From a5b952bf2df11e9c8538b372f2ee0d3c23d1fa90 Mon Sep 17 00:00:00 2001
From: Alexander Sullivan <alexander.j.sullivan@hotmail.com>
Date: Mon, 15 Jan 2024 15:10:51 -0500
Subject: [PATCH] chore: update version and changelog

---
 CHANGELOG.md               | 57 ++++++++++++++++++++++++++++++++++++++
 cgi-bin/core/custom.js     |  2 +-
 cgi-bin/core/custom.min.js |  2 +-
 package.json               |  2 +-
 4 files changed, 60 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f81d8e3..2655b41 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,63 @@ 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).
 
+## [1.3.15] - 2024-01-15
+
+UI/UX:
+
+- Added toast notifications for error messages
+- Centered the loading indicator
+
+Optimization:
+
+- Made SEO improvements
+- Made more accessibility adjustments
+- Optimized images
+- Preload styles
+- Reduced complexity of some functions
+- Refactored some code
+- Removed unused CSS
+- Set loading from lazy to auto for largest LCP
+- Update cookies `SameSite` to `Lax` and `Secure`
+
+Security:
+
+- Update CSP with `base-uri`
+- Update `Permissions-Policy`
+- Update htaccess
+
+Update:
+
+- Migrate to new Google Identity Services library
+- No longer supporting Internet Explorer
+- Update Python 2 to 3
+- Update packages
+- Updated workbox settings
+
+Documentation:
+
+- Added CHANGELOG markdown file
+- Improved readability of some code
+- Sorted uncategorized CSS styles to make them more readable
+- Updated README
+
+Bug fix:
+
+- Fixed "Duplicate without user-selected canonical"
+- Fixed compatibility with Pillow (PIL) 9.5
+- Fixed deprecated `btoa` functions
+- Fixed eFP-Seq Browser web manifest trying to overwrite BAR's web manifest name - now both use same web manifest
+- Fixed issue where if code is run on a non-BAR server, was still trying to access the BAR's GAPI/Google OAuth
+- Fixed issue where loading indicator was not green
+- Fixed issue where submission page was broken on local instances of the eFP-Seq Browser
+- Fixed issue where the title of the uploaded file to a user from an XML was not reachable
+- Fixed issue where variables were not initialized in loops
+- Fixed issue with service worker not working with Python/CGI scripts
+- Fixed missing Apple metadata
+- Fixed missing Math.js source map
+- Fixed service workers trying to register when is not supported for some users
+- Fixed typos
+
 ## [1.3.14] - 2022-06-09
 
 **A brand new version of the [eFP-Seq Browser](https://bar.utoronto.ca/eFP-Seq_Browser/) has dropped!**
diff --git a/cgi-bin/core/custom.js b/cgi-bin/core/custom.js
index 14d55d3..5f31fab 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 = "v1.3.14-p20240113";
+const version = "v1.3.15-p20240115";
 
 /** Selected RPKM mode */
 let colouring_mode = "abs";
diff --git a/cgi-bin/core/custom.min.js b/cgi-bin/core/custom.min.js
index dc5dca0..ff08cab 100644
--- a/cgi-bin/core/custom.min.js
+++ b/cgi-bin/core/custom.min.js
@@ -1 +1 @@
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i="";i=sraDict[t].RPKM&&sraDict[t].RPKM[variantPosition]?sraDict[t].RPKM[variantPosition]:0,0==i&&0==o?exp_info[e].splice(4,1,0):s=Math.log2(i/o),l.push(s),sraDict[t].relativeRPKM=s,exp_info[e].splice(4,1,l),exp_info[e].splice(6,1,o),i>=max_absolute_fpkm&&(max_absolute_fpkm=i),"Missing controls data"!=exp_info[e][4]&&Math.abs(exp_info[e][4])>=max_log_fpkm&&Math.abs(exp_info[e][4])<1e3&&(max_log_fpkm=Math.abs(exp_info[e][4])),"rel"===colouring_mode?exp_info[e][4]||0==exp_info[e][4]||(exp_info[e][4]=-999999):exp_info[e][3][variantPosition]||0==exp_info[e][3][variantPosition]||(exp_info[e][3][variantPosition]=-999999)}else logError("Issue retrieving exp_info for "+t+" within BAM entry point "+e);whichAbsOrRel()}document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update"),change_rpkm_colour_scale(colouring_mode)}function get_input_values(){locus=document.getElementById("locus").value,locus=locus.trim().toUpperCase(),yscale_input=document.getElementById("yscale_input").value,("Auto"==yscale_input||parseInt(yscale_input)<1)&&(yscale_input=parseInt(-1)),max_abs_scale=document.getElementById("rpkm_scale_input").value}function update_all_images(t){null!=document.getElementById("locus")&&(new_locus=document.getElementById("locus").value,new_locus===old_locus?($.xhrPool.abortAll(),variants_radio_options(t)):new_locus!=old_locus&&(getGFF(new_locus),old_locus=new_locus,setTimeout((function(){$.xhrPool.abortAll(),variants_radio_options(t)}),1650)))}function variants_radio_options(t){get_input_values(),$.ajax({url:"./cgi-bin/get_gene_structures.cgi?locus="+locus,dataType:"json",success:function(e){locus_start=e.locus_start,locus_end=e.locus_end,splice_variants=JSON.stringify(e.splice_variants),populate_table(t),populate_efp_modal(t);const n=document.getElementById("variants_div");if(null!==n&&null!==n.firstChild&&void 0!==n.firstChild)for(;n.firstChild;)n.removeChild(n.firstChild);$("#variant_select").ddslick("destroy");let a='<select id="variant_select">';if(e.variant_count&&parseInt(e.variant_count)>0)for(let t=0;t<parseInt(e.variant_count);t++)e.splice_variants&&e.splice_variants[t]&&e.splice_variants[t].gene_structure&&(a+='<option value="'+t+'"',a+=' data-imagesrc="data:image/png;base64,'+e.splice_variants[t].gene_structure+'" style="max-width:none;"></option>');else a+='<option value="'+i+'"',a+=' data-imagesrc="'+img_gene_struct_error+'" style="max-width:none;"></option>';if(e.splice_variants&&e.splice_variants[0]&&e.splice_variants[0].gene_structure){img_gene_struct_1="data:image/png;base64,"+e.splice_variants[0].gene_structure;const t=document.getElementsByClassName("gene_structure_img");for(const n of t)n.src="data:image/png;base64,"+e.splice_variants[0].gene_structure}else{img_gene_struct_1=img_gene_struct_error;const t=document.getElementsByClassName("gene_structure_img");for(const n of t)n.src="data:image/png;base64,"+e.splice_variants[0].gene_structure}$("input[type=radio][name=radio_group]").change((function(){gene_structure_radio_on_change()})),a+="</select></div>",$("#variants_div").append(a),document.getElementById("variant_select")&&$("#variant_select").ddslick({width:"100%",onSelected:function(){gene_structure_radio_on_change()}}),document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update")},error:function(t,e,n){displayError("ERROR IN get_gene_structures !"),generateToastNotification(`Error processing gene structures: ${error.message}`,"ERROR"),console.log(`Error processing gene structures: ${error.message}`)}})}function displayError(t){$("#displayError").empty();let e='<p class="warning_core" style="text-align:center;">'+t+" <br /><br /> PLEASE REFRESH PAGE, RELOAD OR RE-INPUT DATA OR TRY AGAIN AT A LATER TIME </p>";console.error("Error in logic:",t),$("#displayError").append(e),$("#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} - ${datasetName}`}function logError(t){console.error("Error in logic:",t)}let variant_selected,variantPosition=0;function gene_structure_radio_on_change(){if(document.getElementsByClassName("dd-selected-value")&&document.getElementsByClassName("dd-selected-value")[0]&&document.getElementsByClassName("dd-selected-value")[0].value){variant_selected=document.getElementsByClassName("dd-selected-value")[0].value,variantPosition=variant_selected;let t=document.getElementsByClassName("dd-selected-image")[0].src;document.getElementsByClassName("dd-selected-image")&&document.getElementsByClassName("dd-selected-image")[0]&&!document.getElementsByClassName("dd-selected-image")[0].alt&&(document.getElementsByClassName("dd-selected-image")[0].alt="RNA-Seq Coverage");let e=document.getElementsByClassName("gene_structure_img");for(let n=0;n<e.length;n++)e[n].src=t;for(let n=0;n<exp_info.length;n++){let e=exp_info[n][0].split("_")[0];document.getElementById(e+"_gene_structure_img").src=t;let a,o=sraDict[e].r[variant_selected].toFixed(2);document.getElementById(e+"_rpb").innerHTML=o,sraDict[exp_info[n][0].split("_svg")[0]]||(sraDict[exp_info[n][0].split("_svg")[0]]={}),sraDict[exp_info[n][0].split("_svg")[0]].rpb=o,sraDict[e].RPKM&&sraDict[e].RPKM[variant_selected]?a=sraDict[e].RPKM[variant_selected].toFixed(2):sraDict[e].RPKM?logError("Unable to retrieve RPKM values at: [variant_selected] for "+e):sraDict[e]?logError('Unable to retrieve RPKM values at: ["RPKM"] for '+e):logError(sraDict?"Unable to retrieve RPKM values at: SRA within sraDict":"Unable to retrieve RPKM values at: sraDict unreachable"),document.getElementById(e+"_rpkm").innerHTML=a,whichAbsOrRel(!0,n)}}document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update")}function whichAbsOrRel(t=!1,e=0){if(!0===t)absOrRel(e);else if(exp_info.length>0)for(let n=0;n<exp_info.length;n++)absOrRel(n);change_rpkm_colour_scale(colouring_mode)}function absOrRel(t=0){let e=exp_info[t],n=e[0].slice(0,-4);if("rel"==colouring_mode&&sraDict[n].relativeRPKM){document.getElementById("compareGeneVariants").disabled=!0,e&&!e[4]&&0!