@sjcrh/proteinpaint-client 2.76.1 → 2.76.2

package/dist/{mds.survivalplot-9ad7dabc.js → mds.survivalplot-1d8f2b7e.js}

@@ -1 +1 @@
-import{M as e,j as t,U as s,q as n,ae as a,a8 as l,af as p,I as o,d as i,ag as r}from"./app-2cd97738.js";import{b as d,a as u}from"./axis-747c801e.js";async function c(n,a,l){if(l){window.obj=n}n.plots=[];n.menu=new e({padding:"5px"});n.tip=new e({padding:"5px"});n.errordiv=a.append("div").style("margin","10px");n.sayerror=e=>{t(n.errordiv,typeof e=="string"?e:e.message);if(e.stack)console.log(e.stack)};n.uidiv=a.append("div").style("margin","20px");n.plotdiv=a.append("div").style("margin","20px");n.legendtable=a.append("table").style("border-spacing","5px");a.append("button").text("SVG").on("click",(()=>{s(n.plotlist[0].svg.node(),"Survival")}));try{await m(n);if(!n.plotlist){n.plotlist=[]}if(!Array.isArray(n.plotlist))throw".plotlist should be array";if(n.plotlist.length==0){const e={type:n.plottypes[0].key};n.plotlist.push(e)}for(const e of n.plotlist){f(e,n)}}catch(e){if(e.stack)console.log(e.stack);n.sayerror("Cannot make plot: "+(e.message||e))}}function m(e){const t={genome:e.genome.name,dslabel:e.mds.label,init:1};return n("mdssurvivalplot",t).then((t=>{if(t.error)throw t.error;if(!t.plottypes)throw"plottypes[] missing";e.plottypes=t.plottypes;e.samplegroupings=t.samplegroupings}))}function f(e,t){y(e,t);const s=t.uidiv.append("div").style("margin","20px");if(t.plottypes.length>1){const n=s.append("div").style("margin-bottom","10px").append("select").on("change",(t=>{e.type=t.target.options[t.target.selectedIndex].value}));for(const[s,a]of t.plottypes.entries()){n.append("option").text(a.name).property("value",a.key);if(a.key==e.type){n.node().selectedIndex=s}}}if(t.samplegroupings&&!e.samplerule.full.immutable){const n=s.append("div").style("margin-bottom","20px");const a=s.append("div").style("display","none");n.append("span").html("Choose samples from&nbsp;").style("opacity",.5);const l={};const p=n.append("select").style("margin-right","5px").on("change",(t=>{for(const e in l){l[e].style("display","none")}const 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(n="+n.count+")").property("value",n.value);if(t&&n.value==e.samplerule.full.value){o.node().selectedIndex=s}}}p.append("option").text("all samples").property("useall",1);if(e.samplerule.full.useall){p.node().selectedIndex=t.samplegroupings.length}p.append("option").text("custom sampleset").property("usesampleset",1)}x(e,s);e.button=s.append("button").text("Make plot").on("click",(()=>{h(e,t)}));e.d=t.plotdiv.append("div").style("margin","20px"),e.legend={d_pvalue:e.d.append("div").style("margin","10px"),d_samplefull:e.d.append("div").style("margin","10px"),d_curves:e.d.append("div").style("margin","10px")};e.svg=e.d.append("svg");e.resize_handle=e.d.append("div").append("div").attr("class","sja_clbtext").text("drag to resize").style("float","right");if(e.renderplot){h(e,t)}}function y(e,t){if(!e.type){e.type=t.plottypes[0].key}if(!e.samplerule){e.samplerule={}}if(!e.samplerule.full){e.samplerule.full={}}if(t.samplegroupings){if(!e.samplerule.full.useall){e.samplerule.full.byattr=1;if(!e.samplerule.full.key){e.samplerule.full.key=t.samplegroupings[0].key;e.samplerule.full.value=t.samplegroupings[0].values[0].value}}}else{e.samplerule.full.useall=1}if(e.samplerule.set){const t=e.samplerule.set;if(t.geneexpression){if(!t.bymedian&&!t.byquartile){t.bymedian=1}}}if(!e.width)e.width=500;if(!e.height)e.height=500;if(!e.toppad)e.toppad=10;if(!e.rightpad)e.rightpad=10;if(!e.xaxispad)e.xaxispad=10;if(!e.yaxispad)e.yaxispad=10;if(!e.xaxish)e.xaxish=40;if(!e.yaxisw)e.yaxisw=65;if(!e.censorticksize)e.censorticksize=6;if(!e.tickfontsize)e.tickfontsize=14;if(!e.labfontsize)e.labfontsize=15}function g(e,t){const s=l(p);const n=0;let a=0;for(const t of e.samplesets){t.color=s(t.name);for(const e of t.steps){a=Math.max(a,e.x)}}e.svg.selectAll("*").remove();const c=e.svg.append("g");for(const t of e.samplesets){t.path=c.append("path").attr("stroke",t.color).attr("fill","none");t.ticks=c.append("path").attr("stroke",t.color).attr("fill","none")}const m=e.svg.append("g");const f=o().domain([0,1]);const y=e.svg.append("g");const g=y.append("text").text("Survival").attr("transform","rotate(-90)");const h=e.svg.append("g");const x=o().domain([n,a]);const v=e.svg.append("text").attr("font-size",e.labfontsize).text(t.plottypes.find((t=>t.key==e.type)).timelabel).attr("x",e.yaxisw+e.yaxispad+e.width/2).attr("y",e.toppad+e.height+e.xaxispad+e.xaxish-3);function b(){c.attr("transform","translate("+(e.yaxisw+e.yaxispad)+","+e.toppad+")");for(const t of e.samplesets){const s=[];const n=["M 0 0"];for(const l of t.steps){n.push("H "+e.width*l.x/a);const t=e.height*(l.y+l.drop);n.push("V "+t);if(l.censored){const t=e.height*l.y;for(const n of l.censored){const l=e.width*n/a;s.push("M "+(l-e.censorticksize/2)+" "+(t-e.censorticksize/2)+" l "+e.censorticksize+" "+e.censorticksize+" M "+(l+e.censorticksize/2)+" "+(t-e.censorticksize/2)+" l -"+e.censorticksize+" "+e.censorticksize)}}}t.path.attr("d",n.join(" "));if(s.length){t.ticks.attr("d",s.join(" "))}}m.attr("transform","translate("+e.yaxisw+","+e.toppad+")");r({axis:m.call(d().scale(f.range([e.height,0])).ticks(Math.floor(e.height/(e.tickfontsize+20)))),showline:1,fontsize:e.tickfontsize});y.attr("transform","translate("+e.labfontsize+","+(e.toppad+e.height/2)+")");g.attr("font-size",e.labfontsize);h.attr("transform","translate("+(e.yaxisw+e.yaxispad)+","+(e.toppad+e.height+e.xaxispad)+")");let t;h.append("text").text(a).attr("font-size",e.tickfontsize).each((function(){t=Math.floor(e.width/(this.getBBox().width+30))})).remove();r({axis:h.call(u().scale(x.range([0,e.width])).ticks(t)),showline:1,fontsize:e.tickfontsize});v.attr("font-size",e.labfontsize).attr("x",e.yaxisw+e.yaxispad+e.width/2).attr("y",e.toppad+e.height+e.xaxispad+e.xaxish-3);e.svg.attr("width",e.yaxisw+e.yaxispad+e.width+e.rightpad).attr("height",e.toppad+e.height+e.xaxispad+e.xaxish)}b();e.resize_handle.on("mousedown",(t=>{t.preventDefault();const s=i(document.body);const n=t.clientX;const a=t.clientY;const l=e.width;const p=e.height;s.on("mousemove",(()=>{e.width=l+t.clientX-n;e.height=p+t.clientY-a;b()}));s.on("mouseup",(()=>{s.on("mousemove",null).on("mouseup",null)}))}));if(Number.isFinite(e.pvalue)){e.legend.d_pvalue.style("display","block").text("P-value: "+e.pvalue)}else{e.legend.d_pvalue.style("display","none")}e.legend.d_curves.selectAll("*").remove();for(const t of e.samplesets){e.legend.d_curves.append("div").style("margin","3px").html('<span style="background:'+t.color+'">&nbsp;&nbsp;</span> '+t.name+(t.pvalue==undefined?"":", P-value: "+t.pvalue))}}function h(e,t){e.button.text("Loading...").attr("disabled",1);const s={genome:t.genome.name,dslabel:t.mds.label,type:e.type,samplerule:e.samplerule};n("mdssurvivalplot",s).then((s=>{if(s.error)throw s.error;if(!s.samplesets)throw"samplesets[] missing";e.samplesets=s.samplesets;e.pvalue=s.pvalue;g(e,t);if(e.samplerule.set&&e.samplerule.set.mutation){if(e.mutation_count.cnv)e.mutation_count.cnv.html("(n="+s.count_cnv+")&nbsp;");if(e.mutation_count.loh)e.mutation_count.loh.html("(n="+s.count_loh+")&nbsp;");if(e.mutation_count.snvindel)e.mutation_count.snvindel.html("(n="+s.count_snvindel+")&nbsp;");if(e.mutation_count.sv)e.mutation_count.sv.html("(n="+s.count_sv+")&nbsp;");if(e.mutation_count.fusion)e.mutation_count.fusion.html("(n="+s.count_fusion+")&nbsp;");if(e.mutation_count.itd)e.mutation_count.itd.html("(n="+s.count_itd+")&nbsp;")}})).catch((e=>{t.sayerror(e)})).then((()=>{e.button.text("Update plot").attr("disabled",null)}))}function x(e,t){if(!e.samplerule.set)return;const s=e.samplerule.set;if(s.geneexpression){if(!s.bymedian&&!s.byquartile){s.bymedian=1}const n=t.append("div").style("margin-bottom","10px");n.append("span").style("opacity",.5).html("Divide samples by "+s.gene+" expression with&nbsp;");const a=n.append("select").on("change",(t=>{const s=t.target.options[t.target.selectedIndex];if(s.median){e.samplerule.set.bymedian=1;delete e.samplerule.set.byquartile;l.style("display","none")}else if(s.quartile){e.samplerule.set.byquartile=1;delete e.samplerule.set.bymedian;l.style("display","inline")}}));a.append("option").text("median (group=2)").property("median",1);a.append("option").text("quartile (group=4)").property("quartile",1);const l=n.append("span").style("margin-left","10px");l.append("span").html("Compare each quartile against&nbsp;").style("opacity",.5);{const t=l.append("select").on("change",(t=>{delete e.samplerule.set.against1st;delete e.samplerule.set.against4th;switch(t.target.selectedIndex){case 0:break;case 1:e.samplerule.set.against1st=1;break;case 2:e.samplerule.set.against4th=1;break}}));t.append("option").text("none");t.append("option").text("first quartile");t.append("option").text("fourth quartile");if(s.against1st){t.node().selectedIndex=1}else if(t.against4th){t.node().selectedIndex=2}}if(s.bymedian){a.node().selectedIndex=0;l.style("display","none")}else if(s.byquartile){a.node().selectedIndex=1;l.style("display","inline")}}if(s.mutation){e.mutation_count={};if(s.snvindel){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.snvindel=n.append("span");if(s.snvindel.name){n.append("span").html("SNV/indel&nbsp;");const e=n.append("select");e.append("option").text(s.snvindel.name).property("named",1);e.append("option").text("any mutation at "+s.chr+":"+s.start)}else{n.append("span").text("SNV/indel at "+s.chr+":"+(s.start==s.stop?s.start:s.start+"-"+s.stop))}}if(s.cnv){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.cnv=n.append("span");n.append("span").html("Copy number variation over "+s.chr+":"+s.start+"-"+s.stop+' <span style="font-size:.7em">'+a(s.stop-s.start)+"</span>&nbsp;")}if(s.loh){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.loh=n.append("span");n.append("span").html("LOH over "+s.chr+":"+s.start+"-"+s.stop+' <span style="font-size:.7em">'+a(s.stop-s.start)+"</span>&nbsp;")}if(s.sv){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.sv=n.append("span");n.append("span").html("SV at "+s.chr+":"+(s.start==s.stop?s.start:s.start+"-"+s.stop)+"&nbsp;")}if(s.fusion){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.fusion=n.append("span");n.append("span").html("Fusion at "+s.chr+":"+(s.start==s.stop?s.start:s.start+"-"+s.stop)+"&nbsp;")}if(s.itd){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.itd=n.append("span");n.append("span").html("ITD over "+s.chr+":"+s.start+"-"+s.stop+' <span style="font-size:.7em">'+a(s.stop-s.start)+"</span>&nbsp;")}}}function v(e,t){let s=t.selectAll("div").size();if(s)return;const n=t.append("div").style("margin-bottom","10px");const a=n.append("div").style("margin-left","20px");a.append("div").style("vertical-align","top").style("display","inline-block").style("opacity",.5).html("Enter sample names<br>(one sample per line) &nbsp;");const l=a.append("textarea").style("display","inline-block").attr("cols","20").attr("rows","10").on("change",(()=>{let t=e.samplerule.full.sampleset=[];const s=l.property("value").trim();if(!s)return;for(const e of s.split("\n")){t.push(e)}}))}export{c as init};
+import{M as e,j as t,U as s,q as n,ae as a,a8 as l,af as p,I as o,d as i,ag as r}from"./app-6fb77603.js";import{b as d,a as u}from"./axis-747c801e.js";async function c(n,a,l){if(l){window.obj=n}n.plots=[];n.menu=new e({padding:"5px"});n.tip=new e({padding:"5px"});n.errordiv=a.append("div").style("margin","10px");n.sayerror=e=>{t(n.errordiv,typeof e=="string"?e:e.message);if(e.stack)console.log(e.stack)};n.uidiv=a.append("div").style("margin","20px");n.plotdiv=a.append("div").style("margin","20px");n.legendtable=a.append("table").style("border-spacing","5px");a.append("button").text("SVG").on("click",(()=>{s(n.plotlist[0].svg.node(),"Survival")}));try{await m(n);if(!n.plotlist){n.plotlist=[]}if(!Array.isArray(n.plotlist))throw".plotlist should be array";if(n.plotlist.length==0){const e={type:n.plottypes[0].key};n.plotlist.push(e)}for(const e of n.plotlist){f(e,n)}}catch(e){if(e.stack)console.log(e.stack);n.sayerror("Cannot make plot: "+(e.message||e))}}function m(e){const t={genome:e.genome.name,dslabel:e.mds.label,init:1};return n("mdssurvivalplot",t).then((t=>{if(t.error)throw t.error;if(!t.plottypes)throw"plottypes[] missing";e.plottypes=t.plottypes;e.samplegroupings=t.samplegroupings}))}function f(e,t){y(e,t);const s=t.uidiv.append("div").style("margin","20px");if(t.plottypes.length>1){const n=s.append("div").style("margin-bottom","10px").append("select").on("change",(t=>{e.type=t.target.options[t.target.selectedIndex].value}));for(const[s,a]of t.plottypes.entries()){n.append("option").text(a.name).property("value",a.key);if(a.key==e.type){n.node().selectedIndex=s}}}if(t.samplegroupings&&!e.samplerule.full.immutable){const n=s.append("div").style("margin-bottom","20px");const a=s.append("div").style("display","none");n.append("span").html("Choose samples from&nbsp;").style("opacity",.5);const l={};const p=n.append("select").style("margin-right","5px").on("change",(t=>{for(const e in l){l[e].style("display","none")}const s=t.target.options[t.target.selectedIndex];a.style("display",s.usesampleset?"block":"none");if(s.useall){e.samplerule.full.useall=1;delete e.samplerule.full.byattr;return}if(s.usesampleset){delete e.samplerule.full.byattr;delete e.samplerule.full.useall;e.samplerule.full.usesampleset=1;v(e,a);return}delete e.samplerule.full.useall;e.samplerule.full.byattr=1;e.samplerule.key=s.key;const n=l[s.key];n.style("display","inline");e.samplerule.full.value=n.node().options[n.node().selectedIndex].value}));for(const[s,a]of t.samplegroupings.entries()){p.append("option").text(a.label).property("key",a.key);const t=e.samplerule.full.byattr&&e.samplerule.full.key==a.key;if(t){p.node().selectedIndex=s}const o=n.append("select").on("change",(t=>{e.samplerule.full.value=t.target.options[t.target.selectedIndex].value}));l[a.key]=o;o.style("display",t?"inline":"none");for(const[s,n]of a.values.entries()){o.append("option").text(n.value+" (n="+n.count+")").property("value",n.value);if(t&&n.value==e.samplerule.full.value){o.node().selectedIndex=s}}}p.append("option").text("all samples").property("useall",1);if(e.samplerule.full.useall){p.node().selectedIndex=t.samplegroupings.length}p.append("option").text("custom sampleset").property("usesampleset",1)}x(e,s);e.button=s.append("button").text("Make plot").on("click",(()=>{h(e,t)}));e.d=t.plotdiv.append("div").style("margin","20px"),e.legend={d_pvalue:e.d.append("div").style("margin","10px"),d_samplefull:e.d.append("div").style("margin","10px"),d_curves:e.d.append("div").style("margin","10px")};e.svg=e.d.append("svg");e.resize_handle=e.d.append("div").append("div").attr("class","sja_clbtext").text("drag to resize").style("float","right");if(e.renderplot){h(e,t)}}function y(e,t){if(!e.type){e.type=t.plottypes[0].key}if(!e.samplerule){e.samplerule={}}if(!e.samplerule.full){e.samplerule.full={}}if(t.samplegroupings){if(!e.samplerule.full.useall){e.samplerule.full.byattr=1;if(!e.samplerule.full.key){e.samplerule.full.key=t.samplegroupings[0].key;e.samplerule.full.value=t.samplegroupings[0].values[0].value}}}else{e.samplerule.full.useall=1}if(e.samplerule.set){const t=e.samplerule.set;if(t.geneexpression){if(!t.bymedian&&!t.byquartile){t.bymedian=1}}}if(!e.width)e.width=500;if(!e.height)e.height=500;if(!e.toppad)e.toppad=10;if(!e.rightpad)e.rightpad=10;if(!e.xaxispad)e.xaxispad=10;if(!e.yaxispad)e.yaxispad=10;if(!e.xaxish)e.xaxish=40;if(!e.yaxisw)e.yaxisw=65;if(!e.censorticksize)e.censorticksize=6;if(!e.tickfontsize)e.tickfontsize=14;if(!e.labfontsize)e.labfontsize=15}function g(e,t){const s=l(p);const n=0;let a=0;for(const t of e.samplesets){t.color=s(t.name);for(const e of t.steps){a=Math.max(a,e.x)}}e.svg.selectAll("*").remove();const c=e.svg.append("g");for(const t of e.samplesets){t.path=c.append("path").attr("stroke",t.color).attr("fill","none");t.ticks=c.append("path").attr("stroke",t.color).attr("fill","none")}const m=e.svg.append("g");const f=o().domain([0,1]);const y=e.svg.append("g");const g=y.append("text").text("Survival").attr("transform","rotate(-90)");const h=e.svg.append("g");const x=o().domain([n,a]);const v=e.svg.append("text").attr("font-size",e.labfontsize).text(t.plottypes.find((t=>t.key==e.type)).timelabel).attr("x",e.yaxisw+e.yaxispad+e.width/2).attr("y",e.toppad+e.height+e.xaxispad+e.xaxish-3);function b(){c.attr("transform","translate("+(e.yaxisw+e.yaxispad)+","+e.toppad+")");for(const t of e.samplesets){const s=[];const n=["M 0 0"];for(const l of t.steps){n.push("H "+e.width*l.x/a);const t=e.height*(l.y+l.drop);n.push("V "+t);if(l.censored){const t=e.height*l.y;for(const n of l.censored){const l=e.width*n/a;s.push("M "+(l-e.censorticksize/2)+" "+(t-e.censorticksize/2)+" l "+e.censorticksize+" "+e.censorticksize+" M "+(l+e.censorticksize/2)+" "+(t-e.censorticksize/2)+" l -"+e.censorticksize+" "+e.censorticksize)}}}t.path.attr("d",n.join(" "));if(s.length){t.ticks.attr("d",s.join(" "))}}m.attr("transform","translate("+e.yaxisw+","+e.toppad+")");r({axis:m.call(d().scale(f.range([e.height,0])).ticks(Math.floor(e.height/(e.tickfontsize+20)))),showline:1,fontsize:e.tickfontsize});y.attr("transform","translate("+e.labfontsize+","+(e.toppad+e.height/2)+")");g.attr("font-size",e.labfontsize);h.attr("transform","translate("+(e.yaxisw+e.yaxispad)+","+(e.toppad+e.height+e.xaxispad)+")");let t;h.append("text").text(a).attr("font-size",e.tickfontsize).each((function(){t=Math.floor(e.width/(this.getBBox().width+30))})).remove();r({axis:h.call(u().scale(x.range([0,e.width])).ticks(t)),showline:1,fontsize:e.tickfontsize});v.attr("font-size",e.labfontsize).attr("x",e.yaxisw+e.yaxispad+e.width/2).attr("y",e.toppad+e.height+e.xaxispad+e.xaxish-3);e.svg.attr("width",e.yaxisw+e.yaxispad+e.width+e.rightpad).attr("height",e.toppad+e.height+e.xaxispad+e.xaxish)}b();e.resize_handle.on("mousedown",(t=>{t.preventDefault();const s=i(document.body);const n=t.clientX;const a=t.clientY;const l=e.width;const p=e.height;s.on("mousemove",(()=>{e.width=l+t.clientX-n;e.height=p+t.clientY-a;b()}));s.on("mouseup",(()=>{s.on("mousemove",null).on("mouseup",null)}))}));if(Number.isFinite(e.pvalue)){e.legend.d_pvalue.style("display","block").text("P-value: "+e.pvalue)}else{e.legend.d_pvalue.style("display","none")}e.legend.d_curves.selectAll("*").remove();for(const t of e.samplesets){e.legend.d_curves.append("div").style("margin","3px").html('<span style="background:'+t.color+'">&nbsp;&nbsp;</span> '+t.name+(t.pvalue==undefined?"":", P-value: "+t.pvalue))}}function h(e,t){e.button.text("Loading...").attr("disabled",1);const s={genome:t.genome.name,dslabel:t.mds.label,type:e.type,samplerule:e.samplerule};n("mdssurvivalplot",s).then((s=>{if(s.error)throw s.error;if(!s.samplesets)throw"samplesets[] missing";e.samplesets=s.samplesets;e.pvalue=s.pvalue;g(e,t);if(e.samplerule.set&&e.samplerule.set.mutation){if(e.mutation_count.cnv)e.mutation_count.cnv.html("(n="+s.count_cnv+")&nbsp;");if(e.mutation_count.loh)e.mutation_count.loh.html("(n="+s.count_loh+")&nbsp;");if(e.mutation_count.snvindel)e.mutation_count.snvindel.html("(n="+s.count_snvindel+")&nbsp;");if(e.mutation_count.sv)e.mutation_count.sv.html("(n="+s.count_sv+")&nbsp;");if(e.mutation_count.fusion)e.mutation_count.fusion.html("(n="+s.count_fusion+")&nbsp;");if(e.mutation_count.itd)e.mutation_count.itd.html("(n="+s.count_itd+")&nbsp;")}})).catch((e=>{t.sayerror(e)})).then((()=>{e.button.text("Update plot").attr("disabled",null)}))}function x(e,t){if(!e.samplerule.set)return;const s=e.samplerule.set;if(s.geneexpression){if(!s.bymedian&&!s.byquartile){s.bymedian=1}const n=t.append("div").style("margin-bottom","10px");n.append("span").style("opacity",.5).html("Divide samples by "+s.gene+" expression with&nbsp;");const a=n.append("select").on("change",(t=>{const s=t.target.options[t.target.selectedIndex];if(s.median){e.samplerule.set.bymedian=1;delete e.samplerule.set.byquartile;l.style("display","none")}else if(s.quartile){e.samplerule.set.byquartile=1;delete e.samplerule.set.bymedian;l.style("display","inline")}}));a.append("option").text("median (group=2)").property("median",1);a.append("option").text("quartile (group=4)").property("quartile",1);const l=n.append("span").style("margin-left","10px");l.append("span").html("Compare each quartile against&nbsp;").style("opacity",.5);{const t=l.append("select").on("change",(t=>{delete e.samplerule.set.against1st;delete e.samplerule.set.against4th;switch(t.target.selectedIndex){case 0:break;case 1:e.samplerule.set.against1st=1;break;case 2:e.samplerule.set.against4th=1;break}}));t.append("option").text("none");t.append("option").text("first quartile");t.append("option").text("fourth quartile");if(s.against1st){t.node().selectedIndex=1}else if(t.against4th){t.node().selectedIndex=2}}if(s.bymedian){a.node().selectedIndex=0;l.style("display","none")}else if(s.byquartile){a.node().selectedIndex=1;l.style("display","inline")}}if(s.mutation){e.mutation_count={};if(s.snvindel){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.snvindel=n.append("span");if(s.snvindel.name){n.append("span").html("SNV/indel&nbsp;");const e=n.append("select");e.append("option").text(s.snvindel.name).property("named",1);e.append("option").text("any mutation at "+s.chr+":"+s.start)}else{n.append("span").text("SNV/indel at "+s.chr+":"+(s.start==s.stop?s.start:s.start+"-"+s.stop))}}if(s.cnv){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.cnv=n.append("span");n.append("span").html("Copy number variation over "+s.chr+":"+s.start+"-"+s.stop+' <span style="font-size:.7em">'+a(s.stop-s.start)+"</span>&nbsp;")}if(s.loh){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.loh=n.append("span");n.append("span").html("LOH over "+s.chr+":"+s.start+"-"+s.stop+' <span style="font-size:.7em">'+a(s.stop-s.start)+"</span>&nbsp;")}if(s.sv){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.sv=n.append("span");n.append("span").html("SV at "+s.chr+":"+(s.start==s.stop?s.start:s.start+"-"+s.stop)+"&nbsp;")}if(s.fusion){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.fusion=n.append("span");n.append("span").html("Fusion at "+s.chr+":"+(s.start==s.stop?s.start:s.start+"-"+s.stop)+"&nbsp;")}if(s.itd){const n=t.append("div").style("margin-bottom","20px");e.mutation_count.itd=n.append("span");n.append("span").html("ITD over "+s.chr+":"+s.start+"-"+s.stop+' <span style="font-size:.7em">'+a(s.stop-s.start)+"</span>&nbsp;")}}}function v(e,t){let s=t.selectAll("div").size();if(s)return;const n=t.append("div").style("margin-bottom","10px");const a=n.append("div").style("margin-left","20px");a.append("div").style("vertical-align","top").style("display","inline-block").style("opacity",.5).html("Enter sample names<br>(one sample per line) &nbsp;");const l=a.append("textarea").style("display","inline-block").attr("cols","20").attr("rows","10").on("change",(()=>{let t=e.samplerule.full.sampleset=[];const s=l.property("value").trim();if(!s)return;for(const e of s.split("\n")){t.push(e)}}))}export{c as init};

