-expanded")?(document.getElementById("tableToggle").setAttribute("aria-expanded",!0),document.getElementById("filterDropdown").classList.add("show")):(document.getElementById("tableToggle").setAttribute("aria-expanded",!1),document.getElementById("filterDropdown").classList.remove("show"))}function toggleTableOptionsView(){document.getElementById("tableFilter-tab").classList.value.includes("active")?(document.getElementById("tableFilter-tab").classList.remove("active"),document.getElementById("eFPFilter-tab").classList.add("active"),document.getElementById("tableFilter").classList.remove("show","active"),document.getElementById("eFPFilter").classList.add("show","active")):(document.getElementById("tableFilter-tab").classList.add("active"),document.getElementById("eFPFilter-tab").classList.remove("active"),document.getElementById("tableFilter").classList.add("show","active"),document.getElementById("eFPFilter").classList.remove("show","active"))}let downloadDivNum=1;function downloadDiv(id){html2canvas(document.getElementById(id)).then((canvas=>{$("#appendCanvas").empty(),canvas.id="downloadDivNum_"+downloadDivNum,document.getElementById("appendCanvas").appendChild(canvas),document.getElementById("downloadDivNum_"+downloadDivNum).style.width="100%",$("#DownloadImageModal").modal("toggle"),downloadDivNum++}))}function displayNavBAR(hideNavbar=!1){const displayNav=$("#navbar_menu").is(":visible")||hideNavbar;document.getElementById("navbar_menu").style.display=displayNav?"none":"block",document.getElementById("main_content").className=displayNav?"col-sm-12":"col-sm-9",document.getElementById("openMenu").style.display=displayNav?"block":"none",document.getElementById("theTable")&&(displayNav?document.getElementById("theTable").classList.add("RNATable"):document.getElementById("theTable").classList.remove("RNATable"))}function adjustFooterSize(){const navbar=document.getElementById("navbar_menu");navbar&&(document.getElementById("nm_footer").style.width=navbar.offsetWidth+"px",navbar.scrollHeight==navbar.clientHeight?document.getElementById("nm_footer").classList.contains("navbar_menu_footer_overflow_abs")||(document.getElementById("nm_footer").classList.remove("navbar_menu_footer_overflow_sticky"),document.getElementById("nm_footer").classList.add("navbar_menu_footer_overflow_abs")):navbar.scrollHeight>navbar.clientHeight&&(document.getElementById("nm_footer").classList.contains("navbar_menu_footer_overflow_sticky")||(document.getElementById("nm_footer").classList.remove("navbar_menu_footer_overflow_abs"),document.getElementById("nm_footer").classList.add("navbar_menu_footer_overflow_sticky"))))}function adjustTableOptionsDropdownSize(){document.getElementById("filterDropdown").style.left=(document.body.offsetWidth-2*document.getElementById("tableToggle").offsetWidth-document.getElementById("filterDropdown").offsetWidth).toString()+"px"}function adjustSubmissionIFrameSize(){const iFrameSize=.7*window.innerHeight;document.getElementById("submissioniframe").height=iFrameSize+"px"}let usedToggle=!1;function toggleTableCol(colClass,enable){const column=document.getElementsByClassName(colClass);if(enable)for(const element of column)element&&element.removeAttribute("hidden");else if(!enable)for(const element of column)element&&element.setAttribute("hidden",!0)}let responsiveRNAWidthAdjusted=!1;function responsiveRNAWidthResize(){const responsive=document.getElementsByClassName("responsiveRNAWidth");if(window.innerWidth<=575){for(let i=0;i<responsive.length;i++)responsive[i].style.minWidth=.93*window.innerWidth+"px";responsiveRNAWidthAdjusted=!0}else