@sjcrh/proteinpaint-client 2.74.2 → 2.76.0

package/dist/numeric.toggle-7fa2a770.js

@@ -0,0 +1 @@
+import{_ as e}from"./tslib.es6-c3c2d88f.js";import{T as i}from"./toggleButtons-dbdbad01.js";import{o as t,c as n,s as r}from"./termsetting-33ea66f1.js";import{P as s}from"./app-b369b169.js";import"path";function o(e){switch(e){case"./numeric.binary.ts":return import("./numeric.binary-1f9e93f2.js");case"./numeric.continuous.ts":return import("./numeric.continuous-ebcd0567.js");case"./numeric.discrete.ts":return import("./numeric.discrete-7b97044a.js");case"./numeric.spline.ts":return import("./numeric.spline-1be88f3d.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};

package/dist/oncomatrix-351af2a0.js

@@ -0,0 +1 @@
+import{appInit as t}from"./plot.app-30c4b8e5.js";import{d as e,P as r,b as i}from"./app-b369b169.js";import{f as s}from"./termsetting-33ea66f1.js";import{v as a}from"./FilterRxComp-701a1480.js";import"./recover-49e09de0.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./tslib.es6-c3c2d88f.js";import"./toggleButtons-dbdbad01.js";import"path";import"./table-29d5a973.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";const o="hg38";const n="GDC";async function p(i,p,c){const m=c[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 c=await a({state:{vocab:{genome:o,dslabel:n}}});c.getTermdbConfig();const f=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=f.getState().plots.find((t=>t.chartType=="matrix"));if(t)d=f.getComponents(`plots.${t.id}`)}const r=[...i.termgroups||[],{lst:e}];if(d){f.dispatch({type:"plot_edit",id:d.id,config:{termgroups:r}})}else{f.dispatch({type:"plot_create",config:{chartType:"matrix",termgroups:r,divideBy:i.divideBy||undefined,settings:p}})}}},recover:{undoHtml:"Undo",redoHtml:"Redo",resetHtml:"Restore",hide(t){return t.plots[0]?.chartType!="matrix"},adjustTrackedState:t=>{const e=structuredClone(t);delete e.termfilter.filter0;if(e.plots){for(const t of e.plots){if(!t.termgroups)continue;for(const e of t.termgroups){if(!e.lst)continue;for(const t of e.lst){if(!t?.term)continue;delete t.term.category2samplecount;delete t.term.values}}}}return e}},matrix:r({reactsTo(t){if(t.type.startsWith("plot_"))return t.id===this.id;if(t.type.startsWith("filter"))return true;if(t.type=="app_refresh")return true},customInputs:{genes:[{label:`Maximum # Genes`,title:"Limit the number of displayed genes",type:"number",chartType:"matrix",settingsKey:"maxGenes",callback:async t=>{for(const t in i.opts?.app?.callbacks){if(t.startsWith("preDispatch")){i.opts?.app?.callbacks[t]();break}}const e=await l(i,{maxGenes:t,geneFilter:p.matrix.geneFilter},c);u.update({termgroups:[{lst:e}],settings:{matrix:{maxGenes:t}}})}}]},callbacks:{"firstRender.gdcMatrix":async t=>{t.on("firstRender.gdcMatrix",null);if(!g)return;f.dispatch({type:"plot_delete",id:g.id});g=undefined}}},i.opts?.matrix||{})});let d,g;const u={update:async t=>{if(!d){const t=f.getState().plots.find((t=>t.chartType=="matrix"));if(t)d=f.getComponents(`plots.${t.id}`)}if(t.genes){f.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}},c))))}]}})}else if("filter0"in t){f.dispatch({type:"filter_replace",filter0:t.filter0})}else if(d){f.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-e66308cd.js → parseData-21fe9822.js}

@@ -1 +1 @@
-import{_ as r}from"./tslib.es6-1f85f553.js";import{aj as e,q as i,a7 as t}from"./app-a8c4854a.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-b369b169.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/partjson.esm-b3f1fc21.js