=e[4]&&(e[4]=-999999);let t=sraDict[n].relativeRPKM.toFixed(2);document.getElementById(e[0].split("_svg")[0]+"_rpkm").innerHTML=t,sraDict[e[0].split("_svg")[0]].rpkm=t,colour_part_by_id(n+"_svg",sraDict[n].svg_part,sraDict[n].relativeRPKM,colouring_mode)}else{allCheckedOptions.length>0&&(document.getElementById("compareGeneVariants").disabled=!1),e[3]||0==e[3]||(e[3]=-999999);let t="";if(variant_selected&&sraDict[n].RPKM&&sraDict[n].RPKM[variant_selected]){let a=sraDict[n].RPKM[variant_selected].toFixed(2);document.getElementById(e[0].split("_svg")[0]+"_rpkm").innerHTML=a,t=a}else{let n=0;document.getElementById(e[0].split("_svg")[0]+"_rpkm").innerHTML=n,t=n}colour_part_by_id(n+"_svg",sraDict[n].svg_part,t,colouring_mode)}}function parseIntArray(t){for(let e=0,n=t.length;e<n;e++)t[e]=parseInt(t[e],10);return t}let rnaseq_image_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(t){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 e=0;e<count_bam_entries_in_xml;e++){let n=rnaseq_calls[e][0]||"undefined",a=rnaseq_calls[e][1]||"unknown";if("Google Drive"===sraDict[sraList[e]].bam_type){let t=sraDict[sraList[e]].drive_link,n=t.split("?usp=sharing");n=n[0].split("drive.google.com/drive/folders/"),match_drive=n.length>1?n[1]:t}else if("Amazon AWS"===sraDict[sraList[e]].bam_type){let t=sraDict[sraList[e]].drive_link,n=t.split("amazonaws.com/");1===n.length&&(n=t.split("araport.cyverse-cdn.tacc.cloud/")),match_drive=n.length>1?n[1]:t}data={status:t,numberofreads:sraDict[sraList[e]].numberofreads,hexcodecolour:sraDict[sraList[e]].hexColourCode,remoteDrive:match_drive,bamType:sraDict[sraList[e]].bam_type,filename:sraDict[sraList[e]].filenameIn,tissue:n,record:a,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(t){let e=99;count_bam_entries_in_xml>0&&(e=parseInt((count_bam_entries_in_xml-1)/count_bam_entries_in_xml*100)),rnaseq_success++;let n=new Date;if(rnaseq_success_current_time=n.getTime(),progress_percent=rnaseq_change/count_bam_entries_in_xml*100,$("div#progress").width(progress_percent+"%"),progress_percent>e&&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}`,t.status&&"success"===t.status&&t.record){let e=t.record||"unknown";if(listOfRecordsDisplayed.includes(e)?(e=findUnusedRecordDisplayName(e,listOfRecordsDisplayed),listOfRecordsDisplayed.push(e)):listOfRecordsDisplayed.push(e),listOfRecordsDisplayed=[],sraDict[e].bp_length=parseFloat(t.end)-parseFloat(t.start),sraDict[e].bp_start=parseFloat(t.start),sraDict[e].bp_end=parseFloat(t.end),sraDict[e].MappedReads=t.reads_mapped_to_locus,totalreadsMapped_dic[e]=t.totalReadsMapped,sraDict[e].locusValue=t.locus,sraDict[e].r=t.r,sraDict[e].dataVisualization=t.rnaseqbase64,locus!=t.locus)throw new Error(`ERROR: ${locus}'s RNA-Seq API request returned with data for some other locus.`);let n=[];if(t.ss_y&&t.sum_y&&t.sum_xy&&t.sum_x&&t.ss_x&&t.end&&t.start){parseInt(t.ss_y);let e=parseInt(t.sum_y),a=parseInt(t.ss_y),o=parseIntArray(t.sum_xy.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),s=parseIntArray(t.sum_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),l=(parseIntArray(t.sum_xx.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),parseIntArray(t.ss_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),parseIntArray(t.ss_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(","))),i=parseInt(t.end)-parseInt(t.start),r=[];for(let t=0;t<o.length;t++)r.splice(t,0,o[t]-s[t]*e/i),n.splice(t,0,r[t]/Math.sqrt(l[t]*a))}else n=t.r;if(document.getElementById(e+"_rnaseq_img")&&t.rnaseqbase64?"None"!==t.rnaseqbase64&&t.rnaseqbase64.length>=3?(document.getElementById(e+"_rnaseq_img").src="data:image/png;base64,"+t.rnaseqbase64,rnaseq_change+=1):(document.getElementById(e+"_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 - "+e+", dataset - "+base_src)):(document.getElementById(`${e}_rnaseq_img`)&&(document.getElementById(`${e}_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 - "+e+", dataset - "+base_src)),document.getElementById(e+"_rpb").innerHTML=parseFloat(n[0]).toFixed(2),sraDict[e].rpb=parseFloat(n[0]).toFixed(2),document.getElementById(e+"_rpkm").innerHTML=t["absolute-fpkm"],updateRPKMAbsoluteMax(t["absolute-fpkm"]),sraDict[e].RPKM=t["absolute-fpkm"],rpkmCount++,document.getElementById(e+"_totalReadsNum").innerHTML="Total reads = "+t.totalReadsMapped,callDumpOutputs)if(dumpOutputs+='\t\telif (record == "'+t.record+'"):\n',"complex"==dumpMethod){for(dumpOutputs+='\t\t\tdumpJSON(200, "'+t.locus+'", '+t.variant+", "+t.chromosome+", "+t.start+", "+t.end+', "'+t.record+'", "'+t.tissue+'", "'+t.rnaseqbase64+'", '+t.reads_mapped_to_locus+", "+t["absolute-fpkm"]+", ["+t.r+"], "+t.totalReadsMapped+", ["+t.exp_arr+"], [",n=0;n<t.ReadsMappedNucleotidePosition.length;n+=2)dumpOutputs+="["+t.ReadsMappedNucleotidePosition[n]+"]",n!=t.ReadsMappedNucleotidePosition.length-2&&(dumpOutputs+=", ");dumpOutputs+="], {";for(let e=0;e<t.expected_expr_in_variant.length;e++)dumpOutputs+='"'+GFF_List[e].replace(locus,"")+'": ',dumpOutputs+="["+t.expected_expr_in_variant[e]+"]",e!=t.expected_expr_in_variant.length-1&&(dumpOutputs+=", ");dumpOutputs+="})\n"}else dumpOutputs+='\t\t\tdumpJSON(200, "'+t.locus+'", '+t.variant+", "+t.chromosome+", "+t.start+", "+t.end+', "'+t.record+'", "'+t.tissue+'", "'+t.rnaseqbase64+'", '+t.reads_mapped_to_locus+", ["+t["absolute-fpkm"]+"], ["+t.r+"], "+t.totalReadsMapped+")\n";for(let a=0;a<count_bam_entries_in_xml;a++)exp_info&&exp_info[a]&&exp_info[a][0]&&exp_info[a][0]==e+"_svg"&&(exp_info[a].splice(3,1,t["absolute-fpkm"]),exp_info[a].splice(5,1,n));colour_part_by_id(e+"_svg","Shapes",t["absolute-fpkm"][variantPosition],colouring_mode)}else if(t.status&&"fail"===t.status){let e=t.record||"unknown";listOfRecordsDisplayed.includes(e)?(e=findUnusedRecordDisplayName(e,listOfRecordsDisplayed),listOfRecordsDisplayed.push(e)):listOfRecordsDisplayed.push(e),e&&document.getElementById(`${e}_rnaseq_img`)&&(document.getElementById(`${e}_rnaseq_img`).src=`https://${window.location.host}${window.location.pathname}/cgi-bin/img/error.webp`),rnaseq_change+=1,e&&document.getElementById(e+"_rpb")&&(document.getElementById(e+"_rpb").innerHTML=null,sraDict[e]||(sraDict[e]={}),sraDict[e].rpb=null),e&&document.getElementById(e+"_rpkm")&&(document.getElementById(e+"_rpkm").innerHTML=null,updateRPKMAbsoluteMax(null),sraDict[e].RPKM=null),rpkmCount++,e&&document.getElementById(e+"_totalReadsNum")&&t.totalReadsMapped&&(document.getElementById(e+"_totalReadsNum").innerHTML="Total reads = "+t.totalReadsMapped),e&&document.getElementById(e+"_row")&&document.getElementById(e+"_row").classList.add("mainEntriesError"),console.error("Unable to create RNA-Seq map coverage data for: Locus - "+locus+", SRA - "+e+", dataset - "+base_src)}else console.log("Error!",t,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(t,e,n){generateToastNotification(`Error getting RNA-Seq map coverage for ${data.record} - ${n.message}`,"ERROR"),console.error("Error getting RNA-Seq map coverage!",t,e,n)}})}}}function findUnusedRecordDisplayName(t="unknown",e=sraList,n=0){if(Array.isArray(e)){let a=t+"_"+n;if(e.includes(a))findUnusedRecordDisplayName(t,e,n+1);else if(!e.includes(a))return a}else findUnusedRecordDisplayName(t,e=[])}function updateRPKMAbsoluteMax(t){let e=parseInt(document.getElementById("rpkm_scale_input").value);1e3===e&&(e=1);let n=parseInt(t);n>e&&(document.getElementById("rpkm_scale_input").value=n)}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(t,e,n=!1){let a=t.split(".")[0],o=n?svgAgainstData[a].name:e;return svgAgainstData[a]&&!n&&(svgAgainstData[a].subunit?svgAgainstData[a].subunit.includes(e)||(svgAgainstData[a].subunit_name?o=svgAgainstData[a].subunit_name:svgAgainstData[a].subunit[0]&&(o=svgAgainstData[a].subunit[0])):"all"!==e&&(o="all")),o}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(t){$("#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 e='<img loading="lazy" src="data:image/png;base64,'+exon_intron_scale+'" alt="RNA-Seq mapped image" style="float: right; margin-right: 10px;">',n='<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'+e+'</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(n);let a='<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'+e+'</th><th id="compare_colrpb" title="Point biserial correlation coefficient. 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p="";if(m.length>0)for(let t=0;t<m.length;t++)p+=m[t].toString(),t<m.length-2&&(p+=", ");sraDict[e].controlsString=p.trim();let _=$(this).attr("name");sraDict[e].name=_;let h=$(this).attr("svgname");h&&("ath-"===h.trim().substr(0,4)&&(h=h.slice(4,h.length).trim()),".svg"===h.trim().substr(h.length-4,4)&&(h=h.slice(0,h.length-4).trim())),rnaseq_calls.push([h,e]),sraDict[e].tissue=h;let f=$(this).attr("bam_type");sraDict[e].bam_type=f;let b=$(this).attr("name");sraDict[e].drive_link=b;let D=$(this).attr("read_map_method");sraDict[e].read_map_method=D;let A="https://bioviz.org/bar.html?";A+="version=A_thaliana_Jun_2009&",A+="gene_id="+locus+"&",A+="feature_url_0="+b+"&",A+="genome=A_thaliana_Jun_2009&",A+="annotation_set=Araport11&",A+="query_url="+b+"&",A+="server_url=bar";let y='<tr class="mainEntries" id="'+e+'_row">',v="<table id='table_dl'>\n\t<tbody>\n";v+="\t\t<caption>"+document.getElementById("xmlDatabase").value+"</caption>\n",y+='<td class="colTitle" style="width: 250px; font-size: 12px;" id="'+e+'_title">'+n+"</td>\n",y+=`\n\t\t\t\t\t<td class="colRNA" style="max-width: 576px;">\n\t\t\t\t\t\t<img\n\t\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\t\tid="${e}_rnaseq_img"\n\t\t\t\t\t\t\talt="RNA-Seq mapped image for: ${e}"\n\t\t\t\t\t\t\tstyle="min-width:420px; max-width:576px; width:95%; height: auto;"\n\t\t\t\t\t\t\tclass="rnaseq_img responsiveRNAWidth"\n\t\t\t\t\t\t\tsrc="${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="${e}_gene_structure_img"\n\t\t\t\t\t\t\tstyle="max-width: 576px; width:100%; height: auto;"\n\t\t\t\t\t\t\tclass="gene_structure_img"\n\t\t\t\t\t\t\tsrc="${img_gene_struct_1}"\n\t\t\t\t\t\t\talt="Gene variant image for: ${e}"\n\t\t\t\t\t\t/>\n\t\t\t\t\t</td>\n\n\t\t\t\t`,y+='<td id="'+e+'_rpb" class="rpb_value colrpb" style="font-size: 12px; width: 50px; ">'+"-9999</td>",y+='<td class="coleFP" tag="svg_name" style="width:  75px;"><div id="'+e+'_svg" name="'+o.substring(0,o.length-4).slice(4)+'_tissue" tag='+s+'_subtissue" width="75" height="75" style="width: 75px; height: 75px; max-width: 75px; max-height: 75px;">'+document.getElementById(o.substring(4).replace(".svg","_svg")).innerHTML+'</div><div class="mdl-tooltip" for="'+e+'_svg">'+o.substring(4).replace(".svg","")+"</div></td>\n",y+='<td class="colRPKM" id="'+e+'_rpkm" style="font-size: 12px; width: 50px; ">-9999</td>',y+='<td class="colDetails" id="'+e+'_details" style="font-size: 12px;"><div id="'+e+'_description" name="'+a.trim()+'">'+truncateDescription(a)+"</div>","Amazon AWS"===f&&(y+='<div id="igbLink_'+e+'">Show: <a href="'+A+'" target="_blank" rel="noopener">Alignments in IGB</a></div>'),e.includes("unknown")&&!i||(y+='<div id="extraLinks_'+e+'">Go to: ',e.includes("unknown")||(y+='<a href="'+l+'" target="_blank" rel="noopener">NCBI SRA</a>'),e.includes("unknown")&&i&&(y+=" or "),i&&(y+='<a href="'+i+'" target="_blank" rel="noopener">PubMed</a>'),y+="</div>"),y+='<a 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onclick="tableCheckbox(this.id);"></div></td>',y+="</tr>",iteration_num++,$("#theTable").append(y);let w=document.getElementsByClassName("fltrow")[0].childNodes[6];(w&&void 0===w.classList[0]||"undefined"===w.classList[0])&&(w.classList=["colCompare"],w.innerHTML='<input type="checkbox" name="compareCheckbox" class="compareCheckbox" value="compareCheckbox" id="allCheckbox" onclick="disableAllComparison();">'),exp_info.push([e+"_svg",s,m,0,0,0,0]),!0===loadNewDataset?