package/dist/{metaboliteIntensity-ec3176f4.js → metaboliteIntensity-bbb23c76.js}

@@ -1 +1 @@
-import{_ as e}from"./tslib.es6-c3c2d88f.js";import{P as n}from"./app-2cd97738.js";function i(e){switch(e){case"./numeric.binary.ts":return import("./numeric.binary-1dd9a2b4.js");case"./numeric.continuous.ts":return import("./numeric.continuous-ed132eea.js");case"./numeric.discrete.ts":return import("./numeric.discrete-d780d076.js");case"./numeric.spline.ts":return import("./numeric.spline-abe07708.js");case"./numeric.toggle.ts":return import("./numeric.toggle-647423dd.js");default:return new Promise((function(n,i){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(i.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}function t(n){return e(this,void 0,void 0,(function*(){const e=n.opts.numericEditMenuVersion;const i=e.length>1?"toggle":e[0];const t=yield o(i);return yield t.getHandler(n)}))}function r(i,t,r=null){var o;return e(this,void 0,void 0,(function*(){if(!((o=i.q)===null||o===void 0?void 0:o.mode))i.q={mode:"continuous"};if(r)n(i.q,r);if(i.q.mode!="continuous"&&!i.term.bins){yield t.setTermBins(i)}return i}))}function o(n){return e(this,void 0,void 0,(function*(){try{return yield i(`./numeric.${n}.ts`)}catch(e){if(e.stack)console.log(e.stack);throw`Type numeric.${n} does not exist [handlers/numeric.ts importSubtype()]`}}))}export{r as fillTW,t as getHandler};
+import{_ as e}from"./tslib.es6-c3c2d88f.js";import{P as n}from"./app-6fb77603.js";function i(e){switch(e){case"./numeric.binary.ts":return import("./numeric.binary-f382cc98.js");case"./numeric.continuous.ts":return import("./numeric.continuous-6feb34a7.js");case"./numeric.discrete.ts":return import("./numeric.discrete-ed10bbc1.js");case"./numeric.spline.ts":return import("./numeric.spline-a35cfbf0.js");case"./numeric.toggle.ts":return import("./numeric.toggle-2f98d6e5.js");default:return new Promise((function(n,i){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(i.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}function t(n){return e(this,void 0,void 0,(function*(){const e=n.opts.numericEditMenuVersion;const i=e.length>1?"toggle":e[0];const t=yield o(i);return yield t.getHandler(n)}))}function r(i,t,r=null){var o;return e(this,void 0,void 0,(function*(){if(!((o=i.q)===null||o===void 0?void 0:o.mode))i.q={mode:"continuous"};if(r)n(i.q,r);if(i.q.mode!="continuous"&&!i.term.bins){yield t.setTermBins(i)}return i}))}function o(n){return e(this,void 0,void 0,(function*(){try{return yield i(`./numeric.${n}.ts`)}catch(e){if(e.stack)console.log(e.stack);throw`Type numeric.${n} does not exist [handlers/numeric.ts importSubtype()]`}}))}export{r as fillTW,t as getHandler};

package/dist/niceNumLabels-29a7c6ca.js

@@ -0,0 +1 @@
+import{j as t}from"./termsetting-492eefa7.js";function n(n){const o=n.sort(((t,n)=>t-n));const s=Math.abs(o[0]-o[o.length-1]);const e=t(s);const r=s>=10?0:s>=1?1:e+2;return n.map((t=>Number(t.toFixed(r))))}export{n};

package/dist/{nodrag-ab7d5a9f.js → nodrag-b2737073.js}

@@ -1 +1 @@
-import{d as e}from"./app-2cd97738.js";const t={passive:false};const n={capture:true,passive:false};function s(e){e.stopImmediatePropagation()}function a(e){e.preventDefault();e.stopImmediatePropagation()}function o(t){var s=t.document.documentElement,o=e(t).on("dragstart.drag",a,n);if("onselectstart"in s){o.on("selectstart.drag",a,n)}else{s.__noselect=s.style.MozUserSelect;s.style.MozUserSelect="none"}}function l(t,s){var o=t.document.documentElement,l=e(t).on("dragstart.drag",null);if(s){l.on("click.drag",a,n);setTimeout((function(){l.on("click.drag",null)}),0)}if("onselectstart"in o){l.on("selectstart.drag",null)}else{o.style.MozUserSelect=o.__noselect;delete o.__noselect}}export{n as a,s as b,a as c,o as d,t as n,l as y};
+import{d as e}from"./app-6fb77603.js";const t={passive:false};const n={capture:true,passive:false};function s(e){e.stopImmediatePropagation()}function a(e){e.preventDefault();e.stopImmediatePropagation()}function o(t){var s=t.document.documentElement,o=e(t).on("dragstart.drag",a,n);if("onselectstart"in s){o.on("selectstart.drag",a,n)}else{s.__noselect=s.style.MozUserSelect;s.style.MozUserSelect="none"}}function l(t,s){var o=t.document.documentElement,l=e(t).on("dragstart.drag",null);if(s){l.on("click.drag",a,n);setTimeout((function(){l.on("click.drag",null)}),0)}if("onselectstart"in o){l.on("selectstart.drag",null)}else{o.style.MozUserSelect=o.__noselect;delete o.__noselect}}export{n as a,s as b,a as c,o as d,t as n,l as y};

package/dist/{notify-59f61230.js → notify-0cb8904f.js}

@@ -1 +1 @@
-import{d as e}from"./app-2cd97738.js";const t=e("body").append("div").style("position","fixed").style("top",`16px`).style("right","10px").style("font-size","1.2em").style("background-color","rgba(250, 250, 250, 0.75)").style("z-index",1e4);let o,i=0;const s=sessionStorage.getItem("hostURL")||window.testHost||"";const n=s.endsWith("/")?`${s}sse`:`${s}/sse`;a();function a(){o=new EventSource(n);let s=0;o.onmessage=o=>{if(i===0)i=o.timeStamp;if(s===0)s=o.timeStamp;const n=JSON.parse(o.data);if(o.timeStamp>s&&n.find((e=>e.reload)));const a=n;const r=t.selectAll(`:scope>div`).data(a,(e=>e.key));r.exit().remove();r.style("color",(e=>e.color||(e.status=="ok"?"green":"red"))).style("border",(e=>`1px solid ${e.color||"#000"}`)).html((e=>`${e.key}: ${e.message}`)).each((function(t){if(t.reload&&o.timeStamp>s)window.location.reload();else if(t.duration){setTimeout((()=>e(this).transition().duration(t.duration).style("opacity",0).remove()),t.duration)}}));r.enter().append("div").style("margin","5px").style("padding","5px").style("border",(e=>`1px solid ${e.color||"#000"}`)).style("color",(e=>e.color||(e.status=="ok"?"green":"red"))).html((e=>`${e.key}: ${e.message}`)).on("click",(function(){})).each((function(t){if(t.reload&&o.timeStamp>s)window.location.reload();else if(t.duration){setTimeout((()=>e(this).transition().duration(t.duration).style("opacity",0).remove()),t.duration)}}))};o.onerror=e=>console.log(e)}document.addEventListener("visibilitychange",(()=>{if(document.hidden)o.close();else if(!o||o.readyState===2)a()}));
+import{d as e}from"./app-6fb77603.js";const t=e("body").append("div").style("position","fixed").style("top",`16px`).style("right","10px").style("font-size","1.2em").style("background-color","rgba(250, 250, 250, 0.75)").style("z-index",1e4);let o,i=0;const s=sessionStorage.getItem("hostURL")||window.testHost||"";const n=s.endsWith("/")?`${s}sse`:`${s}/sse`;a();function a(){o=new EventSource(n);let s=0;o.onmessage=o=>{if(i===0)i=o.timeStamp;if(s===0)s=o.timeStamp;const n=JSON.parse(o.data);if(o.timeStamp>s&&n.find((e=>e.reload)));const a=n;const r=t.selectAll(`:scope>div`).data(a,(e=>e.key));r.exit().remove();r.style("color",(e=>e.color||(e.status=="ok"?"green":"red"))).style("border",(e=>`1px solid ${e.color||"#000"}`)).html((e=>`${e.key}: ${e.message}`)).each((function(t){if(t.reload&&o.timeStamp>s)window.location.reload();else if(t.duration){setTimeout((()=>e(this).transition().duration(t.duration).style("opacity",0).remove()),t.duration)}}));r.enter().append("div").style("margin","5px").style("padding","5px").style("border",(e=>`1px solid ${e.color||"#000"}`)).style("color",(e=>e.color||(e.status=="ok"?"green":"red"))).html((e=>`${e.key}: ${e.message}`)).on("click",(function(){})).each((function(t){if(t.reload&&o.timeStamp>s)window.location.reload();else if(t.duration){setTimeout((()=>e(this).transition().duration(t.duration).style("opacity",0).remove()),t.duration)}}))};o.onerror=e=>console.log(e)}document.addEventListener("visibilitychange",(()=>{if(document.hidden)o.close();else if(!o||o.readyState===2)a()}));

package/dist/{numeric-4853b665.js → numeric-24dacbee.js}

@@ -1 +1 @@
-import{_ as e}from"./tslib.es6-c3c2d88f.js";function t(e){switch(e){case"./numeric.binary.ts":return import("./numeric.binary-1dd9a2b4.js");case"./numeric.continuous.ts":return import("./numeric.continuous-ed132eea.js");case"./numeric.discrete.ts":return import("./numeric.discrete-d780d076.js");case"./numeric.spline.ts":return import("./numeric.spline-abe07708.js");case"./numeric.toggle.ts":return import("./numeric.toggle-647423dd.js");default:return new Promise((function(t,n){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(n.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}function n(t){return e(this,void 0,void 0,(function*(){const e=t.opts.numericEditMenuVersion;const n=e.length>1?"toggle":e[0];const i=yield r(n);return yield i.getHandler(t)}))}function i(t,n,i=null){return e(this,void 0,void 0,(function*(){if(!t.q.mode){if(!i||i.mode)t.q.mode="discrete"}const e=t.term.type=="float"||t.term.type=="integer"?"toggle":t.q.mode;const o=yield r(e);return yield o.fillTW(t,n,i)}))}function r(n){return e(this,void 0,void 0,(function*(){try{return yield t(`./numeric.${n}.ts`)}catch(e){if(e.stack)console.log(e.stack);throw`Type numeric.${n} does not exist [handlers/numeric.ts importSubtype()]`}}))}export{i as fillTW,n as getHandler};
+import{_ as e}from"./tslib.es6-c3c2d88f.js";function t(e){switch(e){case"./numeric.binary.ts":return import("./numeric.binary-f382cc98.js");case"./numeric.continuous.ts":return import("./numeric.continuous-6feb34a7.js");case"./numeric.discrete.ts":return import("./numeric.discrete-ed10bbc1.js");case"./numeric.spline.ts":return import("./numeric.spline-a35cfbf0.js");case"./numeric.toggle.ts":return import("./numeric.toggle-2f98d6e5.js");default:return new Promise((function(t,n){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(n.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}function n(t){return e(this,void 0,void 0,(function*(){const e=t.opts.numericEditMenuVersion;const n=e.length>1?"toggle":e[0];const i=yield r(n);return yield i.getHandler(t)}))}function i(t,n,i=null){return e(this,void 0,void 0,(function*(){if(!t.q.mode){if(!i||i.mode)t.q.mode="discrete"}const e=t.term.type=="float"||t.term.type=="integer"?"toggle":t.q.mode;const o=yield r(e);return yield o.fillTW(t,n,i)}))}function r(n){return e(this,void 0,void 0,(function*(){try{return yield t(`./numeric.${n}.ts`)}catch(e){if(e.stack)console.log(e.stack);throw`Type numeric.${n} does not exist [handlers/numeric.ts importSubtype()]`}}))}export{i as fillTW,n as getHandler};

package/dist/{numeric.binary-1dd9a2b4.js → numeric.binary-f382cc98.js}

@@ -1 +1 @@
-import{_ as e}from"./tslib.es6-c3c2d88f.js";import{setDensityPlot as t}from"./density-69a732f6.js";import{renderBoundaryInclusionInput as i,renderBoundaryInputDivs as n}from"./numeric.discrete-d780d076.js";import{g as o,a as r}from"./termdb.bins-01e8cce6.js";import{m as d}from"./checkbox-96437f4d.js";import{o as s}from"./termsetting-ad8c4f3a.js";import{convertViolinData as a}from"./tvs.numeric-de14101f.js";import{v as l}from"./violinRenderer-08b3b58c.js";import"./app-2cd97738.js";import"./drag-d8daa62f.js";import"./nodrag-ab7d5a9f.js";import"./pointer-c7475677.js";import"./toggleButtons-04c5ad7c.js";import"./radiobutton-09bff425.js";import"path";import"./tvs.density-b2790080.js";import"./brush-bb4ae2fb.js";import"./niceNumLabels-5f45218a.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";function u(o){return{getPillName(e){return s(o,e)},getPillStatus(){var e;return{text:((e=o.usecase)===null||e===void 0?void 0:e.target)=="regression"?o.data.q.lst.find((e=>e.label!=o.data.refGrp)).label:"binary"}},showEditMenu(r){var d,s,f,y;return e(this,void 0,void 0,(function*(){o.num_obj={};o.num_obj.plot_size={width:500,height:100,xpad:10,ypad:20};r.selectAll("*").remove();r.append("div").style("padding","10px").style("text-align","center").html("Getting distribution data ...<br/>");const v=yield o.vocabApi.getViolinPlotData({tw:{term:o.term,q:o.q},filter:o.filter,filter0:(s=(d=o.vocabApi.state)===null||d===void 0?void 0:d.termfilter)===null||s===void 0?void 0:s.filter0,svgw:o.num_obj.plot_size.width/window.devicePixelRatio},(y=(f=o.opts).getBodyParams)===null||y===void 0?void 0:y.call(f));o.num_obj.density_data=a(v);o.dom.num_holder=r;r.selectAll("*").remove();o.dom.density_div=r.append("div");o.vr=new l(o.dom.density_div,o.num_obj.density_data,o.num_obj.plot_size.width,o.num_obj.plot_size.height);o.num_obj.svg=o.vr.svg;o.dom.bins_div=r.append("div").style("padding","4px");m(o);t(o);i(o);o.dom.cutoff_div=o.dom.bins_div.append("div").style("margin","10px");p(o);o.dom.bins_table=o.dom.bins_div.append("div").style("display","flex").style("color","rgb(136, 136, 136)").style("margin","10px").style("width","100%");o.dom.rangeAndLabelDiv=o.dom.bins_table.append("div");n(o,o.q.lst);const b=r.append("div").style("padding","3px 10px");b.append("button").style("margin","5px").html("Apply").on("click",(()=>e(this,void 0,void 0,(function*(){delete o.q.startinclusive;delete o.q.stopinclusive;delete o.q.bin_size;delete o.q.first_bin;delete o.q.last_bin;o.q.lst=c(o);o.numqByTermIdModeType[o.term.id].binary=JSON.parse(JSON.stringify(o.q));o.q.mode="binary";o.runCallback()}))));b.append("button").style("margin","5px").html("Reset").on("click",(()=>{o.q={};delete o.numqByTermIdModeType[o.term.id];u(o).showEditMenu(o.dom.num_holder)}))}))}}}function m(e){const t=e.num_obj.density_data;const i=e.q&&e.q.lst&&e.q.lst.length?e.q.lst[0].stop:undefined;const n=e.numqByTermIdModeType;if(!e.term)throw`Missing .term{} [numeric.binary, setqDefaults()]`;const d=e.term;if(!n[d.id])n[d.id]={};if(!n[d.id].binary){const o=i!==undefined?Number(i):t.maxvalue!=t.minvalue?t.minvalue+(t.maxvalue-t.minvalue)/2:t.maxvalue;n[d.id].binary={mode:"binary",type:"custom-bin",modeBinaryCutoffType:"normal",modeBinaryCutoffPercentile:50,lst:[{startunbounded:true,stopinclusive:true,stop:o.toFixed(e.term.type=="integer"?0:2)},{stopunbounded:true,start:o.toFixed(e.term.type=="integer"?0:2)}]}}if(!e.q||e.q.mode!=="binary")e.q={};const s=JSON.parse(JSON.stringify(n[d.id].binary));e.q=Object.assign(s,e.q);if(e.q.lst){e.q.lst.forEach((t=>{if(!("label"in t))t.label=o(t,e.q);if(!("range"in t))t.range=r(t,e.q)}))}}function p(i){return e(this,void 0,void 0,(function*(){i.dom.cutoff_div.append("span").style("margin-right","5px").style("opacity",.5).text("Boundary value");i.dom.customBinBoundaryInput=i.dom.cutoff_div.append("input").style("width","100px").attr("type","number").style("margin-right","10px").attr("value",i.q.modeBinaryCutoffType=="normal"?i.q.lst[0].stop:i.q.modeBinaryCutoffPercentile).on("change",s);i.dom.customBinBoundaryPercentileCheckbox=d({holder:i.dom.cutoff_div,labeltext:"Use percentile",checked:i.q.modeBinaryCutoffType=="percentile",divstyle:{display:"inline-block"},callback:l});function s(){return e(this,void 0,void 0,(function*(){const e=+this.value;if(i.q.modeBinaryCutoffType=="normal"){a(e)}else if(i.q.modeBinaryCutoffType=="percentile"){if(e<1||e>99){window.alert("Invalid percentile value: enter integer between 1 and 99");return}i.q.modeBinaryCutoffPercentile=e;yield u()}else{throw"invalid modeBinaryCutoffType value"}}))}function a(e){i.q.lst[0].stop=e;i.q.lst[1].start=e;i.q.lst.forEach((e=>{e.label=o(e,i.q);e.range=r(e,i.q)}));if(!i.num_obj)throw`Missing density data [numeric.binary updateUI()]`;t(i);n(i,i.q.lst)}function l(){return e(this,void 0,void 0,(function*(){i.q.modeBinaryCutoffType=i.q.modeBinaryCutoffType=="percentile"?"normal":"percentile";if(i.q.modeBinaryCutoffType=="normal"){const e=i.q.lst[0].stop;i.dom.customBinBoundaryInput.property("value",e);a(e)}else if(i.q.modeBinaryCutoffType=="percentile"){i.dom.customBinBoundaryInput.property("value",i.q.modeBinaryCutoffPercentile);yield u()}else{throw"invalid modeBinaryCutoffType value"}}))}function u(){return e(this,void 0,void 0,(function*(){const e=yield i.opts.vocabApi.getPercentile(i.term.id,[i.q.modeBinaryCutoffPercentile],i.filter);a(e.values[0])}))}}))}function c(e){const t=e.dom.boundaryInput.property("value")=="startinclusive";const i=e.dom.boundaryInput.property("value")=="stopinclusive";const n=e.dom.bins_table.node().querySelectorAll("input");const r=e.q.lst[0].stop;const d=[{startunbounded:true,stop:r,startinclusive:t,stopinclusive:i},{start:r,startinclusive:t,stopinclusive:i,stopunbounded:true}];d.forEach(((t,i)=>{const r=n[i].value;t.label=r?r:o(t,e.q)}));return d}export{u as getHandler};
+import{_ as e}from"./tslib.es6-c3c2d88f.js";import{setDensityPlot as t}from"./density-09feb0c9.js";import{renderBoundaryInclusionInput as i,renderBoundaryInputDivs as n}from"./numeric.discrete-ed10bbc1.js";import{g as o,a as r}from"./termdb.bins-39d11f24.js";import{m as d}from"./checkbox-96437f4d.js";import{o as s}from"./termsetting-492eefa7.js";import{convertViolinData as a}from"./tvs.numeric-aa1f892f.js";import{v as l}from"./violinRenderer-14fa200d.js";import"./app-6fb77603.js";import"./drag-2e9c80bb.js";import"./nodrag-b2737073.js";import"./pointer-c7475677.js";import"./toggleButtons-c4d6f260.js";import"./radiobutton-09bff425.js";import"path";import"./tvs.density-034b506d.js";import"./brush-9faa7ae7.js";import"./niceNumLabels-29a7c6ca.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";function u(o){return{getPillName(e){return s(o,e)},getPillStatus(){var e;return{text:((e=o.usecase)===null||e===void 0?void 0:e.target)=="regression"?o.data.q.lst.find((e=>e.label!=o.data.refGrp)).label:"binary"}},showEditMenu(r){var d,s,f,y;return e(this,void 0,void 0,(function*(){o.num_obj={};o.num_obj.plot_size={width:500,height:100,xpad:10,ypad:20};r.selectAll("*").remove();r.append("div").style("padding","10px").style("text-align","center").html("Getting distribution data ...<br/>");const v=yield o.vocabApi.getViolinPlotData({tw:{term:o.term,q:o.q},filter:o.filter,filter0:(s=(d=o.vocabApi.state)===null||d===void 0?void 0:d.termfilter)===null||s===void 0?void 0:s.filter0,svgw:o.num_obj.plot_size.width/window.devicePixelRatio},(y=(f=o.opts).getBodyParams)===null||y===void 0?void 0:y.call(f));o.num_obj.density_data=a(v);o.dom.num_holder=r;r.selectAll("*").remove();o.dom.density_div=r.append("div");o.vr=new l(o.dom.density_div,o.num_obj.density_data,o.num_obj.plot_size.width,o.num_obj.plot_size.height);o.num_obj.svg=o.vr.svg;o.dom.bins_div=r.append("div").style("padding","4px");m(o);t(o);i(o);o.dom.cutoff_div=o.dom.bins_div.append("div").style("margin","10px");p(o);o.dom.bins_table=o.dom.bins_div.append("div").style("display","flex").style("color","rgb(136, 136, 136)").style("margin","10px").style("width","100%");o.dom.rangeAndLabelDiv=o.dom.bins_table.append("div");n(o,o.q.lst);const b=r.append("div").style("padding","3px 10px");b.append("button").style("margin","5px").html("Apply").on("click",(()=>e(this,void 0,void 0,(function*(){delete o.q.startinclusive;delete o.q.stopinclusive;delete o.q.bin_size;delete o.q.first_bin;delete o.q.last_bin;o.q.lst=c(o);o.numqByTermIdModeType[o.term.id].binary=JSON.parse(JSON.stringify(o.q));o.q.mode="binary";o.runCallback()}))));b.append("button").style("margin","5px").html("Reset").on("click",(()=>{o.q={};delete o.numqByTermIdModeType[o.term.id];u(o).showEditMenu(o.dom.num_holder)}))}))}}}function m(e){const t=e.num_obj.density_data;const i=e.q&&e.q.lst&&e.q.lst.length?e.q.lst[0].stop:undefined;const n=e.numqByTermIdModeType;if(!e.term)throw`Missing .term{} [numeric.binary, setqDefaults()]`;const d=e.term;if(!n[d.id])n[d.id]={};if(!n[d.id].binary){const o=i!==undefined?Number(i):t.maxvalue!=t.minvalue?t.minvalue+(t.maxvalue-t.minvalue)/2:t.maxvalue;n[d.id].binary={mode:"binary",type:"custom-bin",modeBinaryCutoffType:"normal",modeBinaryCutoffPercentile:50,lst:[{startunbounded:true,stopinclusive:true,stop:o.toFixed(e.term.type=="integer"?0:2)},{stopunbounded:true,start:o.toFixed(e.term.type=="integer"?0:2)}]}}if(!e.q||e.q.mode!=="binary")e.q={};const s=JSON.parse(JSON.stringify(n[d.id].binary));e.q=Object.assign(s,e.q);if(e.q.lst){e.q.lst.forEach((t=>{if(!("label"in t))t.label=o(t,e.q);if(!("range"in t))t.range=r(t,e.q)}))}}function p(i){return e(this,void 0,void 0,(function*(){i.dom.cutoff_div.append("span").style("margin-right","5px").style("opacity",.5).text("Boundary value");i.dom.customBinBoundaryInput=i.dom.cutoff_div.append("input").style("width","100px").attr("type","number").style("margin-right","10px").attr("value",i.q.modeBinaryCutoffType=="normal"?i.q.lst[0].stop:i.q.modeBinaryCutoffPercentile).on("change",s);i.dom.customBinBoundaryPercentileCheckbox=d({holder:i.dom.cutoff_div,labeltext:"Use percentile",checked:i.q.modeBinaryCutoffType=="percentile",divstyle:{display:"inline-block"},callback:l});function s(){return e(this,void 0,void 0,(function*(){const e=+this.value;if(i.q.modeBinaryCutoffType=="normal"){a(e)}else if(i.q.modeBinaryCutoffType=="percentile"){if(e<1||e>99){window.alert("Invalid percentile value: enter integer between 1 and 99");return}i.q.modeBinaryCutoffPercentile=e;yield u()}else{throw"invalid modeBinaryCutoffType value"}}))}function a(e){i.q.lst[0].stop=e;i.q.lst[1].start=e;i.q.lst.forEach((e=>{e.label=o(e,i.q);e.range=r(e,i.q)}));if(!i.num_obj)throw`Missing density data [numeric.binary updateUI()]`;t(i);n(i,i.q.lst)}function l(){return e(this,void 0,void 0,(function*(){i.q.modeBinaryCutoffType=i.q.modeBinaryCutoffType=="percentile"?"normal":"percentile";if(i.q.modeBinaryCutoffType=="normal"){const e=i.q.lst[0].stop;i.dom.customBinBoundaryInput.property("value",e);a(e)}else if(i.q.modeBinaryCutoffType=="percentile"){i.dom.customBinBoundaryInput.property("value",i.q.modeBinaryCutoffPercentile);yield u()}else{throw"invalid modeBinaryCutoffType value"}}))}function u(){return e(this,void 0,void 0,(function*(){const e=yield i.opts.vocabApi.getPercentile(i.term.id,[i.q.modeBinaryCutoffPercentile],i.filter);a(e.values[0])}))}}))}function c(e){const t=e.dom.boundaryInput.property("value")=="startinclusive";const i=e.dom.boundaryInput.property("value")=="stopinclusive";const n=e.dom.bins_table.node().querySelectorAll("input");const r=e.q.lst[0].stop;const d=[{startunbounded:true,stop:r,startinclusive:t,stopinclusive:i},{start:r,startinclusive:t,stopinclusive:i,stopunbounded:true}];d.forEach(((t,i)=>{const r=n[i].value;t.label=r?r:o(t,e.q)}));return d}export{u as getHandler};