@@ -0,0 +1 @@
+class t{constructor(t){this.Pj=t,this.opts=["@delimit","@errmode"],this.contexts=["@branch","@parent","@root","@self","@values","@key"],this.filters=["@split()","@before()","@join()","@ignore()"],this.post=["@after()","@dist()","@end()"],this.terms=[...this.opts,...this.contexts,...this.filters,...this.post]}setFxn(t,e,s,r){this[t]?s[t]=this[t](r,e,s):e.errors.push(["key","UNRECOGNIZED-RESERVED-"+t])}trueFxn(){return!0}notDefined(t){return void 0===t}}t.prototype["@split"]=function(t){const e=t.slice(1,-2),s=this.Pj.opts["="][e];if(!s)throw`missing @split() function ${e}`;this.Pj.split=s},t.prototype["@before"]=function(t,e){const s=t.slice(1,-2),r=this.Pj.opts["="][s];return r||(e.errors.push(["val","MISSING-"+e.term+"-FXN",s]),this.trueFxn)},t.prototype["@after"]=t.prototype["@before"],t.prototype["@done"]=t.prototype["@before"],t.prototype["@join"]=function(t,e,s){return(s,r)=>{let o=!0;for(const i in t){const n=t[i].slice(1,-2),l=this.Pj.opts["="][n];if(l){const t=l(s,r,i);t?this.Pj.joins.set(i,t):o=!1}else e.errors.push(["val","MISSING-@join-FXN",n])}return o}},t.prototype["@dist"]=function(t,e){const s=Array.isArray(t)?t:[t],r={};for(const t of s)r[t]=this.Pj.converter.subs["@"](this.Pj,t);return t=>{t["@dist"]=s=>{for(const o in r){const i=(0,r[o])(null,t);i?Array.isArray(i)?i.includes(s)||i.push(s):t.errors.push([e,"NON-ARRAY-DIST-TARGET",o]):t.errors.push([e,"MISSING-DIST-TARGET",o])}}}},t.prototype["@ignore"]=function(t,e,s){if(!t["@ignore()"])return e;const r=Array.isArray(t["@ignore()"])||"string"==typeof t["@ignore()"]||"object"!=typeof t["@ignore()"],o=r?{"@":t["@ignore()"]}:t["@ignore()"],i={};for(const t in o){const e=o[t];if(Array.isArray(e))i[t]=t=>e.includes(t);else if("string"==typeof e&&"="==e[0]){const r=this.Pj.opts["="][e.slice(1,-2)];r?i[t]=r:(s.errors.push(["val","MISSING-@ignore()-FXN",e]),i[t]=this.notDefined)}else s.errors.push(["val","UNSUPPORTED-@ignore()-VALUE",e]),i[t]=this.notDefined}return r?i:Object.assign({},e,i)};class e{constructor(t){this.Pj=t,this.allowedKeyTypes=new Set(["string","number"])}getFxn(t,e){const[s,r]=this.Pj.converter.default(this.Pj,t,e,t.term);if(s)return this[r.conv](s,t)}getAllowedKeys(t,e,s,r){if(!Array.isArray(t))return r.errors.push(["key","NON-ARRAY-KEYS",e]),[];const o=[];for(const i of t)s.ignore(i)||(this.allowedKeyTypes.has(typeof i)?o.push(i):r.errors.push([s,"INVALID-RESULT-KEY",e]));return o}}e.prototype[""]=function(t,e){return(s,r)=>this.getAllowedKeys([t(s,r)],s,e,r)},e.prototype["()"]=e.prototype[""],e.prototype["[]"]=function(t,e){return(s,r)=>this.getAllowedKeys(t(s,r),s,e,r)},e.prototype["(]"]=e.prototype["[]"];class s{constructor(t){this.Pj=t}getFxn(t,e){return this[this.getValType(t.templateVal)+"Filler"](t,e,t.templateVal)}getValType(t){return"string"==typeof t?"str":Array.isArray(t)?"arr":t&&"object"==typeof t?"obj":"default"}strFiller(t,e,s,r){const[o,i]=this.Pj.converter.default(this.Pj,t,e,s);if(!o)return;const n=(r||i.aggr)+","+i.conv;return n in this?this[n](o,t):void 0}arrFiller(t,e,s){const r=this.getValType(s[0]);return"str"==r?this.strFiller(t,e,s[0],"[]"):"arr"==r?this["[[,]]"](s[0],t):"obj"==r?this["[{}]"](s[0],t):this.defaultFiller(t,e,s)}objFiller(t,e,s){return this.Pj.parseTemplate(s,t.inheritedIgnore,t.lineage),(t,e,r)=>{this.Pj.setResultContext("{}",e,r),this.Pj.processRow(t,s,r[e])}}defaultFiller(t,e,s){const r=JSON.stringify(s);return(t,e,s)=>{s[e]=JSON.parse(r)}}getArrSeed(t){const e=t.templateVal&&t.templateVal.length>1?t.templateVal[1]:1;if("set"==e)return(t,e,s)=>{e in t?Array.isArray(t[e])&&(t[e]=new Set(t[e])):t[e]=new Set,t[e].add(s)};if(0==e)return(t,e,s)=>{e in t||(t[e]=[]),t[e].push(s)};if(this.isNumeric(e)){const t=new Map;return(s,r,o)=>{r in s||(s[r]=[]),t.has(s[r])||t.set(s[r],new Map);const i=t.get(s[r]);i.has(o)||i.set(o,0);const n=i.get(o);n<e&&(s[r].push(o),i.set(o,n+1))}}}isNumeric(t){return!isNaN(parseFloat(t))&&isFinite(t)&&""!==t}}s.prototype[","]=function(t,e){return(s,r,o,i)=>{const n=t(s,i);e.ignore(n,r,s)||(o[r]=n)}},s.prototype[",()"]=s.prototype[","],s.prototype[",[]"]=s.prototype[","],s.prototype[",(]"]=s.prototype[","],s.prototype["[],"]=function(t,e){const s=this.getArrSeed(e);if(s)return(r,o,i,n)=>{const l=t(r,n);e.ignore(l,o,r,n)||s(i,o,l)};e.errors.push(["val","INVALID-[]-OPTION"])},s.prototype["[],()"]=s.prototype["[],"],s.prototype["[],[]"]=function(t,e){const s=this.getArrSeed(e);return(r,o,i,n)=>{const l=t(r,n);if(Array.isArray(l))for(const t of l)e.ignore(t,o,r,n)||s(i,o,t);else n.errors.push([e,"NON-ARRAY-VALS",r])}},s.prototype["[],(]"]=s.prototype["[],[]"],s.prototype["[{}]"]=function(t,e){this.Pj.parseTemplate(t,e.inheritedIgnore,e.lineage);const s=e.templateVal&&e.templateVal.length>1?e.templateVal[1]:"";if(!s)return(e,s,r)=>{this.Pj.setResultContext("[]",s,r);const o=this.Pj.setResultContext("{}",r[s].length,r[s]);this.Pj.processRow(e,t,o)};if("string"==typeof s){const[r,o]=this.Pj.converter.default(this.Pj,Object.assign({},{templateVal:s}),e.inheritedIgnore,s);return o.aggr||o.skip||o.timing?void e.errors.push(["val","INVALID-[{}]-OPTION-TOKEN"]):(o,i,n,l)=>{const c=this.Pj.setResultContext("[]",i,n,!0),p=this.Pj.contexts.get(c).tracker,h=r(o,l),a="]"==s.slice(-1)?h:[h];if(Array.isArray(a))for(const e of a)if(p.has(e))this.Pj.processRow(o,t,p.get(e));else{const s=this.Pj.setResultContext("{}",c.length,c,!1,e,o,t);s&&(p.set(e,s),this.Pj.processRow(o,t,s))}else l.errors.push([e,"NON-ARRAY-VALS",o])}}e.errors.push(["val","INVALID-[{}]-OPTION"])},s.prototype["[[,]]"]=function(t,e){const s=[];for(const r of t){const t=Object.assign({},e,{templateVal:r});s.push(this.getFxn(t,e.inheritedIgnore))}return"map"!=(e.templateVal[1]?e.templateVal[1]:"")?(t,e,r)=>{e in r||(r[e]=[]);const o=[];for(const e in s)s[+e](t,+e,o);r[e].push(o)}:(t,e,r)=>{e in r?r[e]instanceof Map||(r[e]=new Map(r[e])):r[e]=new Map;const o=[];s[0](t,0,o),r[e].has(o[0])&&(o[1]=r[e].get(o[0])),s[1](t,1,o),r[e].set(o[0],o[1])}},s.prototype["+,"]=function(t,e){return(s,r,o,i)=>{r in o||(o[r]=0);const n=t(s,i);e.ignore(n,r,s,i)||(this.isNumeric(n)?o[r]+=+n:i.errors.push([e,"NON-NUMERIC-INCREMENT",s]))}},s.prototype["+,()"]=s.prototype["+,"],s.prototype["+,[]"]=function(t,e){return(s,r,o,i)=>{r in o||(o[r]=0);const n=t(s,i);if(Array.isArray(n))for(const t of n)e.ignore(t,r,s,i)||(this.isNumeric(t)?o[r]+=+t:i.errors.push([e,"NON-NUMERIC-INCREMENT",s]));else e.errors.push(["val","NON-ARRAY-VALS",s])}},s.prototype["+,(]"]=s.prototype["+,[]"],s.prototype["-,"]=function(t,e){return(s,r,o,i)=>{r in o||(o[r]=0);const n=t(s,i);e.ignore(n,r,s,i)||(this.isNumeric(n)?o[r]+=-n:i.errors.push([e,"NON-NUMERIC-DECREMENT",s]))}},s.prototype["-,()"]=s.prototype["-,"],s.prototype["-,[]"]=function(t,e){return(s,r,o,i)=>{const n=t(s,i);if(Array.isArray(n)){r in o||(o[r]=0);for(const t of n)e.ignore(t,r,s,i)||(o[r]+=-t)}else e.errors.push(["val","NON-ARRAY-VALS",s])}},s.prototype["-,(]"]=s.prototype["-,[]"],s.prototype["<,"]=function(t,e){return(s,r,o,i)=>{const n=t(s,i);if(e.ignore(n,r,s,i))return;const l=+n;this.isNumeric(l)?r in o?o[r]<l&&(o[r]=l):o[r]=l:i.errors.push([e,"NON-NUMERIC-THAN",s])}},s.prototype["<,()"]=s.prototype["<,"],s.prototype["<,[]"]=function(t,e){return(s,r,o,i)=>{const n=t(s,i);if(Array.isArray(n))for(const t of n){if(e.ignore(t,r,s,i))return;if(!this.isNumeric(t))return void i.errors.push([e,"NON-NUMERIC-THAN",s]);const n=+t;r in o?o[r]<n&&(o[r]=n):o[r]=n}else e.errors.push(["val","NON-ARRAY-VALS",s])}},s.prototype["<,(]"]=s.prototype["<,[]"],s.prototype[">,"]=function(t,e){return(s,r,o,i)=>{const n=t(s,i);e.ignore(n,r,s,i)||(this.isNumeric(n)?r in o?o[r]>n&&(o[r]=n):o[r]=n:i.errors.push([e,"NON-NUMERIC-THAN",s]))}},s.prototype[">,()"]=s.prototype[">,"],s.prototype[">,[]"]=function(t,e){return(s,r,o,i)=>{const n=t(s,i);if(Array.isArray(n))for(const t of n){if(e.ignore(t,r,s,i))return;if(!this.isNumeric(t))return void i.errors.push([e,"NON-NUMERIC-THAN",s]);const n=+t;r in o?o[r]>n&&(o[r]=n):o[r]=n}else e.errors.push(["val","NON-ARRAY-VALS",s])}},s.prototype[">,(]"]=s.prototype[">,[]"];class r{constructor(t){this.Pj=t,this.allErrSet=new Set,this.allErrObj=Object.create(null),this.mode={input:"{}",result:"{}-",root:"",console:"{}"},this.modeKeys=["input","result","root","console"],this.setMode()}setMode(t={}){Array.isArray(t)?this.modeKeys.forEach(((e,s)=>this.mode[e]=t[s])):"object"==typeof t&&this.modeKeys.forEach((e=>{e in t&&(this.mode[e]=t[e])}))}clear(t={}){this.allErrSet.clear(),this.allErrObj=Object.create(null),this.setMode(t)}markErrors(t,e){if(!e)return;const s="[]"==this.mode.result.slice(0,2)?[]:{};for(const r in e.filler.inputs){const o=e.filler.inputs[r];for(const e of o.errors){const[r,i,n]=e;"key"==r?(this.track(s,e,o.lineage.join(this.Pj.delimit)),this.mode.input&&(t["{{ "+i+" }} "+o.term]=o.templateVal)):"val"==r&&(Array.isArray(o.templateVal)?(this.track(s,e,o.templateVal[0]),this.mode.input&&(t[o.term]=["{{ "+i+" }} ",...o.templateVal])):"string"==typeof o.templateVal?