if(window.innerWidth>575&&responsiveRNAWidthAdjusted)for(let i=0;i<responsive.length;i++)responsive[i].style.minWidth="420px"}function toggleResponsiveTableOptions(colTitleBool,colRNABool,colrpbBool,coleFPBool,colRPKMBool,colDetailsBool,colCompareBool){toggleTableCol("colTitle",colTitleBool),document.getElementById("toggleTitle").checked=colTitleBool,toggleTableCol("colRNA",colRNABool),document.getElementById("toggleRNA").checked=colRNABool,toggleTableCol("colrpb",colrpbBool),document.getElementById("togglerpb").checked=colrpbBool,toggleTableCol("coleFP",coleFPBool),document.getElementById("toggleeFP").checked=coleFPBool,toggleTableCol("colRPKM",colRPKMBool),document.getElementById("toggleRPKM").checked=colRPKMBool,toggleTableCol("colDetails",colDetailsBool),document.getElementById("toggleDetails").checked=colDetailsBool,toggleTableCol("colCompare",colCompareBool),document.getElementById("toggleCompare").checked=colCompareBool,RememberToggleOptions(colTitleBool,colRNABool,colrpbBool,coleFPBool,colRPKMBool,colDetailsBool,colCompareBool)}function determineResponsiveTable(){document.body.offsetWidth<=576?(toggleResponsiveTable(2),displayNavBAR(!0)):toggleResponsiveTable(0)}function toggleResponsiveTable(forceToggle=0){"none"!=document.getElementById("tableToggle").style.display&&(1==forceToggle||window.innerWidth<=575&&!usedToggle?toggleResponsiveTableOptions(!1,!0,!1,!1,!1,!1,!1):2==forceToggle||window.innerWidth>=1100&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!0,!0,!0,!1):3==forceToggle||window.innerWidth<830&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!1,!1,!1,!1,!1):4==forceToggle||window.innerWidth<900&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!1,!1,!1,!1):5==forceToggle||window.innerWidth<990&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!1,!0,!1,!1):(6==forceToggle||window.innerWidth<1100&&!usedToggle)&&toggleResponsiveTableOptions(!0,!0,!0,!0,!0,!1,!1))}let ToggledTable=[!0,!0,!0,!0,!0,!0,!1];function RememberToggleOptions(title=!0,rna=!0,rpb=!0,efp=!0,rpkm=!0,details=!0,compare=!1){ToggledTable=[title,rna,rpb,efp,rpkm,details,compare]}const colSortList=["colTitle","colrpb","colRPKM","colDetails"];function ResizeArrowRow(){for(const col of colSortList){const colRow=col+"Row";document.getElementById(colRow).style.width=document.getElementById(colRow).parentNode.offsetWidth-2+"px";CheckElementWidth(col+"Arrow",8)}}function CheckElementWidth(arrowID,widthCheckFor){document.getElementById(arrowID).offsetWidth<widthCheckFor&&(document.getElementById(arrowID).style.width=widthCheckFor+"px")}function ChangeColArrow(tableArrowID){setTimeout((function(){const arrowColID=tableArrowID+"Arrow";document.getElementById(tableArrowID).classList.contains("headerSortDown")?document.getElementById(arrowColID).src="./cgi-bin/SVGs/arrowSortDown.svg":document.getElementById(tableArrowID).classList.contains("headerSortUp")&&(document.getElementById(arrowColID).src="./cgi-bin/SVGs/arrowSortUp.svg");for(const col of colSortList){CheckElementWidth(col+"Arrow",8)}}),100)}function ScrollToRNARow(rowID){document.getElementById("closemodal_efPOverview").click(),$("#main_content").animate({scrollTop:$("#"+rowID).offset().top},"slow"),document.getElementById(rowID)&&(document.getElementById(rowID).className+=" scrollToRow",setTimeout((function(){document.getElementById(rowID).className+=" scrollToRowRemove"}),2e3),setTimeout((function(){document.getElementById(rowID).classList.remove("scrollToRow"),document.getElementById(rowID).classList.remove("scrollToRowRemove")}),4050))}function IfPressEnter(event,toClickButton){13!