package/dist/{numeric.continuous-ed132eea.js → numeric.continuous-6feb34a7.js}

@@ -1 +1 @@
-import{_ as t}from"./tslib.es6-c3c2d88f.js";import{o as e}from"./termsetting-ad8c4f3a.js";import{convertViolinData as i}from"./tvs.numeric-de14101f.js";import{v as o}from"./violinRenderer-08b3b58c.js";import{m as l}from"./checkbox-96437f4d.js";import"./app-2cd97738.js";import"path";import"./tvs.density-b2790080.js";import"./brush-bb4ae2fb.js";import"./pointer-c7475677.js";import"./nodrag-ab7d5a9f.js";import"./niceNumLabels-5f45218a.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";function n(n){return{getPillName(t){return e(n,t)},getPillStatus(){return{text:"continuous"}},showEditMenu(e){var a,r,p,d,c;return t(this,void 0,void 0,(function*(){s(n);e.style("padding","5px").selectAll("*").remove();const t=e.append("div");const m={width:500,height:100,xpad:10,ypad:20};const u=yield n.vocabApi.getViolinPlotData({tw:{term:n.term,q:n.q},filter:n.filter,filter0:(r=(a=n.vocabApi.state)===null||a===void 0?void 0:a.termfilter)===null||r===void 0?void 0:r.filter0,svgw:m.width/window.devicePixelRatio},(d=(p=n.opts).getBodyParams)===null||d===void 0?void 0:d.call(p));const v=i(u);const f=new o(t,v,m.width,m.height);f.render();let h;if(((c=n.usecase)===null||c===void 0?void 0:c.target)=="matrix"){h=l({holder:e,labeltext:"Convert to z-score",checked:n.q.convert2ZScore?true:false,divstyle:{display:"inline-block",padding:"3px 10px"},callback:t=>{n.q.convert2ZScore=t;if(t){b.property("value",1);delete n.q.scale}}})}const y=e.append("div").style("display","inline-block");y.append("div").style("display","inline-block").style("padding","3px 10px").html("Scale values");const b=y.append("select").on("change",(t=>{if(!n.q)throw`Missing .q{} [numeric.continuous getHandler()]`;if(t.target.value!="1"){if(h)h.property("checked",false);n.q.scale=Number(t.target.value)}else delete n.q.scale}));b.selectAll("option").data([{html:"No Scaling",value:1},{html:"Per 10",value:10},{html:"Per 100",value:100},{html:"Per 1000",value:1e3}]).enter().append("option").attr("value",(t=>t.value)).html((t=>t.html)).property("selected",(t=>"scale"in n.q&&t.value==n.q.scale));const g=e.append("div").style("padding","3px 10px");if(n.term.type=="survival"){g.append("div").style("font-size",".8em").style("margin","20px 5px 5px 5px").html(`\n\t\t\t\t\t\tDisplay survival outcomes as time to event (${n.term.unit})\n\t\t\t\t\t`)}g.append("button").style("margin","5px").html("Apply").on("click",(()=>{n.q.mode="continuous";n.runCallback()}))}))}}}function s(t){const e=t.numqByTermIdModeType;const i=t.term;if(!e[i.id])e[i.id]={};if(!e[i.id].continuous){e[i.id].continuous={mode:"continuous"}}const o=JSON.parse(JSON.stringify(e[i.id].continuous));t.q=Object.assign(o,t.q)}export{n as getHandler};
+import{_ as t}from"./tslib.es6-c3c2d88f.js";import{o as e}from"./termsetting-492eefa7.js";import{convertViolinData as i}from"./tvs.numeric-aa1f892f.js";import{v as o}from"./violinRenderer-14fa200d.js";import{m as l}from"./checkbox-96437f4d.js";import"./app-6fb77603.js";import"path";import"./tvs.density-034b506d.js";import"./brush-9faa7ae7.js";import"./pointer-c7475677.js";import"./nodrag-b2737073.js";import"./niceNumLabels-29a7c6ca.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";function n(n){return{getPillName(t){return e(n,t)},getPillStatus(){return{text:"continuous"}},showEditMenu(e){var a,r,p,d,c;return t(this,void 0,void 0,(function*(){s(n);e.style("padding","5px").selectAll("*").remove();const t=e.append("div");const m={width:500,height:100,xpad:10,ypad:20};const u=yield n.vocabApi.getViolinPlotData({tw:{term:n.term,q:n.q},filter:n.filter,filter0:(r=(a=n.vocabApi.state)===null||a===void 0?void 0:a.termfilter)===null||r===void 0?void 0:r.filter0,svgw:m.width/window.devicePixelRatio},(d=(p=n.opts).getBodyParams)===null||d===void 0?void 0:d.call(p));const v=i(u);const f=new o(t,v,m.width,m.height);f.render();let h;if(((c=n.usecase)===null||c===void 0?void 0:c.target)=="matrix"){h=l({holder:e,labeltext:"Convert to z-score",checked:n.q.convert2ZScore?true:false,divstyle:{display:"inline-block",padding:"3px 10px"},callback:t=>{n.q.convert2ZScore=t;if(t){g.property("value",1);delete n.q.scale}}})}const y=e.append("div").style("display","inline-block");y.append("div").style("display","inline-block").style("padding","3px 10px").html("Scale values");const g=y.append("select").on("change",(t=>{if(!n.q)throw`Missing .q{} [numeric.continuous getHandler()]`;if(t.target.value!="1"){if(h)h.property("checked",false);n.q.scale=Number(t.target.value)}else delete n.q.scale}));g.selectAll("option").data([{html:"No Scaling",value:1},{html:"Per 10",value:10},{html:"Per 100",value:100},{html:"Per 1000",value:1e3}]).enter().append("option").attr("value",(t=>t.value)).html((t=>t.html)).property("selected",(t=>"scale"in n.q&&t.value==n.q.scale));const b=e.append("div").style("padding","3px 10px");if(n.term.type=="survival"){b.append("div").style("font-size",".8em").style("margin","20px 5px 5px 5px").html(`\n\t\t\t\t\t\tDisplay survival outcomes as time to event (${n.term.unit})\n\t\t\t\t\t`)}b.append("button").style("margin","5px").html("Apply").on("click",(()=>{n.q.mode="continuous";n.runCallback()}))}))}}}function s(t){const e=t.numqByTermIdModeType;const i=t.term;if(!e[i.id])e[i.id]={};if(!e[i.id].continuous){e[i.id].continuous={mode:"continuous"}}const o=JSON.parse(JSON.stringify(e[i.id].continuous));t.q=Object.assign(o,t.q)}export{n as getHandler};

