From 853973eb3ef441239e5befe3da7a142d861ba39f Mon Sep 17 00:00:00 2001
From: colin combe <colin.combe@ed.ac.uk>
Date: Tue, 22 Nov 2022 10:27:09 +0100
Subject: [PATCH] update Closure Compiler  built version after uniprot lookup
 fix

---
 build/crosslinkviewer.js | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/build/crosslinkviewer.js b/build/crosslinkviewer.js
index 5f5687e2..eb0b89f8 100644
--- a/build/crosslinkviewer.js
+++ b/build/crosslinkviewer.js
@@ -516,8 +516,9 @@ ResidueLink.prototype.hide=function(){this.controller.sequenceInitComplete&&this
 ResidueLink.prototype.setLineCoordinates=function(c){if(null!=c.x&&null!=c.y&&null!==this.getToProtein()&&this.shown){var g;this.getFromProtein()===c?(0===c.form?(g=c.x,c=c.y):(c=this.getResidueCoordinates(this.fromResidue,c),g=c[0],c=c[1]),this.line.setAttribute("x1",g),this.line.setAttribute("y1",c),this.highlightLine.setAttribute("x1",g),this.highlightLine.setAttribute("y1",c)):this.getToProtein()===c&&(0===c.form?(g=c.x,c=c.y):(c=this.getResidueCoordinates(this.toResidue,c),g=c[0],c=c[1]),this.line.setAttribute("x2",
 g),this.line.setAttribute("y2",c),this.highlightLine.setAttribute("x2",g),this.highlightLine.setAttribute("y2",c))}};
 ResidueLink.prototype.getResidueCoordinates=function(c,g){var f=g.getResXwithStickZoom(c)*this.controller.z,l=0;if(8<Protein.UNITS_PER_RESIDUE*g.stickZoom){var l=this.getFromProtein(),m=this.getToProtein(),p=Math.atan2(l.y-m.y,l.x-m.x)/(2*Math.PI)*360;0>p&&(p+=360);g===l?(l=p-l.rotation,0>l&&(l+=360),m=5,180>l&&(m=-5)):(l=p-m.rotation,0>l&&(l+=360),m=5,180<l&&(m=-5));l=m*this.controller.z}l=Protein.rotatePointAboutPoint([f,l],[0,0],g.rotation);f=l[0]+g.x;l=l[1]+g.y;return[f,l]};
-ResidueLink.prototype.leastAmbiguousMatches=function(){};ResidueLink.prototype.toJSON=function(){for(var c=[],g=this.matches.length,f=0;f<g;f++)c.push(this.matches[f].id);return{}};function xiNET_Storage(){}xiNET_Storage.ns="xiNET.";xiNET_Storage.accessionFromId=function(c){c+="";return-1!==c.indexOf("|")?c.split("|")[1]:c};xiNET_Storage.getUniProtTxt=function(c,g){function f(){d3.text("https://www.uniprot.org/uniprot/"+l+".txt",function(f){"undefined"!==typeof Storage&&localStorage.setItem(xiNET_Storage.ns+"UniProtKB."+l,f);g(c,f)})}var l=xiNET_Storage.accessionFromId(c);if("undefined"!==typeof Storage){var m=localStorage.getItem(xiNET_Storage.ns+"UniProtKB."+l);m?g(c,m):f()}else f()};
-xiNET_Storage.getSequence=function(c,g){function f(){d3.text("https://www.uniprot.org/uniprot/"+l+".fasta",function(f,m){if(f)alert("Failed. Cannot fetch sequence data for "+l+". Is it a valid UniprotKB accession number?");else if(m){for(var s="",u=m.split("\n"),v=u.length,x=1;x<v;x++)var y=u[x],y=u[x],s=s+y;s=s.replace(/[^A-Z]/g,"");"undefined"!==typeof Storage&&localStorage.setItem(xiNET_Storage.ns+"UniProtKB.fasta."+l,s);g(c,s)}})}var l=xiNET_Storage.accessionFromId(c);if("undefined"!==typeof Storage){var m=