(setTimeout((function(){count_bam_num()}),200),setTimeout((function(){rnaseq_images(t)}),10)):rnaseq_images(t)})),$.tablesorter.addParser({id:"rpb_sorter",is:function(t){return!1},format:function(t){return NaN==t?-99999:null==t?-999999:t==1/0?99999:t==-1/0?-99999:parseFloat(t)},type:"numeric"}),$.tablesorter.addParser({id:"rpkm_sorter",is:function(t){return!1},format:function(t){return NaN==t?-99999:null==t?-999999:t==1/0?99999:t==-1/0?-99999:"Missing controls 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e=t.substring(0,t.length-5);document.getElementById(e).removeAttribute("hidden");const n=document.getElementById(document.getElementById(t).name);n.textContent=truncateDescription(n.getAttribute("name"))}}function truncateDescription(t){if(null!=t||null!=t)return t.length>30?t.substring(0,30)+"...":t}let remainder_efp=0,efp_length=0,eFPSortedSRA=[],efp_RPKM_values=[];function populate_efp_modal(t){toggleResponsiveTable(2),$("#efpModalTable").empty(),efp_table_column="",eFPSortedSRA=[];const e=document.getElementsByClassName("colTitle");for(let n=2;n<e.length;n++){let t=e[n].id.substring(0,e[n].id.length-6);"none"!=document.getElementById(t+"_row").style.display&&eFPSortedSRA.push(t)}remainder_efp=eFPSortedSRA.length%11,efp_length=eFPSortedSRA.length,efp_RPKM_values=[];for(let n=0;n<eFPSortedSRA.length;n++)isNaN(parseFloat(sraDict[eFPSortedSRA[n]].RPKM))||efp_RPKM_values.push(parseFloat(sraDict[eFPSortedSRA[n]].RPKM));$("#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?$("#efpModalTable").append(`\n\t\t\t\t<p class="eFP_thead">\n\t\t\t\t\teFP Colour Scale:\n\n\t\t\t\t\t<img\n\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\tsrc="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQD//wD//AD/+QD/9wD/9AD/8gD/7wD/7QD/6gD/6AD/5QD/4gD/4AD/3QD/2wD/2AD/1gD/ 0wD/0QD/zgD/zAD/yQD/xgD/xAD/wQD/vwD/vAD/ugD/twD/tQD/sgD/rwD/rQD/qgD/qAD/pQD/ owD/oAD/ngD/mwD/mQD/lgD/kwD/kQD/jgD/jAD/iQD/hwD/hAD/ggD/fwD/fAD/egD/dwD/dQD/ cgD/cAD/bQD/awD/aAD/ZgD/YwD/YAD/XgD/WwD/WQD/VgD/VAD/UQD/TwD/TAD/SQD/RwD/RAD/ QgD/PwD/PQD/OgD/OAD/NQD/MwD/MAD/LQD/KwD/KAD/JgD/IwD/IQD/HgD/HAD/GQD/FgD/FAD/ EQD/DwD/DAD/CgD/BwD/BQD/AgCkIVxRAAAAs0lEQVQ4jWNg5+Dk4ubh5eMXEBQSFhEVE5eQlJKW 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/>\n\n\t\t\t\t<table>\n\t\t\t\t\t<tbody>\n\t\t\t\t</tbody>\n\t\t\t`),$("#efpModalTable").append('<table id="eFPtable" class="table"></table>');for(let n=0;n<11*~~(eFPSortedSRA.length/11);n+=11)if("null"!=document.getElementById(eFPSortedSRA[n+10]).outerHTML){efp_table_column="<tr>";for(let t=0;t<11;t++)efp_table_column+=generateEFPTableItem(eFPSortedSRA[n+t],sraDict[eFPSortedSRA[n+t]].title);efp_table_column+="</tr>",$("#eFPtable").append(efp_table_column)}for(let n=0;n<12;n++)if(remainder_efp===n){efp_table_column="<tr>";for(let t=remainder_efp;t>0;t--)efp_table_column+=generateEFPTableItem(eFPSortedSRA[efp_length-t],sraDict[eFPSortedSRA[efp_length-t]].title);efp_table_column+="</tr>",$("#eFPtable").append(efp_table_column)}toggleResponsiveTable()}function generateEFPTableItem(t,e){return t&&e?`\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="${t}_rep"\n\t\t\t\t\tonclick="ScrollToRNARow('${t}_row')"\n\t\t\t\t>\n\t\t\t\t\t${document.getElementById(t+"_svg").outerHTML}\n\t\t\t\t\t<span class="efp_table_tooltip_text">\n\t\t\t\t\t${t} - ${e}\n\t\t\t\t\t</span>\n\t\t\t\t</div>\n\t\t\t</td>\n\t\t`:""}function change_rpkm_colour_scale(t){if(null===svg_colouring_element&&document.getElementById("flt3_theTable")&&document.getElementById("flt3_theTable").parentElement&&(svg_colouring_element=document.getElementById("flt3_theTable").parentElement),svg_colouring_element&&svg_colouring_element.innerHTML&&(svg_colouring_element.innerHTML=""),"rel"==t){const t=document.createElement("img");t.src="data:image/png;base64,"+relative_rpkm_scale,t.style="margin-top: 10px;",svg_colouring_element&&svg_colouring_element.appendChild(t)}else{const t=document.createElement("img");t.src="data:image/png;base64,"+absolute_rpkm_scale,t.style="margin-top: 10px;",t.alt="Absolute RPKM Scale",svg_colouring_element&&svg_colouring_element.appendChild(t)}const e=["colTitle","colRNA","colrpb","coleFP","colRPKM","colDetails"];let n=[];document.getElementsByClassName("fltrow")&&document.getElementsByClassName("fltrow")[0]&&(n=document.getElementsByClassName("fltrow")[0].getElementsByTagName("td"));for(let a=0;a<n.length;a++)n[a].style="border: 1px solid #D3D3D3",n[a].classList.add(e[a])}function locus_validation(){const t=document.getElementById("locus").value;9==t.length&&("A"==t[0]||"a"==t[0])&&("T"==t[1]||"t"==t[1])&&(t[2]>=1&&t[2]<=5||"C"==t[2]||"M"==t[2]||"c"==t[2]||"m"==t[2])&&("G"==t[3]||"g"==t[3])&&t[4]>=0&&t[4]<=9&&t[5]>=0&&t[5]<=9&&t[6]>=0&&t[6]<=9&&t[7]>=0&&t[7]<=9&&t[8]>=0&&t[8]<=9?$("#locus_button").removeAttr("disabled"):$("#locus_button").prop("disabled",!0)}function yscale_validation(){const 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occurred with your account, you have now been logged out. Please log back in")):$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/get_xml_list.php?user="+users_email,dataType:"json",failure:function(){console.log("ERROR! 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Please log back in"))):users_email===t?$.ajax({method:"POST",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/upload.php",data:{user:users_email,xml:upload_src,title:datasetName}}):""!=users_email&&users_email!=t&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in"))):users_email===t?$.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!=t&&(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 t=findAuthUser();""!=users_email&&users_email===t?document.getElementById("upload_modal").click():""!=users_email&&users_email!=t?(signOut(),alert("Error occurred with your account, you have now been logged out. 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confirm_deleteUser(){const t=findAuthUser();""!=users_email&&users_email===t&&$("#logoutModal").is(":visible")&&delete_allXMLs(t)}function delete_allXMLs(t){const e=findAuthUser();if(t===e){for(let t=0;t<title_list.length;t++){const n="deleteBox_"+(t+2);users_email===e&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_xml.php?user="+users_email+"&file="+match_title[document.getElementById(n).value]})}delete_user(),databasesAdded=!1}}function delete_user(){const t=findAuthUser();""!=users_email&&users_email===t&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_user.php?user="+users_email}),signOut()}let warningActive_index_XML="nope",warningActive_index_account="nope";function showWarning_index(t){1===t?isDeletePublicDisabled||("nope"==warningActive_index_XML?(document.getElementById("warning_index_xml").className="warning_index",warningActive_index_XML="yes"):"yes"==warningActive_index_XML&&hideWarning_index(t)):2===t&&("nope"==warningActive_index_account?(document.getElementById("warning_index_account").className="warning_index",warningActive_index_account="yes"):"yes"==warningActive_index_account&&hideWarning_index(t))}function hideWarning_index(t){1===t?(document.getElementById("warning_index_xml").className="warning_nope_index",warningActive_index_XML="nope"):2===t&&(document.getElementById("warning_index_account").className="warning_nope_index",warningActive_index_account="nope")}function manage_DownloadXML(){const t=title_list.length+2;for(let e=0;e<t;e++){const t="deleteBox_"+e;document.getElementById(t).checked&&($("#downloadXML").attr("href",dataset_dictionary[document.getElementById(t).value]).attr("download",document.getElementById(t).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(){$("#XMLtoCSVtable").empty();for(let t=0;t<total_amount_of_datasets;t++){const e="deleteBox_"+t;$.ajax({url:dataset_dictionary[document.getElementById(e).value],dataType:"xml",failure:function(){console.log("Failed at opening XML for conversion into a CSV file. 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${locus}`,document.getElementById("progress").title="0%",$("div#progress").width(progress_percent+"%");for(const t in public_dataset_dictionary){if(base_src===public_dataset_dictionary[t]){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: ${locus}`)}function verifyLoci(t){if("string"==typeof t){const e=new RegExp("^[A][T][MC0-9][G][0-9]{5}[.][0-9]{1,2}$|^[A][T][MC0-9][G][0-9]{5}$","i");return t.trim().match(e)}return!1}let parse_output,GFF_List=[];function getGFF(t){GFF_List=[],$.ajax({url:`https://bar.utoronto.ca/webservices/bar_araport/gene_structure_by_locus.php?locus=${t}`,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(t){if(parse_output=t,parse_output.wasSuccessful){let t=parse_output.features[0].subfeatures;for(let e=0;e<t.length;e++)null!=t[e].uniqueID?GFF_List.push(t[e].