package/dist/{numeric.discrete-d780d076.js → numeric.discrete-ed10bbc1.js}

@@ -1 +1 @@
-import{_ as t}from"./tslib.es6-c3c2d88f.js";import{W as e,k as n}from"./app-2cd97738.js";import{setDensityPlot as i}from"./density-69a732f6.js";import{g as s,a}from"./termdb.bins-01e8cce6.js";import{T as r}from"./toggleButtons-04c5ad7c.js";import{m as o}from"./radiobutton-09bff425.js";import{o as l}from"./termsetting-ad8c4f3a.js";import{convertViolinData as d}from"./tvs.numeric-de14101f.js";import{v as u}from"./violinRenderer-08b3b58c.js";import"./drag-d8daa62f.js";import"./nodrag-ab7d5a9f.js";import"./pointer-c7475677.js";import"path";import"./tvs.density-b2790080.js";import"./brush-bb4ae2fb.js";import"./niceNumLabels-5f45218a.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";function p(e){return{getPillName(t){return l(e,t)},getPillStatus(){var t,n;if(!e.q)throw`Missing .q{} [numeric.discrete getPillStatus()]`;const i=((t=e.q)===null||t===void 0?void 0:t.name)||((n=e.q)===null||n===void 0?void 0:n.reuseId);if(i)return{text:i};if(e.q.type=="regular-bin")return{text:"bin size="+e.q.bin_size};return{text:e.q.lst.length+" bins"}},showEditMenu(n){return t(this,void 0,void 0,(function*(){m(e,n)}))}}}function m(e,n){var s,a,r,o;return t(this,void 0,void 0,(function*(){e.num_obj={};e.num_obj.plot_size={width:500,height:100,xpad:10,ypad:20};n.selectAll("*").remove();n.append("div").style("padding","10px").style("text-align","center").html("Getting distribution data ...<br/>");try{const t=yield e.vocabApi.getViolinPlotData({tw:{term:e.term,q:{mode:"continuous"}},filter:e.filter,filter0:(a=(s=e.vocabApi.state)===null||s===void 0?void 0:s.termfilter)===null||a===void 0?void 0:a.filter0,svgw:e.num_obj.plot_size.width/window.devicePixelRatio,strokeWidth:.2},(o=(r=e.opts).getBodyParams)===null||o===void 0?void 0:o.call(r));e.num_obj.density_data=d(t)}catch(t){console.log(t)}n.selectAll("*").remove();if(e.term.type=="survival"){e.dom.discreteSur_div=n.append("div").style("padding","4px");w(e);return}e.dom.num_holder=n;e.dom.density_div=n.append("div");e.vr=new u(e.dom.density_div,e.num_obj.density_data,e.num_obj.plot_size.width,e.num_obj.plot_size.height);e.num_obj.svg=e.vr.svg;e.dom.bins_div=n.append("div").style("padding","4px");y(e);i(e);v(e);f(e);I(e)}))}function c(t){var e;if(t.q.type=="regular-bin"){if(!t.q.first_bin){t.q.first_bin={stop:Number(t.dom.first_stop_input.property("value"))}}t.q.startinclusive=t.dom.boundaryInput.property("value")=="startinclusive";t.q.stopinclusive=t.dom.boundaryInput.property("value")=="stopinclusive";const n=t.dom.bin_size_input.property("value");t.q.bin_size=Number(n);if(n.includes(".")&&!n.endsWith(".")){t.q.rounding="."+n.split(".")[1].length+"f"}else{t.q.rounding=".0f"}if(t.q.scale)delete t.q.scale;if(Number.isFinite((e=t.q.last_bin)===null||e===void 0?void 0:e.start));else{delete t.q.last_bin}t.numqByTermIdModeType[t.term.id].discrete["regular-bin"]=JSON.parse(JSON.stringify(t.q))}else if(t.term.type!=="survival"){if(t.dom.bins_table.selectAll("input").node().value){t.q.lst=b(t);t.numqByTermIdModeType[t.term.id].discrete["custom-bin"]=JSON.parse(JSON.stringify(t.q))}}t.q.mode="discrete";t.dom.tip.hide();t.runCallback()}function b(t){var e;const n=t.dom.boundaryInput.property("value")=="startinclusive";const i=t.dom.boundaryInput.property("value")=="stopinclusive";const r=t.dom.bins_table.node().querySelectorAll("input");let o;const l=t.dom.customBinBoundaryInput.property("value").split("\n").filter((t=>t!=""&&!isNaN(t)));const d=new Set(l);const u=Array.from(d).map((t=>+t)).sort(((t,e)=>t-e)).map(((e,l)=>{const d={start:+e,startinclusive:n,stopinclusive:i};if(o){delete o.stopunbounded;o.stop=d.start;const e=r[l].value;o.label=e?e:s(o,t.q,t.term.valueConversion);o.range=a(o,t.q)}o=d;return d}));if(u.length==0)return;o.stopunbounded=true;const p=(e=r[u.length])===null||e===void 0?void 0:e.value;o.label=p?p:s(o,t.q,t.term.valueConversion);o.range=a(o,t.q);u.unshift({startunbounded:true,stop:u[0].start,startinclusive:n,stopinclusive:i,label:r[0].value});if(!u[0].label)u[0].label=s(u[0],t.q,t.term.valueConversion);if(!u[0].range)u[0].range=a(u[0],t.q);return u}function y(t){var e,n;const i=t.num_obj.density_data;const r=t.numqByTermIdModeType;const o=t.term;if(!r[o.id])r[o.id]={};if(!r[o.id].discrete){const e=!Number.isFinite(i.minvalue)||!Number.isFinite(i.maxvalue)?0:i.maxvalue!=i.minvalue?i.minvalue+(i.maxvalue-i.minvalue)/2:i.maxvalue;r[o.id].discrete={"regular-bin":t.q&&t.q.type=="regular-bin"?JSON.parse(JSON.stringify(t.q)):t.opts.use_bins_less&&o.bins.less?JSON.parse(JSON.stringify(o.bins.less)):JSON.parse(JSON.stringify(o.bins.default)),"custom-bin":t.q&&t.q.type=="custom-bin"?t.q:{type:"custom-bin",mode:"discrete",lst:[{startunbounded:true,startinclusive:true,stopinclusive:false,stop:+e.toFixed(o.type=="integer"?0:2)},{stopunbounded:true,startinclusive:true,stopinclusive:false,start:+e.toFixed(o.type=="integer"?0:2)}]}};if(!r[o.id].discrete["regular-bin"].type){r[o.id].discrete["regular-bin"].type="regular-bin"}}if(t.q&&!t.q.mode)t.q.mode="discrete";if(!t.q||t.q.mode!=="discrete")t.q={};if(!t.q.type){t.q.type=((n=(e=t.term.bins)===null||e===void 0?void 0:e.default)===null||n===void 0?void 0:n.type)||"regular-bin"}const l=JSON.parse(JSON.stringify(r[o.id].discrete[t.q.type]));t.q=Object.assign(l,t.q);const d="bin_size"in t.q&&t.q.bin_size.toString();if(!t.q.rounding&&typeof d=="string"&&d.includes(".")&&!d.endsWith(".")){const e=d.split(".")[1].length;t.q.rounding="."+e+"f"}if(t.q.lst){t.q.lst.forEach((e=>{if(!("label"in e))e.label=s(e,t.q,t.term.valueConversion);if(!("range"in e))e.range=a(e,t.q)}))}}function v(t){t.dom.boundaryInclusionDiv=t.dom.bins_div.append("div").style("margin-left","5px");t.dom.boundaryInclusionDiv.append("span").style("padding","5px").style("color","rgb(136, 136, 136)").html("Boundary Inclusion");const e='<span style="font-family:Times;font-style:italic">x</span>';t.dom.boundaryInput=t.dom.boundaryInclusionDiv.append("select").style("margin-left","10px").on("change",(function(){const e=t.q.mode=="binary"?t.numqByTermIdModeType[t.term.id].binary:t.numqByTermIdModeType[t.term.id].discrete[t.q.type];e.lst=t.q.lst;if(e.type=="regular-bin"){n(e)}else{e.lst.forEach((e=>{n(e);e.label=s(e,t.q,t.term.valueConversion);e.range=a(e,t.q)}));z(t,e.lst)}function n(e){e.startinclusive=t.dom.boundaryInput.node().selectedIndex==1;e.stopinclusive=t.dom.boundaryInput.node().selectedIndex==0}}));t.dom.boundaryInput.selectAll("option").data([{value:"stopinclusive",html:"start &lt; "+e+" &le; end"},{value:"startinclusive",html:"start &le; "+e+" &lt; end"}]).enter().append("option").property("value",(t=>t.value)).property("selected",(e=>{if(t.q.type=="regular-bin")return t.q[e.value]==true;else return t.q.lst[0][e.value]==true})).html((t=>t.html))}function f(e){const n=e.dom.bins_div.append("div").style("margin","10px");if(e.term.bins.default.type=="custom-bin"){e.q.type="custom-bin";y(e);i(e);j(e,n);return}if(e.term.bins.default.type!="regular-bin")throw"self.bins.default.type is neither regular-bin or custom-bin, cannot render ui";const s=[{active:e.q.type=="regular-bin",label:"Same bin size",callback:(n,a)=>t(this,void 0,void 0,(function*(){e.q.type="regular-bin";y(e);i(e);if(!s[0].isInitialized){q(e,a.contentHolder);s[0].isInitialized=true}}))},{active:e.q.type=="custom-bin",label:"Varying bin sizes",callback:(n,a)=>t(this,void 0,void 0,(function*(){e.q.type="custom-bin";y(e);i(e);if(!s[1].isInitialized){j(e,a.contentHolder);s[1].isInitialized=true}}))}];new r({holder:n,tabs:s}).main()}function g(t,e){if(!t.term.valueConversion)return;e.append("div").style("margin-bottom","5px").style("opacity",.6).text(`Note: using values by the unit of ${t.term.valueConversion.fromUnit}.`)}function q(t,e){g(t,e);t.dom.bins_table=e.append("table");_(t,t.dom.bins_table.append("tr"));h(t,t.dom.bins_table.append("tr"));x(t,t.dom.bins_table.append("tr"))}function _(t,n){n.append("td").style("margin","5px").style("opacity",.5).text("Bin Size");const s=t.num_obj.density_data;const a=t.q.bin_size;t.dom.bin_size_input=n.append("td").append("input").attr("type","number").attr("value","rounding"in t.q?e(t.q.rounding)(t.q.bin_size):t.q.bin_size).style("margin-left","15px").style("width","100px").style("color",(()=>t.q.bin_size>Math.abs(s.maxvalue-s.minvalue)?"red":"")).on("change",(e=>{const n=Number(e.target.value);if(n<=0){window.alert("Please enter non-negative bin size.");e.target.value=a;return}if((s.maxvalue-s.minvalue)/n>100){window.alert("Bin size too small. Try setting a bigger value.");e.target.value=a;return}t.q.bin_size=n;t.dom.bin_size_input.style("color",t.q.bin_size>s.maxvalue-s.minvalue?"red":n!=a?"green":"");i(t)}))}function h(t,e){if(!t.q.first_bin)throw"missing q.first_bin";e.append("td").style("margin","5px").style("opacity",.5).text("First Bin Stop");const n=t.num_obj.density_data;const i=t.q.first_bin.stop;t.dom.first_stop_input=e.append("td").append("input").attr("type","number").property("value",i).style("width","100px").style("margin-left","15px").on("change",(e=>{const s=Number(e.target.value);if(s<n.minvalue||s>n.maxvalue){window.alert("First bin stop value out of bound.");e.target.value=i;return}if(t.q.first_bin)t.q.first_bin.stop=s;t.renderBinLines(t,t.q)}));e.append("td").append("div").style("font-size",".6em").style("opacity",.5).style("display",t.num_obj.no_density_data?"none":"block").text("Indicated by left-most red line. Drag to change.")}function x(t,e){const n=!t.q.last_bin||!Number.isFinite(t.q.last_bin.start);e.append("td").style("margin","5px").style("opacity",.5).text("Last Bin Start");const s=t.num_obj.density_data;const a=e.append("td").style("padding-left","15px").style("vertical-align","top");const r=a.append("div");o({holder:r,options:[{label:"Automatic",value:"auto",checked:n},{label:"Fixed",value:"fixed",checked:!n}],callback:e=>{if(e=="auto"){delete t.q.last_bin;l.style("display","none");t.renderBinLines(t,t.q);i(t);return}l.style("display","inline-block");if(!t.q.last_bin)t.q.last_bin={};if(t.dom.last_start_input.property("value")==""){t.dom.last_start_input.property("value",s.maxvalue)}d();i(t)}});const l=e.append("td").append("div").style("display",n?"none":"inline-block");t.dom.last_start_input=l.append("input").attr("type","number").property("value",t.q.last_bin?t.q.last_bin.start:"").style("width","100px").on("change",d);l.append("div").style("font-size",".6em").style("opacity",.5).style("display",t.num_obj.no_density_data?"none":"block").text("Indicated by right-most red line. Drag to change.");function d(){const e=Number(t.dom.last_start_input.property("value"));if(t.q.first_bin&&e<=t.q.first_bin.stop){window.alert("Last bin start cannot be smaller than first bin stop.");t.dom.last_start_input.property("value",s.maxvalue);return}if(e>s.maxvalue){window.alert("Last bin start value out of bound.");t.dom.last_start_input.property("value",s.maxvalue);return}if(!t.q.last_bin)t.q.last_bin={};t.q.last_bin.start=e;t.renderBinLines(t,t.q)}}function j(e,i){g(e,i);e.dom.bins_table=i.append("div").style("display","flex").style("width","100%");const s=e.dom.bins_table.append("div").style("margin-right","20px");e.dom.rangeAndLabelDiv=e.dom.bins_table.append("div");s.append("div").style("margin-bottom","5px").style("color","rgb(136, 136, 136)").text("Bin boundaries");e.dom.customBinBoundaryInput=s.append("textarea").style("width","100px").style("height","70px").text(e.q.lst.slice(1).map((t=>t.start)).join("\n")).on("change",a).on("keyup",(function(i){return t(this,void 0,void 0,(function*(){if(!n(i)&&i.key!=8)return;if(!e.dom.bins_table.selectAll("input").node().value)return;a.call(this)}))}));s.append("div").style("font-size",".6em").style("margin-left","1px").style("color","#858585").html("Enter numeric values </br>seperated by ENTER");function a(){const t=e.dom.bins_table.selectAll("input");t.property("value","");const n=b(e);if(n==undefined){return}const i=e.numqByTermIdModeType[e.term.id].discrete[e.q.type];if(e.q.hiddenValues)i.hiddenValues=e.q.hiddenValues;if(r(n,i.lst)){i.lst=n;e.renderBinLines(e,i)}z(e,i.lst);e.q.lst=i.lst}function r(t,e){if(t.length!=e.length)return true;if(Object.keys(t[0]).length!==Object.keys(e[0]).length)return true;for(const[n,i]of e.entries()){for(const e of Object.keys(i)){if(i[e]&&i[e]!==t[n][e]){return true}}}return false}z(e,e.q.lst)}function z(t,e){const n=t.dom.rangeAndLabelDiv;n.selectAll("*").remove();const i=n.append("div").style("display","grid").style("grid-template-columns","auto auto").style("column-gap","20px").style("align-items","center");i.append("div").style("margin-bottom","3px").style("color","rgb(136, 136, 136)").text("Range");i.append("div").style("margin-bottom","3px").style("color","rgb(136, 136, 136)").text("Bin label");for(const[t,n]of e.entries()){i.append("div").attr("name","range").html(n.range);i.append("div").append("input").attr("type","text").style("margin","2px 0px").property("value",n.label).on("change",(function(){e[t].label=this.value}))}t.dom.customBinRanges=t.dom.bins_table.selectAll('div[name="range"]').data(e);t.dom.customBinLabelInput=t.dom.bins_table.selectAll("input").data(e)}function I(t){const e=t.dom.bins_div.append("div");e.append("button").style("margin","5px").html("Apply").on("click",(()=>c(t)));e.append("button").style("margin","5px").html("Reset").on("click",(()=>{t.q={};delete t.numqByTermIdModeType[t.term.id];m(t,t.dom.num_holder)}))}function w(t){const e=t.dom.discreteSur_div.append("div");e.append("div").style("font-size",".8em").style("margin","5px").html(`\n\t\t\tDisplay survival outcomes as exit codes <br>\n\t\t`);const n=t.dom.discreteSur_div.append("div");n.append("button").style("margin","5px").html("Apply").on("click",(()=>c(t)))}export{p as getHandler,v as renderBoundaryInclusionInput,z as renderBoundaryInputDivs};
+import{_ as t}from"./tslib.es6-c3c2d88f.js";import{W as e,k as n}from"./app-6fb77603.js";import{setDensityPlot as i}from"./density-09feb0c9.js";import{g as s,a}from"./termdb.bins-39d11f24.js";import{T as r}from"./toggleButtons-c4d6f260.js";import{m as o}from"./radiobutton-09bff425.js";import{o as l}from"./termsetting-492eefa7.js";import{convertViolinData as d}from"./tvs.numeric-aa1f892f.js";import{v as u}from"./violinRenderer-14fa200d.js";import"./drag-2e9c80bb.js";import"./nodrag-b2737073.js";import"./pointer-c7475677.js";import"path";import"./tvs.density-034b506d.js";import"./brush-9faa7ae7.js";import"./niceNumLabels-29a7c6ca.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";function p(e){return{getPillName(t){return l(e,t)},getPillStatus(){var t,n;if(!e.q)throw`Missing .q{} [numeric.discrete getPillStatus()]`;const i=((t=e.q)===null||t===void 0?void 0:t.name)||((n=e.q)===null||n===void 0?void 0:n.reuseId);if(i)return{text:i};if(e.q.type=="regular-bin")return{text:"bin size="+e.q.bin_size};return{text:e.q.lst.length+" bins"}},showEditMenu(n){return t(this,void 0,void 0,(function*(){m(e,n)}))}}}function m(e,n){var s,a,r,o;return t(this,void 0,void 0,(function*(){e.num_obj={};e.num_obj.plot_size={width:500,height:100,xpad:10,ypad:20};n.selectAll("*").remove();n.append("div").style("padding","10px").style("text-align","center").html("Getting distribution data ...<br/>");try{const t=yield e.vocabApi.getViolinPlotData({tw:{term:e.term,q:{mode:"continuous"}},filter:e.filter,filter0:(a=(s=e.vocabApi.state)===null||s===void 0?void 0:s.termfilter)===null||a===void 0?void 0:a.filter0,svgw:e.num_obj.plot_size.width/window.devicePixelRatio,strokeWidth:.2},(o=(r=e.opts).getBodyParams)===null||o===void 0?void 0:o.call(r));e.num_obj.density_data=d(t)}catch(t){console.log(t)}n.selectAll("*").remove();if(e.term.type=="survival"){e.dom.discreteSur_div=n.append("div").style("padding","4px");w(e);return}e.dom.num_holder=n;e.dom.density_div=n.append("div");e.vr=new u(e.dom.density_div,e.num_obj.density_data,e.num_obj.plot_size.width,e.num_obj.plot_size.height);e.num_obj.svg=e.vr.svg;e.dom.bins_div=n.append("div").style("padding","4px");y(e);i(e);v(e);f(e);I(e)}))}function c(t){var e;if(t.q.type=="regular-bin"){if(!t.q.first_bin){t.q.first_bin={stop:Number(t.dom.first_stop_input.property("value"))}}t.q.startinclusive=t.dom.boundaryInput.property("value")=="startinclusive";t.q.stopinclusive=t.dom.boundaryInput.property("value")=="stopinclusive";const n=t.dom.bin_size_input.property("value");t.q.bin_size=Number(n);if(n.includes(".")&&!n.endsWith(".")){t.q.rounding="."+n.split(".")[1].length+"f"}else{t.q.rounding=".0f"}if(t.q.scale)delete t.q.scale;if(Number.isFinite((e=t.q.last_bin)===null||e===void 0?void 0:e.start));else{delete t.q.last_bin}t.numqByTermIdModeType[t.term.id].discrete["regular-bin"]=JSON.parse(JSON.stringify(t.q))}else if(t.term.type!=="survival"){if(t.dom.bins_table.selectAll("input").node().value){t.q.lst=b(t);t.numqByTermIdModeType[t.term.id].discrete["custom-bin"]=JSON.parse(JSON.stringify(t.q))}}t.q.mode="discrete";t.dom.tip.hide();t.runCallback()}function b(t){var e;const n=t.dom.boundaryInput.property("value")=="startinclusive";const i=t.dom.boundaryInput.property("value")=="stopinclusive";const r=t.dom.bins_table.node().querySelectorAll("input");let o;const l=t.dom.customBinBoundaryInput.property("value").split("\n").filter((t=>t!=""&&!isNaN(t)));const d=new Set(l);const u=Array.from(d).map((t=>+t)).sort(((t,e)=>t-e)).map(((e,l)=>{const d={start:+e,startinclusive:n,stopinclusive:i};if(o){delete o.stopunbounded;o.stop=d.start;const e=r[l].value;o.label=e?e:s(o,t.q,t.term.valueConversion);o.range=a(o,t.q)}o=d;return d}));if(u.length==0)return;o.stopunbounded=true;const p=(e=r[u.length])===null||e===void 0?void 0:e.value;o.label=p?p:s(o,t.q,t.term.valueConversion);o.range=a(o,t.q);u.unshift({startunbounded:true,stop:u[0].start,startinclusive:n,stopinclusive:i,label:r[0].value});if(!u[0].label)u[0].label=s(u[0],t.q,t.term.valueConversion);if(!u[0].range)u[0].range=a(u[0],t.q);return u}function y(t){var e,n;const i=t.num_obj.density_data;const r=t.numqByTermIdModeType;const o=t.term;if(!r[o.id])r[o.id]={};if(!r[o.id].discrete){const e=!Number.isFinite(i.minvalue)||!Number.isFinite(i.maxvalue)?0:i.maxvalue!=i.minvalue?i.minvalue+(i.maxvalue-i.minvalue)/2:i.maxvalue;r[o.id].discrete={"regular-bin":t.q&&t.q.type=="regular-bin"?JSON.parse(JSON.stringify(t.q)):t.opts.use_bins_less&&o.bins.less?JSON.parse(JSON.stringify(o.bins.less)):JSON.parse(JSON.stringify(o.bins.default)),"custom-bin":t.q&&t.q.type=="custom-bin"?t.q:{type:"custom-bin",mode:"discrete",lst:[{startunbounded:true,startinclusive:true,stopinclusive:false,stop:+e.toFixed(o.type=="integer"?0:2)},{stopunbounded:true,startinclusive:true,stopinclusive:false,start:+e.toFixed(o.type=="integer"?0:2)}]}};if(!r[o.id].discrete["regular-bin"].type){r[o.id].discrete["regular-bin"].type="regular-bin"}}if(t.q&&!t.q.mode)t.q.mode="discrete";if(!t.q||t.q.mode!=="discrete")t.q={};if(!t.q.type){t.q.type=((n=(e=t.term.bins)===null||e===void 0?void 0:e.default)===null||n===void 0?void 0:n.type)||"regular-bin"}const l=JSON.parse(JSON.stringify(r[o.id].discrete[t.q.type]));t.q=Object.assign(l,t.q);const d="bin_size"in t.q&&t.q.bin_size.toString();if(!t.q.rounding&&typeof d=="string"&&d.includes(".")&&!d.endsWith(".")){const e=d.split(".")[1].length;t.q.rounding="."+e+"f"}if(t.q.lst){t.q.lst.forEach((e=>{if(!("label"in e))e.label=s(e,t.q,t.term.valueConversion);if(!("range"in e))e.range=a(e,t.q)}))}}function v(t){t.dom.boundaryInclusionDiv=t.dom.bins_div.append("div").style("margin-left","5px");t.dom.boundaryInclusionDiv.append("span").style("padding","5px").style("color","rgb(136, 136, 136)").html("Boundary Inclusion");const e='<span style="font-family:Times;font-style:italic">x</span>';t.dom.boundaryInput=t.dom.boundaryInclusionDiv.append("select").style("margin-left","10px").on("change",(function(){const e=t.q.mode=="binary"?t.numqByTermIdModeType[t.term.id].binary:t.numqByTermIdModeType[t.term.id].discrete[t.q.type];e.lst=t.q.lst;if(e.type=="regular-bin"){n(e)}else{e.lst.forEach((e=>{n(e);e.label=s(e,t.q,t.term.valueConversion);e.range=a(e,t.q)}));z(t,e.lst)}function n(e){e.startinclusive=t.dom.boundaryInput.node().selectedIndex==1;e.stopinclusive=t.dom.boundaryInput.node().selectedIndex==0}}));t.dom.boundaryInput.selectAll("option").data([{value:"stopinclusive",html:"start &lt; "+e+" &le; end"},{value:"startinclusive",html:"start &le; "+e+" &lt; end"}]).enter().append("option").property("value",(t=>t.value)).property("selected",(e=>{if(t.q.type=="regular-bin")return t.q[e.value]==true;else return t.q.lst[0][e.value]==true})).html((t=>t.html))}function f(e){const n=e.dom.bins_div.append("div").style("margin","10px");if(e.term.bins.default.type=="custom-bin"){e.q.type="custom-bin";y(e);i(e);j(e,n);return}if(e.term.bins.default.type!="regular-bin")throw"self.bins.default.type is neither regular-bin or custom-bin, cannot render ui";const s=[{active:e.q.type=="regular-bin",label:"Same bin size",callback:(n,a)=>t(this,void 0,void 0,(function*(){e.q.type="regular-bin";y(e);i(e);if(!s[0].isInitialized){q(e,a.contentHolder);s[0].isInitialized=true}}))},{active:e.q.type=="custom-bin",label:"Varying bin sizes",callback:(n,a)=>t(this,void 0,void 0,(function*(){e.q.type="custom-bin";y(e);i(e);if(!s[1].isInitialized){j(e,a.contentHolder);s[1].isInitialized=true}}))}];new r({holder:n,tabs:s}).main()}function g(t,e){if(!t.term.valueConversion)return;e.append("div").style("margin-bottom","5px").style("opacity",.6).text(`Note: using values by the unit of ${t.term.valueConversion.fromUnit}.`)}function q(t,e){g(t,e);t.dom.bins_table=e.append("table");_(t,t.dom.bins_table.append("tr"));h(t,t.dom.bins_table.append("tr"));x(t,t.dom.bins_table.append("tr"))}function _(t,n){n.append("td").style("margin","5px").style("opacity",.5).text("Bin Size");const s=t.num_obj.density_data;const a=t.q.bin_size;t.dom.bin_size_input=n.append("td").append("input").attr("type","number").attr("value","rounding"in t.q?e(t.q.rounding)(t.q.bin_size):t.q.bin_size).style("margin-left","15px").style("width","100px").style("color",(()=>t.q.bin_size>Math.abs(s.maxvalue-s.minvalue)?"red":"")).on("change",(e=>{const n=Number(e.target.value);if(n<=0){window.alert("Please enter non-negative bin size.");e.target.value=a;return}if((s.maxvalue-s.minvalue)/n>100){window.alert("Bin size too small. Try setting a bigger value.");e.target.value=a;return}t.q.bin_size=n;t.dom.bin_size_input.style("color",t.q.bin_size>s.maxvalue-s.minvalue?"red":n!=a?"green":"");i(t)}))}function h(t,e){if(!t.q.first_bin)throw"missing q.first_bin";e.append("td").style("margin","5px").style("opacity",.5).text("First Bin Stop");const n=t.num_obj.density_data;const i=t.q.first_bin.stop;t.dom.first_stop_input=e.append("td").append("input").attr("type","number").property("value",i).style("width","100px").style("margin-left","15px").on("change",(e=>{const s=Number(e.target.value);if(s<n.minvalue||s>n.maxvalue){window.alert("First bin stop value out of bound.");e.target.value=i;return}if(t.q.first_bin)t.q.first_bin.stop=s;t.renderBinLines(t,t.q)}));e.append("td").append("div").style("font-size",".6em").style("opacity",.5).style("display",t.num_obj.no_density_data?"none":"block").text("Indicated by left-most red line. Drag to change.")}function x(t,e){const n=!t.q.last_bin||!Number.isFinite(t.q.last_bin.start);e.append("td").style("margin","5px").style("opacity",.5).text("Last Bin Start");const s=t.num_obj.density_data;const a=e.append("td").style("padding-left","15px").style("vertical-align","top");const r=a.append("div");o({holder:r,options:[{label:"Automatic",value:"auto",checked:n},{label:"Fixed",value:"fixed",checked:!n}],callback:e=>{if(e=="auto"){delete t.q.last_bin;l.style("display","none");t.renderBinLines(t,t.q);i(t);return}l.style("display","inline-block");if(!t.q.last_bin)t.q.last_bin={};if(t.dom.last_start_input.property("value")==""){t.dom.last_start_input.property("value",s.maxvalue)}d();i(t)}});const l=e.append("td").append("div").style("display",n?"none":"inline-block");t.dom.last_start_input=l.append("input").attr("type","number").property("value",t.q.last_bin?t.q.last_bin.start:"").style("width","100px").on("change",d);l.append("div").style("font-size",".6em").style("opacity",.5).style("display",t.num_obj.no_density_data?"none":"block").text("Indicated by right-most red line. Drag to change.");function d(){const e=Number(t.dom.last_start_input.property("value"));if(t.q.first_bin&&e<=t.q.first_bin.stop){window.alert("Last bin start cannot be smaller than first bin stop.");t.dom.last_start_input.property("value",s.maxvalue);return}if(e>s.maxvalue){window.alert("Last bin start value out of bound.");t.dom.last_start_input.property("value",s.maxvalue);return}if(!t.q.last_bin)t.q.last_bin={};t.q.last_bin.start=e;t.renderBinLines(t,t.q)}}function j(e,i){g(e,i);e.dom.bins_table=i.append("div").style("display","flex").style("width","100%");const s=e.dom.bins_table.append("div").style("margin-right","20px");e.dom.rangeAndLabelDiv=e.dom.bins_table.append("div");s.append("div").style("margin-bottom","5px").style("color","rgb(136, 136, 136)").text("Bin boundaries");e.dom.customBinBoundaryInput=s.append("textarea").style("width","100px").style("height","70px").text(e.q.lst.slice(1).map((t=>t.start)).join("\n")).on("change",a).on("keyup",(function(i){return t(this,void 0,void 0,(function*(){if(!n(i)&&i.key!=8)return;if(!e.dom.bins_table.selectAll("input").node().value)return;a.call(this)}))}));s.append("div").style("font-size",".6em").style("margin-left","1px").style("color","#858585").html("Enter numeric values </br>seperated by ENTER");function a(){const t=e.dom.bins_table.selectAll("input");t.property("value","");const n=b(e);if(n==undefined){return}const i=e.numqByTermIdModeType[e.term.id].discrete[e.q.type];if(e.q.hiddenValues)i.hiddenValues=e.q.hiddenValues;if(r(n,i.lst)){i.lst=n;e.renderBinLines(e,i)}z(e,i.lst);e.q.lst=i.lst}function r(t,e){if(t.length!=e.length)return true;if(Object.keys(t[0]).length!==Object.keys(e[0]).length)return true;for(const[n,i]of e.entries()){for(const e of Object.keys(i)){if(i[e]&&i[e]!==t[n][e]){return true}}}return false}z(e,e.q.lst)}function z(t,e){const n=t.dom.rangeAndLabelDiv;n.selectAll("*").remove();const i=n.append("div").style("display","grid").style("grid-template-columns","auto auto").style("column-gap","20px").style("align-items","center");i.append("div").style("margin-bottom","3px").style("color","rgb(136, 136, 136)").text("Range");i.append("div").style("margin-bottom","3px").style("color","rgb(136, 136, 136)").text("Bin label");for(const[t,n]of e.entries()){i.append("div").attr("name","range").html(n.range);i.append("div").append("input").attr("type","text").style("margin","2px 0px").property("value",n.label).on("change",(function(){e[t].label=this.value}))}t.dom.customBinRanges=t.dom.bins_table.selectAll('div[name="range"]').data(e);t.dom.customBinLabelInput=t.dom.bins_table.selectAll("input").data(e)}function I(t){const e=t.dom.bins_div.append("div");e.append("button").style("margin","5px").html("Apply").on("click",(()=>c(t)));e.append("button").style("margin","5px").html("Reset").on("click",(()=>{t.q={};delete t.numqByTermIdModeType[t.term.id];m(t,t.dom.num_holder)}))}function w(t){const e=t.dom.discreteSur_div.append("div");e.append("div").style("font-size",".8em").style("margin","5px").html(`\n\t\t\tDisplay survival outcomes as exit codes <br>\n\t\t`);const n=t.dom.discreteSur_div.append("div");n.append("button").style("margin","5px").html("Apply").on("click",(()=>c(t)))}export{p as getHandler,v as renderBoundaryInclusionInput,z as renderBoundaryInputDivs};