+ResidueLink.prototype.leastAmbiguousMatches=function(){};ResidueLink.prototype.toJSON=function(){for(var c=[],g=this.matches.length,f=0;f<g;f++)c.push(this.matches[f].id);return{}};function xiNET_Storage(){}xiNET_Storage.ns="xiNET.";xiNET_Storage.accessionFromId=function(c){c+="";return-1!==c.indexOf("|")?c.split("|")[1]:c};
+xiNET_Storage.getUniProtTxt=function(c,g){function f(){d3.text("https://rest.uniprot.org/uniprotkb/"+l+".txt",function(f){"undefined"!==typeof Storage&&localStorage.setItem(xiNET_Storage.ns+"UniProtKB."+l,f);g(c,f)})}var l=xiNET_Storage.accessionFromId(c);if("undefined"!==typeof Storage){var m=localStorage.getItem(xiNET_Storage.ns+"UniProtKB."+l);m?g(c,m):f()}else f()};
+xiNET_Storage.getSequence=function(c,g){function f(){d3.text("https://rest.uniprot.org/uniprotkb/"+l+".fasta",function(f,m){if(f)alert("Failed. Cannot fetch sequence data for "+l+". Is it a valid UniprotKB accession number?");else if(m){for(var s="",u=m.split("\n"),v=u.length,x=1;x<v;x++)var y=u[x],y=u[x],s=s+y;s=s.replace(/[^A-Z]/g,"");"undefined"!==typeof Storage&&localStorage.setItem(xiNET_Storage.ns+"UniProtKB.fasta."+l,s);g(c,s)}})}var l=xiNET_Storage.accessionFromId(c);if("undefined"!==typeof Storage){var m=
 localStorage.getItem(xiNET_Storage.ns+"UniProtKB.fasta."+l);m?(console.log(l+" UniProt from local storage."),g(c,m)):f()}else f()};xiNET_Storage.getUniProtFeatures=function(c,g){xiNET_Storage.accessionFromId(c);xiNET_Storage.getUniProtTxt(c,function(c,l){var m=[];if(null!==l)for(var p=l.split("\n"),r=p.length,s=0;s<r;s++){var u=p[s];0===u.indexOf("FT")&&(u=u.split(/\s{2,}/g),4<u.length&&"CHAIN"!==u[1]&&m.push(new Annotation(u[1],u[2],u[3],null,u[4])))}g(c,m)})};
 xiNET_Storage.getSuperFamFeatures=function(c,g){function f(){d3.xml("http://supfam.org/SUPERFAMILY/cgi-bin/das/up/features?segment="+m,function(c){c=(new XMLSerializer).serializeToString(c);"undefined"!==typeof Storage&&localStorage.setItem(xiNET_Storage.ns+"SuperFamDAS."+m,c);l(c)})}function l(f){if(window.DOMParser)var l=(new DOMParser).parseFromString(f,"text/xml");else l=new ActiveXObject("Microsoft.XMLDOM"),l.async=!1,l.loadXML(f);f=[];for(var l=l.getElementsByTagName("FEATURE"),m=l.length,p=
 0;p<m;p++){var x=l[p],y=x.getElementsByTagName("TYPE")[0];if("miscellaneous"===y.getAttribute("category")){var y=y.getAttribute("id"),C=x.getElementsByTagName("START")[0].textContent,x=x.getElementsByTagName("END")[0].textContent;f.push(new Annotation(y,C,x))}}g(c,f)}var m=xiNET_Storage.accessionFromId(c);if("undefined"!==typeof Storage){var p=localStorage.getItem(xiNET_Storage.ns+"SuperFamDAS."+m);p?l(p):f()}else f()};function Rotator(c,g,f){var l=this;this.ctrl=f;this.proteinOrPartThereof=c;this.upperOrLower=g;this.svg=document.createElementNS(xiNET.svgns,"g");this.rotatorSymbol=document.createElementNS(xiNET.svgns,"g");c=document.createElementNS(xiNET.svgns,"circle");c.setAttribute("r",14);c.setAttribute("stroke","none");c.setAttribute("fill","gray");c.setAttribute("fill-opacity","0.0");this.svg.appendChild(c);c=document.createElementNS(xiNET.svgns,"circle");c.setAttribute("r",20);c.setAttribute("stroke","black");