(this.track(s,e,o.templateVal),this.mode.input&&(t[o.term]="{{ "+i+" }} "+o.templateVal)):(this.track(s,e,o.templateVal),this.mode.input&&(t[o.term]="{{ "+i+" }} ")))}}if(e.errors.length){const r={};t["@errors"]=r;for(const t of e.errors){const[e,o,i]=t;if(this.track(s,t,e.term),!this.mode.input)continue;const n="{{ "+o+" }} "+e.term;n in r||(r[n]=0),r[n]+=1}}if(e.filler.errors.length)for(const t of e.filler.errors)this.track(s,t,t[2],!1);Object.keys(s).length&&this.mode.result&&(t["@errors"]=s)}track(t,e,s,r=!0){this.allErrSet.add(e),this.trackAsObj(this.allErrObj,e,s),r&&"-"==this.mode.result.slice(-1)||(Array.isArray(t)?t.push(e):this.trackAsObj(t,e,s))}trackAsObj(t,e,s){const[r,o,i]=e;o in t||(t[o]=Object.create(null)),s in t[o]||(t[o][s]=i?[]:0),i?t[o][s].includes(i)||t[o][s].push(i):t[o][s]+=1}log(){const t=[...this.allErrSet];if(t.length){if(this.mode.root){const e=this.mode.root;this.Pj.tree["@errorsAll"]="[]"==e?t:this.allErrObj}if(this.mode.console){const e=this.mode.console.slice(0,2);console.log("[]"==e?t:this.allErrObj)}}}}function o(t,e){const s=t.skipSymbols.includes(e[0])?e[0]:"",r=e.slice(s.length,s.length+3),o=t.timeSymbols.includes(r)?r:"",i=s.length+o.length,n=e[i],l=e.slice(-2),c=t.aggrSymbols.includes(n)&&n!=e?n:"",p=t.convSymbols.includes(l)&&l!=e?l:"",h=c&&p?e.slice(i+1,-2):c?e.slice(i+1):p?e.slice(i,-2):s||o?e.slice(i):e,a=t.subsSymbols.includes(h[0])?h[0]:"",u=c+a+p,f=a?h.slice(1):h;return[h,u,{skip:s,time:o,aggr:c,subs:a,stem:f,conv:p,subterm:h},t.steps.indexOf(o)]}const i={"#":function(t,e,s){t.commentedTerms.has(s)||t.commentedTerms.set(s,[]),t.commentedTerms.get(s).push(e)},"*":function(t,e,s){t.focusTemplate[s.term.slice(1)]=s.templateVal},"":function(t,e,s){return t.valFiller.isNumeric(e)?()=>+e:()=>e},$:function(t,e,s){if("$"==e||e=="$"+t.delimit)return t=>t;if(e.includes(t.delimit)){const s=e.slice(1).split(t.delimit);""==s[0]&&s.shift();const r=(t,e)=>t?t[e]:void 0;return t=>s.reduce(r,t)}{const t=e.slice(1);return e=>e[t]}},"=":function(t,e,s){const r=e.slice(1).split(t.delimit).reduce(((t,e)=>t&&e in t?t[e]:void 0),t.opts["="]);if(r)return t=>r;s.errors.push(["val","MISSING-EXTERNAL-SUBS"])},"@":function(t,e,s){if(!t.reserved.opts.includes(e)){if("@"==e||e=="@"+t.delimit)return(t,e)=>e.self;if(e.includes(t.delimit)){const r=e.split(t.delimit),o=(r,o)=>{if("@"==o[0]&&o.length>1&&!t.reserved.contexts.includes(o))return s.errors.push(["val","UNRECOGNIZED-CONTEXT-"+e,s.lineage.join(".")+"."+o]),[null,null];const[i,n]=r;return i&&o?"@"==o?[n.self,n]:"@values"==o?[Object.values(i),n]:"@"==o[0]?[n[o.slice(1)],t.contexts.get(n[o.slice(1)])]:[i[o],t.contexts.get(i[o])]:[null,null]};return(t,e)=>r.reduce(o,[e.self,e])[0]}if(t.reserved.contexts.includes(e)){const t=e.slice(1);return(e,s)=>s[t]}s.errors.push(["val","UNRECOGNIZED-CONTEXT-"+e])}},"&":function(t,e,s){const r=e.slice(1).split(t.delimit),o=r.shift();if(r.length){if(1==r.length){const e=r[0];return()=>{const s=t.joins.get(o);return s?s[e]:null}}{const e=(t,e)=>t?t[e]:null;t.joins.get(o);return s=>r.reduce(e,t.joins.get(o))}}return()=>t.joins.get(o)}},n={"":function(t,e,s){return t},"()":function(t,e,s){if("="==s.subs){const r=t();return"function"!=typeof r?void e.errors.push(["val","NOT-A-FUNCTION",s.subs+s.term+s.conv]):r}return(s,r)=>{const o=t(s,r);if("function"==typeof o)return o(s,r);e.errors.push(["val","NOT-A-FUNCTION",s])}}};n["[]"]=n[""],n["(]"]=n["()"];var l=Object.freeze({__proto__:null,default:function(t,e,s,r){const[l,c,p]=o(t,r);if(t.reserved.opts.includes(l))return[];const h=l+p.conv;if(e.ignore=h in s?s[h]:s["@"],p.skip&&"~"!=p.skip)return i[p.skip](t,l,e),[];if(p.subs in i){const s=i[p.subs](t,l,e);return s?[n[p.conv](s,e,p),p]:[]}return e.errors.push(["val","UNSUPPORTED-SYMBOL-"+p.subs]),[]},parseTerm:o,subs:i,conv:n});class c{constructor(o={}){this.defaultOpts={template:{},seed:"{}","=":{}},this.opts=Object.assign(this.defaultOpts,o),this.delimit=".",this.subsSymbols=["$","=","@","&"],this.convSymbols=["()","[]","(]"],this.aggrSymbols=["+","-","<",">"],this.timePost=["_0:","_1:","_2:","_3:","_4:","_5:","_6:","_7:","_8:","_9:"],this.timeSymbols=[":__","_:_","__:",...this.timePost],this.skipSymbols=["#","*","~"],this.steps=[":__","","_:_"],this.errors=new r(this),this.reserved=new t(this),this.keyFiller=new e(this),this.valFiller=new s(this),this.commentedTerms=new Map,this.joins=new Map,this.fillers=new Map,this.contexts=new Map,this.temps=new Map,this.refresh()}refresh(t={}){this.times={start:+new Date},Object.assign(this.opts,t),"string"!=typeof this.opts.template&&(this.opts.template=JSON.stringify(this.opts.template));const e=JSON.parse(this.opts.template);this.errors.clear(e["@errmode"]),e["@delimit"]&&(this.delimit=e["@delimit"]),this.commentedTerms.clear(),this.joins.clear(),this.fillers.clear(),this.contexts.clear(),this.temps.clear(),delete this.tree,this.tree=this.setResultContext(this.opts.seed),this.focusTemplate=Object.create(null),this.parseTemplate(e,{"@":this.reserved.notDefined}),this.times.parse=+new Date-this.times.start,Object.keys(this.focusTemplate).length?(this.parseTemplate(this.focusTemplate,{"@":this.reserved.notDefined}),this.template=this.focusTemplate):this.template=e,this.postLoopTerms=Object.create(null),this.done=[],this.opts.data&&this.add(this.opts.data,!1),this.errors.log(this.fillers)}setResultContext(t,e=null,s=null,r=!1,o,i=null,n=null){const l=null!==e&&e in s?s[e]:JSON.parse(t);if(this.contexts.has(l))return l;const c={branch:e,parent:s,context:this.contexts.get(s),self:l,root:this.tree?this.tree:l,joins:this.joins,errors:[],key:o};if(r&&(c.tracker=new Map),i&&n){const t=this.fillers.get(n);if(!t["@before"](i,c))return;if(t["@join"]&&!t["@join"](i,c))return}return this.contexts.set(l,c),null!==e&&(s[e]=l),l}parseTemplate(t,e,s=[]){const r=Object.create(null);r.inputs=Object.create(null),r["@before"]=this.reserved.trueFxn,r["@after"]=this.reserved.trueFxn,r.postTerms={},r.errors=[];const i=this.reserved["@ignore"](t,e,r);r["@ignore"]=i,this.fillers.set(t,r);const n=this.steps.map((t=>[]));for(const e in t){const[l,c,p,h]=o(this,e),a=t[e],u=r.inputs[e]={term:e,subterm:l,symbols:c,keyTokens:p,templateVal:a,lineage:[...s,e],inheritedIgnore:i,errors:[]};"@()"==c?this.reserved.setFxn(l,u,r,a):(u.keyFxn=this.keyFiller.getFxn(u,i),u.keyFxn&&(u.valFxn=this.valFiller.getFxn(u,i),"__:"==p.time||this.timePost.includes(p.time)?(r.postTerms[p.time]||(r.postTerms[p.time]=[]),r.postTerms[p.time].includes(e)||r.postTerms[p.time].push(e)):n[h].push(e)))}r.steps=n.filter((t=>t.length))}add(t,e=!0){this.times.start||(this.times.start=+new Date),e&&this.errors.clear(),this.joins.clear();for(const e of t)if(this.split)for(const t of this.split(e))this.processRow(t,this.template,this.tree),this.joins.clear();else this.processRow(e,this.template,this.tree),this.joins.clear();this.processResult(this.tree);for(const t of this.timePost)if(this.postLoopTerms[t])for(const e of this.postLoopTerms[t])this.postLoop(e.self,e,t);for(const t of this.done)t.done(t.self,t);for(const[t,e]of this.temps)for(const s of e)delete t[s];this.times.total=+new Date-this.times.start,delete this.times.start,e&&this.errors.log()}processRow(t,e,s){const r=this.contexts.get(s),o=this.fillers.get(e);if(r.filler=o,o["@before"](t,r)&&(!o["@join"]||o["@join"](t,r))){for(const e of o.steps)for(const i of e){const e=o.inputs[i];if(e.keyFxn&&e.valFxn){const o=e.keyFxn(t,r);for(const i of o)e.valFxn(t,i,s,r),"~"==e.keyTokens.skip&&(this.temps.has(s)||this.temps.set(s,new Set),this.temps.get(s).add(i))}}o["@after"](t,r),o["@dist"]&&o["@dist"](r),o["@done"]&&!this.done.includes(r)&&(r.done=o["@done"],this.done.push(r));for(const t in o.postTerms)this.postLoopTerms[t]||(this.postLoopTerms[t]=[]),this.postLoopTerms[t].includes(r)||this.postLoopTerms[t].push(r);return!0}}postLoop(t,e,s="__:"){if(e&&e.filler&&e.filler.postTerms[s])for(const r of e.filler.postTerms[s]){const s=e.filler.inputs[r];if(s.keyFxn&&s.valFxn){const r=s.keyFxn(null,e);for(const o of r)s.valFxn(null,o,t,e)}}}processResult(t){const e=this.contexts.get(t);this.postLoop(t,e,"__:");for(const e in t){const s=t[e];if(s)if(Array.isArray(s)||s instanceof Set||s instanceof Map)for(const t of s)"object"==typeof t&&this.processResult(t);else if("object"==typeof s){const t=this.contexts.get(s);t&&t["@dist"]&&t["@dist"](s),this.processResult(s)}}e&&e.filler&&this.errors.markErrors(t,e)}copyResult(t,e={}){if(arguments.length&&void 0===t)return;const s=arguments.length?t:this.tree;for(const t in s){const r=s[t];if(r instanceof Set||r instanceof Map)e[t]=[...r];else if(Array.isArray(r)){e[t]=[];for(const s of r)if(Array.isArray(s)){const r=[];e[t].push(r),this.copyResult(s,r)}else if(s&&"object"==typeof s){const r=Object.create(null);e[t].push(r),this.copyResult(s,r)}else e[t]=JSON.parse(JSON.stringify(r))}else r&&"object"==typeof r?(e[t]=Object.create(null),this.copyResult(r,e[t])):e[t]=JSON.parse(JSON.stringify(r))}return e}}c.prototype.converter=l;export{c};