package/dist/{numeric.spline-abe07708.js → numeric.spline-a35cfbf0.js}

@@ -1 +1 @@
-import{_ as t}from"./tslib.es6-c3c2d88f.js";import{setDensityPlot as e}from"./density-69a732f6.js";import{k as n}from"./app-2cd97738.js";import{o}from"./termsetting-ad8c4f3a.js";import{convertViolinData as i}from"./tvs.numeric-de14101f.js";import{v as s}from"./violinRenderer-08b3b58c.js";import"./termdb.bins-01e8cce6.js";import"./drag-d8daa62f.js";import"./nodrag-ab7d5a9f.js";import"./pointer-c7475677.js";import"path";import"./tvs.density-b2790080.js";import"./brush-bb4ae2fb.js";import"./niceNumLabels-5f45218a.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";function l(n){return{getPillName(t){return o(n,t)},getPillStatus(){return{text:"cubic spline"}},showEditMenu(o){var l,p,a,m;return t(this,void 0,void 0,(function*(){n.num_obj={};n.num_obj.plot_size={width:500,height:100,xpad:10,ypad:20};o.selectAll("*").remove();o.append("div").style("padding","10px").style("text-align","center").html("Getting distribution data ...<br/>");try{const t=yield n.vocabApi.getViolinPlotData({tw:{term:n.term,q:n.q},filter:n.filter,filter0:(p=(l=n.vocabApi.state)===null||l===void 0?void 0:l.termfilter)===null||p===void 0?void 0:p.filter0,svgw:n.num_obj.plot_size.width/window.devicePixelRatio},(m=(a=n.opts).getBodyParams)===null||m===void 0?void 0:m.call(a));n.num_obj.density_data=i(t)}catch(t){console.log(t)}o.selectAll("*").remove();n.dom.density_div=o.append("div");n.vr=new s(n.dom.density_div,n.num_obj.density_data,n.num_obj.plot_size.width,n.num_obj.plot_size.height);n.num_obj.svg=n.vr.svg;n.dom.num_holder=o;n.dom.knots_div=o.append("div").style("padding","5px");yield d(n);e(n);r(n);y(n)}))}}}function d(e){return t(this,void 0,void 0,(function*(){const t=e.numqByTermIdModeType;const n=e.term;if(!t[n.id])t[n.id]={};if(!t[n.id]["spline"]){t[n.id]["spline"]={mode:"spline",knots:[]}}const o=JSON.parse(JSON.stringify(t[n.id]["spline"]));e.q=Object.assign(o,e.q);if(!e.q.knots.length){const t=4;yield u(e,t);e.numqByTermIdModeType[e.term.id]["spline"].knots=e.q.knots}}))}function r(t){const e=t.dom.knots_div;p(t,e);c(t,e)}function p(e,o){e.dom.custom_knots_div=o.append("div");e.dom.custom_knots_div.append("div").style("display","inline-block").style("vertical-align","top").style("padding","3px 15px").style("font-weight","normal").style("color","rgb(136, 136, 136)").html("Knots");e.dom.customKnotsInput=e.dom.custom_knots_div.append("div").style("display","inline-block").style("padding","3px 15px").style("padding-left","5px").append("textarea").style("height","100px").style("width","100px").text(e.q.knots.map((t=>t.value)).join("\n")).on("change",i).on("keyup",(function(e){return t(this,void 0,void 0,(function*(){if(!n(e)&&e.key!=8)return;i.call(this)}))}));e.dom.custom_knots_div.append("div").style("display","inline-block").style("vertical-align","top").style("font-size",".7em").style("padding","3px 15px").style("padding-left","5px").style("color","rgb(136, 136, 136)").html(`Enter knot values, one knot per line.</br> \n\t\t\tAdjust knot by dragging on the vertical line.</br>\n\t\t \tOr autocompute knots from below.`);function i(){const t=m(e);const n=e.q;if(s(t,n.knots)){n.knots=t;e.renderBinLines(e,n)}e.q=n}function s(t,e){if(t.length!=e.length)return true;if(Object.keys(t[0]).length!==Object.keys(e[0]).length)return true;for(const[n,o]of e.entries()){for(const e of Object.keys(o)){if(o[e]&&o[e]!==t[n][e]){return true}}}return false}}function a(t){t.dom.customKnotsInput.property("value",t.q.knots.map((t=>t.value)).join("\n"))}function m(t){const e=t.dom.customKnotsInput.property("value").split("\n").filter((t=>t!="")).map((t=>+t)).sort(((t,e)=>t-e)).map((t=>{const e={value:+t};return e}));return e}function c(n,o){const i=4;const s=i;n.dom.knot_select_div=o.append("div");n.dom.knot_select_div.append("div").style("display","inline-block").style("margin-left","15px").style("color","rgb(136, 136, 136)").html("Autocompute");const l=n.dom.knot_select_div.append("select").style("margin-left","10px").style("margin-bottom","7px");for(let t=s-1;t<s+5;t++){l.append("option").attr("value",t).html(t)}const d=n.q.knots&&n.q.knots.length?n.q.knots.length:s;l.node().value=d;n.dom.knot_select_div.append("div").style("display","inline-block").style("margin-left","10px").style("color","rgb(136, 136, 136)").html("knots");n.dom.knot_select_div.append("button").style("margin","15px").html("Compute").on("click",(()=>t(this,void 0,void 0,(function*(){const t=Number.parseInt(l.node().value);let o=Number.parseInt(l.node().value);while(n.q.knots.length!=t){yield u(n,o);o=o+1}a(n);e(n)}))));n.dom.knot_select_div.append("div").style("display","inline-block").style("font-size",".7em").style("padding","3px 15px").style("padding-left","5px").style("color","rgb(136, 136, 136)").html("Will overwrite existing values.")}function u(e,n){return t(this,void 0,void 0,(function*(){const t=n-2;const o=e.term;const i=e.q.knots=[];const s=[5];const l=(90/(t+1)).toFixed(0);for(let e=1;e<t+1;e++){s.push(e*l)}s.push(95);const d=yield v(e,s);for(const t of d){i.push({value:t.toFixed(o.type=="integer"?0:2)})}}))}function v(e,n){return t(this,void 0,void 0,(function*(){const t=yield e.vocabApi.getPercentile(e.term.id,n,e.filter);if(t.error||!t.values.length||!t.values.every((t=>Number.isFinite(t))))throw"cannot get median value: "+(t.error||"no data");const o=[...new Set(t.values)];return o}))}function y(t){const e=t.dom.knots_div.append("div");e.append("button").style("margin","5px").html("Apply").on("click",(()=>f(t)));e.append("button").style("margin","5px").html("Reset").on("click",(()=>{t.q={};delete t.numqByTermIdModeType[t.term.id];t.handler=l(t);t.handler.showEditMenu(t.dom.num_holder)}))}function f(t){t.q.mode="spline";t.dom.tip.hide();t.runCallback()}export{l as getHandler};
+import{_ as t}from"./tslib.es6-c3c2d88f.js";import{setDensityPlot as e}from"./density-09feb0c9.js";import{k as n}from"./app-6fb77603.js";import{o}from"./termsetting-492eefa7.js";import{convertViolinData as i}from"./tvs.numeric-aa1f892f.js";import{v as s}from"./violinRenderer-14fa200d.js";import"./termdb.bins-39d11f24.js";import"./drag-2e9c80bb.js";import"./nodrag-b2737073.js";import"./pointer-c7475677.js";import"path";import"./tvs.density-034b506d.js";import"./brush-9faa7ae7.js";import"./niceNumLabels-29a7c6ca.js";import"./axis-747c801e.js";import"./line-264f8f9e.js";import"./constant-426a1483.js";import"./basis-3870f5ba.js";function l(n){return{getPillName(t){return o(n,t)},getPillStatus(){return{text:"cubic spline"}},showEditMenu(o){var l,p,a,m;return t(this,void 0,void 0,(function*(){n.num_obj={};n.num_obj.plot_size={width:500,height:100,xpad:10,ypad:20};o.selectAll("*").remove();o.append("div").style("padding","10px").style("text-align","center").html("Getting distribution data ...<br/>");try{const t=yield n.vocabApi.getViolinPlotData({tw:{term:n.term,q:n.q},filter:n.filter,filter0:(p=(l=n.vocabApi.state)===null||l===void 0?void 0:l.termfilter)===null||p===void 0?void 0:p.filter0,svgw:n.num_obj.plot_size.width/window.devicePixelRatio},(m=(a=n.opts).getBodyParams)===null||m===void 0?void 0:m.call(a));n.num_obj.density_data=i(t)}catch(t){console.log(t)}o.selectAll("*").remove();n.dom.density_div=o.append("div");n.vr=new s(n.dom.density_div,n.num_obj.density_data,n.num_obj.plot_size.width,n.num_obj.plot_size.height);n.num_obj.svg=n.vr.svg;n.dom.num_holder=o;n.dom.knots_div=o.append("div").style("padding","5px");yield d(n);e(n);r(n);f(n)}))}}}function d(e){return t(this,void 0,void 0,(function*(){const t=e.numqByTermIdModeType;const n=e.term;if(!t[n.id])t[n.id]={};if(!t[n.id]["spline"]){t[n.id]["spline"]={mode:"spline",knots:[]}}const o=JSON.parse(JSON.stringify(t[n.id]["spline"]));e.q=Object.assign(o,e.q);if(!e.q.knots.length){const t=4;yield u(e,t);e.numqByTermIdModeType[e.term.id]["spline"].knots=e.q.knots}}))}function r(t){const e=t.dom.knots_div;p(t,e);c(t,e)}function p(e,o){e.dom.custom_knots_div=o.append("div");e.dom.custom_knots_div.append("div").style("display","inline-block").style("vertical-align","top").style("padding","3px 15px").style("font-weight","normal").style("color","rgb(136, 136, 136)").html("Knots");e.dom.customKnotsInput=e.dom.custom_knots_div.append("div").style("display","inline-block").style("padding","3px 15px").style("padding-left","5px").append("textarea").style("height","100px").style("width","100px").text(e.q.knots.map((t=>t.value)).join("\n")).on("change",i).on("keyup",(function(e){return t(this,void 0,void 0,(function*(){if(!n(e)&&e.key!=8)return;i.call(this)}))}));e.dom.custom_knots_div.append("div").style("display","inline-block").style("vertical-align","top").style("font-size",".7em").style("padding","3px 15px").style("padding-left","5px").style("color","rgb(136, 136, 136)").html(`Enter knot values, one knot per line.</br> \n\t\t\tAdjust knot by dragging on the vertical line.</br>\n\t\t \tOr autocompute knots from below.`);function i(){const t=m(e);const n=e.q;if(s(t,n.knots)){n.knots=t;e.renderBinLines(e,n)}e.q=n}function s(t,e){if(t.length!=e.length)return true;if(Object.keys(t[0]).length!==Object.keys(e[0]).length)return true;for(const[n,o]of e.entries()){for(const e of Object.keys(o)){if(o[e]&&o[e]!==t[n][e]){return true}}}return false}}function a(t){t.dom.customKnotsInput.property("value",t.q.knots.map((t=>t.value)).join("\n"))}function m(t){const e=t.dom.customKnotsInput.property("value").split("\n").filter((t=>t!="")).map((t=>+t)).sort(((t,e)=>t-e)).map((t=>{const e={value:+t};return e}));return e}function c(n,o){const i=4;const s=i;n.dom.knot_select_div=o.append("div");n.dom.knot_select_div.append("div").style("display","inline-block").style("margin-left","15px").style("color","rgb(136, 136, 136)").html("Autocompute");const l=n.dom.knot_select_div.append("select").style("margin-left","10px").style("margin-bottom","7px");for(let t=s-1;t<s+5;t++){l.append("option").attr("value",t).html(t)}const d=n.q.knots&&n.q.knots.length?n.q.knots.length:s;l.node().value=d;n.dom.knot_select_div.append("div").style("display","inline-block").style("margin-left","10px").style("color","rgb(136, 136, 136)").html("knots");n.dom.knot_select_div.append("button").style("margin","15px").html("Compute").on("click",(()=>t(this,void 0,void 0,(function*(){const t=Number.parseInt(l.node().value);let o=Number.parseInt(l.node().value);while(n.q.knots.length!=t){yield u(n,o);o=o+1}a(n);e(n)}))));n.dom.knot_select_div.append("div").style("display","inline-block").style("font-size",".7em").style("padding","3px 15px").style("padding-left","5px").style("color","rgb(136, 136, 136)").html("Will overwrite existing values.")}function u(e,n){return t(this,void 0,void 0,(function*(){const t=n-2;const o=e.term;const i=e.q.knots=[];const s=[5];const l=(90/(t+1)).toFixed(0);for(let e=1;e<t+1;e++){s.push(e*l)}s.push(95);const d=yield v(e,s);for(const t of d){i.push({value:t.toFixed(o.type=="integer"?0:2)})}}))}function v(e,n){return t(this,void 0,void 0,(function*(){const t=yield e.vocabApi.getPercentile(e.term.id,n,e.filter);if(t.error||!t.values.length||!t.values.every((t=>Number.isFinite(t))))throw"cannot get median value: "+(t.error||"no data");const o=[...new Set(t.values)];return o}))}function f(t){const e=t.dom.knots_div.append("div");e.append("button").style("margin","5px").html("Apply").on("click",(()=>y(t)));e.append("button").style("margin","5px").html("Reset").on("click",(()=>{t.q={};delete t.numqByTermIdModeType[t.term.id];t.handler=l(t);t.handler.showEditMenu(t.dom.num_holder)}))}function y(t){t.q.mode="spline";t.dom.tip.hide();t.runCallback()}export{l as getHandler};

package/dist/{numeric.toggle-647423dd.js → numeric.toggle-2f98d6e5.js}

@@ -1 +1 @@
-import{_ as e}from"./tslib.es6-c3c2d88f.js";import{T as i}from"./toggleButtons-04c5ad7c.js";import{o as t,c as n,s as r}from"./termsetting-ad8c4f3a.js";import{P as s}from"./app-2cd97738.js";import"path";function o(e){switch(e){case"./numeric.binary.ts":return import("./numeric.binary-1dd9a2b4.js");case"./numeric.continuous.ts":return import("./numeric.continuous-ed132eea.js");case"./numeric.discrete.ts":return import("./numeric.discrete-d780d076.js");case"./numeric.spline.ts":return import("./numeric.spline-abe07708.js");case"./numeric.toggle.ts":return Promise.resolve().then((function(){return c}));default:return new Promise((function(i,t){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(t.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}function u(n){return e(this,void 0,void 0,(function*(){n.tabCallback=(i,t)=>e(this,void 0,void 0,(function*(){if(!t)return;if(!n.q)throw`Missing .q{} [numeric.toggle getHandler()]`;n.q.mode=t.mode;const e=`numeric.${t.mode}`;if(!n.handlerByType[e]){const i=yield o(`./numeric.${t.mode}.ts`);n.handlerByType[e]=yield i.getHandler(n)}t.isRendered=true;yield n.handlerByType[e].showEditMenu(t.contentHolder)}));const r=[];if(n.opts.numericEditMenuVersion.includes("continuous")){r.push({mode:"continuous",label:n.term.type=="survival"?"Time to Event":"Continuous",callback:n.tabCallback})}if(n.opts.numericEditMenuVersion.includes("discrete")){r.push({mode:"discrete",label:n.term.type=="survival"?"Exit code":"Discrete",callback:n.tabCallback})}if(n.opts.numericEditMenuVersion.includes("spline")){r.push({mode:"spline",label:"Cubic spline",callback:n.tabCallback})}if(n.opts.numericEditMenuVersion.includes("binary")){r.push({mode:"binary",label:"Binary",callback:n.tabCallback})}return{getPillName(e){return t(n,e)},getPillStatus(){var e;if(!n.q)throw`Missing .q{} [numeric.toggle getPillStatus()]`;let i=n.q.mode;if(n.q.mode=="spline"){i="cubic spline"}else if(n.q.mode=="discrete"){if(((e=n.usecase)===null||e===void 0?void 0:e.target)=="regression"){i="discrete"}else if(n.q.type=="custom-bin"){i=n.q.lst.length+" bins"}else{i="bin size="+n.q.bin_size}}return{text:i}},showEditMenu(t){return e(this,void 0,void 0,(function*(){for(const e of r){delete e.isRendered;e.active=n.q.mode==e.mode||e.mode=="continuous"&&!n.q.mode}const e=t.append("div").style("padding","10px");e.append("span").html("Use as&nbsp;");new i({holder:e.append("div").style("display","inline-block"),contentHolder:t.append("div"),noTopContentStyle:true,tabs:r}).main()}))}}}))}function l(i,t,o){return e(this,void 0,void 0,(function*(){if(!i.q.mode&&!(o===null||o===void 0?void 0:o.mode))i.q.mode="discrete";if(i.q.mode!=="continuous"&&!a(i.q)){s(i.q,i.term.bins.default)}if(o){o.isAtomic=true;const e=o;const r=o;if(e.preferredBins=="median"){const r=e;if(!r.type||r.type!="custom-bin")throw".type must be custom-bin when .preferredBins=median";const s=yield t.getPercentile(i.term.id,[50]);if(!s.values)throw".values[] missing from vocab.getPercentile()";const u=n(s.values[0]);if(!Number.isFinite(u))throw"median value not a number";const l=JSON.parse(JSON.stringify(o));delete l.preferredBins;i.q=l;i.q.lst=[{startunbounded:true,stop:u,stopinclusive:false,label:"<"+u},{start:u,startinclusive:true,stopunbounded:true,label:"≥"+u}]}else if(r.preferredBins=="less"||r.preferredBins=="default"){i.q=JSON.parse(JSON.stringify(i.term.bins[r.preferredBins]))}else{s(i.q,o)}}r(i.q,i.term)}))}function a(e){if(e.type=="custom-bin"){if(!Array.isArray(e.lst))return false;return true}if(Number.isFinite(e.bin_size)&&e.first_bin){if(Number.isFinite(e.first_bin.stop))return true}return false}var c=Object.freeze({__proto__:null,getHandler:u,fillTW:l});export{l as fillTW,u as getHandler};
+import{_ as e}from"./tslib.es6-c3c2d88f.js";import{T as i}from"./toggleButtons-c4d6f260.js";import{o as t,c as n,s as r}from"./termsetting-492eefa7.js";import{P as s}from"./app-6fb77603.js";import"path";function o(e){switch(e){case"./numeric.binary.ts":return import("./numeric.binary-f382cc98.js");case"./numeric.continuous.ts":return import("./numeric.continuous-6feb34a7.js");case"./numeric.discrete.ts":return import("./numeric.discrete-ed10bbc1.js");case"./numeric.spline.ts":return import("./numeric.spline-a35cfbf0.js");case"./numeric.toggle.ts":return Promise.resolve().then((function(){return a}));default:return new Promise((function(i,t){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(t.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}function u(n){return e(this,void 0,void 0,(function*(){n.tabCallback=(i,t)=>e(this,void 0,void 0,(function*(){if(!t)return;if(!n.q)throw`Missing .q{} [numeric.toggle getHandler()]`;n.q.mode=t.mode;const e=`numeric.${t.mode}`;if(!n.handlerByType[e]){const i=yield o(`./numeric.${t.mode}.ts`);n.handlerByType[e]=yield i.getHandler(n)}t.isRendered=true;yield n.handlerByType[e].showEditMenu(t.contentHolder)}));const r=[];if(n.opts.numericEditMenuVersion.includes("continuous")){r.push({mode:"continuous",label:n.term.type=="survival"?"Time to Event":"Continuous",callback:n.tabCallback})}if(n.opts.numericEditMenuVersion.includes("discrete")){r.push({mode:"discrete",label:n.term.type=="survival"?"Exit code":"Discrete",callback:n.tabCallback})}if(n.opts.numericEditMenuVersion.includes("spline")){r.push({mode:"spline",label:"Cubic spline",callback:n.tabCallback})}if(n.opts.numericEditMenuVersion.includes("binary")){r.push({mode:"binary",label:"Binary",callback:n.tabCallback})}return{getPillName(e){return t(n,e)},getPillStatus(){var e;if(!n.q)throw`Missing .q{} [numeric.toggle getPillStatus()]`;let i=n.q.mode;if(n.q.mode=="spline"){i="cubic spline"}else if(n.q.mode=="discrete"){if(((e=n.usecase)===null||e===void 0?void 0:e.target)=="regression"){i="discrete"}else if(n.q.type=="custom-bin"){i=n.q.lst.length+" bins"}else{i="bin size="+n.q.bin_size}}return{text:i}},showEditMenu(t){return e(this,void 0,void 0,(function*(){for(const e of r){delete e.isRendered;e.active=n.q.mode==e.mode||e.mode=="continuous"&&!n.q.mode}const e=t.append("div").style("padding","10px");e.append("span").html("Use as&nbsp;");new i({holder:e.append("div").style("display","inline-block"),contentHolder:t.append("div"),noTopContentStyle:true,tabs:r}).main()}))}}}))}function l(i,t,o){return e(this,void 0,void 0,(function*(){if(!i.q.mode&&!(o===null||o===void 0?void 0:o.mode))i.q.mode="discrete";if(i.q.mode!=="continuous"&&!c(i.q)){s(i.q,i.term.bins.default)}if(o){o.isAtomic=true;const e=o;const r=o;if(e.preferredBins=="median"){const r=e;if(!r.type||r.type!="custom-bin")throw".type must be custom-bin when .preferredBins=median";const s=yield t.getPercentile(i.term.id,[50]);if(!s.values)throw".values[] missing from vocab.getPercentile()";const u=n(s.values[0]);if(!Number.isFinite(u))throw"median value not a number";const l=JSON.parse(JSON.stringify(o));delete l.preferredBins;i.q=l;i.q.lst=[{startunbounded:true,stop:u,stopinclusive:false,label:"<"+u},{start:u,startinclusive:true,stopunbounded:true,label:"≥"+u}]}else if(r.preferredBins=="less"||r.preferredBins=="default"){i.q=JSON.parse(JSON.stringify(i.term.bins[r.preferredBins]))}else{s(i.q,o)}}r(i.q,i.term)}))}function c(e){if(e.type=="custom-bin"){if(!Array.isArray(e.lst))return false;return true}if(Number.isFinite(e.bin_size)&&e.first_bin){if(Number.isFinite(e.first_bin.stop))return true}return false}var a=Object.freeze({__proto__:null,getHandler:u,fillTW:l});export{l as fillTW,u as getHandler};