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(t,e,n){generateToastNotification(`Error getting GFFs (getGFF) information failed to retrieve locus information from Araport11: ${n.message}`,"ERROR"),console.log(`Error getting GFFs (getGFF) information failed to retrieve locus information from Araport11: ${n.message}`)}})}function addGFF(){if(document.getElementsByClassName("dd-option").length>0)for(let t=0;t<GFF_List.length;t++)document.getElementsByClassName("dd-option")[t]&&document.getElementsByClassName("dd-option")[t].setAttribute("title",GFF_List[t])}function hiddenGoogleSignin(){const t=document.getElementsByClassName("abcRioButtonLightBlue");for(let e=0;e<t.length;e++)t[e]&&t[e].setAttribute("id","loginClick"+e)}function remove_private_database(){databasesAdded=!1,document.getElementById("private_dataset_header").style.display="none";const t=document.getElementsByClassName("userAdded");for(let e=0;e<t.length;e++)$("#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 t=document.getElementById("locus").value.trim().split("/");t[0]?document.getElementById("locus").value=t[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 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t=document.getElementById("navbar_menu");t&&(document.getElementById("nm_footer").style.width=t.offsetWidth+"px",t.scrollHeight==t.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")):t.scrollHeight>t.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 t=.7*window.innerHeight;document.getElementById("submissioniframe").height=t+"px"}let usedToggle=!1;function toggleTableCol(t,e){const n=document.getElementsByClassName(t);if(e)for(const a of n)a&&a.removeAttribute("hidden");else if(!e)for(const a of n)a&&a.setAttribute("hidden",!0)}let responsiveRNAWidthAdjusted=!1;function responsiveRNAWidthResize(){const t=document.getElementsByClassName("responsiveRNAWidth");if(window.innerWidth<=575){for(let e=0;e<t.length;e++)t[e].style.minWidth=.93*window.innerWidth+"px";responsiveRNAWidthAdjusted=!0}else if(window.innerWidth>575&&responsiveRNAWidthAdjusted)for(let e=0;e<t.length;e++)t[e].style.minWidth="420px"}function toggleResponsiveTableOptions(t,e,n,a,o,s,l){toggleTableCol("colTitle",t),document.getElementById("toggleTitle").checked=t,toggleTableCol("colRNA",e),document.getElementById("toggleRNA").checked=e,toggleTableCol("colrpb",n),document.getElementById("togglerpb").checked=n,toggleTableCol("coleFP",a),document.getElementById("toggleeFP").checked=a,toggleTableCol("colRPKM",o),document.getElementById("toggleRPKM").checked=o,toggleTableCol("colDetails",s),document.getElementById("toggleDetails").checked=s,toggleTableCol("colCompare",l),document.getElementById("toggleCompare").checked=l,RememberToggleOptions(t,e,n,a,o,s,l)}function determineResponsiveTable(){document.body.offsetWidth<=576?(toggleResponsiveTable(2),displayNavBAR(!0)):toggleResponsiveTable(0)}function toggleResponsiveTable(t=0){"none"!=document.getElementById("tableToggle").style.display&&(1==t||window.innerWidth<=575&&!usedToggle?toggleResponsiveTableOptions(!1,!0,!1,!1,!1,!1,!1):2==t||window.innerWidth>=1100&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!0,!0,!0,!1):3==t||window.innerWidth<830&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!1,!1,!1,!1,!1):4==t||window.innerWidth<900&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!1,!1,!1,!1):5==t||window.innerWidth<990&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!1,!0,!1,!1):(6==t||window.innerWidth<1100&&!usedToggle)&&toggleResponsiveTableOptions(!0,!0,!0,!0,!0,!1,!1))}let ToggledTable=[!0,!0,!0,!0,!0,!0,!1];function RememberToggleOptions(t=!0,e=!0,n=!0,a=!0,o=!0,s=!0,l=!1){ToggledTable=[t,e,n,a,o,s,l]}const colSortList=["colTitle","colrpb","colRPKM","colDetails"];function ResizeArrowRow(){for(const t of colSortList){const e=t+"Row";document.getElementById(e).style.width=document.getElementById(e).parentNode.offsetWidth-2+"px";CheckElementWidth(t+"Arrow",8)}}function CheckElementWidth(t,e){document.getElementById(t).offsetWidth<e&&(document.getElementById(t).style.width=e+"px")}function ChangeColArrow(t){setTimeout((function(){const e=t+"Arrow";document.getElementById(t).classList.contains("headerSortDown")?document.getElementById(e).src="./cgi-bin/SVGs/arrowSortDown.min.svg":document.getElementById(t).classList.contains("headerSortUp")&&(document.getElementById(e).src="./cgi-bin/SVGs/arrowSortUp.min.svg");for(const t of colSortList){CheckElementWidth(t+"Arrow",8)}}),100)}function ScrollToRNARow(t){document.getElementById("closemodal_efPOverview").click(),$("#main_content").animate({scrollTop:$("#"+t).offset().top},"slow"),document.getElementById(t)&&(document.getElementById(t).className+=" scrollToRow",setTimeout((function(){document.getElementById(t).className+=" 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a=t.split("=");if(a.length>1)if("locus"===a[0].split("%20").join(" ").trim()){const n=t.substring(6).split("%20").join(" ").trim();shareLinkInputs.locus=n,document.getElementById("locus").value=n,e=!0}else if("dataset"===a[0].split("%20").join(" ").trim()){const e=t.substring(8).split("%20").join(" ").trim();shareLinkInputs.dataset=e,base_src=e,n=!0}}e&&n?(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(e&&!1===n?"ERROR IN SHARE LINK! Missing dataset":!1===e&&n?"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(t,e=!1){const n=t.split("_")[0];if(e)disableAllComparison();else if(!1===e&&document.getElementById(t)&&document.getElementById(t).checked){allCheckedOptions.push(n);const e={};for(let t=0;t<GFF_List.length;t++){let a='<tr class="compareDataRow" id="'+n+"_compareRow"+t+'">';parseInt(t)===parseInt(variantPosition)?a+='<td style="width: 250px; font-size: 12px;" id="'+n+"_compareTitle"+t+'">'+document.getElementById(n+"_title").innerHTML+" ... ("+GFF_List[t]+")</td>\n":a+='<td style="width: 250px; font-size: 12px;" id="'+n+"_compareTitle"+t+'">^^^ ... ('+GFF_List[t]+")</td>\n",a+='<td style="max-width: 576px;"><img loading="lazy" id="'+n+"_rnaseq_img"+t+'" alt="RNA-Seq mapped image for:'+n+'" style="min-width:420px; max-width:576px; width:95%; height: auto;" src="" /><br/><img loading="lazy" id="'+n+"_gene_structure_img"+t+'" style="max-width: 576px; width:100%; height: auto;" src="" alt="Gene variant image for:'+n+'"/></td>\n',a+='<td id="'+n+"_rpb"+t+'" style="font-size: 12px; width: 50px; ">'+sraDict[n].r[t].toFixed(2)+"</td>",a+='<td tag="svg_name" style="width:  75px;"><div id="'+n+"_svg"+t+'" name="'+sraDict[n].svg.substr(4).replace(".","_")+'_tissue" tag='+sraDict[n].svg_part+'_subtissue" width="75" height="75" style="width: 75px; height: 75px; max-width: 75px; max-height: 75px;">'+document.getElementById(sraDict[n].svg.substr(4).replace(".svg","_svg")).innerHTML+'</div><div class="mdl-tooltip" for="'+n+"_svg"+t+'">'+sraDict[n].svg.substring(4).replace(".svg","")+"</div></td>\n",a+='<td id="'+n+"_rpkm"+t+'" style="font-size: 12px; width: 50px; ">'+sraDict[n].RPKM[t].toFixed(2)+"</td>",parseInt(t)===parseInt(variantPosition)?a+='<td style="width: 250px; font-size: 12px;" id="'+n+"_compareTitle"+t+'"><div id="'+n+'_descriptionCompare" name="'+document.getElementById(n+"_description").getAttribute("name")+'">'+document.getElementById(n+"_description").innerHTML+'</div><div id="igbLinkCompare_'+n+'">'+document.getElementById("igbLink_"+n).innerHTML+'</div><div id="extraLinksCompare_'+n+'">'+document.getElementById("extraLinks_"+n).innerHTML+"</div></td>\n":a+='<td style="width: 250px; font-size: 12px;" id="'+n+"_compareTitle"+t+'">^^^</td>\n',a+="</tr>",e[t]=n+"_compareRow"+t,document.getElementById("compareTable").innerHTML+=a,document.getElementById(n+"_rnaseq_img"+t)&&document.getElementById(n+"_rnaseq_img"+t).setAttribute("src",document.getElementById(n+"_rnaseq_img").src),document.getElementById(n+"_gene_structure_img"+t)&&document.getElementById(n+"_gene_structure_img"+t).setAttribute("src",document.getElementsByClassName("dd-option-image")[t].src),sraDict[n].RPKM&&sraDict[n].RPKM[t]&&colour_part_by_id(n+"_svg"+t,sraDict[n].svg_part,sraDict[n].RPKM[t],colouring_mode)}document.getElementById(t).checked=!0,document.getElementById("allCheckbox").checked=!0,"rel"!=colouring_mode&&(document.getElementById("compareGeneVariants").disabled=!1)}else!1===e?(disableCompare(n),allCheckedOptions.splice(allCheckedOptions.indexOf(n),1),document.getElementById(t).checked=!1):!0===e&&disableAllComparison(),0===allCheckedOptions.length&&(document.getElementById("compareGeneVariants").disabled=!0)}function disableCompare(t){for(let e=0;e<GFF_List.length;e++)null!=document.getElementById(t+"_compareRow"+e)&&document.getElementById(t+"_compareRow"+e).remove()}function disableAllComparison(){if(document.getElementById("allCheckbox")){let t=document.getElementsByClassName("compareDataRow");for(let a=t.length-1;a>=0;a--)document.getElementsByClassName("compareDataRow")[a].remove();allCheckedOptions=[],t=document.getElementsByClassName("compareCheckbox");for(let a=0;a<t.length;a++)document.getElementsByClassName("compareCheckbox")[a].checked=!1;document.getElementById("allCheckbox").checked=!1;const e=[],n=document.getElementsByClassName("mainEntries");for(let a=0;a<n.length;a++){const t=n[a].id;!1===e.includes(t)?e.push(t):document.getElementsByClassName("mainEntries")[a].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 t=document.cookie.split(";");let e,n;for(const a of t){const t=a.split("=");if(t[0]&&"eSBAcceptedCookies"===t[0].trim()&&(e=t[1].trim()),t[0]&&"eSBVersion"===t[0].trim()&&(n=t[1].trim()),e&&n)break}e&&"1"===e?document.getElementById("PrivacyAndCookies").setAttribute("hidden",!1):document.getElementById("PrivacyAndCookies").removeAttribute("hidden"),n&&n!==version&&(document.getElementById("PrivacyAndCookies").removeAttribute("hidden"),document.cookie="eSBAcceptedCookies=0; SameSite=Lax; Secure")}function displayVersionNumber(){document.getElementById("feedbackText").innerHTML+="<br><br>The eFP-Seq Browser's current version number is: "+version}let toastCounter=0;function generateToastNotification(t,e="Notification"){if(t){let n=`toast-${toastCounter}`;const a=`\n\t\t<div class="toast" role="alert" aria-live="assertive" aria-atomic="true" data-toast="${n}" style="background-color: rgba(255, 255, 255, 1);">\n\t\t\t<div class="toast-header">\n\t\t\t\t<img\n\t\t\t\t\tsrc="cgi-bin/img/BAR-logo.svg"\n\t\t\t\t\tclass="rounded me-2"\n\t\t\t\t\talt="BAR notification"\n\t\t\t\t\tstyle="width: 20px; 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\ No newline at end of file