=event.which&&13!=event.keyCode||$("#"+toClickButton).click()}let shareLink,BrowserDetected=!1;function DetectBrowser(){if(!1===BrowserDetected){const userAgentParser={"Microsoft+Edge":{Contain:["Edge"]},Opera:{Contain:["OPR","Opera"]},Firefox:{Contain:["Firefox"],NContain:["Seamonkey"]},Seamonkey:{Contain:["Seamonkey"]},Chrome:{Contain:["Chrome"],NContain:["Chromium"]},Chromium:{Contain:["Chromium"]},"Internet+Explorer":{Contain:["MSIE"]},Safari:{Contain:["Safari"],NContain:["Chromium","Chrome"]}};let userAgentParserKeys,detectBrowser;userAgentParser?userAgentParserKeys=Object.keys(userAgentParser):logError("Unable retrieve userAgentParser");let notDetectedBrowser=!0;for(const userAgent of userAgentParserKeys)for(let c=0;c<userAgentParser[userAgent].Contain.length;c++)if(notDetectedBrowser&&-1!==navigator.userAgent.indexOf(userAgentParser[element].Contain[c])){if(!userAgentParser[element].NContain){detectBrowser=element,notDetectedBrowser=!1;break}{const failLength=userAgentParser[element].NContain.length;let passLength=0;if(userAgentParser[element].NContain.forEach((agent=>{-1!==navigator.userAgent.indexOf(agent)&&passLength++})),passLength!=failLength){detectBrowser=element,notDetectedBrowser=!1;break}}}if(detectBrowser){$("#notChrome").empty();const append_str=' or through the following <a href="https://www.google.com/search?q=manage+cookies+in+'+detectBrowser+'" target="_blank" rel="noopener">Google search results</a>';$("#notChrome").append(append_str)}BrowserDetected=!0}}function CreateFilteredeFPList(){if($("#filtereFPList").empty(),tissueSRADic){const allTissuesDisplayed=Object.keys(tissueSRADic);for(const tissue of allTissuesDisplayed){let append_str='<li class="form-check">';append_str+='<input class="form-check-input" type="checkbox" id="'+tissue.replace(" ","_")+'" onclick="ToggleFilteredeFP(this.id, this.checked);" style="margin: 6px 5px 0;" value="toggleeFP" checked>',append_str+='<p class="form-check-label" for="toggleTitle" style="padding-left: 20px; font-weight: 10;">'+tissue+"</p>",append_str+="</li>",$("#filtereFPList").append(append_str)}}else logError("Unable to use tissueSRADic")}function ToggleFilteredeFP(whichToToggle,OnOrOff){const whichSVG=whichToToggle.replace("_"," "),whichSRA=tissueSRADic[whichSVG];if(!0===OnOrOff)for(let i=0;i<whichSRA.length;i++)document.getElementById(whichSRA[i]+"_row")&&document.getElementById(whichSRA[i]+"_row").removeAttribute("hidden");else if(!1===OnOrOff)for(let i=0;i<whichSRA.length;i++)document.getElementById(whichSRA[i]+"_row")&&document.getElementById(whichSRA[i]+"_row").setAttribute("hidden",!0)}function LoadSubmittedData(){emptyLanding(),progress_percent=0,document.title=`eFP-Seq Browser: Loading 0% - ${locus}`,loadingScreen(!1),setTimeout((function(){count_bam_num(),disableAllComparison()}),200),update_all_images(0)}function generateShareLink(changeURL=!1){let url="https://"+window.location.host+window.location.pathname;url+="?locus="+locus+"&dataset="+base_src,shareLink=url,changeURL&&window.history.pushState&&window.history.pushState({},"Title",window.location.pathname+"?locus="+locus+"&dataset="+base_src),document.getElementById("shareLinkTextArea").textContent=shareLink}const shareLinkInputs={};function readShareLink(){const query=window.location.search.substr(1);let locusInput=!1,datasetInput=!1;if(""!