package/dist/oncomatrix-c0b2d635.js

@@ -0,0 +1 @@
+import{appInit as t}from"./plot.app-2a805759.js";import{d as e,P as r,b as i}from"./app-6fb77603.js";import{f as s}from"./termsetting-492eefa7.js";import{v as a}from"./FilterRxComp-02e68f1b.js";import"./recover-299ffdb3.js";import"./FilterStateless-16a33070.js";import"./app-d215327f.js";import"./termInfo-491b10af.js";import"./tslib.es6-c3c2d88f.js";import"./toggleButtons-c4d6f260.js";import"path";import"./table-0daf2b89.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-39d11f24.js";import"./genesearch-ffd88bf2.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";const o="hg38";const n="GDC";async function p(i,p,f){const m=f[o];try{if(!m)throw o+" missing";const p=i.settings||{};if(typeof p!="object")throw"arg.settings{} not object";if(!p.matrix)p.matrix={};if(typeof p.matrix!="object")throw"arg.settings.matrix{} not object";if(!p.matrix.geneFilter)p.matrix.geneFilter="CGC";if(!Number.isInteger(p.matrix.maxGenes))p.matrix.maxGenes=50;if(i.filter0&&typeof i.filter0!="object")throw"arg.filter0 not object";const f=await a({state:{vocab:{genome:o,dslabel:n}}});f.getTermdbConfig();const c=await t({holder:e(i.holder).select(".sja_root_holder"),genome:m,state:{genome:o,dslabel:n,termfilter:{filter0:i.filter0},plots:[{chartType:"geneset",toolName:"OncoMatrix",settings:{maxGenes:p.matrix.maxGenes,geneFilter:p.matrix.geneFilter}}]},app:i.opts?.app||{},geneset:{mode:"geneVariant",genome:m,genes:i.genes,reactsTo(t){if(t.type.startsWith("plot_"))return t.id===this.id;if(t.type.startsWith("filter"))return true;if(t.type=="app_refresh")return true},showWaitMessage(t){t.style("margin","20px");t.append("div").text("Loading the top mutated genes in the current cohort...")},async callback(t,e){if(!t)return;g=t;if(!d){const t=c.getState().plots.find((t=>t.chartType=="matrix"));if(t)d=c.getComponents(`plots.${t.id}`)}const r=[...i.termgroups||[],{lst:e}];if(d){c.dispatch({type:"plot_edit",id:d.id,config:{termgroups:r}})}else{c.dispatch({type:"plot_create",config:{chartType:"matrix",termgroups:r,divideBy:i.divideBy||undefined,settings:p}})}}},recover:{undoHtml:"Undo",redoHtml:"Redo",resetHtml:"Restore",hide(t){return t.plots[0]?.chartType!="matrix"},adjustTrackedState:t=>{const e=structuredClone(t);delete e.termfilter.filter0;if(e.plots){for(const t of e.plots){if(!t.termgroups)continue;for(const e of t.termgroups){if(!e.lst)continue;for(const t of e.lst){if(!t?.term)continue;delete t.term.category2samplecount;delete t.term.values}}}}return e}},matrix:r({reactsTo(t){if(t.type.startsWith("plot_"))return t.id===this.id;if(t.type.startsWith("filter"))return true;if(t.type=="app_refresh")return true},customInputs:{genes:[{label:`Maximum # Genes`,title:"Limit the number of displayed genes",type:"number",chartType:"matrix",settingsKey:"maxGenes",callback:async t=>{for(const t in i.opts?.app?.callbacks){if(t.startsWith("preDispatch")){i.opts?.app?.callbacks[t]();break}}const e=await l(i,{maxGenes:t,geneFilter:p.matrix.geneFilter},f);u.update({termgroups:[{lst:e}],settings:{matrix:{maxGenes:t}}})}}]},callbacks:{"firstRender.gdcMatrix":async t=>{t.on("firstRender.gdcMatrix",null);if(!g)return;c.dispatch({type:"plot_delete",id:g.id});g=undefined}}},i.opts?.matrix||{})});let d,g;const u={update:async t=>{if(!d){const t=c.getState().plots.find((t=>t.chartType=="matrix"));if(t)d=c.getComponents(`plots.${t.id}`)}if(t.genes){c.dispatch({type:"plot_edit",id:d.id,config:{termgroups:[{lst:await Promise.all(t.genes.map((async t=>await s({term:{gene:t.gene,type:"geneVariant",name:t.gene}},f))))}]}})}else if("filter0"in t){c.dispatch({type:"filter_replace",filter0:t.filter0})}else if(d){c.dispatch({type:"plot_edit",id:d.id,config:t})}}};return u}catch(t){throw t}}async function l(t,e,r){const a={maxGenes:e.maxGenes,geneFilter:e.geneFilter};if(t.filter0)a.filter0=t.filter0;const o=await i("gdc/topMutatedGenes",{body:a});if(o.error)throw o.error;if(!o.genes)return;return await Promise.all(o.genes.map((async t=>await s({term:{gene:t.gene,type:"geneVariant"}},r))))}export{p as init};

package/dist/{parseData-567f3d70.js → parseData-292648dd.js}

@@ -1 +1 @@
-import{_ as r}from"./tslib.es6-c3c2d88f.js";import{aj as e,q as i,a7 as t}from"./app-2cd97738.js";function n(e,n,o=[]){return r(this,void 0,void 0,(function*(){if(n)window["hic"]=e;if(e.tklst){const r=[];for(const i of e.tklst){if(!i.type){o.push("type missing from one of the tracks accompanying HiC")}else{i.iscustom=true;r.push(i)}}if(r.length){e.tklst=r}else{delete e.tklst}}if(e.enzyme){if(e.genome.hicenzymefragment){let r=null;for(const i of e.genome.hicenzymefragment){if(i.enzyme==e.enzyme){r=i;break}}if(r){e.enzymefile=r.file}else{o.push("unknown enzyme: "+e.enzyme);delete e.enzyme}}else{o.push("no enzyme fragment information available for this genome");delete e.enzyme}}try{if(e.sv&&e.sv.file){const r=yield i(e.hostURL+"/textfile",{method:"POST",body:JSON.stringify({file:e.sv.file,jwt:e.jwt})});const t=r.json();const[n,o,a]=s(t.text);if(n)throw{message:"Error parsing SV: "+n};e.sv.header=o;e.sv.items=a}const r=yield t("hicstat?"+(e.file?"file="+e.file:"url="+e.url));if(r.error){o.push(r.error);return}const n=f(e,r.out);if(n)throw{message:n}}catch(r){o.push(r.message||r);if(r.stack){console.log(r.stack)}}return e}))}function s(r){const e=r.trim().split(/\r?\n/);const[i,t]=o(e[0]);if(i)return["header error: "+i];const n=[];for(let r=1;r<e.length;r++){const i=e[r];if(i[0]=="#")continue;const[s,o]=a(i,t);if(s)return["line "+(r+1)+" error: "+s];n.push(o)}return[null,t,n]}function o(r){const e=r.toLowerCase().split("\t");if(e.length<=1)return"invalid file header for fusions";const i=(...r)=>{for(const i of r){const r=e.indexOf(i);if(r!=-1)return r}return-1};let t=i("chr_a","chr1","chra");if(t==-1)return"chr_A missing from header";e[t]="chr1";t=i("chr_b","chr2","chrb");if(t==-1)return"chr_B missing from header";e[t]="chr2";t=i("pos_a","position_a","position1","posa");if(t==-1)return"pos_a missing from header";e[t]="position1";t=i("pos_b","position_b","position2","posb");if(t==-1)return"pos_b missing from header";e[t]="position2";t=i("strand_a","orta","orienta");if(t==-1)return"strand_a missing from header";e[t]="strand1";t=i("strand_b","ortb","orientb");if(t==-1)return"strand_b missing from header";e[t]="strand2";t=i("numreadsa");if(t!=-1)e[t]="reads1";t=i("numreadsb");if(t!=-1)e[t]="reads2";return[null,e]}function a(r,e){const i=r.split("\t");const t={};for(let r=0;r<e.length;r++){t[e[r]]=i[r]}if(!t.chr1)return["missing chr1"];if(t.chr1.toLowerCase().indexOf("chr")!=0){t.chr1="chr"+t.chr1}if(!t.chr2)return["missing chr2"];if(t.chr2.toLowerCase().indexOf("chr")!=0){t.chr2="chr"+t.chr2}if(!t.position1)return["missing position1"];let n=Number.parseInt(t.position1);if(Number.isNaN(n)||n<=0)return["position1 invalid value"];t.position1=n;if(!t.position2)return["missing position2"];n=Number.parseInt(t.position2);if(Number.isNaN(n)||n<=0)return["position2 invalid value"];t.position2=n;if(t.reads1){n=Number.parseInt(t.reads1);if(Number.isNaN(n))return["reads1 invalid value"];t.reads1=n}if(t.reads2){n=Number.parseInt(t.reads2);if(Number.isNaN(n))return["reads2 invalid value"];t.reads2=n}return[null,t]}function f(r,i){if(!i)return"cannot stat hic file";r.normalization=i.normalization;r.version=i.version;if(!i.Chromosomes)return"Chromosomes not found in file stat";if(!Array.isArray(i.chrorder))return".chrorder[] missing";if(i.chrorder.length==0)return".chrorder[] empty array";r.chrorder=i.chrorder;if(!i["Base pair-delimited resolutions"])return"Base pair-delimited resolutions not found in file stat";if(!Array.isArray(i["Base pair-delimited resolutions"]))return"Base pair-delimited resolutions should be array";r.bpresolution=i["Base pair-delimited resolutions"];if(!i["Fragment-delimited resolutions"])return"Fragment-delimited resolutions not found in file stat";if(!Array.isArray(i["Fragment-delimited resolutions"]))return"Fragment-delimited resolutions is not array";r.fragresolution=i["Fragment-delimited resolutions"];const t=[];for(const r in i.Chromosomes){t.push(r)}const[n,s]=e(r.genome,t);if(n+s==0)return"chromosome names do not match with genome build";if(n>0){r.nochr=true;for(let e=0;e<r.chrorder.length;e++)r.chrorder[e]="chr"+r.chrorder[e]}r.chrlst=[];for(const e of r.genome.majorchrorder){const i=r.nochr?e.replace("chr",""):e;if(t.indexOf(i)!=-1){r.chrlst.push(e)}}}function l(r){const e=new Map;let i=null,t;for(const n of r){if(!n.rest||!n.rest[0]){return["items[].rest data problem"]}const r=Number.parseInt(n.rest[0]);if(Number.isNaN(r)){return[n.start+"."+n.stop+" invalid fragment id: "+n.rest[0]]}e.set(r,[n.start,n.stop]);if(i==null){i=r;t=r}else{i=Math.min(i,r);t=Math.max(t,r)}}return[null,e,i,t]}export{f as a,l as b,n as h};
+import{_ as r}from"./tslib.es6-c3c2d88f.js";import{aj as e,q as i,a7 as t}from"./app-6fb77603.js";function n(e,n,o=[]){return r(this,void 0,void 0,(function*(){if(n)window["hic"]=e;if(e.tklst){const r=[];for(const i of e.tklst){if(!i.type){o.push("type missing from one of the tracks accompanying HiC")}else{i.iscustom=true;r.push(i)}}if(r.length){e.tklst=r}else{delete e.tklst}}if(e.enzyme){if(e.genome.hicenzymefragment){let r=null;for(const i of e.genome.hicenzymefragment){if(i.enzyme==e.enzyme){r=i;break}}if(r){e.enzymefile=r.file}else{o.push("unknown enzyme: "+e.enzyme);delete e.enzyme}}else{o.push("no enzyme fragment information available for this genome");delete e.enzyme}}try{if(e.sv&&e.sv.file){const r=yield i(e.hostURL+"/textfile",{method:"POST",body:JSON.stringify({file:e.sv.file,jwt:e.jwt})});const t=r.json();const[n,o,a]=s(t.text);if(n)throw{message:"Error parsing SV: "+n};e.sv.header=o;e.sv.items=a}const r=yield t("hicstat?"+(e.file?"file="+e.file:"url="+e.url));if(r.error){o.push(r.error);return}const n=f(e,r.out);if(n)throw{message:n}}catch(r){o.push(r.message||r);if(r.stack){console.log(r.stack)}}return e}))}function s(r){const e=r.trim().split(/\r?\n/);const[i,t]=o(e[0]);if(i)return["header error: "+i];const n=[];for(let r=1;r<e.length;r++){const i=e[r];if(i[0]=="#")continue;const[s,o]=a(i,t);if(s)return["line "+(r+1)+" error: "+s];n.push(o)}return[null,t,n]}function o(r){const e=r.toLowerCase().split("\t");if(e.length<=1)return"invalid file header for fusions";const i=(...r)=>{for(const i of r){const r=e.indexOf(i);if(r!=-1)return r}return-1};let t=i("chr_a","chr1","chra");if(t==-1)return"chr_A missing from header";e[t]="chr1";t=i("chr_b","chr2","chrb");if(t==-1)return"chr_B missing from header";e[t]="chr2";t=i("pos_a","position_a","position1","posa");if(t==-1)return"pos_a missing from header";e[t]="position1";t=i("pos_b","position_b","position2","posb");if(t==-1)return"pos_b missing from header";e[t]="position2";t=i("strand_a","orta","orienta");if(t==-1)return"strand_a missing from header";e[t]="strand1";t=i("strand_b","ortb","orientb");if(t==-1)return"strand_b missing from header";e[t]="strand2";t=i("numreadsa");if(t!=-1)e[t]="reads1";t=i("numreadsb");if(t!=-1)e[t]="reads2";return[null,e]}function a(r,e){const i=r.split("\t");const t={};for(let r=0;r<e.length;r++){t[e[r]]=i[r]}if(!t.chr1)return["missing chr1"];if(t.chr1.toLowerCase().indexOf("chr")!=0){t.chr1="chr"+t.chr1}if(!t.chr2)return["missing chr2"];if(t.chr2.toLowerCase().indexOf("chr")!=0){t.chr2="chr"+t.chr2}if(!t.position1)return["missing position1"];let n=Number.parseInt(t.position1);if(Number.isNaN(n)||n<=0)return["position1 invalid value"];t.position1=n;if(!t.position2)return["missing position2"];n=Number.parseInt(t.position2);if(Number.isNaN(n)||n<=0)return["position2 invalid value"];t.position2=n;if(t.reads1){n=Number.parseInt(t.reads1);if(Number.isNaN(n))return["reads1 invalid value"];t.reads1=n}if(t.reads2){n=Number.parseInt(t.reads2);if(Number.isNaN(n))return["reads2 invalid value"];t.reads2=n}return[null,t]}function f(r,i){if(!i)return"cannot stat hic file";r.normalization=i.normalization;r.version=i.version;if(!i.Chromosomes)return"Chromosomes not found in file stat";if(!Array.isArray(i.chrorder))return".chrorder[] missing";if(i.chrorder.length==0)return".chrorder[] empty array";r.chrorder=i.chrorder;if(!i["Base pair-delimited resolutions"])return"Base pair-delimited resolutions not found in file stat";if(!Array.isArray(i["Base pair-delimited resolutions"]))return"Base pair-delimited resolutions should be array";r.bpresolution=i["Base pair-delimited resolutions"];if(!i["Fragment-delimited resolutions"])return"Fragment-delimited resolutions not found in file stat";if(!Array.isArray(i["Fragment-delimited resolutions"]))return"Fragment-delimited resolutions is not array";r.fragresolution=i["Fragment-delimited resolutions"];const t=[];for(const r in i.Chromosomes){t.push(r)}const[n,s]=e(r.genome,t);if(n+s==0)return"chromosome names do not match with genome build";if(n>0){r.nochr=true;for(let e=0;e<r.chrorder.length;e++)r.chrorder[e]="chr"+r.chrorder[e]}r.chrlst=[];for(const e of r.genome.majorchrorder){const i=r.nochr?e.replace("chr",""):e;if(t.indexOf(i)!=-1){r.chrlst.push(e)}}}function l(r){const e=new Map;let i=null,t;for(const n of r){if(!n.rest||!n.rest[0]){return["items[].rest data problem"]}const r=Number.parseInt(n.rest[0]);if(Number.isNaN(r)){return[n.start+"."+n.stop+" invalid fragment id: "+n.rest[0]]}e.set(r,[n.start,n.stop]);if(i==null){i=r;t=r}else{i=Math.min(i,r);t=Math.max(t,r)}}return[null,e,i,t]}export{f as a,l as b,n as h};