package/dist/{plot.2dvaf-73dbfbd1.js → plot.2dvaf-18a35e4b.js}

@@ -1 +1 @@
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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};
+import{M as t,I as e,ah as a,a9 as r,ag as i}from"./app-b369b169.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 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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};

package/dist/plot.app-30c4b8e5.js

@@ -0,0 +1 @@
+import{o as t,M as s,y as r}from"./app-b369b169.js";import{s as e,r as o}from"./recover-49e09de0.js";import{v as i}from"./FilterRxComp-701a1480.js";import"./termsetting-33ea66f1.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./table-29d5a973.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";function a(t){switch(t){case"../plots/DEanalysis.js":return import("./DEanalysis-95bad59a.js");case"../plots/Disco.js":return import("./Disco-a6e921a0.js");case"../plots/DziViewer.js":return import("./DziViewer-354a790d.js");case"../plots/WSIViewer.js":return import("./WSIViewer-dc7f8eb0.js");case"../plots/barchart.data.js":return import("./FilterRxComp-701a1480.js").then((function(t){return t.j}));case"../plots/barchart.events.js":return import("./barchart.events-da29c90d.js");case"../plots/barchart.js":return import("./barchart-8277ed43.js");case"../plots/bars.renderer.js":return import("./bars.renderer-dcfdd59b.js");case"../plots/bars.settings.js":return import("./bars.settings-64bb4642.js");case"../plots/boxplot.js":return import("./boxplot-e17a17b7.js");case"../plots/brainImaging.js":return import("./brainImaging-bf2ceee9.js");case"../plots/controls.btns.js":return import("./controls.btns-79b805dd.js");case"../plots/controls.config.js":return import("./controls.config-28d6d6a8.js");case"../plots/controls.js":return import("./controls-287e6efa.js");case"../plots/cuminc.js":return import("./cuminc-9e275854.js");case"../plots/dataDownload.js":return import("./dataDownload-3a3d4f33.js");case"../plots/dictionary.js":return import("./dictionary-c5a19d90.js");case"../plots/facet.js":return import("./facet-a9b44ef3.js");case"../plots/geneExpression.js":return import("./geneExpression-589f485b.js");case"../plots/geneORA.js":return import("./geneORA-903a780f.js");case"../plots/geneset.js":return import("./geneset-108a39d2.js");case"../plots/genomeBrowser.controls.js":return import("./genomeBrowser.controls-d5067811.js");case"../plots/genomeBrowser.js":return import("./genomeBrowser-12f86a36.js");case"../plots/gsea.js":return import("./gsea-543dab25.js");case"../plots/hierCluster.config.js":return import("./hierCluster.config-98e82dff.js");case"../plots/hierCluster.interactivity.js":return import("./hierCluster.interactivity-e56f6542.js").then((function(t){return t.i}));case"../plots/hierCluster.js":return import("./hierCluster-26e14090.js");case"../plots/hierCluster.renderers.js":return import("./hierCluster.renderers-74a64cf5.js").then((function(t){return t.r}));case"../plots/imagePlot.js":return import("./imagePlot-b9eae4ae.js");case"../plots/matrix.cells.js":return import("./matrix.cells-914dd0c6.js");case"../plots/matrix.cluster.js":return import("./matrix.cluster-783ceab0.js");case"../plots/matrix.config.js":return import("./matrix.config-6ce74dfe.js");case"../plots/matrix.controls.js":return import("./matrix.controls-7b2a6f95.js");case"../plots/matrix.data.js":return import("./matrix.data-dac4f1b7.js").then((function(t){return t.m}));case"../plots/matrix.dom.js":return import("./matrix.dom-4e10bbe9.js");case"../plots/matrix.groups.js":return import("./matrix.groups-b9fca14a.js").then((function(t){return t.m}));case"../plots/matrix.interactivity.js":return import("./matrix.interactivity-84169b43.js");case"../plots/matrix.js":return import("./matrix-00bb50ff.js");case"../plots/matrix.layout.js":return import("./matrix.layout-dd5a44fd.js").then((function(t){return t.m}));case"../plots/matrix.legend.js":return import("./matrix.legend-ac6d45e6.js").then((function(t){return t.m}));case"../plots/matrix.renderers.js":return import("./matrix.renderers-78010275.js");case"../plots/matrix.serieses.js":return import("./matrix.serieses-9b4fd744.js").then((function(t){return t.m}));case"../plots/matrix.sort.js":return import("./matrix.sort-014d798d.js");case"../plots/matrix.sorterUi.js":return import("./matrix.sorterUi-9bf7e6f9.js");case"../plots/plot.app.js":return Promise.resolve().then((function(){return c}));case"../plots/plot.brainImaging.js":return import("./plot.brainImaging-2ceb6023.js");case"../plots/plot.disco.js":return import("./plot.disco-6011f87f.js");case"../plots/plot.ssgq.js":return import("./plot.ssgq-5581dc56.js");case"../plots/profileBarchart.js":return import("./profileBarchart-0476f1f8.js");case"../plots/profilePlot.js":return import("./profilePlot-c7e099e8.js");case"../plots/profilePolar.js":return import("./profilePolar-6b981e63.js");case"../plots/profileRadar.js":return import("./profileRadar-bca1cc03.js");case"../plots/profileRadarFacility.js":return import("./profileRadarFacility-bbb1ecd8.js");case"../plots/profileSummary.js":return import("./profileSummary-b114204f.js");case"../plots/regression.inputs.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.b}));case"../plots/regression.inputs.term.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.a}));case"../plots/regression.inputs.values.table.js":return import("./regression.inputs.values.table-5929d25a.js");case"../plots/regression.js":return import("./regression.inputs-a761f40d.js").then((function(t){return t.r}));case"../plots/regression.results.js":return import("./regression.results-69bc42d0.js").then((function(t){return t.r}));case"../plots/sampleScatter.interactivity.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.a}));case"../plots/sampleScatter.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.b}));case"../plots/sampleScatter.renderer.js":return import("./sampleScatter-2d0ed680.js").then((function(t){return t.s}));case"../plots/sampleScatter.rendererThree.js":return import("./sampleScatter.rendererThree-0b12ac61.js").then((function(t){return t.c}));case"../plots/sampleView.js":return import("./sampleView-484ab133.js");case"../plots/scatter.js":return import("./scatter-205e013f.js");case"../plots/singleCellPlot.js":return import("./singleCellPlot-73b2738f.js");case"../plots/stattable.js":return import("./stattable-7c5ecc2f.js");case"../plots/summary.js":return import("./summary-5ec455d3.js");case"../plots/survival.js":return import("./survival-92250664.js");case"../plots/table.js":return import("./table-ad744310.js");case"../plots/variantBrowser.js":return import("./variantBrowser-7c540224.js");case"../plots/violin.interactivity.js":return import("./violin.interactivity-4da6d7a9.js");case"../plots/violin.js":return import("./violin-2ba509eb.js");case"../plots/violin.renderer.js":return import("./violin.renderer-ce024265.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-7c4865a2.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-b369b169.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-641da058.js → plot.boxplot-fe3046c6.js}

@@ -1 +1 @@
-import{a8 as t,af as e,ah as r,I as a,ag as n}from"./app-a8c4854a.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-b369b169.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-2ceb6023.js

@@ -0,0 +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-30c4b8e5.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-6011f87f.js

@@ -0,0 +1 @@
+import{b as e,B as t}from"./app-b369b169.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-30c4b8e5.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-41ea26e5.js → plot.dzi-6728a7c8.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-aa916e0e.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-30c4b8e5.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-5581dc56.js

@@ -0,0 +1 @@
+import{b as t,w as e,f as o}from"./app-b369b169.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 b;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));b=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(b){b.jump_1basedcoordinate({chr:o,start:m,stop:d});return}b=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-6aedd569.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-80e58833.js → plot.vaf2cov-b2284c64.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-a8c4854a.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 V=S.append("text").text("VAF").attr("text-anchor","middle").attr("dominant-baseline","middle").attr("fill",m).attr("font-family",a).attr("transform","rotate(-90)");const X=A.append("g");const Y=A.append("g");const E=A.append("g");const C=E.append("rect").attr("stroke",m).attr("stroke-dasharray","2,2").attr("fill","none").attr("shape-rendering","crispEdges");const D=E.append("line").attr("stroke",m).attr("stroke-dasharray","2,2").attr("shape-rendering","crispEdges");const G=A.append("g");const I=G.selectAll().data(g).enter().append("rect");const W=A.append("g");const _=A.append("g");const q=_.selectAll().data(y).enter().append("rect");const B=A.append("g");let H=null,J,K,L,N,O;if(p.genotype){const t=r(e);const o=new Set;for(const a of p.data){if(a.genotype){o.add(a.genotype);a.color=t(a.genotype)}}const n=[...o];H=A.append("g");J=H.append("text").text("Genotype").attr("dominant-baseline","central").attr("font-family",a);K=H.selectAll().data(n).enter().append("g");L=K.append("line").attr("stroke",(a=>t(a)));N=K.append("line").attr("stroke",(a=>t(a)));O=K.append("text").text((t=>t)).attr("fill",(a=>t(a))).attr("dominant-baseline","central").attr("font-family",a)}const P=E.selectAll().data(p.data).enter().append("g");const Q=P.append("line").attr("stroke-opacity",.6).attr("stroke",(t=>t.color?t.color:t.sampleobj.color||p.samplecolor)).each((function(t){t.crosshair1=o(this)}));const R=P.append("line").attr("stroke-opacity",.6).attr("stroke",(t=>t.color?t.color:t.sampleobj.color||p.samplecolor)).each((function(t){t.crosshair2=o(this)}));const 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 resize").attr("class","sja_clbtext").attr("font-size",13).attr("text-anchor","end").attr("fill",m).on("mousedown",(t=>{t.preventDefault();const a=o(document.body);const r=t.clientX,e=t.clientY,n=d,s=f;a.on("mousemove",(t=>{d=n+t.clientX-r;f=s+t.clientY-e;Z()}));a.on("mouseup",(()=>{a.on("mousemove",null).on("mouseup",null)}))}));function Z(){const t=Math.max(12,Math.min(d,f)/25);const a=f/20;h=Math.ceil(t/3);const r=h,e=r+t*3,o=r+20,n=t*1.3,p=t*1.6,u=f/5,y=d/5;v.range([0,d]);z.range([f,0]);j.range([u,0]);M.range([0,y]);A.attr("width",t+e+p+d+n+y+a+r).attr("height",t/2+u+n+f+p+o+r+t);F.attr("font-size",t).attr("x",t+e+p+d/2).attr("y",t/2+u+n+f+p+o+r+t-5);S.attr("transform","translate("+t+","+(t/2+u+n+f/2)+")");V.attr("font-size",t);X.attr("transform","translate("+(t+e+p)+","+(t/2+u+n+f+p)+")").call(c().scale(v).ticks(4).tickSize(r));s({axis:X,color:m,fontsize:t,showline:true});Y.attr("transform","translate("+(t+e)+","+(t/2+u+n)+")").call(i().scale(z).ticks(5).tickSize(r));s({axis:Y,color:m,fontsize:t,showline:true});E.attr("transform","translate("+(t+e+p)+","+(t/2+u+n)+")");C.attr("width",d).attr("height",f);D.attr("y1",f/2).attr("x2",d).attr("y2",f/2);P.attr("transform",(t=>"translate("+v(t.total>x?x:t.total)+","+z(t.maf)+")"));Q.attr("x1",-h).attr("y1",-h).attr("x2",h).attr("y2",h);R.attr("x1",h).attr("y1",-h).attr("x2",-h).attr("y2",h);T.attr("r",h);G.attr("transform","translate("+(t+e+p+d+n)+","+(t/2+u+n+f)+")");const g=f/k;I.attr("y",((t,a)=>-g*(a+1))).attr("width",(t=>M(t))).attr("height",g).attr("fill",m);W.attr("transform","translate("+(t+e+p+d+n)+","+(t/2+u+n+f+p)+")").call(c().scale(M).tickValues([0,b]).tickFormat(l("d")));s({axis:W,color:m,showline:true});_.attr("transform","translate("+(t+e+p)+","+(t/2+u)+")");const Z=d/k;q.attr("x",((t,a)=>Z*a)).attr("y",(t=>j(t)-u)).attr("height",(t=>u-j(t))).attr("width",Z).attr("fill",m);B.attr("transform","translate("+(t+e)+","+t/2+")").call(i().scale(j).tickValues([0,w]).tickFormat(l("d")));s({axis:B,color:m,showline:true});U.attr("x",t+e+p+d+n+y+a+r-5).attr("y",t/2+u+n+f+p+o+r+t-5);if(H){H.attr("transform","translate("+(t+e+p+d+n)+","+t/2+")");J.attr("font-size",t);K.attr("transform",((a,r)=>"translate(0,"+(t/2+3+(t+1)*r+t/2)+")"));L.attr("y1",-t/2).attr("x2",t).attr("y2",t/2);N.attr("x1",t).attr("y1",-t/2).attr("y2",t/2);O.attr("x",t+5).attr("font-size",t)}}Z();return P}export{p as default};
+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-b369b169.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 V=S.append("text").text("VAF").attr("text-anchor","middle").attr("dominant-baseline","middle").attr("fill",m).attr("font-family",a).attr("transform","rotate(-90)");const X=A.append("g");const Y=A.append("g");const E=A.append("g");const C=E.append("rect").attr("stroke",m).attr("stroke-dasharray","2,2").attr("fill","none").attr("shape-rendering","crispEdges");const D=E.append("line").attr("stroke",m).attr("stroke-dasharray","2,2").attr("shape-rendering","crispEdges");const G=A.append("g");const I=G.selectAll().data(g).enter().append("rect");const W=A.append("g");const _=A.append("g");const q=_.selectAll().data(y).enter().append("rect");const B=A.append("g");let H=null,J,K,L,N,O;if(p.genotype){const t=r(e);const o=new Set;for(const a of p.data){if(a.genotype){o.add(a.genotype);a.color=t(a.genotype)}}const n=[...o];H=A.append("g");J=H.append("text").text("Genotype").attr("dominant-baseline","central").attr("font-family",a);K=H.selectAll().data(n).enter().append("g");L=K.append("line").attr("stroke",(a=>t(a)));N=K.append("line").attr("stroke",(a=>t(a)));O=K.append("text").text((t=>t)).attr("fill",(a=>t(a))).attr("dominant-baseline","central").attr("font-family",a)}const P=E.selectAll().data(p.data).enter().append("g");const Q=P.append("line").attr("stroke-opacity",.6).attr("stroke",(t=>t.color?t.color:t.sampleobj.color||p.samplecolor)).each((function(t){t.crosshair1=o(this)}));const R=P.append("line").attr("stroke-opacity",.6).attr("stroke",(t=>t.color?t.color:t.sampleobj.color||p.samplecolor)).each((function(t){t.crosshair2=o(this)}));const 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 resize").attr("class","sja_clbtext").attr("font-size",13).attr("text-anchor","end").attr("fill",m).on("mousedown",(t=>{t.preventDefault();const a=o(document.body);const r=t.clientX,e=t.clientY,n=d,s=f;a.on("mousemove",(t=>{d=n+t.clientX-r;f=s+t.clientY-e;Z()}));a.on("mouseup",(()=>{a.on("mousemove",null).on("mouseup",null)}))}));function Z(){const t=Math.max(12,Math.min(d,f)/25);const a=f/20;h=Math.ceil(t/3);const r=h,e=r+t*3,o=r+20,n=t*1.3,p=t*1.6,u=f/5,y=d/5;v.range([0,d]);z.range([f,0]);j.range([u,0]);M.range([0,y]);A.attr("width",t+e+p+d+n+y+a+r).attr("height",t/2+u+n+f+p+o+r+t);F.attr("font-size",t).attr("x",t+e+p+d/2).attr("y",t/2+u+n+f+p+o+r+t-5);S.attr("transform","translate("+t+","+(t/2+u+n+f/2)+")");V.attr("font-size",t);X.attr("transform","translate("+(t+e+p)+","+(t/2+u+n+f+p)+")").call(c().scale(v).ticks(4).tickSize(r));s({axis:X,color:m,fontsize:t,showline:true});Y.attr("transform","translate("+(t+e)+","+(t/2+u+n)+")").call(i().scale(z).ticks(5).tickSize(r));s({axis:Y,color:m,fontsize:t,showline:true});E.attr("transform","translate("+(t+e+p)+","+(t/2+u+n)+")");C.attr("width",d).attr("height",f);D.attr("y1",f/2).attr("x2",d).attr("y2",f/2);P.attr("transform",(t=>"translate("+v(t.total>x?x:t.total)+","+z(t.maf)+")"));Q.attr("x1",-h).attr("y1",-h).attr("x2",h).attr("y2",h);R.attr("x1",h).attr("y1",-h).attr("x2",-h).attr("y2",h);T.attr("r",h);G.attr("transform","translate("+(t+e+p+d+n)+","+(t/2+u+n+f)+")");const g=f/k;I.attr("y",((t,a)=>-g*(a+1))).attr("width",(t=>M(t))).attr("height",g).attr("fill",m);W.attr("transform","translate("+(t+e+p+d+n)+","+(t/2+u+n+f+p)+")").call(c().scale(M).tickValues([0,b]).tickFormat(l("d")));s({axis:W,color:m,showline:true});_.attr("transform","translate("+(t+e+p)+","+(t/2+u)+")");const Z=d/k;q.attr("x",((t,a)=>Z*a)).attr("y",(t=>j(t)-u)).attr("height",(t=>u-j(t))).attr("width",Z).attr("fill",m);B.attr("transform","translate("+(t+e)+","+t/2+")").call(i().scale(j).tickValues([0,w]).tickFormat(l("d")));s({axis:B,color:m,showline:true});U.attr("x",t+e+p+d+n+y+a+r-5).attr("y",t/2+u+n+f+p+o+r+t-5);if(H){H.attr("transform","translate("+(t+e+p+d+n)+","+t/2+")");J.attr("font-size",t);K.attr("transform",((a,r)=>"translate(0,"+(t/2+3+(t+1)*r+t/2)+")"));L.attr("y1",-t/2).attr("x2",t).attr("y2",t/2);N.attr("x1",t).attr("y1",-t/2).attr("y2",t/2);O.attr("x",t+5).attr("font-size",t)}}Z();return P}export{p as default};