=query){const inputs=query.split("&");for(const input of inputs){const queryInputs=input.split("=");if(queryInputs.length>1)if("locus"===queryInputs[0].split("%20").join(" ").trim()){const qIValue=input.substring(6).split("%20").join(" ").trim();shareLinkInputs.locus=qIValue,document.getElementById("locus").value=qIValue,locusInput=!0}else if("dataset"===queryInputs[0].split("%20").join(" ").trim()){const qIValue=input.substring(8).split("%20").join(" ").trim();shareLinkInputs.dataset=qIValue,base_src=qIValue,datasetInput=!0}}locusInput&&datasetInput?(emptyLanding(),progress_percent=0,document.title=`eFP-Seq Browser: Loading 0% - ${locus}`,sraDict={},sraCountDic={},loadNewDataset=!1,setTimeout((function(){count_bam_num(),disableAllComparison(),checkPreload()}),200),toggleResponsiveTable(0)):displayError(locusInput&&!1===datasetInput?"ERROR IN SHARE LINK! Missing dataset":!1===locusInput&&datasetInput?"ERROR IN SHARE LINK! Missing locus":"ERROR IN SHARE LINK! Missing locus and dataset")}}function copyToClipboard(){""!==document.getElementById("shareLinkTextArea").trim()&&(document.getElementById("shareLinkTextArea").select(),document.execCommand("copy"))}let allCheckedOptions=[];function tableCheckbox(whatID,disableAll=!1){const whatSRA=whatID.split("_")[0];if(disableAll)disableAllComparison();else if(!1===disableAll&&document.getElementById(whatID)&&document.getElementById(whatID).checked){allCheckedOptions.push(whatSRA);const iterationProcess={};for(let i=0;i<GFF_List.length;i++){let append_str='<tr class="compareDataRow" id="'+whatSRA+"_compareRow"+i+'">';parseInt(i)===parseInt(variantPosition)?append_str+='<td style="width: 250px; font-size: 12px;" id="'+whatSRA+"_compareTitle"+i+'">'+document.getElementById(whatSRA+"_title").innerHTML+" ... ("+GFF_List[i]+")</td>\n":append_str+='<td style="width: 250px; font-size: 12px;" id="'+whatSRA+"_compareTitle"+i+'">^^^ ... ('+GFF_List[i]+")</td>\n",append_str+='<td style="max-width: 576px;"><img loading="lazy" id="'+whatSRA+"_rnaseq_img"+i+'" alt="RNA-Seq mapped image for:'+whatSRA+'" style="min-width:420px; max-width:576px; width:95%; height: auto;" src="" /><br/><img loading="lazy" id="'+whatSRA+"_gene_structure_img"+i+'" style="max-width: 576px; width:100%; height: auto;" src="" alt="Gene variant image for:'+whatSRA+'"/></td>\n',append_str+='<td id="'+whatSRA+"_rpb"+i+'" style="font-size: 12px; width: 50px; ">'+sraDict[whatSRA].r[i].toFixed(2)+"</td>",append_str+='<td tag="svg_name" style="width:  75px;"><div id="'+whatSRA+"_svg"+i+'" name="'+sraDict[whatSRA].svg.substr(4).replace(".","_")+'_tissue" tag='+sraDict[whatSRA].svg_part+'_subtissue" width="75" height="75" style="width: 75px; height: 75px; max-width: 75px; max-height: 75px;">'+document.getElementById(sraDict[whatSRA].svg.substr(4).replace(".svg","_svg")).innerHTML+'</div><div class="mdl-tooltip" for="'+whatSRA+"_svg"+i+'">'+sraDict[whatSRA].svg.substring(4).replace(".svg","")+"</div></td>\n",append_str+='<td id="'+whatSRA+"_rpkm"+i+'" style="font-size: 12px; width: 50px; ">'+sraDict[whatSRA].RPKM[i].toFixed(2)+"</td>",parseInt(i)===parseInt(variantPosition)?append_str+='<td style="width: 250px; font-size: 12px;" id="'+whatSRA+"_compareTitle"+i+'"><div id="'+whatSRA+'_descriptionCompare" name="'+document.getElementById(whatSRA+"_description").getAttribute("name")+'">'+document.getElementById(whatSRA+"_description").innerHTML+'</div><div id="igbLinkCompare_'+whatSRA+'">'+document.getElementById("igbLink_"+whatSRA).innerHTML+'</div><div id="extraLinksCompare_'+whatSRA+'">'+document.getElementById("extraLinks_"+whatSRA).innerHTML+"</div></td>\n":append_str+='<td style="width: 250px; font-size: 