package/dist/{plot.2dvaf-4016e75e.js → plot.2dvaf-6ae22dc1.js}

@@ -1 +1 @@
-import{M as t,I as e,ah as a,a9 as r,ag as i}from"./app-2cd97738.js";import{b as l,d as s,a as o}from"./axis-747c801e.js";const n="#999";const p="#d95f02";const c="#7570b3";const f="#1b9e77";const d="#f3f3f3";const y=.9;function m(m,g,h){if(g.individualcategories){for(const t of m){const e=t[g.individualcategories.categorykey];if(e&&g.individualcategories.categories[e]){t.color=g.individualcategories.categories[e].color}}}const x=g.individualkey;{const t=h.append("div").style("margin","5px 10px 10px 30px");const e=new Set;for(const t of m){e.add(t[x])}t.append("div").text(e.size+" "+x+(e.size>1?"s":""));if(g.individualcategories){for(const e in g.individualcategories.categories){const a=new Set;for(const t of m){const r=t[x];if(!r)continue;if(t[g.individualcategories.categorykey]==e){a.add(r)}}const r=t.append("div").style("margin","5px");r.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background-color",g.individualcategories.categories[e].color).style("padding","1px 3px").text(a.size).style("margin-right","5px");r.append("span").text(g.individualcategories.categories[e].label||e).style("color",g.individualcategories.categories[e].color)}}}const u=new t({border:"none",padding:"0px"});const v=(t,e,a)=>{if(st){st.filter((e=>e[x]==t[x])).attr("fill-opacity",.5)}if(dt){dt.filter((e=>e[x]==t[x])).attr("fill-opacity",.5)}vt.filter((e=>e[x]==t[x])).attr("fill-opacity",.5);At.filter((e=>e[x]==t[x])).attr("fill-opacity",.5);u.show(e,a);u.clear();const i=[{k:x,v:t[x]},{k:g.xsampletype,v:t.sampletypes[g.xsampletype].vaf.toFixed(2)+", "+t.sampletypes[g.xsampletype].total}];if(g.individualcategories){const 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m){I=Math.max(I,t.sampletypes[g.xsampletype].total);if(t.sampletypes[g.yleftsampletype]){_=Math.max(_,t.sampletypes[g.yleftsampletype].total)}if(t.sampletypes[g.yrightsampletype]){q=Math.max(_,t.sampletypes[g.yrightsampletype].total)}}let B=1;let D=0;const E=e().domain([D,B]);const G=e().domain([D,B]);const H=e().domain([0,I]);let J;let K;if(_){J=e().domain([0,_])}if(q){K=e().domain([0,q])}const L=h.append("svg").style("margin","10px");let N,O,P,Q;if(_){N=L.append("g");O=N.append("g");P=N.append("g");Q=P.append("text").attr("transform","rotate(-90)").text(g.yleftsampletype+" VAF").attr("font-family",a).attr("fill",f).attr("text-anchor","middle").attr("dominant-baseline","central")}let R,T,U,W;if(q){R=L.append("g");T=R.append("g");U=R.append("g");W=U.append("text").attr("transform","rotate(-90)").text(g.yrightsampletype+" VAF").attr("font-family",a).attr("fill",f).attr("text-anchor","middle").attr("dominant-baseline","central")}const Z=L.append("g");const $=Z.append("g");const tt=Z.append("text").text(g.xsampletype+" VAF").attr("font-family",a).attr("fill",c).attr("text-anchor","middle");let et,at,rt,it,lt,st;if(_){et=L.append("g");at=et.append("rect").attr("fill",d);rt=et.append("line").attr("stroke","white").attr("stroke-width",2);it=et.append("g");lt=et.append("g").selectAll().data(m.filter((t=>t.sampletypes[g.yleftsampletype]))).enter().append("g");st=lt.append("circle").attr("fill",(t=>t.color||f)).attr("fill-opacity",0).attr("stroke",(t=>t.color||f)).attr("stroke-opacity",y).on("mouseover",((t,e)=>v(e,t.clientX,t.clientY))).on("mouseout",k)}let ot,nt,pt,ct,ft,dt;if(q){ot=L.append("g");nt=ot.append("rect").attr("fill",d);pt=et.append("line").attr("stroke","white").attr("stroke-width",2);ct=ot.append("g");ft=ot.append("g").selectAll().data(m.filter((t=>t.sampletypes[g.yrightsampletype]))).enter().append("g");dt=ft.append("rect").attr("fill",(t=>t.color||f)).attr("fill-opacity",0).attr("stroke",(t=>t.color||f)).attr("stroke-opacity",y).on("mouseover",((t,e)=>v(e,t.clientX,t.clientY))).on("mouseout",k)}const yt=L.append("g");const mt=yt.append("rect").attr("fill",d);const gt=yt.append("line").attr("stroke","white").attr("stroke-width",2);const ht=yt.append("text").text("Coverage").attr("text-anchor","end").attr("dominant-baseline","central").attr("font-family",a).attr("fill",n);const xt=yt.append("g");const ut=yt.append("g").selectAll().data(m).enter().append("g");const vt=ut.append("circle").attr("fill",(t=>t.color||c)).attr("fill-opacity",0).attr("stroke",(t=>t.color||c)).attr("stroke-opacity",y).on("mouseover",((t,e)=>v(e,t.clientX,t.clientY))).on("mouseout",k);const kt=L.append("g");const wt=kt.append("rect").attr("fill",d);const zt=kt.append("line").attr("stroke","white").attr("stroke-width",2);const bt=kt.append("line").attr("stroke","white").attr("stroke-width",2);const St=kt.append("g").selectAll().data(m).enter().append("g");const At=St.append("circle").attr("fill",(t=>t.color||p)).attr("fill-opacity",0).attr("stroke",(t=>t.color||p)).attr("stroke-opacity",y).on("mouseover",((t,e)=>v(e,t.clientX,t.clientY))).on("mouseout",k);const Ft=()=>{b=C+j+10+j*2;S=C+j*2+10+j*2;V=Y*2;M=C+j+Y+10;E.range([0,w]);G.range([0,-z]);H.range([0,A]);if(J){J.range([0,-F])}if(K){K.range([0,F])}if(N){N.attr("transform","translate("+S+","+(X+z)+")");P.attr("transform","translate(-"+(S-j)+",-"+z/2+")");Q.attr("font-size",j*2)}if(R){R.attr("transform","translate("+((_?S+V+F:0)+M+w+M+F+V)+","+(X+z)+")");U.attr("transform","translate("+(S-j)+",-"+z/2+")");W.attr("font-size",j*2)}Z.attr("transform","translate("+(S+V+F+M)+","+(X+z+M+A+V)+")");tt.attr("font-size",j*2).attr("x",w/2).attr("y",b);if(et){et.attr("transform","translate("+(S+V+F)+","+(X+z)+")");it.attr("transform","translate(0,"+(5+Y)+")");at.attr("x",-F).attr("y",-z).attr("width",F).attr("height",z);rt.attr("x1",-F).attr("y1",-z/2).attr("y2",-z/2)}if(ot){ot.attr("transform","translate("+((_?S+V+F:0)+M+w+M)+","+(X+z)+")");ct.attr("transform","translate(0,"+(5+Y)+")");nt.attr("y",-z).attr("width",F).attr("height",z);pt.attr("y1",-z/2).attr("y2",-z/2).attr("x2",F)}yt.attr("transform","translate("+(S+V+F+M)+","+(X+z+M)+")");xt.attr("transform","translate(-"+(5+Y)+",0)");mt.attr("width",w).attr("height",A);gt.attr("x1",w/2).attr("x2",w/2).attr("y2",A);ht.attr("x",-40).attr("y",A/2).attr("font-size",j*1.5);kt.attr("transform","translate("+(S+V+F+M)+","+(X+z)+")");wt.attr("y",-z).attr("width",w).attr("height",z);zt.attr("y1",-z/2).attr("y2",-z/2).attr("x2",w);bt.attr("x1",w/2).attr("x2",w/2).attr("y2",-z);if(O){i({axis:O.call(l().scale(G).tickSize(C-2)),showline:true,color:n,fontsize:j})}if(T){i({axis:T.call(s().scale(G).tickSize(C-2)),showline:true,color:n,fontsize:j})}i({axis:$.call(o().scale(E).tickSize(C-2)),showline:true,color:n,fontsize:j});i({axis:xt.call(l().scale(H).tickSize(C-2).tickValues([0,I])),showline:true,color:n,fontsize:j});if(it){i({axis:it.call(o().scale(J).tickSize(C-2).tickValues([0,_])),showline:true,color:n,fontsize:j})}if(ct){i({axis:ct.call(o().scale(K).tickSize(C-2).tickValues([0,q])),showline:true,color:n,fontsize:j})}if(lt){lt.attr("transform",(t=>{const e=t.sampletypes[g.yleftsampletype];return"translate("+J(e.total)+","+G(e.vaf)+")"}))}if(ft){ft.attr("transform",(t=>{const e=t.sampletypes[g.yrightsampletype];return"translate("+K(e.total)+","+G(e.vaf)+")"}))}ut.attr("transform",(t=>{const e=t.sampletypes[g.xsampletype];return"translate("+E(e.vaf)+","+H(e.total)+")"}));St.attr("transform",(t=>{const e=t.sampletypes[g.xsampletype];const a=t.sampletypes[g.yleftsampletype]||t.sampletypes[g.yrightsampletype];return"translate("+E(e.vaf)+","+G(a.vaf)+")"}));vt.attr("r",Y);At.attr("r",Y);if(st){st.attr("r",Y)}if(dt){dt.attr("x",-Y).attr("y",-Y).attr("width",Y*2).attr("height",Y*2)}L.attr("width",(_?S+V+F:0)+M+w+M+(q?F+V+S:0)).attr("height",X+z+M+A+V+b)};Ft()}export{m as default};
+import{M as t,I as e,ah as a,a9 as r,ag as i}from"./app-6fb77603.js";import{b as l,d as s,a as o}from"./axis-747c801e.js";const n="#999";const p="#d95f02";const c="#7570b3";const f="#1b9e77";const d="#f3f3f3";const y=.9;function m(m,g,h){if(g.individualcategories){for(const t of m){const e=t[g.individualcategories.categorykey];if(e&&g.individualcategories.categories[e]){t.color=g.individualcategories.categories[e].color}}}const x=g.individualkey;{const t=h.append("div").style("margin","5px 10px 10px 30px");const e=new Set;for(const t of m){e.add(t[x])}t.append("div").text(e.size+" "+x+(e.size>1?"s":""));if(g.individualcategories){for(const e in g.individualcategories.categories){const a=new Set;for(const t of m){const r=t[x];if(!r)continue;if(t[g.individualcategories.categorykey]==e){a.add(r)}}const r=t.append("div").style("margin","5px");r.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background-color",g.individualcategories.categories[e].color).style("padding","1px 3px").text(a.size).style("margin-right","5px");r.append("span").text(g.individualcategories.categories[e].label||e).style("color",g.individualcategories.categories[e].color)}}}const u=new t({border:"none",padding:"0px"});const v=(t,e,a)=>{if(st){st.filter((e=>e[x]==t[x])).attr("fill-opacity",.5)}if(dt){dt.filter((e=>e[x]==t[x])).attr("fill-opacity",.5)}vt.filter((e=>e[x]==t[x])).attr("fill-opacity",.5);At.filter((e=>e[x]==t[x])).attr("fill-opacity",.5);u.show(e,a);u.clear();const i=[{k:x,v:t[x]},{k:g.xsampletype,v:t.sampletypes[g.xsampletype].vaf.toFixed(2)+", "+t.sampletypes[g.xsampletype].total}];if(g.individualcategories){const 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tt=Z.append("text").text(g.xsampletype+" VAF").attr("font-family",a).attr("fill",c).attr("text-anchor","middle");let et,at,rt,it,lt,st;if(_){et=L.append("g");at=et.append("rect").attr("fill",d);rt=et.append("line").attr("stroke","white").attr("stroke-width",2);it=et.append("g");lt=et.append("g").selectAll().data(m.filter((t=>t.sampletypes[g.yleftsampletype]))).enter().append("g");st=lt.append("circle").attr("fill",(t=>t.color||f)).attr("fill-opacity",0).attr("stroke",(t=>t.color||f)).attr("stroke-opacity",y).on("mouseover",((t,e)=>v(e,t.clientX,t.clientY))).on("mouseout",k)}let ot,nt,pt,ct,ft,dt;if(q){ot=L.append("g");nt=ot.append("rect").attr("fill",d);pt=et.append("line").attr("stroke","white").attr("stroke-width",2);ct=ot.append("g");ft=ot.append("g").selectAll().data(m.filter((t=>t.sampletypes[g.yrightsampletype]))).enter().append("g");dt=ft.append("rect").attr("fill",(t=>t.color||f)).attr("fill-opacity",0).attr("stroke",(t=>t.color||f)).attr("stroke-opacity",y).on("mouseover",((t,e)=>v(e,t.clientX,t.clientY))).on("mouseout",k)}const yt=L.append("g");const mt=yt.append("rect").attr("fill",d);const gt=yt.append("line").attr("stroke","white").attr("stroke-width",2);const ht=yt.append("text").text("Coverage").attr("text-anchor","end").attr("dominant-baseline","central").attr("font-family",a).attr("fill",n);const xt=yt.append("g");const ut=yt.append("g").selectAll().data(m).enter().append("g");const vt=ut.append("circle").attr("fill",(t=>t.color||c)).attr("fill-opacity",0).attr("stroke",(t=>t.color||c)).attr("stroke-opacity",y).on("mouseover",((t,e)=>v(e,t.clientX,t.clientY))).on("mouseout",k);const kt=L.append("g");const wt=kt.append("rect").attr("fill",d);const zt=kt.append("line").attr("stroke","white").attr("stroke-width",2);const bt=kt.append("line").attr("stroke","white").attr("stroke-width",2);const St=kt.append("g").selectAll().data(m).enter().append("g");const At=St.append("circle").attr("fill",(t=>t.color||p)).attr("fill-opacity",0).attr("stroke",(t=>t.color||p)).attr("stroke-opacity",y).on("mouseover",((t,e)=>v(e,t.clientX,t.clientY))).on("mouseout",k);const Ft=()=>{b=C+j+10+j*2;S=C+j*2+10+j*2;V=Y*2;M=C+j+Y+10;E.range([0,w]);G.range([0,-z]);H.range([0,A]);if(J){J.range([0,-F])}if(K){K.range([0,F])}if(N){N.attr("transform","translate("+S+","+(X+z)+")");P.attr("transform","translate(-"+(S-j)+",-"+z/2+")");Q.attr("font-size",j*2)}if(R){R.attr("transform","translate("+((_?S+V+F:0)+M+w+M+F+V)+","+(X+z)+")");U.attr("transform","translate("+(S-j)+",-"+z/2+")");W.attr("font-size",j*2)}Z.attr("transform","translate("+(S+V+F+M)+","+(X+z+M+A+V)+")");tt.attr("font-size",j*2).attr("x",w/2).attr("y",b);if(et){et.attr("transform","translate("+(S+V+F)+","+(X+z)+")");it.attr("transform","translate(0,"+(5+Y)+")");at.attr("x",-F).attr("y",-z).attr("width",F).attr("height",z);rt.attr("x1",-F).attr("y1",-z/2).attr("y2",-z/2)}if(ot){ot.attr("transform","translate("+((_?S+V+F:0)+M+w+M)+","+(X+z)+")");ct.attr("transform","translate(0,"+(5+Y)+")");nt.attr("y",-z).attr("width",F).attr("height",z);pt.attr("y1",-z/2).attr("y2",-z/2).attr("x2",F)}yt.attr("transform","translate("+(S+V+F+M)+","+(X+z+M)+")");xt.attr("transform","translate(-"+(5+Y)+",0)");mt.attr("width",w).attr("height",A);gt.attr("x1",w/2).attr("x2",w/2).attr("y2",A);ht.attr("x",-40).attr("y",A/2).attr("font-size",j*1.5);kt.attr("transform","translate("+(S+V+F+M)+","+(X+z)+")");wt.attr("y",-z).attr("width",w).attr("height",z);zt.attr("y1",-z/2).attr("y2",-z/2).attr("x2",w);bt.attr("x1",w/2).attr("x2",w/2).attr("y2",-z);if(O){i({axis:O.call(l().scale(G).tickSize(C-2)),showline:true,color:n,fontsize:j})}if(T){i({axis:T.call(s().scale(G).tickSize(C-2)),showline:true,color:n,fontsize:j})}i({axis:$.call(o().scale(E).tickSize(C-2)),showline:true,color:n,fontsize:j});i({axis:xt.call(l().scale(H).tickSize(C-2).tickValues([0,I])),showline:true,color:n,fontsize:j});if(it){i({axis:it.call(o().scale(J).tickSize(C-2).tickValues([0,_])),showline:true,color:n,fontsize:j})}if(ct){i({axis:ct.call(o().scale(K).tickSize(C-2).tickValues([0,q])),showline:true,color:n,fontsize:j})}if(lt){lt.attr("transform",(t=>{const e=t.sampletypes[g.yleftsampletype];return"translate("+J(e.total)+","+G(e.vaf)+")"}))}if(ft){ft.attr("transform",(t=>{const e=t.sampletypes[g.yrightsampletype];return"translate("+K(e.total)+","+G(e.vaf)+")"}))}ut.attr("transform",(t=>{const e=t.sampletypes[g.xsampletype];return"translate("+E(e.vaf)+","+H(e.total)+")"}));St.attr("transform",(t=>{const e=t.sampletypes[g.xsampletype];const a=t.sampletypes[g.yleftsampletype]||t.sampletypes[g.yrightsampletype];return"translate("+E(e.vaf)+","+G(a.vaf)+")"}));vt.attr("r",Y);At.attr("r",Y);if(st){st.attr("r",Y)}if(dt){dt.attr("x",-Y).attr("y",-Y).attr("width",Y*2).attr("height",Y*2)}L.attr("width",(_?S+V+F:0)+M+w+M+(q?F+V+S:0)).attr("height",X+z+M+A+V+b)};Ft()}export{m as default};

package/dist/plot.app-2a805759.js

@@ -0,0 +1 @@
+import{o as t,M as s,y as r}from"./app-6fb77603.js";import{s as e,r as o}from"./recover-299ffdb3.js";import{v as i}from"./FilterRxComp-02e68f1b.js";import"./termsetting-492eefa7.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./FilterStateless-16a33070.js";import"./app-d215327f.js";import"./termInfo-491b10af.js";import"./toggleButtons-c4d6f260.js";import"./table-0daf2b89.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-39d11f24.js";import"./genesearch-ffd88bf2.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";function a(t){switch(t){case"../plots/DEanalysis.js":return import("./DEanalysis-bbfad00d.js");case"../plots/Disco.js":return import("./Disco-b7c9bf72.js");case"../plots/DziViewer.js":return import("./DziViewer-28915c11.js");case"../plots/WSIViewer.js":return import("./WSIViewer-957695a8.js");case"../plots/barchart.data.js":return import("./FilterRxComp-02e68f1b.js").then((function(t){return t.j}));case"../plots/barchart.events.js":return import("./barchart.events-426d737a.js");case"../plots/barchart.js":return import("./barchart-2898d229.js");case"../plots/bars.renderer.js":return import("./bars.renderer-71935d34.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-4c9a5479.js");case"../plots/brainImaging.js":return import("./brainImaging-7716bc66.js");case"../plots/controls.btns.js":return import("./controls.btns-5bf9e7d7.js");case"../plots/controls.config.js":return import("./controls.config-2f0fa061.js");case"../plots/controls.js":return import("./controls-268e40e6.js");case"../plots/cuminc.js":return import("./cuminc-8dffb765.js");case"../plots/dataDownload.js":return import("./dataDownload-452ae3cd.js");case"../plots/dictionary.js":return import("./dictionary-a132a3cc.js");case"../plots/facet.js":return import("./facet-fa4fe49c.js");case"../plots/geneExpression.js":return import("./geneExpression-66208299.js");case"../plots/geneORA.js":return import("./geneORA-9456872c.js");case"../plots/geneset.js":return import("./geneset-0315daf8.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-2601cab5.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-608b924e.js");case"../plots/gsea.js":return import("./gsea-0c0cf8de.js");case"../plots/hierCluster.config.js":return import("./hierCluster.config-f4daaf92.js");case"../plots/hierCluster.interactivity.js":return import("./hierCluster.interactivity-7f475259.js").then((function(t){return t.i}));case"../plots/hierCluster.js":return import("./hierCluster-7ab62ca5.js");case"../plots/hierCluster.renderers.js":return import("./hierCluster.renderers-19b79639.js").then((function(t){return t.r}));case"../plots/imagePlot.js":return import("./imagePlot-1ef24562.js");case"../plots/matrix.cells.js":return import("./matrix.cells-a018d731.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-a6e713e8.js");case"../plots/matrix.config.js":return import("./matrix.config-2c550b5d.js");case"../plots/matrix.controls.js":return import("./matrix.controls-42ad4912.js");case"../plots/matrix.data.js":return import("./matrix.data-2b814c9f.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-1e0da5b3.js");case"../plots/matrix.groups.js":return import("./matrix.groups-824a7244.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-1cb56534.js");case"../plots/matrix.js":return import("./matrix-38cd47c3.js");case"../plots/matrix.layout.js":return import("./matrix.layout-47e44357.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-9af0c757.js").then((function(t){return t.m}));case"../plots/matrix.renderers.js":return import("./matrix.renderers-337ce240.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-7b7184c9.js").then((function(t){return t.m}));case"../plots/matrix.sort.js":return import("./matrix.sort-1ac05842.js");case"../plots/matrix.sorterUi.js":return import("./matrix.sorterUi-1c60c145.js");case"../plots/plot.app.js":return Promise.resolve().then((function(){return c}));case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-32a484b6.js");case"../plots/plot.disco.js":return import("./plot.disco-1fdfee3c.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-d33113d5.js");case"../plots/profileBarchart.js":return import("./profileBarchart-58f0a8c0.js");case"../plots/profilePlot.js":return import("./profilePlot-4db8ca78.js");case"../plots/profilePolar.js":return import("./profilePolar-50b8e40e.js");case"../plots/profileRadar.js":return import("./profileRadar-fff0b004.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-d6d34c15.js");case"../plots/profileSummary.js":return import("./profileSummary-04b8b15b.js");case"../plots/regression.inputs.js":return import("./regression.inputs-14df7c31.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-14df7c31.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-d79efa9e.js");case"../plots/regression.js":return import("./regression.inputs-14df7c31.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-4767144e.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter-55d9eb74.js").then((function(t){return t.a}));case"../plots/sampleScatter.js":return import("./sampleScatter-55d9eb74.js").then((function(t){return t.b}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-55d9eb74.js").then((function(t){return t.s}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-ef289434.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-1dff3fca.js");case"../plots/scatter.js":return import("./scatter-f8285107.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-eff5760b.js");case"../plots/stattable.js":return import("./stattable-46cde32c.js");case"../plots/summary.js":return import("./summary-a6c15c9e.js");case"../plots/survival.js":return import("./survival-52714cd3.js");case"../plots/table.js":return import("./table-bf40249b.js");case"../plots/variantBrowser.js":return import("./variantBrowser-14d5c3f6.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-bf40ddde.js");case"../plots/violin.js":return import("./violin-74d26b75.js");case"../plots/violin.renderer.js":return import("./violin.renderer-469fa0ff.js");default:return new Promise((function(s,r){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(r.bind(null,new Error("Unknown variable dynamic import: "+t)))}))}}class n{constructor(t){this.type="app";const s=t.violin?.mode=="minimal"?null:t.holder.append("div").style("white-space","nowrap");this.dom={holder:t.holder,errdiv:t.holder.append("div"),plotDiv:t.holder.append("div")};if(s){this.dom.plotControls=s.append("div").style("display","inline-block");this.dom.recoverControls=s.append("div").style("display","inline-block")}}validateOpts(t={}){if(!t.holder)throw`missing opts.holder in the MassApp constructor argument`;if(!t.callbacks)t.callbacks={};return t}async preApiFreeze(t){try{t.tip=new s({padding:"5px"});t.printError=t=>this.printError(t);const r=this.opts.state.vocab;t.vocabApi=this.opts.vocabApi?this.opts.vocabApi:await i({app:t,state:{vocab:{genome:r?.genome||this.opts.state.genome,dslabel:r?.dslabel||this.opts.state.dslabel,terms:r?.terms}},fetchOpts:this.opts.fetchOpts});this.opts.state.vocab=t.vocabApi.vocab}catch(t){throw t}}async init(){try{this.opts.state.nav={header_mode:"hidden"};this.store=await e({app:this.api,state:this.opts.state});this.state=await this.store.copyState();this.components={plots:{}};if(this.opts.app?.features?.includes("recover"))this.components.recover=await o({app:this.api,holder:this.dom.recoverControls,getState:t=>t,maxHistoryLen:10});await this.api.dispatch()}catch(t){this.printError(t);throw t}}async main(){this.api.vocabApi.main();for(const t in this.components.plots){const s=this.components.plots[t];if(!this.state.plots.find((t=>t.id===s.id))){s.destroy();delete this.components.plots[t]}}for(const[t,s]of this.state.plots.entries()){if(!this.components.plots[s.id]){const t=this.opts?.app?.getPlotHolder?this.opts.app.getPlotHolder(s,this.dom.holder):this.dom.holder.append("div");if(!this.dom.plotDiv)this.dom.plotDiv=t;const r=await a(`../plots/${s.chartType}.js`);const e=await r.componentInit({id:s.id,app:this.api,holder:t,controls:this.dom.plotControls});this.components.plots[s.id]=e}}}printError(t){r(this.dom.errdiv,"Error: "+(t.message||t));if(t.stack)console.log(t.stack);this.bus.emit("error")}destroy(){this.dom.holder.selectAll("*").remove()}}const p=t(n);var c=Object.freeze({__proto__:null,appInit:p});export{p as appInit};

package/dist/plot.barplot-34841e70.js

@@ -0,0 +1 @@
+import{Z as t,U as a,ah as e,I as o,W as n,ag as i}from"./app-6fb77603.js";import{c as l}from"./axis-747c801e.js";function r(a,e,o,n){const i=t({x:n.left+200,y:n.top});i.body.style("padding","10px");i.header.html(o);a.sort(((t,a)=>a.size-t.size));s({lst:a,holder:i.body,barcolor:e,limit:Math.min(a.length,20)})}function s(t){t.holder.selectAll("*").remove();const r=t.holder.append("div").style("margin-bottom","10px");r.append("button").text("more").on("click",(()=>{t.limit=Math.min(t.lst.length,t.limit+10);s(t)}));r.append("button").text("less").on("click",(()=>{t.limit=Math.max(1,t.limit-10);s(t)}));r.append("button").text("screenshot").on("click",(()=>a(b.node(),"barplot")));let m=20,c=300,d=5,p=m+5,h=m/8,x=0,f=0;const b=t.holder.append("svg");const g=b.append("g");for(let a=0;a<t.limit;a++){let o=t.lst[a];f=Math.max(f,o.size);b.append("text").text(o.name).attr("font-size",m-2).attr("font-family",e).each((function(){x=Math.max(x,this.getBBox().width)})).remove()}b.attr("width",x+d+c+d).attr("height",p+d+t.limit*(m+h));g.attr("transform","translate("+(x+d)+","+p+")").call(l().scale(o().domain([0,f]).range([0,c])).tickFormat(n("d")));i({axis:g,showline:true,fontsize:m*.8,color:"black"});let y=p+d;const u=c/f;for(let a=0;a<t.limit;a++){const o=t.lst[a];b.append("text").text(o.name).attr("x",x).attr("y",y+m/2).attr("text-anchor","end").attr("font-size",m-2).attr("font-family",e).attr("dominant-baseline","central");b.append("rect").attr("x",x+d).attr("y",y).attr("width",u*o.size).attr("height",m-1).attr("fill",t.barcolor);y+=m+h}}export{r as default};