package/dist/{plot.wsi-51cc48ef.js → plot.wsi-9a9d4034.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-aa916e0e.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-30c4b8e5.js");const p=await i.appInit(n);o.remove()}catch(e){o.text("Error: "+(e.message||e))}}export{e as default};

package/dist/profileBarchart-0476f1f8.js

@@ -0,0 +1 @@
+import{P as t,h as e,I as r}from"./app-b369b169.js";import{m as o}from"./termsetting-33ea66f1.js";import{getDefaultProfilePlotSettings as s,loadFilterTerms as a,profilePlot as n}from"./profilePlot-c7e099e8.js";import{c as i}from"./axis-747c801e.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./svg.download-35926549.js";import"./FilterRxComp-701a1480.js";import"./table-29d5a973.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./controls-287e6efa.js";import"./controls.btns-79b805dd.js";import"./controls.config-28d6d6a8.js";import"./recover-49e09de0.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";let p=500;const c=400;class l extends n{constructor(){super();this.type="profileBarchart"}async init(t){await super.init(t);const e=t.plots.find((t=>t.id===this.id));this.componentNames=e.plotByComponent.map((t=>({value:t.component.name,label:t.component.name})));this.componentInput={label:"Component",type:"dropdown",chartType:"profileBarchart",options:this.componentNames,settingsKey:"component",callback:t=>this.setComponent(t)}}setComponent(t){this.settings.component=t;this.app.dispatch({type:"plot_edit",id:this.id,config:this.config})}async main(){await super.main();this.configComponent=this.config.plotByComponent.find((t=>t.component.name==this.settings.component))||this.config.plotByComponent[0];this.twLst=[];this.rowCount=0;for(const t of this.configComponent.groups)for(const e of t.rows){this.rowCount++;if(e.term1){this.twLst.push(e.term1.score);this.twLst.push(e.term1.maxScore)}if(e.term2){this.twLst.push(e.term2.score);this.twLst.push(e.term2.maxScore)}}await this.setControls([this.componentInput]);this.component=this.settings.component||this.componentNames[0].value;this.plot()}onMouseOut(t){if(t.target.tagName=="rect"&&t.target.getAttribute("fill-opacity")==.3){const e=t.target;e.setAttribute("fill-opacity",0)}}onMouseOver(t){if(t.target.tagName=="rect"&&t.target.getAttribute("fill-opacity")==0){const e=t.target;e.setAttribute("fill-opacity",.3)}}plot(){const t=this.config;this.dom.plotDiv.selectAll("*").remove();const e=this.configComponent.hasSubjectiveData;const o=1400;const s=this.rowCount*32+600;this.svg=this.dom.plotDiv.append("svg").attr("width",o).attr("height",s);const a=this.state.dslabel=="ProfileAbbrev"?`Score-based Results for the ${this.component} Component by Module and Domain Compared with End-User Impression`:`Objective ${this.component=="Patients and Outcomes"?"":"and Subjective "}Score-based Results for the ${this.component} Component by Module and Domain`;this.svg.append("text").attr("transform",`translate(50, 30)`).attr("font-weight","bold").text(a);const n=this.svg;const l=this.configComponent.component.color;this.svg.append("defs").append("pattern").attr("id",`${this.id}_diagonalHatch`).attr("patternUnits","userSpaceOnUse").attr("width",4).attr("height",4).append("path").attr("d","M-1,1 l2,-2 M0,4 l4,-4 M3,5 l2,-2").attr("stroke-width",1).attr("stroke","gray");let m;let d;let h=30;for(const[r,o]of t.columnNames.entries()){if(r==1&&!e)break;m=r%2==0?400:900;m+=10;d=70;n.append("text").attr("transform",`translate(${m}, ${d})`).attr("text-anchor","start").style("font-weight","bold").text(o);g(m,d+30);m+=p}d=70;for(const t of this.configComponent.groups){n.append("text").attr("transform",`translate(${50}, ${d+40})`).attr("text-anchor","start").text(`${t.label}`).style("font-weight","bold");d+=h+20;for(const r of t.rows){const t=n.append("g");t.append("rect").attr("transform",`translate(${20}, ${d-6})`).attr("x",0).attr("y",0).attr("width",e?1500:850).attr("height",30).attr("fill","#f8d335").attr("fill-opacity",0);m=400;if(r.term1)this.drawRect(m,d,r,"term1",t);if(r.term2)this.drawRect(m+p,d,r,"term2",t);d+=h}}u(410,120,50,d,"B");u(410,120,75,d,"A");this.legendG=this.svg.append("g").attr("transform",`translate(${50},${d+60})`);this.filterG=this.svg.append("g").attr("transform",`translate(${50},${d+180})`);this.legendG.append("text").attr("text-anchor","left").style("font-weight","bold").text("Overall Score").attr("transform",`translate(0, -5)`);this.addLegendItem("A","More than 75% of possible scorable items",1);this.addLegendItem("B","50-75% of possible scorable items",2);this.addLegendItem("C","Less than 50% of possible scorable items",3);this.addFilterLegend();if(this.state.dslabel=="ProfileAbbrev"){const t=this.legendG.append("g").attr("transform",`translate(420, 0)`);this.addEndUserImpressionNote(t)}else this.addPOCNote(this.legendG.append("g").attr("transform",`translate(550, -80)`));if(!e)return;u(910,120,50,d,"B");u(910,120,75,d,"A");d+=40;m=600;const f=n.append("g");this.drawLegendRect(m,d,"and",l,f);m+=300;this.drawLegendRect(m,d,"or",l,f);function g(t,e){const o=r().domain([0,100]).range([0,c]);n.append("g").attr("transform",`translate(${t}, ${e})`).call(i(o))}function u(t,e,r,o,s){const a=t+r/100*c;n.append("line").style("stroke","#aaa").style("stroke-width",1).style("stroke-dasharray","5, 5").attr("x1",a).attr("y1",e).attr("x2",a).attr("y2",o);n.append("text").attr("transform",`translate(${a+.125*c}, ${o+20})`).attr("text-anchor","middle").text(s).style("font-weight","bold");if(r==50)n.append("text").attr("transform",`translate(${a-.25*c}, ${o+20})`).attr("text-anchor","middle").text("C").style("font-weight","bold")}}drawRect(t,e,r,o,s){const a=this.configComponent.hasSubjectiveData;const n=r[o];let i=false;if((r.name=="Total Module"||r.name=="End-user Impression*")&&!r.term2)i=true;const l=n.score.term.color;const m=this.getPercentage(n);const d=o=="term1"||o=="term2"&&!r.term1;const h=o=="term1"?this.getPercentage(r.term2):this.getPercentage(r.term1);const f=m?m/100*c:0;if(m){const r=this.state.dslabel=="ProfileFull"&&this.settings.component=="Patients and Outcomes"?true:!i&&(h||!a);const o=s.append("rect").attr("transform",`translate(${t+10}, ${e})`).attr("pointer-events","none").attr("x",0).attr("y",0).attr("width",f).attr("height",20);if(r)o.attr("fill",l);else{const t=this.id+n.score.term.id;s.append("defs").append("pattern").attr("id",t).attr("patternUnits","userSpaceOnUse").attr("width",4).attr("height",4).append("path").attr("d","M-1,1 l2,-2 M0,4 l4,-4 M3,5 l2,-2").attr("stroke-width",1).attr("stroke",l);o.attr("fill",`url(#${t})`)}}const g=s.append("text").attr("pointer-events","none").attr("text-anchor","end").text(`${m||0}%`);if(f>0)g.attr("transform",`translate(${t+f+55}, ${e+15})`);else if(!h&&o=="term1")g.attr("transform",`translate(${t+35}, ${e+15})`);if(d)s.append("text").attr("transform",`translate(${o=="term1"?t:t-p}, ${e+15})`).attr("text-anchor","end").text(r.name).attr("pointer-events","none")}drawLegendRect(t,e,r,o,s){const a=s.append("g").attr("transform",`translate(${t}, ${e})`).append("rect").attr("x",0).attr("y",0).attr("width",20).attr("height",20);if(r=="and")a.attr("fill","gray");else a.attr("fill",`url(#${this.id}_diagonalHatch)`);const n=this.svg.append("text").attr("transform",`translate(${t+25}, ${e+15})`).attr("text-anchor","start").text("Objective ");n.append("tspan").attr("font-weight","bold").text(r);n.append("tspan").text(" Subjective data")}}async function m(e,r){try{const n=r.vocabApi.termdbConfig?.chartConfigByType?.profileBarchart;n.settings={profileBarchart:s()};const i=t(structuredClone(n),e);i.settings.controls={isOpen:false};const p=[];for(const t of i.plotByComponent){t.hasSubjectiveData=false;for(const e of t.groups)for(const r of e.rows){if(r.term1){r.term1.score.q=r.term1.maxScore.q={mode:"continuous"};p.push(r.term1.score);p.push(r.term1.maxScore)}if(r.term2){r.term2.score.q=r.term2.maxScore.q={mode:"continuous"};p.push(r.term2.score);p.push(r.term2.maxScore)}if(r.term1&&r.term2)t.hasSubjectiveData=true}}await o(p,r.vocabApi);await a(i,r);return i}catch(t){throw`${t} [profileBarchart getPlotConfig()]`}}const d=e(l);const h=d;function f(){return{}}export{h as componentInit,f as getDefaultProfileBarchartSettings,m as getPlotConfig,d as profileBarchartInit};