12px;" id="'+whatSRA+"_compareTitle"+i+'">^^^</td>\n',append_str+="</tr>",iterationProcess[i]=whatSRA+"_compareRow"+i,document.getElementById("compareTable").innerHTML+=append_str,document.getElementById(whatSRA+"_rnaseq_img"+i)&&document.getElementById(whatSRA+"_rnaseq_img"+i).setAttribute("src",document.getElementById(whatSRA+"_rnaseq_img").src),document.getElementById(whatSRA+"_gene_structure_img"+i)&&document.getElementById(whatSRA+"_gene_structure_img"+i).setAttribute("src",document.getElementsByClassName("dd-option-image")[i].src),sraDict[whatSRA].RPKM&&sraDict[whatSRA].RPKM[i]&&colour_part_by_id(whatSRA+"_svg"+i,sraDict[whatSRA].svg_part,sraDict[whatSRA].RPKM[i],colouring_mode)}document.getElementById(whatID).checked=!0,document.getElementById("allCheckbox").checked=!0,"rel"!=colouring_mode&&(document.getElementById("compareGeneVariants").disabled=!1)}else!1===disableAll?(disableCompare(whatSRA),allCheckedOptions.splice(allCheckedOptions.indexOf(whatSRA),1),document.getElementById(whatID).checked=!1):!0===disableAll&&disableAllComparison(),0===allCheckedOptions.length&&(document.getElementById("compareGeneVariants").disabled=!0)}function disableCompare(whatSRA){for(let i=0;i<GFF_List.length;i++)null!=document.getElementById(whatSRA+"_compareRow"+i)&&document.getElementById(whatSRA+"_compareRow"+i).remove()}function disableAllComparison(){if(document.getElementById("allCheckbox")){let compareDataRows=document.getElementsByClassName("compareDataRow");for(let c=compareDataRows.length-1;c>=0;c--)document.getElementsByClassName("compareDataRow")[c].remove();allCheckedOptions=[],compareDataRows=document.getElementsByClassName("compareCheckbox");for(let c=0;c<compareDataRows.length;c++)document.getElementsByClassName("compareCheckbox")[c].checked=!1;document.getElementById("allCheckbox").checked=!1;const listOfEntries=[],mainEntries=document.getElementsByClassName("mainEntries");for(let m=0;m<mainEntries.length;m++){const mainID=mainEntries[m].id;!1===listOfEntries.includes(mainID)?listOfEntries.push(mainID):document.getElementsByClassName("mainEntries")[m].remove()}document.getElementById("compareGeneVariants").disabled=!0}}function PnCDisappear(){document.getElementById("PrivacyAndCookies").setAttribute("hidden",!0),document.cookie="eSBAcceptedCookies=1; expires=Friday, December 31, 9999 at 7:00:00 AM; SameSite=Lax; Secure",document.cookie="eSBVersion="+version+"; expires=Friday, December 31, 9999 at 7:00:00 AM; SameSite=Lax; Secure"}function setUpCookies(){const cookies=document.cookie.split(";");let cookieAccept,cookieVersion;for(const cookie of cookies){const whichCookie=cookie.split("=");if(whichCookie[0]&&"eSBAcceptedCookies"===whichCookie[0].trim()&&(cookieAccept=whichCookie[1].trim()),whichCookie[0]&&"eSBVersion"===whichCookie[0].trim()&&(cookieVersion=whichCookie[1].trim()),cookieAccept&&cookieVersion)break}cookieAccept&&"1"===cookieAccept?document.getElementById("PrivacyAndCookies").setAttribute("hidden",!1):document.getElementById("PrivacyAndCookies").removeAttribute("hidden"),cookieVersion&&cookieVersion!==version&&(document.getElementById("PrivacyAndCookies").removeAttribute("hidden"),document.cookie="eSBAcceptedCookies=0; SameSite=Lax; Secure")}function appendVersionNumber(elementId){const versionText=`<br><br>The eFP-Seq Browser's current version number is: ${version}`;document.getElementById(elementId).innerHTML+=versionText}function displayVersionNumber(){appendVersionNumber("citationText"),appendVersionNumber("feedbackText")}let toastCounter=0;function generateToastNotification(message,header="Notification"){if(message){let dataAttributeValue=`toast-${toastCounter}`;const