package/dist/{plot.boxplot-76229491.js → plot.boxplot-87ac2ce9.js}

@@ -1 +1 @@
-import{a8 as t,af as e,ah as r,I as a,ag as n}from"./app-2cd97738.js";import{c as i}from"./axis-747c801e.js";function s(s){if(!s.holder)return".holder missing for boxplot";if(!s.list)return".list[] missing";if(!Array.isArray(s.list))return".list should be array";for(const t of s.list){if(!t.label)return".label missing for a group";if(t.samples){for(const e of t.samples){if(!Number.isFinite(e.value))return".value missing from a sample"}}else{if(!Number.isFinite(t.minvalue))return".minvalue missing for a group";if(!Number.isFinite(t.maxvalue))return".maxvalue missing for a group";if(!t.percentile)return".percentile{} missing from a group";if(!Number.isFinite(t.percentile.p05))return".percentile.p05 missing for a group";if(!Number.isFinite(t.percentile.p25))return".percentile.p25 missing for a group";if(!Number.isFinite(t.percentile.p50))return".percentile.p50 missing for a group";if(!Number.isFinite(t.percentile.p75))return".percentile.p75 missing for a group";if(!Number.isFinite(t.percentile.p95))return".percentile.p95 missing for a group"}}const l=t(e);const o=s.holder.append("svg");let p=40,f=300,u=10,c=10,m=30,g=12,h=15;let d=0;let x=null;let b=null;for(const t of s.list){const e=t.samplecount?t.samplecount:t.samples?t.samples.length:null;o.append("text").text(t.label+(e?" (n="+e+")":"")).attr("font-family",r).attr("font-size",h).each((function(){d=Math.max(d,this.getBBox().width)})).remove();if(t.samples){for(const e of t.samples){if(e.value==undefined)continue;if(x==null){x=e.value;b=e.value}else{x=Math.min(x,e.value);b=Math.max(b,e.value)}}}else{if(x==null){x=t.minvalue;b=t.maxvalue}else{x=Math.min(x,t.minvalue);b=Math.max(b,t.maxvalue)}}}o.attr("width",d+c+f+c).attr("height",p+(u+m)*s.list.length+10);const v=o.append("g").attr("transform","translate("+(d+c)+","+p+")");const y=a().domain([x,b]).range([0,f]);const M=v.append("g");n({axis:M.call(i().scale(y).ticks(5)),showline:true,fontsize:g,color:"black"});if(s.axislabel){v.append("text").text(s.axislabel).attr("x",f/2).attr("y",-g-13).attr("font-family",r).attr("font-size",h).attr("text-anchor","middle")}let k=0;for(const t of s.list){k+=u;const e=v.append("g").attr("transform","translate(0,"+k+")");k+=m;const a=t.samplecount?t.samplecount:t.samples?t.samples.length:null;e.append("text").text(t.label+(a?" (n="+a+")":"")).attr("x",-c).attr("y",m/2).attr("text-anchor","end").attr("dominant-baseline","central").attr("font-family",r).attr("font-size",h).attr("fill","black");let n,i,s,o,p;if(t.samples){const e=t.samples.map((t=>t.value));e.sort(((t,e)=>t-e));n=e[Math.floor(e.length*.05)];i=e[Math.floor(e.length*.25)];s=e[Math.floor(e.length*.5)];o=e[Math.floor(e.length*.75)];p=e[Math.floor(e.length*.95)]}else{n=t.percentile.p05;i=t.percentile.p25;s=t.percentile.p50;o=t.percentile.p75;p=t.percentile.p95}const f=y(n);const g=y(i);const d=y(s);const x=y(o);const b=y(p);const M=t.color||l(t.label);e.append("line").attr("y1",m/2).attr("y2",m/2).attr("x1",f).attr("x2",b).attr("stroke",M).attr("shape-rendering","crispEdges");e.append("line").attr("y2",m).attr("x1",f).attr("x2",f).attr("stroke",M).attr("shape-rendering","crispEdges");e.append("line").attr("y2",m).attr("x1",b).attr("x2",b).attr("stroke",M).attr("shape-rendering","crispEdges");e.append("rect").attr("x",g).attr("width",x-g).attr("height",m).attr("stroke",M).attr("fill","white").attr("shape-rendering","crispEdges");e.append("line").attr("y2",m).attr("x1",d).attr("x2",d).attr("stroke",M).attr("shape-rendering","crispEdges")}return null}export{s as default};
+import{a8 as t,af as e,ah as r,I as a,ag as n}from"./app-6fb77603.js";import{c as i}from"./axis-747c801e.js";function s(s){if(!s.holder)return".holder missing for boxplot";if(!s.list)return".list[] missing";if(!Array.isArray(s.list))return".list should be array";for(const t of s.list){if(!t.label)return".label missing for a group";if(t.samples){for(const e of t.samples){if(!Number.isFinite(e.value))return".value missing from a sample"}}else{if(!Number.isFinite(t.minvalue))return".minvalue missing for a group";if(!Number.isFinite(t.maxvalue))return".maxvalue missing for a group";if(!t.percentile)return".percentile{} missing from a group";if(!Number.isFinite(t.percentile.p05))return".percentile.p05 missing for a group";if(!Number.isFinite(t.percentile.p25))return".percentile.p25 missing for a group";if(!Number.isFinite(t.percentile.p50))return".percentile.p50 missing for a group";if(!Number.isFinite(t.percentile.p75))return".percentile.p75 missing for a group";if(!Number.isFinite(t.percentile.p95))return".percentile.p95 missing for a group"}}const l=t(e);const o=s.holder.append("svg");let p=40,f=300,u=10,m=10,c=30,g=12,h=15;let d=0;let x=null;let b=null;for(const t of s.list){const e=t.samplecount?t.samplecount:t.samples?t.samples.length:null;o.append("text").text(t.label+(e?" (n="+e+")":"")).attr("font-family",r).attr("font-size",h).each((function(){d=Math.max(d,this.getBBox().width)})).remove();if(t.samples){for(const e of t.samples){if(e.value==undefined)continue;if(x==null){x=e.value;b=e.value}else{x=Math.min(x,e.value);b=Math.max(b,e.value)}}}else{if(x==null){x=t.minvalue;b=t.maxvalue}else{x=Math.min(x,t.minvalue);b=Math.max(b,t.maxvalue)}}}o.attr("width",d+m+f+m).attr("height",p+(u+c)*s.list.length+10);const v=o.append("g").attr("transform","translate("+(d+m)+","+p+")");const y=a().domain([x,b]).range([0,f]);const M=v.append("g");n({axis:M.call(i().scale(y).ticks(5)),showline:true,fontsize:g,color:"black"});if(s.axislabel){v.append("text").text(s.axislabel).attr("x",f/2).attr("y",-g-13).attr("font-family",r).attr("font-size",h).attr("text-anchor","middle")}let k=0;for(const t of s.list){k+=u;const e=v.append("g").attr("transform","translate(0,"+k+")");k+=c;const a=t.samplecount?t.samplecount:t.samples?t.samples.length:null;e.append("text").text(t.label+(a?" (n="+a+")":"")).attr("x",-m).attr("y",c/2).attr("text-anchor","end").attr("dominant-baseline","central").attr("font-family",r).attr("font-size",h).attr("fill","black");let n,i,s,o,p;if(t.samples){const e=t.samples.map((t=>t.value));e.sort(((t,e)=>t-e));n=e[Math.floor(e.length*.05)];i=e[Math.floor(e.length*.25)];s=e[Math.floor(e.length*.5)];o=e[Math.floor(e.length*.75)];p=e[Math.floor(e.length*.95)]}else{n=t.percentile.p05;i=t.percentile.p25;s=t.percentile.p50;o=t.percentile.p75;p=t.percentile.p95}const f=y(n);const g=y(i);const d=y(s);const x=y(o);const b=y(p);const M=t.color||l(t.label);e.append("line").attr("y1",c/2).attr("y2",c/2).attr("x1",f).attr("x2",b).attr("stroke",M).attr("shape-rendering","crispEdges");e.append("line").attr("y2",c).attr("x1",f).attr("x2",f).attr("stroke",M).attr("shape-rendering","crispEdges");e.append("line").attr("y2",c).attr("x1",b).attr("x2",b).attr("stroke",M).attr("shape-rendering","crispEdges");e.append("rect").attr("x",g).attr("width",x-g).attr("height",c).attr("stroke",M).attr("fill","white").attr("shape-rendering","crispEdges");e.append("line").attr("y2",c).attr("x1",d).attr("x2",d).attr("stroke",M).attr("shape-rendering","crispEdges")}return null}export{s as default};

package/dist/{plot.brainImaging-39b80a1c.js → plot.brainImaging-32a484b6.js}

@@ -1 +1 @@
-async function e(e,a,o,n,i,r,s={}){const m=t(s);const c=i.append("div").style("margin","20px").text("Loading...");try{if(typeof e?.queries?.NIdata!="object")throw"termdbConfig.queries.NIdata{} not object";const t=e.queries.NIdata[o];if(!t)throw"invalid queryKey";if(typeof n!="object")throw"sample{} not object";if(typeof r!="object")throw"genomeObj{} not object";const s={sampleName:n.sample_id,genome:r,queryKey:o};const d={holder:i,state:{genome:r.name,dslabel:a,plots:[{chartType:"brainImaging",selectedSampleFileNames:[n.sample_id+".nii"],queryKey:o,overrides:m}]}};const p=await import("./plot.app-d6fe76e2.js");const l=await p.appInit(d);c.remove()}catch(e){c.text("Error: "+(e.message||e))}}function t(e){const t=structuredClone(e);if(!t.brainImaging)t.brainImaging={};if(!t.downloadImgName){t.downloadImgName="brainImaging"}return t}export{e as default};
+async function e(e,a,o,n,i,r,s={}){const m=t(s);const c=i.append("div").style("margin","20px").text("Loading...");try{if(typeof e?.queries?.NIdata!="object")throw"termdbConfig.queries.NIdata{} not object";const t=e.queries.NIdata[o];if(!t)throw"invalid queryKey";if(typeof n!="object")throw"sample{} not object";if(typeof r!="object")throw"genomeObj{} not object";const s={sampleName:n.sample_id,genome:r,queryKey:o};const d={holder:i,state:{genome:r.name,dslabel:a,plots:[{chartType:"brainImaging",selectedSampleFileNames:[n.sample_id+".nii"],queryKey:o,overrides:m}]}};const p=await import("./plot.app-2a805759.js");const l=await p.appInit(d);c.remove()}catch(e){c.text("Error: "+(e.message||e))}}function t(e){const t=structuredClone(e);if(!t.brainImaging)t.brainImaging={};if(!t.downloadImgName){t.downloadImgName="brainImaging"}return t}export{e as default};

package/dist/{plot.disco-9a544f9a.js → plot.disco-1fdfee3c.js}

@@ -1 +1 @@
-import{b as e,B as t}from"./app-2cd97738.js";async function o(o,a,i,r,n,l={},m=true){const p=s(l,o,n,i);const c=r.append("div").style("margin","20px").text("Loading...");try{if(typeof o?.queries?.singleSampleMutation!="object")throw"termdbConfig.queries.singleSampleMutation{} not object";if(typeof i!="object")throw"sample{} not object";if(typeof n!="object")throw"genomeObj{} not object";const s={genome:n.name,dslabel:a,sample:i[o.queries.singleSampleMutation.sample_id_key]};const l=await e("termdb/singleSampleMutation",{body:s});if(l.error)throw l.error;if(!Array.isArray(l.mlst))throw"data.mlst is not array";if(l.dt2total?.length){for(const e of l.dt2total){r.append("div").style("margin","20px 20px 0px 40px").text(`(Displaying ${l.mlst.filter((t=>t.dt==e.dt)).length} out of total ${e.total} ${t[e.dt]})`)}}const m=l.mlst;for(const e of m)e.position=e.pos;const d={sampleName:i[o.queries.singleSampleMutation.sample_id_key],data:m,genome:n};if(o.queries.singleSampleMutation.discoSkipChrM){d.chromosomes={};for(const e in n.majorchr){if(e.toLowerCase()=="chrm")continue;d.chromosomes[e]=n.majorchr[e]}}const f={holder:r,state:{genome:n.name,dslabel:a,args:d,plots:[{chartType:"Disco",subfolder:"disco",extension:"ts",overrides:p}]}};const u=await import("./plot.app-d6fe76e2.js");const g=await u.appInit(f);c.remove();return true}catch(e){if(m)c.text("Error: "+(e.message||e));else c.remove();return false}}function s(e,t,o,s){const a=structuredClone(e);if(!a.Disco)a.Disco={};a.Disco.showPrioritizeGeneLabelsByGeneSets=!!o.geneset;if(!a.downloadImgName){a.downloadImgName=s[t.queries.singleSampleMutation.sample_id_key]+" Disco"}return a}export{o as default};
+import{b as e,B as t}from"./app-6fb77603.js";async function o(o,a,i,r,n,l={},m=true){const p=s(l,o,n,i);const c=r.append("div").style("margin","20px").text("Loading...");try{if(typeof o?.queries?.singleSampleMutation!="object")throw"termdbConfig.queries.singleSampleMutation{} not object";if(typeof i!="object")throw"sample{} not object";if(typeof n!="object")throw"genomeObj{} not object";const s={genome:n.name,dslabel:a,sample:i[o.queries.singleSampleMutation.sample_id_key]};const l=await e("termdb/singleSampleMutation",{body:s});if(l.error)throw l.error;if(!Array.isArray(l.mlst))throw"data.mlst is not array";if(l.dt2total?.length){for(const e of l.dt2total){r.append("div").style("margin","20px 20px 0px 40px").text(`(Displaying ${l.mlst.filter((t=>t.dt==e.dt)).length} out of total ${e.total} ${t[e.dt]})`)}}const m=l.mlst;for(const e of m)e.position=e.pos;const d={sampleName:i[o.queries.singleSampleMutation.sample_id_key],data:m,genome:n};if(o.queries.singleSampleMutation.discoSkipChrM){d.chromosomes={};for(const e in n.majorchr){if(e.toLowerCase()=="chrm")continue;d.chromosomes[e]=n.majorchr[e]}}const f={holder:r,state:{genome:n.name,dslabel:a,args:d,plots:[{chartType:"Disco",subfolder:"disco",extension:"ts",overrides:p}]}};const u=await import("./plot.app-2a805759.js");const g=await u.appInit(f);c.remove();return true}catch(e){if(m)c.text("Error: "+(e.message||e));else c.remove();return false}}function s(e,t,o,s){const a=structuredClone(e);if(!a.Disco)a.Disco={};a.Disco.showPrioritizeGeneLabelsByGeneSets=!!o.geneset;if(!a.downloadImgName){a.downloadImgName=s[t.queries.singleSampleMutation.sample_id_key]+" Disco"}return a}export{o as default};

package/dist/{plot.dzi-f1658ebf.js → plot.dzi-e3d0f610.js}

@@ -1 +1 @@
-async function e(e,t,a,s,o){const i=t.append("div").style("margin","20px").text("Loading...");try{const n={holder:t,state:{genome:a.name,dslabel:e,sample_id:s,dzimages:o,plots:[{chartType:"DziViewer",subfolder:"dziviewer",extension:"ts"}]}};const p=await import("./plot.app-d6fe76e2.js");const r=await p.appInit(n);i.remove()}catch(e){i.text("Error: "+(e.message||e))}}export{e as default};
+async function e(e,t,a,s,o){const i=t.append("div").style("margin","20px").text("Loading...");try{const n={holder:t,state:{genome:a.name,dslabel:e,sample_id:s,dzimages:o,plots:[{chartType:"DziViewer",subfolder:"dziviewer",extension:"ts"}]}};const p=await import("./plot.app-2a805759.js");const r=await p.appInit(n);i.remove()}catch(e){i.text("Error: "+(e.message||e))}}export{e as default};

package/dist/{plot.ssgq-aeb2dabc.js → plot.ssgq-d33113d5.js}

@@ -1 +1 @@
-import{b as t,w as e,f as o}from"./app-2cd97738.js";async function i(o,i,a,r,s,c,l,p=true){const m=s.append("div").text("Loading...");try{if(typeof o?.queries?.singleSampleGenomeQuantification!="object")throw"termdbConfig.queries.singleSampleGenomeQuantification{} missing, cannot plot";const p=o.queries.singleSampleGenomeQuantification[a];if(!p)throw"invalid queryKey";if(typeof r!="object")throw"sample{} not object";if(typeof c!="object")throw"genomeObj{} not object";const d={genome:c.name,dslabel:i,devicePixelRatio:window.devicePixelRatio>1?window.devicePixelRatio:1,singleSampleGenomeQuantification:{dataType:a,sample:r[p.sample_id_key]}};const f=await t("mds3",{body:d});if(f.error)throw f.error;const h=o.queries.singleSampleGbtk?.[p.singleSampleGbtk];s.append("div").attr("data-testid","sjpp_ssgq_sandbox").text(p.description||a);if(h){s.append("div").text(`Click a chromosomal position to zoom in and view ${h.description||p.singleSampleGbtk}`)}const g=s.append("img").attr("width",f.canvasWidth).attr("height",f.canvasHeight).attr("src",f.src);m.remove();if(!h)return;let u;if(l){const o=await t("genelookup",{body:{genome:c.name,input:l,deep:1}});if(o.error)throw o.error;if(o.gmlst&&o.gmlst.length){const t=e(o.gmlst);const a=t[0].chr;const l=Math.max(0,t[0].start-(t[0].stop-t[0].start));const m=f.chrLst.filter((t=>t.chr==a))[0].chrLen;const d=Math.min(m,t[0].stop+(t[0].stop-t[0].start));u=await n(i,r,s,c,p,h,a,l,d)}}g.on("click",(async t=>{const e=t.offsetX-f.xoff;let o,a,l;for(const t of f.chrLst){if(t.xStart<=e&&t.xStop>=e){o=t.chr;a=t.chrLen;l=Math.ceil(t.chrLen/(t.xStop-t.xStart)*(e-t.xStart));break}}if(!o)return;const m=Math.max(0,l-5e5),d=Math.min(l+5e5,a);if(u){u.jump_1basedcoordinate({chr:o,start:m,stop:d});return}u=await n(i,r,s,c,p,h,o,m,d)}));return true}catch(t){if(p)m.text("Error: "+(t.message||t));else m.remove();return false}}async function n(e,i,n,a,r,s,c,l,p){const m={genome:a.name,dslabel:e,singleSampleGbtk:{dataType:r.singleSampleGbtk,sample:i[s.sample_id_key]}};const d=await t("mds3",{body:m});if(!d.path)return;const f=[{type:"bigwig",name:i[s.sample_id_key],file:d.path,height:100,scale:{min:s.min,max:s.max},pcolor:r.positiveColor,ncolor:r.negativeColor}];o(a,f);const h=new((await import("./block-4134e823.js").then((function(t){return t.c}))).Block)({genome:a,holder:n.append("div"),nobox:true,tklst:f,chr:c,start:l,stop:p});return h}export{i as plotSingleSampleGenomeQuantification};
+import{b as t,w as e,f as o}from"./app-6fb77603.js";async function i(o,i,a,r,s,c,l,p=true){const m=s.append("div").text("Loading...");try{if(typeof o?.queries?.singleSampleGenomeQuantification!="object")throw"termdbConfig.queries.singleSampleGenomeQuantification{} missing, cannot plot";const p=o.queries.singleSampleGenomeQuantification[a];if(!p)throw"invalid queryKey";if(typeof r!="object")throw"sample{} not object";if(typeof c!="object")throw"genomeObj{} not object";const d={genome:c.name,dslabel:i,devicePixelRatio:window.devicePixelRatio>1?window.devicePixelRatio:1,singleSampleGenomeQuantification:{dataType:a,sample:r[p.sample_id_key]}};const f=await t("mds3",{body:d});if(f.error)throw f.error;const h=o.queries.singleSampleGbtk?.[p.singleSampleGbtk];s.append("div").attr("data-testid","sjpp_ssgq_sandbox").text(p.description||a);if(h){s.append("div").text(`Click a chromosomal position to zoom in and view ${h.description||p.singleSampleGbtk}`)}const g=s.append("img").attr("width",f.canvasWidth).attr("height",f.canvasHeight).attr("src",f.src);m.remove();if(!h)return;let u;if(l){const o=await t("genelookup",{body:{genome:c.name,input:l,deep:1}});if(o.error)throw o.error;if(o.gmlst&&o.gmlst.length){const t=e(o.gmlst);const a=t[0].chr;const l=Math.max(0,t[0].start-(t[0].stop-t[0].start));const m=f.chrLst.filter((t=>t.chr==a))[0].chrLen;const d=Math.min(m,t[0].stop+(t[0].stop-t[0].start));u=await n(i,r,s,c,p,h,a,l,d)}}g.on("click",(async t=>{const e=t.offsetX-f.xoff;let o,a,l;for(const t of f.chrLst){if(t.xStart<=e&&t.xStop>=e){o=t.chr;a=t.chrLen;l=Math.ceil(t.chrLen/(t.xStop-t.xStart)*(e-t.xStart));break}}if(!o)return;const m=Math.max(0,l-5e5),d=Math.min(l+5e5,a);if(u){u.jump_1basedcoordinate({chr:o,start:m,stop:d});return}u=await n(i,r,s,c,p,h,o,m,d)}));return true}catch(t){if(p)m.text("Error: "+(t.message||t));else m.remove();return false}}async function n(e,i,n,a,r,s,c,l,p){const m={genome:a.name,dslabel:e,singleSampleGbtk:{dataType:r.singleSampleGbtk,sample:i[s.sample_id_key]}};const d=await t("mds3",{body:m});if(!d.path)return;const f=[{type:"bigwig",name:i[s.sample_id_key],file:d.path,height:100,scale:{min:s.min,max:s.max},pcolor:r.positiveColor,ncolor:r.negativeColor}];o(a,f);const h=new((await import("./block-75d4ff92.js").then((function(t){return t.c}))).Block)({genome:a,holder:n.append("div"),nobox:true,tklst:f,chr:c,start:l,stop:p});return h}export{i as plotSingleSampleGenomeQuantification};

package/dist/{plot.vaf2cov-ba8332ed.js → plot.vaf2cov-9f4f1776.js}

@@ -1 +1 @@
-import{I as t,ah as a,a8 as r,af as e,d as o,a9 as n,ag as s,W as l}from"./app-2cd97738.js";import{a as c,b as i}from"./axis-747c801e.js";function p(p){for(const t of p.data){if(!t.sampleobj)t.sampleobj={}}let d=p.width||200;let f=p.height||200;const m=p.color||"#999";let h;let x=p.maxtotal||0;if(p.automax){for(const t of p.data){x=Math.max(x,t.total)}}let u=1;const y=[];const g=[];const k=p.bincount||20;for(let t=0;t<k;t++){y.push(0);g.push(0)}{const t=x/k;const a=u/k;for(const r of p.data){if(r.total>=x){y[k-1]++}else{y[Math.floor(r.total/t)]++}g[Math.floor((r.maf==1?.99:r.maf)/a)]++}}const w=Math.max(...y);const b=Math.max(...g);const v=t().domain([0,x]),z=t().domain([0,u]),j=t().domain([0,w]),M=t().domain([0,b]);const A=p.holder.append("svg").style("margin","10px");const F=A.append("text").text("Coverage").attr("text-anchor","middle").attr("fill",m).attr("font-family",a);const S=A.append("g");const 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+import{I as t,ah as a,a8 as r,af as e,d as o,a9 as n,ag as s,W as l}from"./app-6fb77603.js";import{a as c,b as i}from"./axis-747c801e.js";function p(p){for(const t of p.data){if(!t.sampleobj)t.sampleobj={}}let d=p.width||200;let f=p.height||200;const m=p.color||"#999";let h;let x=p.maxtotal||0;if(p.automax){for(const t of p.data){x=Math.max(x,t.total)}}let u=1;const y=[];const g=[];const k=p.bincount||20;for(let t=0;t<k;t++){y.push(0);g.push(0)}{const t=x/k;const a=u/k;for(const r of p.data){if(r.total>=x){y[k-1]++}else{y[Math.floor(r.total/t)]++}g[Math.floor((r.maf==1?.99:r.maf)/a)]++}}const w=Math.max(...y);const b=Math.max(...g);const v=t().domain([0,x]),z=t().domain([0,u]),j=t().domain([0,w]),M=t().domain([0,b]);const A=p.holder.append("svg").style("margin","10px");const F=A.append("text").text("Coverage").attr("text-anchor","middle").attr("fill",m).attr("font-family",a);const S=A.append("g");const 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T=P.append("circle").attr("fill","white").attr("fill-opacity",0).on("mouseover",((t,a)=>{a.crosshair1.attr("stroke-width",3).attr("x1",-h-2).attr("y1",-h-2).attr("x2",h+2).attr("y2",h+2);a.crosshair2.attr("stroke-width",3).attr("x1",h+2).attr("y1",-h-2).attr("x2",-h-2).attr("y2",h+2);p.tip.clear();p.tip.show(t.clientX,t.clientY);const r=[{k:"mut",v:a.mut},{k:"total",v:a.total}];if(a.genotype){r.push({k:"genotype",v:a.genotype})}for(const t in a.sampleobj){if(t=="color")continue;r.push({k:t,v:a.sampleobj[t]})}n(p.tip.d,r).style("margin","none");if(p.mouseover){p.mouseover(a)}})).on("mouseout",((t,a)=>{a.crosshair1.attr("stroke-width",1).attr("x1",-h).attr("y1",-h).attr("x2",h).attr("y2",h);a.crosshair2.attr("stroke-width",1).attr("x1",h).attr("y1",-h).attr("x2",-h).attr("y2",h);p.tip.hide();if(p.mouseout){p.mouseout(a)}}));if(p.click){T.on("click",((t,a)=>{p.click(a)}))}const U=A.append("text").text("drag to 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package/dist/{plot.wsi-2d802557.js → plot.wsi-dea124a7.js}

@@ -1 +1 @@
-async function e(e,t,a,s){const o=t.append("div").style("margin","20px").text("Loading...");try{const n={holder:t,state:{genome:a.name,dslabel:e,sample_id:s,plots:[{chartType:"WSIViewer",subfolder:"wsiviewer",extension:"ts"}]}};const i=await import("./plot.app-d6fe76e2.js");const p=await i.appInit(n);o.remove()}catch(e){o.text("Error: "+(e.message||e))}}export{e as default};
+async function e(e,t,a,s){const o=t.append("div").style("margin","20px").text("Loading...");try{const n={holder:t,state:{genome:a.name,dslabel:e,sample_id:s,plots:[{chartType:"WSIViewer",subfolder:"wsiviewer",extension:"ts"}]}};const i=await import("./plot.app-2a805759.js");const p=await i.appInit(n);o.remove()}catch(e){o.text("Error: "+(e.message||e))}}export{e as default};