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i="";i=sraDict[t].RPKM&&sraDict[t].RPKM[variantPosition]?sraDict[t].RPKM[variantPosition]:0,0==i&&0==o?exp_info[e].splice(4,1,0):s=Math.log2(i/o),l.push(s),sraDict[t].relativeRPKM=s,exp_info[e].splice(4,1,l),exp_info[e].splice(6,1,o),i>=max_absolute_fpkm&&(max_absolute_fpkm=i),"Missing controls data"!=exp_info[e][4]&&Math.abs(exp_info[e][4])>=max_log_fpkm&&Math.abs(exp_info[e][4])<1e3&&(max_log_fpkm=Math.abs(exp_info[e][4])),"rel"===colouring_mode?exp_info[e][4]||0==exp_info[e][4]||(exp_info[e][4]=-999999):exp_info[e][3][variantPosition]||0==exp_info[e][3][variantPosition]||(exp_info[e][3][variantPosition]=-999999)}else logError("Issue retrieving exp_info for "+t+" within BAM entry point "+e);whichAbsOrRel()}document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update"),change_rpkm_colour_scale(colouring_mode)}function 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t)n.src="data:image/png;base64,"+e.splice_variants[0].gene_structure}else{img_gene_struct_1=img_gene_struct_error;const t=document.getElementsByClassName("gene_structure_img");for(const n of t)n.src="data:image/png;base64,"+e.splice_variants[0].gene_structure}$("input[type=radio][name=radio_group]").change((function(){gene_structure_radio_on_change()})),a+="</select></div>",$("#variants_div").append(a),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")},error:function(t,e,n){displayError("ERROR IN get_gene_structures !"),generateToastNotification(`Error processing gene structures: ${error.message}`,"ERROR"),console.log(`Error processing gene structures: ${error.message}`)}})}function displayError(t){$("#displayError").empty();let e='<p class="warning_core" style="text-align:center;">'+t+" <br /><br 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t=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 e=document.getElementsByClassName("gene_structure_img");for(let n=0;n<e.length;n++)e[n].src=t;for(let n=0;n<exp_info.length;n++){let e=exp_info[n][0].split("_")[0];document.getElementById(e+"_gene_structure_img").src=t;let a,o=sraDict[e].r[variant_selected].toFixed(2);document.getElementById(e+"_rpb").innerHTML=o,sraDict[exp_info[n][0].split("_svg")[0]]||(sraDict[exp_info[n][0].split("_svg")[0]]={}),sraDict[exp_info[n][0].split("_svg")[0]].rpb=o,sraDict[e].RPKM&&sraDict[e].RPKM[variant_selected]?a=sraDict[e].RPKM[variant_selected].toFixed(2):sraDict[e].RPKM?logError("Unable to retrieve RPKM values at: [variant_selected] for "+e):sraDict[e]?logError('Unable to retrieve RPKM values at: ["RPKM"] for '+e):logError(sraDict?"Unable to retrieve RPKM values at: SRA within sraDict":"Unable to retrieve RPKM values at: sraDict unreachable"),document.getElementById(e+"_rpkm").innerHTML=a,whichAbsOrRel(!0,n)}}document.getElementById("landing").setAttribute("hidden","true"),$("#theTable").trigger("update")}function whichAbsOrRel(t=!1,e=0){if(!0===t)absOrRel(e);else if(exp_info.length>0)for(let n=0;n<exp_info.length;n++)absOrRel(n);change_rpkm_colour_scale(colouring_mode)}function absOrRel(t=0){let e=exp_info[t],n=e[0].slice(0,-4);if("rel"==colouring_mode&&sraDict[n].relativeRPKM){document.getElementById("compareGeneVariants").disabled=!0,e&&!e[4]&&0!=e[4]&&(e[4]=-999999);let t=sraDict[n].relativeRPKM.toFixed(2);document.getElementById(e[0].split("_svg")[0]+"_rpkm").innerHTML=t,sraDict[e[0].split("_svg")[0]].rpkm=t,colour_part_by_id(n+"_svg",sraDict[n].svg_part,sraDict[n].relativeRPKM,colouring_mode)}else{allCheckedOptions.length>0&&(document.getElementById("compareGeneVariants").disabled=!1),e[3]||0==e[3]||(e[3]=-999999);let t="";if(variant_selected&&sraDict[n].RPKM&&sraDict[n].RPKM[variant_selected]){let a=sraDict[n].RPKM[variant_selected].toFixed(2);document.getElementById(e[0].split("_svg")[0]+"_rpkm").innerHTML=a,t=a}else{let n=0;document.getElementById(e[0].split("_svg")[0]+"_rpkm").innerHTML=n,t=n}colour_part_by_id(n+"_svg",sraDict[n].svg_part,t,colouring_mode)}}function parseIntArray(t){for(let e=0,n=t.length;e<n;e++)t[e]=parseInt(t[e],10);return t}let rnaseq_image_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(t){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 e=0;e<count_bam_entries_in_xml;e++){let n=rnaseq_calls[e][0]||"undefined",a=rnaseq_calls[e][1]||"unknown";if("Google Drive"===sraDict[sraList[e]].bam_type){let t=sraDict[sraList[e]].drive_link,n=t.split("?usp=sharing");n=n[0].split("drive.google.com/drive/folders/"),match_drive=n.length>1?n[1]:t}else if("Amazon AWS"===sraDict[sraList[e]].bam_type){let t=sraDict[sraList[e]].drive_link,n=t.split("amazonaws.com/");1===n.length&&(n=t.split("araport.cyverse-cdn.tacc.cloud/")),match_drive=n.length>1?n[1]:t}data={status:t,numberofreads:sraDict[sraList[e]].numberofreads,hexcodecolour:sraDict[sraList[e]].hexColourCode,remoteDrive:match_drive,bamType:sraDict[sraList[e]].bam_type,filename:sraDict[sraList[e]].filenameIn,tissue:n,record:a,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(){$("#failure").show()},success:function(t){let e=99;count_bam_entries_in_xml>0&&(e=parseInt((count_bam_entries_in_xml-1)/count_bam_entries_in_xml*100)),rnaseq_success++;let n=new Date;if(rnaseq_success_current_time=n.getTime(),progress_percent=rnaseq_change/count_bam_entries_in_xml*100,$("div#progress").width(progress_percent+"%"),progress_percent>e&&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}`,t.status&&"success"===t.status&&t.record){let e=t.record||"unknown";if(listOfRecordsDisplayed.includes(e)?(e=findUnusedRecordDisplayName(e,listOfRecordsDisplayed),listOfRecordsDisplayed.push(e)):listOfRecordsDisplayed.push(e),listOfRecordsDisplayed=[],sraDict[e].bp_length=parseFloat(t.end)-parseFloat(t.start),sraDict[e].bp_start=parseFloat(t.start),sraDict[e].bp_end=parseFloat(t.end),sraDict[e].MappedReads=t.reads_mapped_to_locus,totalreadsMapped_dic[e]=t.totalReadsMapped,sraDict[e].locusValue=t.locus,sraDict[e].r=t.r,sraDict[e].dataVisualization=t.rnaseqbase64,locus!=t.locus)throw new Error(`ERROR: ${locus}'s RNA-Seq API request returned with data for some other locus.`);let n=[];if(t.ss_y&&t.sum_y&&t.sum_xy&&t.sum_x&&t.ss_x&&t.end&&t.start){parseInt(t.ss_y);let e=parseInt(t.sum_y),a=parseInt(t.ss_y),o=parseIntArray(t.sum_xy.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),s=parseIntArray(t.sum_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),l=(parseIntArray(t.sum_xx.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),parseIntArray(t.ss_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(",")),parseIntArray(t.ss_x.replace(/\[/g,"").replace(/\]/g,"").replace(/"/g,"").split(","))),i=parseInt(t.end)-parseInt(t.start),r=[];for(let t=0;t<o.length;t++)r.splice(t,0,o[t]-s[t]*e/i),n.splice(t,0,r[t]/Math.sqrt(l[t]*a))}else n=t.r;if(document.getElementById(e+"_rnaseq_img")&&t.rnaseqbase64?"None"!==t.rnaseqbase64&&t.rnaseqbase64.length>=3?(document.getElementById(e+"_rnaseq_img").src="data:image/png;base64,"+t.rnaseqbase64,rnaseq_change+=1):(document.getElementById(e+"_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 - "+e+", dataset - "+base_src)):(document.getElementById(`${e}_rnaseq_img`)&&(document.getElementById(`${e}_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 - "+e+", dataset - "+base_src)),document.getElementById(e+"_rpb").innerHTML=parseFloat(n[0]).toFixed(2),sraDict[e].rpb=parseFloat(n[0]).toFixed(2),document.getElementById(e+"_rpkm").innerHTML=t["absolute-fpkm"],updateRPKMAbsoluteMax(t["absolute-fpkm"]),sraDict[e].RPKM=t["absolute-fpkm"],rpkmCount++,document.getElementById(e+"_totalReadsNum").innerHTML="Total reads = "+t.totalReadsMapped,callDumpOutputs)if(dumpOutputs+='\t\telif (record == "'+t.record+'"):\n',"complex"==dumpMethod){for(dumpOutputs+='\t\t\tdumpJSON(200, "'+t.locus+'", '+t.variant+", "+t.chromosome+", "+t.start+", "+t.end+', "'+t.record+'", "'+t.tissue+'", "'+t.rnaseqbase64+'", '+t.reads_mapped_to_locus+", "+t["absolute-fpkm"]+", ["+t.r+"], "+t.totalReadsMapped+", ["+t.exp_arr+"], [",n=0;n<t.ReadsMappedNucleotidePosition.length;n+=2)dumpOutputs+="["+t.ReadsMappedNucleotidePosition[n]+"]",n!=t.ReadsMappedNucleotidePosition.length-2&&(dumpOutputs+=", ");dumpOutputs+="], {";for(let e=0;e<t.expected_expr_in_variant.length;e++)dumpOutputs+='"'+GFF_List[e].replace(locus,"")+'": ',dumpOutputs+="["+t.expected_expr_in_variant[e]+"]",e!=t.expected_expr_in_variant.length-1&&(dumpOutputs+=", ");dumpOutputs+="})\n"}else dumpOutputs+='\t\t\tdumpJSON(200, "'+t.locus+'", '+t.variant+", "+t.chromosome+", "+t.start+", "+t.end+', "'+t.record+'", "'+t.tissue+'", "'+t.rnaseqbase64+'", '+t.reads_mapped_to_locus+", ["+t["absolute-fpkm"]+"], ["+t.r+"], "+t.totalReadsMapped+")\n";for(let a=0;a<count_bam_entries_in_xml;a++)exp_info&&exp_info[a]&&exp_info[a][0]&&exp_info[a][0]==e+"_svg"&&(exp_info[a].splice(3,1,t["absolute-fpkm"]),exp_info[a].splice(5,1,n));colour_part_by_id(e+"_svg","Shapes",t["absolute-fpkm"][variantPosition],colouring_mode)}else if(t.status&&"fail"===t.status){let e=t.record||"unknown";listOfRecordsDisplayed.includes(e)?