package/dist/profileHome-32eb9b50.js

@@ -0,0 +1 @@
+import"./app-3320ab6f.js";import{d as e}from"./app-b369b169.js";import"./termsetting-33ea66f1.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./FilterRxComp-701a1480.js";import"./table-29d5a973.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";function t(t){const a=e(t.holder);a.append("img").attr("src","images/Button_Full_Version.png").attr("width","15%").on("click",(e=>o(a,"ProfileFull")));a.append("img").attr("src","images/Button_Abbreviated_Version.png").attr("width","15%").on("click",(e=>o(a,"ProfileAbbrev")))}async function o(t,o){const r=document.getElementById("profileIntro");r.innerHTML="";t.selectAll("*").remove();const n=e(document.getElementById("aaa"));n.selectAll("*").remove();const l={holder:n,state:{nav:{header_mode:"hidden"},vocab:{dslabel:o,genome:"hg38"}}};const s=await import("./app-649f8357.js");const p=await s.appInit(l);a(t,p,o,logged,site);i(p,"profilePolar","Polar Graph",logged,site)}function a(e,t,a,l,s){const p=a=="ProfileFull";const c=e.append("div").style("display","inline-flex").style("gap","5px").style("padding-left","10px").style("font-size","1.1em");c.append("button").text("Full PrOFILE").style("font-size","1.1em").style("background-color",a=="ProfileFull"?"orange":"").on("click",(t=>{o(e,"ProfileFull")}));c.append("button").text("Abbreviated PrOFILE").style("background-color",a=="ProfileAbbrev"?"orange":"").style("font-size","1.1em").on("click",(t=>o(e,"ProfileAbbrev")));c.append("button").text("Polar Graph").style("font-size","1.1em").on("click",(e=>i(t,"profilePolar","Polar Graph",l,s)));c.append("button").text("Bar Graph").style("font-size","1.1em").on("click",(e=>i(t,"profileBarchart","Bar Graph",l,s)));if(l)c.append("button").text("Radar 1-Score-based(Site)").style("font-size","1.1em").on("click",(e=>r(t,"profileRadarFacility","Radar 1-Score-based(Site)","plot1",l,s)));c.append("button").text("Radar 2-Impressions").style("font-size","1.1em").on("click",(e=>r(t,"profileRadar","Radar 2-Impressions","plot1",l,s)));if(p)c.append("button").text("Radar 3-Score-based(SC & POC)").style("font-size","1.1em").on("click",(e=>r(t,"profileRadar","Radar 3-Score-based(SC & POC)","plot2",l,s)));c.append("button").style("font-size","1.1em").on("click",(e=>n(t))).text("Delete All")}async function i(e,t,o,a,i){await e.dispatch({type:"plot_create",config:{chartType:t,header:o,logged:a,site:i}})}async function r(e,t,o,a,i,r){await e.dispatch({type:"plot_create",config:{chartType:t,plot:a,header:o,logged:i,site:r}})}async function n(e){for(const t of e.getState().plots){await e.dispatch({type:"plot_delete",id:t.id})}}export{t as init};