toast=`\n\t\t<div class="toast" role="alert" aria-live="assertive" aria-atomic="true" data-toast="${dataAttributeValue}" style="background-color: rgba(255, 255, 255, 1);">\n\t\t\t<div class="toast-header">\n\t\t\t\t<img\n\t\t\t\t\tsrc="cgi-bin/img/BAR-logo.svg"\n\t\t\t\t\tclass="rounded me-2"\n\t\t\t\t\talt="BAR notification"\n\t\t\t\t\tstyle="width: 20px; height: 20px"\n\t\t\t\t/>\n\t\t\t\t<strong class="me-auto">${header}</strong>\n\t\t\t\t<button type="button" class="btn-close" data-bs-dismiss="toast" aria-label="Close"></button>\n\t\t\t</div>\n\t\t\t<div class="toast-body">${message}</div>\n\t\t</div>\n\t\t`;document.getElementById("toast-container").innerHTML+=toast,$(`[data-toast="${dataAttributeValue}"]`).toast({autohide:!1}),$(`[data-toast="${dataAttributeValue}"]`).toast("show")}}function init(){document.getElementById("locus").value="AT2G24270",document.getElementById("xmlDatabase").value="Araport 11 RNA-seq data",locus_validation(),old_locus=locus,yscale_validation(),rpkm_validation(),adjustFooterSize(),displayVersionNumber(),adjustTableOptionsDropdownSize(),setUpCookies(),$("input[type=radio][name=radio_group]").change((function(){gene_structure_radio_on_change()})),$("#locus").keyup((function(){locus_validation()})),$("#yscale_input").keyup((function(){yscale_validation()})),$("#rpkm_scale_input").keyup((function(){rpkm_validation()})),document.getElementsByClassName("abcRioButtonLightBlue").length>0&&hiddenGoogleSignin(),getGFF(locus),$("#locus").autocomplete({source:function(request,response){const last=request.term.split(/,\s*/).pop();$.ajax({type:"GET",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/idautocomplete.cgi?species=Arabidopsis_thaliana&term="+last,dataType:"json"}).done((function(data){data&&data.length>=7?response(data.slice(0,7)):response(data)}))},close:function(e,ui){correctAGIIDInput()}});const subiFrame=document.getElementById("submissioniframe");subiFrame&&subiFrame.setAttribute("src",subiFrame.getAttribute("data-src")),adjustSubmissionIFrameSize(),readShareLink();document&&"bar.utoronto.ca"===document.location.host&&document.location.href&&document.querySelector('link[rel="canonical"]')&&document.querySelector('link[rel="canonical"]').setAttribute("href",document.location.href)}$(window).resize((function(){adjustFooterSize(),adjustSubmissionIFrameSize(),responsiveRNAWidthResize(),toggleResponsiveTable(),adjustTableOptionsDropdownSize(),setTimeout((function(){adjustFooterSize()}),10)})),adjustFooterSize(),window.addEventListener("load",(function(){init()}));
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index 075930b..820d5b7 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
 	"name": "efp-seq_browser",
-	"version": "1.3.15",
+	"version": "1.4.0",
 	"lockfileVersion": 2,
 	"requires": true,
 	"packages": {
 		"": {
 			"name": "efp-seq_browser",
-			"version": "1.3.15",
+			"version": "1.4.0",
 			"license": "GPL-2.0",
 			"devDependencies": {
 				"concurrently": "^8.2.2",
diff --git a/package.json b/package.json
index 442d3a8..7fa55f8 100644
--- a/package.json
+++ b/package.json
@@ -59,7 +59,7 @@
 			"url": "https://bar.utoronto.ca/"
 		}
 	],
-	"version": "1.3.15",
+	"version": "1.4.0",
 	"private": true,
 	"description": "Search among 113 RNA-seq data sets used by Araport 11 to reannotate the Arabidopsis genome (Cheng et al. 2016, http://biorxiv.org/content/early/2016/04/05/047308). The eFP-Seq Browser will retrieve the number of reads mapped and display these above the desired Araport 11 gene model. You can sort or filter the columns.",
 	"devDependencies": {