(e=findUnusedRecordDisplayName(e,listOfRecordsDisplayed),listOfRecordsDisplayed.push(e)):listOfRecordsDisplayed.push(e),e&&document.getElementById(`${e}_rnaseq_img`)&&(document.getElementById(`${e}_rnaseq_img`).src=`https://${window.location.host}${window.location.pathname}/cgi-bin/img/error.webp`),rnaseq_change+=1,e&&document.getElementById(e+"_rpb")&&(document.getElementById(e+"_rpb").innerHTML=null,sraDict[e]||(sraDict[e]={}),sraDict[e].rpb=null),e&&document.getElementById(e+"_rpkm")&&(document.getElementById(e+"_rpkm").innerHTML=null,updateRPKMAbsoluteMax(null),sraDict[e].RPKM=null),rpkmCount++,e&&document.getElementById(e+"_totalReadsNum")&&t.totalReadsMapped&&(document.getElementById(e+"_totalReadsNum").innerHTML="Total reads = "+t.totalReadsMapped),e&&document.getElementById(e+"_row")&&document.getElementById(e+"_row").classList.add("mainEntriesError"),console.error("Unable to create RNA-Seq map coverage data for: Locus - "+locus+", SRA - "+e+", dataset - "+base_src)}else console.log("Error!",t,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(t,e,n){generateToastNotification(`Error getting RNA-Seq map coverage for ${data.record} - ${n.message}`,"ERROR"),console.error("Error getting RNA-Seq map coverage!",t,e,n)}})}}}function findUnusedRecordDisplayName(t="unknown",e=sraList,n=0){if(Array.isArray(e)){let a=t+"_"+n;if(e.includes(a))findUnusedRecordDisplayName(t,e,n+1);else if(!e.includes(a))return a}else findUnusedRecordDisplayName(t,e=[])}function updateRPKMAbsoluteMax(t){let e=parseInt(document.getElementById("rpkm_scale_input").value);1e3===e&&(e=1);let n=parseInt(t);n>e&&(document.getElementById("rpkm_scale_input").value=n)}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(t,e,n=!1){let a=t.split(".")[0],o=n?svgAgainstData[a].name:e;return svgAgainstData[a]&&!n&&(svgAgainstData[a].subunit?svgAgainstData[a].subunit.includes(e)||(svgAgainstData[a].subunit_name?o=svgAgainstData[a].subunit_name:svgAgainstData[a].subunit[0]&&(o=svgAgainstData[a].subunit[0])):"all"!==e&&(o="all")),o}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(t){$("#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 e='<img loading="lazy" src="data:image/png;base64,'+exon_intron_scale+'" alt="RNA-Seq mapped image" style="float: right; margin-right: 10px;">',n='<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'+e+'</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(n);let a='<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'+e+'</th><th id="compare_colrpb" title="Point biserial correlation coefficient. 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r,d=$(this).attr("total_reads_mapped");null!=d&&""!=d||(d="0"),sraDict[e].numberofreads=d,r=null==$(this).attr("hex_colour")||""==$(this).attr("hex_colour")?"0x64cc65":$(this).attr("hex_colour"),sraDict[e].hexColourCode=r;let c=$(this).attr("filename");null!=c&&""!=c&&null!=c||(c="accepted_hits.bam"),sraDict[e].filenameIn=c;let u=$(this).attr("species");sraDict[e].species=u;let m=[];if(null==$(this).find("controls")[0].innerHTML)for(let t=1;t<$(this).find("controls")[0].childNodes.length;t+2)m.push($(this).find("controls")[0].childNodes[t].firstChild.textContent);else null!=$(this).find("controls")[0].innerHTML&&(m=$(this).find("controls")[0].innerHTML.replace(/<bam_exp>/g,"").replace(/<\/bam_exp>/g,",").replace(/\n/g," ").replace(/ /g,"").split(","));sraDict[e].controls=m;let g="";if(m.length>0)for(let t=m.length;t--;)"MEDIAN"!=m[t]?g+='<a href="https://www.ncbi.nlm.nih.gov/Traces/sra/?run='+m[t]+'"target="_blank" rel="noopener">'+m[t]+"</a> ":g+=m[t];sraDict[e].links=g;let p="";if(m.length>0)for(let t=0;t<m.length;t++)p+=m[t].toString(),t<m.length-2&&(p+=", ");sraDict[e].controlsString=p.trim();let _=$(this).attr("name");sraDict[e].name=_;let h=$(this).attr("svgname");h&&("ath-"===h.trim().substr(0,4)&&(h=h.slice(4,h.length).trim()),".svg"===h.trim().substr(h.length-4,4)&&(h=h.slice(0,h.length-4).trim())),rnaseq_calls.push([h,e]),sraDict[e].tissue=h;let f=$(this).attr("bam_type");sraDict[e].bam_type=f;let b=$(this).attr("name");sraDict[e].drive_link=b;let D=$(this).attr("read_map_method");sraDict[e].read_map_method=D;let A="https://bioviz.org/bar.html?";A+="version=A_thaliana_Jun_2009&",A+="gene_id="+locus+"&",A+="feature_url_0="+b+"&",A+="genome=A_thaliana_Jun_2009&",A+="annotation_set=Araport11&",A+="query_url="+b+"&",A+="server_url=bar";let y='<tr class="mainEntries" id="'+e+'_row">',v="<table id='table_dl'>\n\t<tbody>\n";v+="\t\t<caption>"+document.getElementById("xmlDatabase").value+"</caption>\n",y+='<td class="colTitle" style="width: 250px; font-size: 12px;" id="'+e+'_title">'+n+"</td>\n",y+=`\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="${e}_rnaseq_img"\n\t\t\t\t\t\t\talt="RNA-Seq mapped image for: ${e}"\n\t\t\t\t\t\t\tstyle="min-width:420px; max-width:576px; width:95%; height: auto;"\n\t\t\t\t\t\t\tclass="rnaseq_img responsiveRNAWidth"\n\t\t\t\t\t\t\tsrc="${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="${e}_gene_structure_img"\n\t\t\t\t\t\t\tstyle="max-width: 576px; width:100%; height: auto;"\n\t\t\t\t\t\t\tclass="gene_structure_img"\n\t\t\t\t\t\t\tsrc="${img_gene_struct_1}"\n\t\t\t\t\t\t\talt="Gene variant image for: ${e}"\n\t\t\t\t\t\t/>\n\t\t\t\t\t</td>\n\n\t\t\t\t`,y+='<td id="'+e+'_rpb" class="rpb_value colrpb" style="font-size: 12px; width: 50px; ">'+"-9999</td>",y+='<td class="coleFP" tag="svg_name" style="width:  75px;"><div id="'+e+'_svg" name="'+o.substring(0,o.length-4).slice(4)+'_tissue" tag='+s+'_subtissue" width="75" height="75" style="width: 75px; height: 75px; max-width: 75px; max-height: 75px;">'+document.getElementById(o.substring(4).replace(".svg","_svg")).innerHTML+'</div><div class="mdl-tooltip" for="'+e+'_svg">'+o.substring(4).replace(".svg","")+"</div></td>\n",y+='<td class="colRPKM" id="'+e+'_rpkm" style="font-size: 12px; width: 50px; ">-9999</td>',y+='<td class="colDetails" id="'+e+'_details" style="font-size: 12px;"><div id="'+e+'_description" name="'+a.trim()+'">'+truncateDescription(a)+"</div>","Amazon AWS"===f&&(y+='<div id="igbLink_'+e+'">Show: <a href="'+A+'" target="_blank" rel="noopener">Alignments in IGB</a></div>'),e.includes("unknown")&&!i||(y+='<div id="extraLinks_'+e+'">Go to: ',e.includes("unknown")||(y+='<a href="'+l+'" target="_blank" rel="noopener">NCBI SRA</a>'),e.includes("unknown")&&i&&(y+=" or "),i&&(y+='<a href="'+i+'" target="_blank" rel="noopener">PubMed</a>'),y+="</div>"),y+='<a id="clickForMoreDetails_'+iteration_num+'" name="'+e+'_description" onclick="clickDetailsTextChange(this.id)" href="javascript:(function(){$(\'#'+e+"').toggle();})()\">"+moreDetails.trim()+"</a>",y+='<div id="'+e+'" class="moreDetails" style="display:none">',g&&(y+="Controls: "+g+"<br/>"),y+="Species: "+u+"<br>",y+='<div id="'+e+'_sra">SRA: '+e+"</div>",y+='<div id="'+e+'_totalReadsNum">Total reads = '+d+"</div>",null!=D&&D.length>0&&(y+='<div id="'+e+'_readMappedMethod">Read map method = '+D.trim()+"</div>"),y+='<a id="clickForMoreDetails_'+iteration_num+'_less" name="'+e+'_description" onclick="clickDetailsTextChange(this.id)" href="javascript:(function(){$(\'#'+e+"').toggle();})()\">"+lessDetails+"</a></div></td>\n",y+='<td class="colCompare" style="font-size: 12px; max-width: 30px;"><div id="'+e+'_compareVariant"><input type="checkbox" name="compareCheckbox" class="compareCheckbox" value="compareCheckbox" id="'+e+'_compareCheckbox" onclick="tableCheckbox(this.id);"></div></td>',y+="</tr>",iteration_num++,$("#theTable").append(y);let w=document.getElementsByClassName("fltrow")[0].childNodes[6];(w&&void 0===w.classList[0]||"undefined"===w.classList[0])&&(w.classList=["colCompare"],w.innerHTML='<input type="checkbox" name="compareCheckbox" class="compareCheckbox" value="compareCheckbox" id="allCheckbox" onclick="disableAllComparison();">'),exp_info.push([e+"_svg",s,m,0,0,0,0]),!0===loadNewDataset?(setTimeout((function(){count_bam_num()}),200),setTimeout((function(){rnaseq_images(t)}),10)):rnaseq_images(t)})),$.tablesorter.addParser({id:"rpb_sorter",is:function(t){return!1},format:function(t){return NaN==t?-99999:null==t?-999999:t==1/0?99999:t==-1/0?-99999:parseFloat(t)},type:"numeric"}),$.tablesorter.addParser({id:"rpkm_sorter",is:function(t){return!1},format:function(t){return NaN==t?-99999:null==t?-999999:t==1/0?99999:t==-1/0?-99999:"Missing controls 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e=t.substring(0,t.length-5);document.getElementById(e).removeAttribute("hidden");const n=document.getElementById(document.getElementById(t).name);n.textContent=truncateDescription(n.getAttribute("name"))}}function truncateDescription(t){if(null!=t||null!=t)return t.length>30?t.substring(0,30)+"...":t}let remainder_efp=0,efp_length=0,eFPSortedSRA=[],efp_RPKM_values=[];function populate_efp_modal(t){toggleResponsiveTable(2),$("#efpModalTable").empty(),efp_table_column="",eFPSortedSRA=[];const e=document.getElementsByClassName("colTitle");for(let n=2;n<e.length;n++){let t=e[n].id.substring(0,e[n].id.length-6);"none"!=document.getElementById(t+"_row").style.display&&eFPSortedSRA.push(t)}remainder_efp=eFPSortedSRA.length%11,efp_length=eFPSortedSRA.length,efp_RPKM_values=[];for(let n=0;n<eFPSortedSRA.length;n++)isNaN(parseFloat(sraDict[eFPSortedSRA[n]].RPKM))||efp_RPKM_values.push(parseFloat(sraDict[eFPSortedSRA[n]].RPKM));$("#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?$("#efpModalTable").append(`\n\t\t\t\t<p class="eFP_thead">\n\t\t\t\t\teFP Colour Scale:\n\n\t\t\t\t\t<img\n\t\t\t\t\t\tloading="lazy"\n\t\t\t\t\t\tsrc="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGQAAAAPCAMAAAAlD5r/AAABQVBMVEX///8AAADcFDz/jAAAAP+m 3KYAfQD//wD//AD/+QD/9wD/9AD/8gD/7wD/7QD/6gD/6AD/5QD/4gD/4AD/3QD/2wD/2AD/1gD/ 0wD/0QD/zgD/zAD/yQD/xgD/xAD/wQD/vwD/vAD/ugD/twD/tQD/sgD/rwD/rQD/qgD/qAD/pQD/ owD/oAD/ngD/mwD/mQD/lgD/kwD/kQD/jgD/jAD/iQD/hwD/hAD/ggD/fwD/fAD/egD/dwD/dQD/ cgD/cAD/bQD/awD/aAD/ZgD/YwD/YAD/XgD/WwD/WQD/VgD/VAD/UQD/TwD/TAD/SQD/RwD/RAD/ QgD/PwD/PQD/OgD/OAD/NQD/MwD/MAD/LQD/KwD/KAD/JgD/IwD/IQD/HgD/HAD/GQD/FgD/FAD/ EQD/DwD/DAD/CgD/BwD/BQD/AgCkIVxRAAAAs0lEQVQ4jWNg5+Dk4ubh5eMXEBQSFhEVE5eQlJKW 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/>\n\n\t\t\t\t<table>\n\t\t\t\t\t<tbody>\n\t\t\t\t</tbody>\n\t\t\t`),$("#efpModalTable").append('<table id="eFPtable" class="table"></table>');for(let n=0;n<11*~~(eFPSortedSRA.length/11);n+=11)if("null"!=document.getElementById(eFPSortedSRA[n+10]).outerHTML){efp_table_column="<tr>";for(let t=0;t<11;t++)efp_table_column+=generateEFPTableItem(eFPSortedSRA[n+t],sraDict[eFPSortedSRA[n+t]].title);efp_table_column+="</tr>",$("#eFPtable").append(efp_table_column)}for(let n=0;n<12;n++)if(remainder_efp===n){efp_table_column="<tr>";for(let t=remainder_efp;t>0;t--)efp_table_column+=generateEFPTableItem(eFPSortedSRA[efp_length-t],sraDict[eFPSortedSRA[efp_length-t]].title);efp_table_column+="</tr>",$("#eFPtable").append(efp_table_column)}toggleResponsiveTable()}function generateEFPTableItem(t,e){return t&&e?