package/dist/profilePlot-c7e099e8.js

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+import{d as t}from"./svg.download-35926549.js";import{d as e,M as i,L as s}from"./app-b369b169.js";import{m as a}from"./termsetting-33ea66f1.js";import{c as o}from"./FilterRxComp-701a1480.js";import{controlsInit as n}from"./controls-287e6efa.js";import{k as l}from"./recover-49e09de0.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./table-29d5a973.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./controls.btns-79b805dd.js";import"./controls.config-28d6d6a8.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";const r=["Low income","Lower middle income","Upper middle income","High income"];const p=["Small (1-25 annual newly diagnoses)","Medium (26-80 annual newly diagnoses)","Large (81-120 annual newly diagnoses)","Very large (>120 annual newly diagnoses)"];class d{constructor(){this.type="profilePlot";this.downloadCount=0}getState(t){const e=t.plots.find((t=>t.id===this.id));if(!e)throw`No plot with id='${this.id}' found`;return{config:e,termfilter:t.termfilter,dslabel:t.vocab.dslabel,vocab:t.vocab,logged:e.logged,site:e.site}}async init(t){const a=t.plots.find((t=>t.id===this.id));if(this.opts.header){const t=a.logged?a.site?a.site:"Admin":"Public";this.opts.header.text(a.header?a.header:a.chartType+` / ${t}`)}const o=this.opts.holder.append("div").style("display","inline-block");const n=o.append("div").style("display","inline-block").style("vertical-align","top");const l=o.append("div").style("display","inline-block").style("vertical-align","top");const r=this.opts.holder.append("div");const p=n.append("div").style("display","inline-block").style("font-size","0.9em");const d=n.append("div").style("margin-left","16px").style("margin-top","8px");const h=l.insert("div").style("display","inline-block");const c=h.append("div");this.dom={controlsDiv:p,iconsDiv:d,holder:h,plotDiv:c,holder2:r};e(".sjpp-output-sandbox-content").on("scroll",(t=>this.onMouseOut(t)));this.dom.plotDiv.on("mousemove",(t=>this.onMouseOver(t)));this.dom.plotDiv.on("mouseleave",(t=>this.onMouseOut(t)));this.dom.plotDiv.on("mouseout",(t=>this.onMouseOut(t)));this.sampleidmap=await this.app.vocabApi.getSamplesByName();if(a.site){if(Object.keys(this.sampleidmap).length==0)throw"You must login to view site info";const t=this.sampleidmap[a.site]?.id;if(!t)throw"Invalid site"}this.tip=new i({padding:"4px",offsetX:10,offsetY:15});document.addEventListener("scroll",(t=>this?.tip?.hide()));s["pdf"](d.append("div").style("padding","0px 5px 15px 5px"),{title:"Prints page, select Save as PDF in the options to download as a pdf",handler:()=>{window.print()}});if(this.type!="profileRadarFacility"&&!a.settings[this.type].comparison){const t=d.append("div").style("margin-bottom","20px");const e=t.append("button").style("border","none").style("background-color","transparent");s["compare"](e,{title:"Compare with another plot"});e.on("click",(async t=>{const i=this.settings.comparison=!this.settings.comparison;e.style("background-color",i?"rgb(207, 226, 243)":"transparent");this.dom.holder2.selectAll("*").remove();if(i)await this.comparePlots()}))}if(this.type!="profileBarchart"){const t=d.append("div").style("padding-bottom","15px");this.dom.tableBt=t.append("button").style("border","none").style("background-color","rgb(207, 226, 243)");s["table"](this.dom.tableBt,{title:"Show table with data"});this.dom.tableBt.on("click",(t=>{const e=!this.settings.showTable;this.dom.tableBt.style("background-color",e?"rgb(207, 226, 243)":"transparent");this.showTable(e)}))}s["restart"](d.append("div").style("padding","0px 5px 15px 5px"),{title:"Clear filters",handler:async()=>{this.clearFiltersExcept([]);this.app.dispatch({type:"plot_edit",id:this.id,config:{filter:this.getFilter(),settings:{[this.type]:this.settings}}})}});if(!a.settings[this.type].comparison)s["add"](d.append("div").style("padding","3px"),{title:"Open a new plot",handler:async()=>{const t={chartType:this.type,insertBefore:this.id,header:this.opts.header.text(),logged:this.state.config.logged,site:this.state.config.site};if(this.type=="profileRadarFacility"||this.type=="profileRadar")t.plot=this.state.config.plot;this.app.dispatch({type:"plot_create",config:t})}})}async showTable(t){this.settings.showTable=t;await this.app.dispatch({type:"plot_edit",id:this.id,config:{settings:{[this.type]:this.settings}}})}getList(t){const e=Object.values(t.term.values);const i=this.filtersData.lst.filter((e=>this.samplesPerFilter[t.term.id].includes(parseInt(e.sample))));const s=Array.from(new Set(i.map((e=>e[t.$id]?.value))));for(const t of e){t.value=t.label;t.disabled=!s.includes(t.label)}e.unshift({label:"",value:""});if(!(t.term.id in this.settings))this.settings[t.term.id]=e[0].label;return e}async main(){this.config=JSON.parse(JSON.stringify(this.state.config));this.settings=this.config.settings[this.type];if(this.dom.tableBt)this.dom.tableBt.style("background-color",this.settings.showTable?"rgb(207, 226, 243)":"transparent")}async comparePlots(){this.plotAdded=true;const t=this.state;const e=await import("./plot.app-30c4b8e5.js");const i={chartType:this.type,settings:{[this.type]:{comparison:true}}};if(this.type=="profileRadar"||this.type=="profileRadarFacility")i.plot=this.config.plot;const s={holder:this.dom.holder2,state:{plots:[i],vocab:t.vocab}};await e.appInit(s)}async setControls(e=[]){const i={};for(const t of this.config.filterTWs){const e=this.getFilter(t);if(e)i[t.term.id]=e}this.samplesPerFilter=await this.app.vocabApi.getSamplesPerFilter({filters:i});this.filtersData=await this.app.vocabApi.getAnnotatedSampleData({terms:this.config.filterTWs,termsPerRequest:10});this.regions=Object.keys(this.config.regionTW.term.values).map((t=>({label:t,value:t})));this.regions.unshift({label:"",value:""});this.countries=this.getList(this.config.countryTW);this.incomes=this.getList(this.config.incomeTW);this.teachingStates=this.getList(this.config.teachingStatusTW);this.referralStates=this.getList(this.config.referralStatusTW);this.fundingSources=this.getList(this.config.fundingSourceTW);this.hospitalVolumes=this.getList(this.config.hospitalVolumeTW);this.yearsOfImplementation=this.getList(this.config.yearOfImplementationTW);this.incomes.sort(((t,e)=>{const i=r.indexOf(t.value);const s=r.indexOf(e.value);if(i<s)return-1;return 1}));this.hospitalVolumes.sort(((t,e)=>{const i=p.indexOf(t.value);const s=p.indexOf(e.value);if(i<s)return-1;return 1}));this.types=this.getList(this.config.typeTW);const s=this.config.filter||this.getFilter();this.data=await this.app.vocabApi.getAnnotatedSampleData({terms:this.twLst,filter:s,termsPerRequest:30});const a=this.type;this.dom.controlsDiv.selectAll("*").remove();let o=[];if(this.state.logged&&this.state.site&&a!="profileRadarFacility"){const t={label:"Data",type:"radio",chartType:a,settingsKey:"isAggregate",options:[{label:this.state.site,value:false},{label:"Aggregate",value:true}]};o.push(t)}if(!this.state.logged||!this.state.site||this.settings.isAggregate||a=="profileRadarFacility"){o.push(...[{label:"Region",type:"dropdown",chartType:a,options:this.regions,settingsKey:this.config.regionTW.term.id,callback:t=>this.setRegion(t)},{label:"Country",type:"dropdown",chartType:a,options:this.countries,settingsKey:this.config.countryTW.term.id,callback:t=>this.setFilterValue(this.config.countryTW.term.id,t)},{label:"Income group",type:"dropdown",chartType:a,options:this.incomes,settingsKey:this.config.incomeTW.term.id,callback:t=>this.setFilterValue(this.config.incomeTW.term.id,t)},{label:"Facility type",type:"dropdown",chartType:a,options:this.types,settingsKey:this.config.typeTW.term.id,callback:t=>this.setFilterValue(this.config.typeTW.term.id,t)},{label:this.config.teachingStatusTW.term.name,type:"dropdown",chartType:a,options:this.teachingStates,settingsKey:this.config.teachingStatusTW.term.id,callback:t=>this.setFilterValue(this.config.teachingStatusTW.term.id,t)},{label:this.config.referralStatusTW.term.name,type:"dropdown",chartType:a,options:this.referralStates,settingsKey:this.config.referralStatusTW.term.id,callback:t=>this.setFilterValue(this.config.referralStatusTW.term.id,t)},{label:this.config.fundingSourceTW.term.name,type:"dropdown",chartType:a,options:this.fundingSources,settingsKey:this.config.fundingSourceTW.term.id,callback:t=>this.setFilterValue(this.config.fundingSourceTW.term.id,t)},{label:this.config.hospitalVolumeTW.term.name,type:"dropdown",chartType:a,options:this.hospitalVolumes,settingsKey:this.config.hospitalVolumeTW.term.id,callback:t=>this.setFilterValue(this.config.hospitalVolumeTW.term.id,t)},{label:this.config.yearOfImplementationTW.term.name,type:"dropdown",chartType:a,options:this.yearsOfImplementation,settingsKey:this.config.yearOfImplementationTW.term.id,callback:t=>this.setFilterValue(this.config.yearOfImplementationTW.term.id,t)}])}await this.loadSampleData(a,o);o.unshift(...e);this.components={controls:await n({app:this.app,id:this.id,holder:this.dom.controlsDiv,inputs:o})};this.components.controls.on(`downloadClick.${a}`,(()=>t(this.svg,this.getDownloadFilename(),this.dom.holder.node())));this.components.controls.on(`helpClick.${a}`,(()=>{let t;if(this.state.dslabel=="ProfileAbbrev"){if(a=="profileBarchart")t="https://global.stjude.org/content/dam/global/en-us/documents/no-index/bar-graph-abbr-profiledash.pdf";else if(a=="profilePolar")t="https://global.stjude.org/content/dam/global/en-us/documents/no-index/polar-graph-abbr-profiledash.pdf";else if(a.startsWith("profileRadar"))t="https://global.stjude.org/content/dam/global/en-us/documents/no-index/radar-abbr-profiledash.pdf"}else if(this.state.dslabel=="ProfileFull"){if(a=="profileBarchart")t="https://global.stjude.org/content/dam/global/en-us/documents/no-index/bar-graph-full-profiledash.pdf";else if(a=="profilePolar")t="https://global.stjude.org/content/dam/global/en-us/documents/no-index/polar-graph-full-profiledash.pdf";else if(a.startsWith("profileRadar"))t="https://global.stjude.org/content/dam/global/en-us/documents/no-index/radar-full-profiledash.pdf"}if(t)window.open(t)}));this.filtersCount=0}async loadSampleData(t,e){if(t!="profileRadarFacility"){if(this.state.logged){if(this.state.site&&!this.settings.isAggregate){const t=this.sampleidmap[this.state.site].id;this.settings.site=t;this.sites=[{label:this.state.site,value:t}]}else if(!this.state.site){this.sites=this.data.lst.map((t=>({label:this.data.refs.bySampleId[t.sample].label,value:t.sample})));this.sites.unshift({label:"",value:""});e.push({label:"Site",type:"dropdown",chartType:t,options:this.sites,settingsKey:"site",callback:t=>this.setSite(t)})}if(this.settings.site)this.sampleData=this.data.samples[Number(this.settings.site)];else this.sampleData=null}}else{if(this.state.logged){let i;if(this.state.site){const t=this.sampleidmap[this.state.site].id;this.settings.site=t;this.sites=[{label:this.state.site,value:t}];i=await this.app.vocabApi.getAnnotatedSampleData({terms:this.twLst,termsPerRequest:30,filter:l(parseInt(t))});this.sampleData=i.lst[0]}else{i=await this.app.vocabApi.getAnnotatedSampleData({terms:this.twLst,termsPerRequest:30});this.sites=i.lst.map((t=>({label:i.refs.bySampleId[t.sample].label,value:t.sample})));if(!this.settings.site)this.settings.site=i.lst[0].sample;this.sampleData=i.samples[Number(this.settings.site)]}e.unshift({label:"Site",type:"dropdown",chartType:t,options:this.sites,settingsKey:"site",callback:t=>this.setSite(t)})}}}setFilterValue(t,e){const i=this.config;this.settings[t]=e;this.settings.site="";i.filter=this.getFilter();this.app.dispatch({type:"plot_edit",id:this.id,config:this.config})}setRegion(t){const e=this.config;this.settings[e.regionTW.term.id]=t;this.clearFiltersExcept([e.regionTW.term.id]);e.filter=this.getFilter();this.app.dispatch({type:"plot_edit",id:this.id,config:e})}clearFiltersExcept(t){for(const e of this.config.filterTWs)if(!t.includes(e.term.id))this.settings[e.term.id]="";if(this.config.chartType!="profileRadarFacility")this.settings.site=""}setSite(t){this.settings.site=t;this.sampleData=null;this.app.dispatch({type:"plot_edit",id:this.id,config:this.config})}getFilter(t=null){const e=[];if(t)e.push(t.$id);const i=[];for(const t of this.config.filterTWs)this.processTW(t,this.settings[t.term.id],e,i);const s={type:"tvslst",in:true,join:"and",lst:i};const a=o([this.state.termfilter.filter,s]);return a}processTW(t,e,i,s){if(e&&!i.includes(t.$id))s.push({type:"tvs",tvs:{term:t.term,values:[{key:e}]}})}addFilterLegend(){if(!this.settings.site||this.config.chartType=="profileRadarFacility"){const t=this.config.filterTWs.some((t=>this.settings[t.term.id]));const e=t?"Filters":"No filter applied";this.filterG.attr("font-size","0.9em").append("text").attr("text-anchor","left").style("font-weight","bold").text(`${e} (n=${this.data.lst.length})`).attr("transform",`translate(0, -5)`);for(const t of this.config.filterTWs)this.addFilterLegendItem(t.term.name,this.settings[t.term.id])}if(this.settings.site&&this.config.chartType!="profileRadarFacility"){const t=this.sites.find((t=>t.value==this.settings.site)).label;this.addFilterLegendItem("Facility",t)}}addFilterLegendItem(t,e){if(!e)return;this.filtersCount++;const i=this.filterG.append("g").attr("font-size","0.8em");const s=i.append("text").attr("transform",`translate(0, ${this.filtersCount*22})`).attr("text-anchor","left");s.append("tspan").attr("font-size","bold").text(t);s.append("tspan").text(`: ${e?e:"None"}`)}addEndUserImpressionNote(t){t.attr("font-size","0.8em");let e=t.append("text").attr("transform",`translate(0, 115)`);e.append("tspan").attr("font-weight","bold").text("End-user Impression: ");e.append("tspan").text("It is provided by the local liaison who completed the assessment ");t.append("text").attr("transform",`translate(0, 140)`).text("in consultation with the PHO medical director or directly by the PHO medical director.");t.append("text").attr("transform",`translate(0, 165)`).text("The end-user was asked to rate the current status of the domains and subdomains included.")}addPOCNote(t){t.attr("font-size","0.8em");let e=t.append("text").attr("transform",`translate(0, 115)`);e.append("tspan").attr("font-weight","bold").text("Point of Care (POC) Staff: ");e.append("tspan").text("All members of the assessment team, ");t.append("text").attr("transform",`translate(0, 140)`).text("excluding the Site Coordinator. POC staff provide subjective information based ");t.append("text").attr("transform",`translate(0, 165)`).text("on their experience and perception about service delivery at the PHO facility.")}addLegendItem(t,e,i){const s=this.legendG.append("text").attr("font-size","0.9em").attr("transform",`translate(0, ${i*20})`).attr("text-anchor","left");s.append("tspan").attr("font-weight","bold").text(t);s.append("tspan").text(`: ${e}`)}getDownloadFilename(){this.downloadCount++;let t=`${this.type}${this.downloadCount}.svg`;t=t.split(" ").join("_");return t}getPercentage(t,e=null){if(!t)return null;if(e==null)e=this.settings.isAggregate||this.sampleData==null;if(e){const e=t.maxScore.term?this.data.lst[0]?.[t.maxScore.$id]?.value:t.maxScore;let i=this.data.lst.map((i=>i[t.score.$id]?.value/e*100));i.sort(((t,e)=>t-e));const s=Math.floor(i.length/2);const a=i.length%2!==0?i[s]:(i[s-1]+i[s])/2;return Math.round(a)}else{const e=this.sampleData[t.score.$id]?.value;const i=t.maxScore.term?this.sampleData[t.maxScore.$id]?.value:t.maxScore;const s=e/i*100;return Math.round(s)}}}async function h(t,e){const i=[];t.countryTW={id:"country"};t.regionTW={id:"WHO_region"};t.incomeTW={id:"Income_group"};t.typeTW={id:"FC_TypeofFacility"};t.teachingStatusTW={id:"FC_TeachingFacility"};t.referralStatusTW={id:"FC_ReferralFacility"};t.fundingSourceTW={id:"FC_FundingSrc"};t.hospitalVolumeTW={id:"PO_HospitalVolume"};t.yearOfImplementationTW={id:"Year_implementation"};i.push(...[t.countryTW,t.regionTW,t.incomeTW,t.typeTW,t.teachingStatusTW,t.referralStatusTW,t.fundingSourceTW,t.hospitalVolumeTW,t.yearOfImplementationTW]);await a(i,e.vocabApi);t.filterTWs=i}function c(){return{isAggregate:false,showTable:true}}export{c as getDefaultProfilePlotSettings,h as loadFilterTerms,d as profilePlot};