`\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="${t}_rep"\n\t\t\t\t\tonclick="ScrollToRNARow('${t}_row')"\n\t\t\t\t>\n\t\t\t\t\t${document.getElementById(t+"_svg").outerHTML}\n\t\t\t\t\t<span class="efp_table_tooltip_text">\n\t\t\t\t\t${t} - ${e}\n\t\t\t\t\t</span>\n\t\t\t\t</div>\n\t\t\t</td>\n\t\t`:""}function change_rpkm_colour_scale(t){if(null===svg_colouring_element&&document.getElementById("flt3_theTable")&&document.getElementById("flt3_theTable").parentElement&&(svg_colouring_element=document.getElementById("flt3_theTable").parentElement),svg_colouring_element&&svg_colouring_element.innerHTML&&(svg_colouring_element.innerHTML=""),"rel"==t){const t=document.createElement("img");t.src="data:image/png;base64,"+relative_rpkm_scale,t.style="margin-top: 10px;",svg_colouring_element&&svg_colouring_element.appendChild(t)}else{const t=document.createElement("img");t.src="data:image/png;base64,"+absolute_rpkm_scale,t.style="margin-top: 10px;",t.alt="Absolute RPKM Scale",svg_colouring_element&&svg_colouring_element.appendChild(t)}const e=["colTitle","colRNA","colrpb","coleFP","colRPKM","colDetails"];let n=[];document.getElementsByClassName("fltrow")&&document.getElementsByClassName("fltrow")[0]&&(n=document.getElementsByClassName("fltrow")[0].getElementsByTagName("td"));for(let a=0;a<n.length;a++)n[a].style="border: 1px solid #D3D3D3",n[a].classList.add(e[a])}function locus_validation(){const t=document.getElementById("locus").value;9==t.length&&("A"==t[0]||"a"==t[0])&&("T"==t[1]||"t"==t[1])&&(t[2]>=1&&t[2]<=5||"C"==t[2]||"M"==t[2]||"c"==t[2]||"m"==t[2])&&("G"==t[3]||"g"==t[3])&&t[4]>=0&&t[4]<=9&&t[5]>=0&&t[5]<=9&&t[6]>=0&&t[6]<=9&&t[7]>=0&&t[7]<=9&&t[8]>=0&&t[8]<=9?$("#locus_button").removeAttr("disabled"):$("#locus_button").prop("disabled",!0)}function yscale_validation(){const t=document.getElementById("yscale_input").value;parseInt(t)>0||"Auto"==t||""==t?$("#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"):$("#abs_scale_button").prop("disabled",!0)}const base_dataset_dictionary={"Araport 11 RNA-seq data":"cgi-bin/data/bamdata_araport11.xml","Developmental transcriptome - Klepikova et al":"cgi-bin/data/bamdata_Developmental_transcriptome.xml"};let databasesAdded=!1;function reset_database_options(){$(".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 t=findAuthUser();""==users_email&&null==users_email&&null==users_email||users_email!==t?""!=users_email&&users_email!=t&&(signOut(),alert("Error occurred with your account, you have now been logged out. Please log back in")):$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/get_xml_list.php?user="+users_email,dataType:"json",failure:function(){console.log("ERROR! 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confirm_deleteUser(){const t=findAuthUser();""!=users_email&&users_email===t&&$("#logoutModal").is(":visible")&&delete_allXMLs(t)}function delete_allXMLs(t){const e=findAuthUser();if(t===e){for(let t=0;t<title_list.length;t++){const n="deleteBox_"+(t+2);users_email===e&&$.ajax({url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/delete_xml.php?user="+users_email+"&file="+match_title[document.getElementById(n).value]})}delete_user(),databasesAdded=!1}}function delete_user(){const t=findAuthUser();""!=users_email&&users_email===t&&$.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 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t="deleteBox_"+e;document.getElementById(t).checked&&($("#downloadXML").attr("href",dataset_dictionary[document.getElementById(t).value]).attr("download",document.getElementById(t).value+".xml"),document.getElementById("downloadXML_button").click())}}const table_base="\t\t<tr>\n\t\t\t<th>Title*</th>\n\t\t\t<th>Description*</th>\n\t\t\t<th>Record Number *</th>\n\t\t\t<th>RNA-Seq Data/BAM file repository link*</th>\n\t\t\t<th>Repository type*</th>\n\t\t\t<th>BAM Filename*</th>\n\t\t\t<th>Publication Link</th>\n\t\t\t<th>SRA/NCBI Link</th>\n\t\t\t<th>Total Reads Mapped*</th>\n\t\t\t<th>Read Map Method</th>\n\t\t\t<th>Species*</th>\n\t\t\t<th>Tissue*</th>\n\t\t\t<th>Tissue subunit*</th>\n\t\t\t<th>Controls</th>\n\t\t\t<th>Replicate Controls</th>\n\t\t</tr>\n";function fill_tableCSV(){$("#XMLtoCSVtable").empty();for(let t=0;t<total_amount_of_datasets;t++){const e="deleteBox_"+t;$.ajax({url:dataset_dictionary[document.getElementById(e).value],dataType:"xml",failure:function(){console.log("Failed at opening XML for conversion into a CSV file. 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${locus}`,document.getElementById("progress").title="0%",$("div#progress").width(progress_percent+"%");for(const t in public_dataset_dictionary){if(base_src===public_dataset_dictionary[t]){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: ${locus}`)}function verifyLoci(t){if("string"==typeof t){const e=new RegExp("^[A][T][MC0-9][G][0-9]{5}[.][0-9]{1,2}$|^[A][T][MC0-9][G][0-9]{5}$","i");return t.trim().match(e)}return!1}let parse_output,GFF_List=[];function getGFF(t){GFF_List=[],$.ajax({url:`https://bar.utoronto.ca/webservices/bar_araport/gene_structure_by_locus.php?locus=${t}`,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(t){if(parse_output=t,parse_output.wasSuccessful){let t=parse_output.features[0].subfeatures;for(let e=0;e<t.length;e++)null!=t[e].uniqueID?GFF_List.push(t[e].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(t,e,n){generateToastNotification(`Error getting GFFs (getGFF) information failed to retrieve locus information from Araport11: ${n.message}`,"ERROR"),console.log(`Error getting GFFs (getGFF) information failed to retrieve locus information from Araport11: ${n.message}`)}})}function addGFF(){if(document.getElementsByClassName("dd-option").length>0)for(let t=0;t<GFF_List.length;t++)document.getElementsByClassName("dd-option")[t]&&document.getElementsByClassName("dd-option")[t].setAttribute("title",GFF_List[t])}function hiddenGoogleSignin(){const t=document.getElementsByClassName("abcRioButtonLightBlue");for(let e=0;e<t.length;e++)t[e]&&t[e].setAttribute("id","loginClick"+e)}function remove_private_database(){databasesAdded=!1,document.getElementById("private_dataset_header").style.display="none";const t=document.getElementsByClassName("userAdded");for(let e=0;e<t.length;e++)$("#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 t=document.getElementById("locus").value.trim().split("/");t[0]?document.getElementById("locus").value=t[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(t){html2canvas(document.getElementById(t)).then((t=>{$("#appendCanvas").empty(),t.id="downloadDivNum_"+downloadDivNum,document.getElementById("appendCanvas").appendChild(t),document.getElementById("downloadDivNum_"+downloadDivNum).style.width="100%",$("#DownloadImageModal").modal("toggle"),downloadDivNum++}))}function displayNavBAR(t=!1){const e=$("#navbar_menu").is(":visible")||t;document.getElementById("navbar_menu").style.display=e?"none":"block",document.getElementById("main_content").className=e?"col-sm-12":"col-sm-9",document.getElementById("openMenu").style.display=e?"block":"none",document.getElementById("theTable")&&(e?document.getElementById("theTable").classList.add("RNATable"):document.getElementById("theTable").classList.remove("RNATable"))}function adjustFooterSize(){const t=document.getElementById("navbar_menu");t&&(document.getElementById("nm_footer").style.width=t.offsetWidth+"px",t.scrollHeight==t.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")):t.scrollHeight>t.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 t=.7*window.innerHeight;document.getElementById("submissioniframe").height=t+"px"}let usedToggle=!1;function toggleTableCol(t,e){const n=document.getElementsByClassName(t);if(e)for(const a of n)a&&a.removeAttribute("hidden");else if(!e)for(const a of n)a&&a.setAttribute("hidden",!0)}let responsiveRNAWidthAdjusted=!1;function responsiveRNAWidthResize(){const t=document.getElementsByClassName("responsiveRNAWidth");if(window.innerWidth<=575){for(let e=0;e<t.length;e++)t[e].style.minWidth=.93*window.innerWidth+"px";responsiveRNAWidthAdjusted=!0}else if(window.innerWidth>575&&responsiveRNAWidthAdjusted)for(let e=0;e<t.length;e++)t[e].style.minWidth="420px"}function toggleResponsiveTableOptions(t,e,n,a,o,s,l){toggleTableCol("colTitle",t),document.getElementById("toggleTitle").checked=t,toggleTableCol("colRNA",e),document.getElementById("toggleRNA").checked=e,toggleTableCol("colrpb",n),document.getElementById("togglerpb").checked=n,toggleTableCol("coleFP",a),document.getElementById("toggleeFP").checked=a,toggleTableCol("colRPKM",o),document.getElementById("toggleRPKM").checked=o,toggleTableCol("colDetails",s),document.getElementById("toggleDetails").checked=s,toggleTableCol("colCompare",l),document.getElementById("toggleCompare").checked=l,RememberToggleOptions(t,e,n,a,o,s,l)}function determineResponsiveTable(){document.body.offsetWidth<=576?(toggleResponsiveTable(2),displayNavBAR(!0)):toggleResponsiveTable(0)}function toggleResponsiveTable(t=0){"none"!=document.getElementById("tableToggle").style.display&&(1==t||window.innerWidth<=575&&!usedToggle?toggleResponsiveTableOptions(!1,!0,!1,!1,!1,!1,!1):2==t||window.innerWidth>=1100&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!0,!0,!0,!1):3==t||window.innerWidth<830&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!1,!1,!1,!1,!1):4==t||window.innerWidth<900&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!1,!1,!1,!1):5==t||window.innerWidth<990&&!usedToggle?toggleResponsiveTableOptions(!0,!0,!0,!1,!0,!1,!1):(6==t||window.innerWidth<1100&&!usedToggle)&&toggleResponsiveTableOptions(!0,!0,!0,!0,!0,!1,!1))}let ToggledTable=[!0,!0,!0,!0,!0,!0,!1];function RememberToggleOptions(t=!0,e=!0,n=!0,a=!0,o=!0,s=!0,l=!1){ToggledTable=[t,e,n,a,o,s,l]}const colSortList=["colTitle","colrpb","colRPKM","colDetails"];function ResizeArrowRow(){for(const t of colSortList){const e=t+"Row";document.getElementById(e).style.width=document.getElementById(e).parentNode.offsetWidth-2+"px";CheckElementWidth(t+"Arrow",8)}}function CheckElementWidth(t,e){document.getElementById(t).offsetWidth<e&&(document.getElementById(t).style.width=e+"px")}function ChangeColArrow(t){setTimeout((function(){const e=t+"Arrow";document.getElementById(t).classList.contains("headerSortDown")?document.getElementById(e).src="./cgi-bin/SVGs/arrowSortDown.min.svg":document.getElementById(t).classList.contains("headerSortUp")&&(document.getElementById(e).src="./cgi-bin/SVGs/arrowSortUp.min.svg");for(const t of colSortList){CheckElementWidth(t+"Arrow",8)}}),100)}function ScrollToRNARow(t){document.getElementById("closemodal_efPOverview").click(),$("#main_content").animate({scrollTop:$("#"+t).offset().top},"slow"),document.getElementById(t)&&(document.getElementById(t).className+=" scrollToRow",setTimeout((function(){document.getElementById(t).className+=" 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o=0;if(t[element].NContain.forEach((t=>{-1!==navigator.userAgent.indexOf(t)&&o++})),o!=e){n=element,a=!1;break}}}if(n){$("#notChrome").empty();const t=' or through the following <a href="https://www.google.com/search?q=manage+cookies+in+'+n+'" target="_blank" rel="noopener">Google search results</a>';$("#notChrome").append(t)}BrowserDetected=!0}}function CreateFilteredeFPList(){if($("#filtereFPList").empty(),tissueSRADic){const t=Object.keys(tissueSRADic);for(const e of t){let t='<li class="form-check">';t+='<input class="form-check-input" type="checkbox" id="'+e.replace(" ","_")+'" onclick="ToggleFilteredeFP(this.id, this.checked);" style="margin: 6px 5px 0;" value="toggleeFP" checked>',t+='<p class="form-check-label" for="toggleTitle" style="padding-left: 20px; font-weight: 10;">'+e+"</p>",t+="</li>",$("#filtereFPList").append(t)}}else logError("Unable to use tissueSRADic")}function ToggleFilteredeFP(t,e){const n=t.replace("_"," "),a=tissueSRADic[n];if(!0===e)for(let o=0;o<a.length;o++)document.getElementById(a[o]+"_row")&&document.getElementById(a[o]+"_row").removeAttribute("hidden");else if(!1===e)for(let o=0;o<a.length;o++)document.getElementById(a[o]+"_row")&&document.getElementById(a[o]+"_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(t=!1){let e="https://"+window.location.host+window.location.pathname;e+="?locus="+locus+"&dataset="+base_src,shareLink=e,t&&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 t=window.location.search.substr(1);let e=!1,n=!1;if(""!=t){const a=t.split("&");for(const t of a){const a=t.split("=");if(a.length>1)if("locus"===a[0].split("%20").join(" ").trim()){const n=t.substring(6).split("%20").join(" ").trim();shareLinkInputs.locus=n,document.getElementById("locus").value=n,e=!0}else if("dataset"===a[0].split("%20").join(" ").trim()){const e=t.substring(8).split("%20").join(" ").trim();shareLinkInputs.dataset=e,base_src=e,n=!0}}e&&n?(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(e&&!1===n?"ERROR IN SHARE LINK! Missing dataset":!1===e&&n?"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(t,e=!1){const n=t.split("_")[0];if(e)disableAllComparison();else if(!1===e&&document.getElementById(t)&&document.getElementById(t).checked){allCheckedOptions.push(n);const e={};for(let t=0;t<GFF_List.length;t++){let a='<tr class="compareDataRow" id="'+n+"_compareRow"+t+'">';parseInt(t)===parseInt(variantPosition)?a+='<td style="width: 250px; font-size: 12px;" id="'+n+"_compareTitle"+t+'">'+document.getElementById(n+"_title").innerHTML+" ... ("+GFF_List[t]+")</td>\n":a+='<td style="width: 250px; font-size: 12px;" id="'+n+"_compareTitle"+t+'">^^^ ... ('+GFF_List[t]+")</td>\n",a+='<td style="max-width: 576px;"><img loading="lazy" id="'+n+"_rnaseq_img"+t+'" alt="RNA-Seq mapped image for:'+n+'" style="min-width:420px; max-width:576px; width:95%; height: auto;" src="" /><br/><img loading="lazy" id="'+n+"_gene_structure_img"+t+'" style="max-width: 576px; width:100%; height: auto;" src="" alt="Gene variant image for:'+n+'"/></td>\n',a+='<td id="'+n+"_rpb"+t+'" style="font-size: 12px; width: 50px; ">'+sraDict[n].r[t].toFixed(2)+"</td>",a+='<td tag="svg_name" style="width:  75px;"><div id="'+n+"_svg"+t+'" name="'+sraDict[n].svg.substr(4).replace(".","_")+'_tissue" tag='+sraDict[n].svg_part+'_subtissue" width="75" height="75" style="width: 75px; height: 75px; max-width: 75px; max-height: 75px;">'+document.getElementById(sraDict[n].svg.substr(4).replace(".svg","_svg")).innerHTML+'</div><div class="mdl-tooltip" for="'+n+"_svg"+t+'">'+sraDict[n].svg.substring(4).replace(".svg","")+"</div></td>\n",a+='<td id="'+n+"_rpkm"+t+'" style="font-size: 12px; width: 50px; ">'+sraDict[n].RPKM[t].toFixed(2)+"</td>",parseInt(t)===parseInt(variantPosition)?a+='<td style="width: 250px; font-size: 12px;" id="'+n+"_compareTitle"+t+'"><div id="'+n+'_descriptionCompare" name="'+document.getElementById(n+"_description").getAttribute("name")+'">'+document.getElementById(n+"_description").innerHTML+'</div><div id="igbLinkCompare_'+n+'">'+document.getElementById("igbLink_"+n).innerHTML+'</div><div id="extraLinksCompare_'+n+'">'+document.getElementById("extraLinks_"+n).innerHTML+"</div></td>\n":a+='<td style="width: 250px; font-size: 12px;" id="'+n+"_compareTitle"+t+'">^^^</td>\n',a+="</tr>",e[t]=n+"_compareRow"+t,document.getElementById("compareTable").innerHTML+=a,document.getElementById(n+"_rnaseq_img"+t)&&document.getElementById(n+"_rnaseq_img"+t).setAttribute("src",document.getElementById(n+"_rnaseq_img").src),document.getElementById(n+"_gene_structure_img"+t)&&document.getElementById(n+"_gene_structure_img"+t).setAttribute("src",document.getElementsByClassName("dd-option-image")[t].src),sraDict[n].RPKM&&sraDict[n].RPKM[t]&&colour_part_by_id(n+"_svg"+t,sraDict[n].svg_part,sraDict[n].RPKM[t],colouring_mode)}document.getElementById(t).checked=!0,document.getElementById("allCheckbox").checked=!0,"rel"!=colouring_mode&&(document.getElementById("compareGeneVariants").disabled=!1)}else!1===e?(disableCompare(n),allCheckedOptions.splice(allCheckedOptions.indexOf(n),1),document.getElementById(t).checked=!1):!0===e&&disableAllComparison(),0===allCheckedOptions.length&&(document.getElementById("compareGeneVariants").disabled=!0)}function disableCompare(t){for(let e=0;e<GFF_List.length;e++)null!=document.getElementById(t+"_compareRow"+e)&&document.getElementById(t+"_compareRow"+e).remove()}function disableAllComparison(){if(document.getElementById("allCheckbox")){let t=document.getElementsByClassName("compareDataRow");for(let a=t.length-1;a>=0;a--)document.getElementsByClassName("compareDataRow")[a].remove();allCheckedOptions=[],t=document.getElementsByClassName("compareCheckbox");for(let a=0;a<t.length;a++)document.getElementsByClassName("compareCheckbox")[a].checked=!1;document.getElementById("allCheckbox").checked=!1;const e=[],n=document.getElementsByClassName("mainEntries");for(let a=0;a<n.length;a++){const t=n[a].id;!1===e.includes(t)?e.push(t):document.getElementsByClassName("mainEntries")[a].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 t=document.cookie.split(";");let e,n;for(const a of t){const t=a.split("=");if(t[0]&&"eSBAcceptedCookies"===t[0].trim()&&(e=t[1].trim()),t[0]&&"eSBVersion"===t[0].trim()&&(n=t[1].trim()),e&&n)break}e&&"1"===e?document.getElementById("PrivacyAndCookies").setAttribute("hidden",!1):document.getElementById("PrivacyAndCookies").removeAttribute("hidden"),n&&n!==version&&(document.getElementById("PrivacyAndCookies").removeAttribute("hidden"),document.cookie="eSBAcceptedCookies=0; SameSite=Lax; Secure")}function displayVersionNumber(){document.getElementById("feedbackText").innerHTML+="<br><br>The eFP-Seq Browser's current version number is: "+version}let toastCounter=0;function generateToastNotification(t,e="Notification"){if(t){let n=`toast-${toastCounter}`;const a=`\n\t\t<div class="toast" role="alert" aria-live="assertive" aria-atomic="true" data-toast="${n}" style="background-color: rgba(255, 255, 255, 1);">\n\t\t\t<div class="toast-header">\n\t\t\t\t<img\n\t\t\t\t\tsrc="cgi-bin/img/BAR-logo.svg"\n\t\t\t\t\tclass="rounded me-2"\n\t\t\t\t\talt="BAR notification"\n\t\t\t\t\tstyle="width: 20px; height: 20px"\n\t\t\t\t/>\n\t\t\t\t<strong class="me-auto">${e}</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">${t}</div>\n\t\t</div>\n\t\t`;document.getElementById("toast-container").innerHTML+=a,$(`[data-toast="${n}"]`).toast({autohide:!1}),$(`[data-toast="${n}"]`).toast("show")}}function init(){document.getElementById("locus").value="AT2G24270",document.getElementById("xmlDatabase").value="Araport 11 RNA-seq data",locus_validation(),old_locus=locus,yscale_validation(),rpkm_validation(),adjustFooterSize(),displayVersionNumber(),adjustTableOptionsDropdownSize(),setUpCookies(),$("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(t,e){const n=t.term.split(/,\s*/).pop();$.ajax({type:"GET",url:"https://bar.utoronto.ca/webservices/eFP-Seq_Browser/idautocomplete.cgi?species=Arabidopsis_thaliana&term="+n,dataType:"json"}).done((function(t){t&&t.length>=7?e(t.slice(0,7)):e(t)}))},close:function(t,e){correctAGIIDInput()}});const t=document.getElementById("submissioniframe");t&&t.setAttribute("src",t.getAttribute("data-src")),adjustSubmissionIFrameSize(),readShareLink();document&&"bar.utoronto.ca"===document.location.host&&document.location.href&&document.querySelector('link[rel="canonical"]')&&document.querySelector('link[rel="canonical"]').setAttribute("href",document.location.href)}$(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.json b/package.json
index e7adee2..2f69dd6 100644
--- a/package.json
+++ b/package.json
@@ -59,7 +59,7 @@
 			"url": "https://bar.utoronto.ca/"
 		}
 	],
-	"version": "1.3.14",
+	"version": "1.3.15",
 	"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": {