package/dist/profilePolar-6b981e63.js

@@ -0,0 +1 @@
+import{P as t,h as e}from"./app-b369b169.js";import{m as s}from"./termsetting-33ea66f1.js";import{getDefaultProfilePlotSettings as o,loadFilterTerms as r,profilePlot as i}from"./profilePlot-c7e099e8.js";import{r as a}from"./table-29d5a973.js";import{d as n}from"./arc-3d6751aa.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./svg.download-35926549.js";import"./FilterRxComp-701a1480.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./controls-287e6efa.js";import"./controls.btns-79b805dd.js";import"./controls.config-28d6d6a8.js";import"./recover-49e09de0.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";import"./constant-426a1483.js";import"./math-2fb199c6.js";class l extends i{constructor(){super();this.type="profilePolar";this.radius=250}async init(t){await super.init(t);const e=t.plots.find((t=>t.id===this.id));this.twLst=[];for(const[t,s]of e.terms.entries()){this.twLst.push(s.score);this.twLst.push(s.maxScore)}this.arcGenerator=n().innerRadius(0)}async main(){await super.main();await this.setControls();this.angle=Math.PI*2/this.config.terms.length;this.plot()}onMouseOut(t){if(t.target.tagName=="path"){const e=t.target;e.setAttribute("stroke","white");if(e.getAttribute("stroke-opacity")==0)e.setAttribute("stroke-opacity",1)}this.tip.hide()}onMouseOver(t){if(t.target.tagName=="path"){const e=t.target;e.setAttribute("stroke-opacity",0);const s=e.__data__;const o=this.tip.clear();const r=this.getPercentage(s);o.d.text(`${s.module} ${r}%`);o.show(t.clientX,t.clientY,true,true)}else this.onMouseOut(t)}plot(){const t=this.config;this.dom.plotDiv.selectAll("*").remove();const e=1e3;const s=700;this.svg=this.dom.plotDiv.append("div").style("display","inline-block").append("svg").attr("width",e).attr("height",s);this.dom.tableDiv=this.dom.plotDiv.append("div").style("display","inline-block").style("vertical-align","top").style("margin","45px 20px");if(!this.settings.comparison)this.svg.append("text").attr("transform",`translate(130, ${40})`).attr("font-weight","bold").text(t.title);const o=[];const r=[{label:"Color"},{label:"Module"},{label:"Score",align:"center"}];const i=this.radius;const n=280;const l=330;const c=this.svg.append("g").attr("transform",`translate(${n},${l})`);this.polarG=c;this.legendG=this.svg.append("g").attr("transform",`translate(${n+280}, ${l-200})`);this.filterG=this.svg.append("g").attr("transform",`translate(${n+260},${l+170})`);for(let t=0;t<=10;t++)h(t*10);const p=this.angle;let d=0;for(let e of t.terms){const t=e.module;e.i=d;const s=e.score.term.color;const r=this.getPercentage(e);o.push([{color:s,disabled:true},{value:t},{value:r}]);c.append("g").append("path").datum(e).attr("fill",s).attr("stroke","white").attr("d",this.arcGenerator({outerRadius:r/100*i,startAngle:d*p,endAngle:(d+1)*p})).on("click",(t=>this.onMouseOver(t)));d++}this.dom.tableDiv.selectAll("*").remove();if(this.settings.showTable)a({rows:o,columns:r,div:this.dom.tableDiv,showLines:true,resize:true,maxHeight:"50vh"});h(50,"C");h(75,"B");h(100,"A");for(let t=0;t<=10;t++){const e=t*10;c.append("text").attr("transform",`translate(-10, ${-e/100*i+5})`).attr("text-anchor","end").style("font-size","0.8rem").text(`${e}%`).attr("pointer-events","none")}this.legendG.append("text").attr("text-anchor","left").style("font-weight","bold").text("Overall Score").attr("transform",`translate(0, -5)`);this.addLegendItem("A","More than 75% of possible scorable items",1);this.addLegendItem("B","50-75% of possible scorable items",2);this.addLegendItem("C","Less than 50% of possible scorable items",3);this.addFilterLegend();function h(t,e=null){const s=c.append("circle").attr("r",t/100*i).style("fill","none").style("opacity","0.5");if(t!=50)s.style("stroke","#aaa");if(e){if(t!=100)s.style("stroke-dasharray","5, 5").style("stroke-width","2").style("stroke","black");c.append("text").attr("transform",`translate(15, ${-(t/100-.125)*i+10})`).attr("text-anchor","middle").text(e).style("font-weight","bold").style("font-size","24px").attr("pointer-events","none")}}}}async function c(e,i){try{const a=i.vocabApi.termdbConfig?.chartConfigByType?.profilePolar;a.settings={profilePolar:o()};if(!a)throw"default config not found in termdbConfig.chartConfigByType.profilePolar";const n=t(structuredClone(a),e);n.settings.controls={isOpen:false};const l=[];for(const t of n.terms){const e=t.score;const s=t.maxScore;e.q={mode:"continuous"};s.q={mode:"continuous"};l.push(e);l.push(s)}await s(l,i.vocabApi);await r(n,i);return n}catch(t){throw`${t} [profilePolar getPlotConfig()]`}}const p=e(l);const d=p;export{d as componentInit,c as getPlotConfig,p as profilePolarInit};

package/dist/profileRadar-bca1cc03.js

@@ -0,0 +1 @@
+import{P as t,h as e}from"./app-b369b169.js";import{m as s}from"./termsetting-33ea66f1.js";import{getDefaultProfilePlotSettings as r,loadFilterTerms as a,profilePlot as o}from"./profilePlot-c7e099e8.js";import{r as n}from"./table-29d5a973.js";import{l as i}from"./line-264f8f9e.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./svg.download-35926549.js";import"./FilterRxComp-701a1480.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./controls-287e6efa.js";import"./controls.btns-79b805dd.js";import"./controls.config-28d6d6a8.js";import"./recover-49e09de0.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";import"./constant-426a1483.js";class l extends o{constructor(){super();this.type="profileRadar";this.radius=250}async init(t){await super.init(t);const e=t.plots.find((t=>t.id===this.id));this.lineGenerator=i();this.twLst=[];this.terms=e[e.plot].terms;for(const t of this.terms){this.twLst.push(t.term1.score);if(t.term1.maxScore.term)this.twLst.push(t.term1.maxScore);this.twLst.push(t.term2.score);if(t.term2.maxScore.term)this.twLst.push(t.term2.maxScore)}}async main(){await super.main();await this.setControls();this.angle=Math.PI*2/this.terms.length;this.plot()}plot(){const t=this.config;this.dom.plotDiv.selectAll("*").remove();if(this.data.lst.length==0)return;const e=1200;const s=800;this.svg=this.dom.plotDiv.append("div").style("display","inline-block").append("svg").attr("width",e).attr("height",s);this.tableDiv=this.dom.plotDiv.append("div").style("display","inline-block").style("vertical-align","top").style("margin-top","45px");const r=[];const a=[{label:"Color"},{label:"Module"},{label:t[t.plot].term1.abbrev},{label:t[t.plot].term2.abbrev},{label:"Diff"}];const o=this.radius;const i=370;const l=340;if(!this.settings.comparison)this.svg.append("text").attr("transform",`translate(40, ${40})`).attr("font-weight","bold").attr("font-size","0.9rem").text(t[t.plot].title);const p=this.svg.append("g").attr("transform",`translate(${i},${l})`);this.polarG=p;this.legendG=this.svg.append("g").attr("transform",`translate(${i+320},${l+240})`);this.filterG=this.svg.append("g").attr("transform",`translate(${40},${l+340})`);for(let t=0;t<=10;t++)this.addPoligon(t*10);let d=0;const c=[],h=[];for(let{module:t,term1:e,term2:s}of this.terms){const a=d*this.angle-Math.PI/2;this.addData("term2",a,d,h);this.addData("term1",a,d,c);const n=e.score.term.color;const i=this.getPercentage(e);const l=this.getPercentage(s);const m=Math.abs(i-l);const f={value:m};if(m>=20)f.color=l>i?"red":"blue";r.push([{color:n,disabled:true},{value:t},{value:i},{value:l},f]);d++;const g=a>Math.PI/2&&a<=3/2*Math.PI;let u=o*1.1*Math.cos(a);let b=o*1.1*Math.sin(a)-10;const x=p.append("text").attr("x",`${u}px`).attr("y",`${b}px`);const v=t.split(" ");let y;v.forEach(((t,e)=>{if(t!="and"){b+=15;y=x.append("tspan").attr("x",`${u}px`).attr("y",`${b}px`).text(t+"")}else y.append("tspan").text(" and")}));if(g)x.attr("text-anchor","end")}if(this.settings.showTable)n({rows:r,columns:a,div:this.tableDiv,showLines:true,resize:true,maxHeight:"60vh"});c.push(c[0]);h.push(h[0]);const m="blue",f="gray";p.append("g").append("path").style("stroke",m).attr("fill","none").attr("stroke-width","2px").attr("d",this.lineGenerator(c));p.append("g").append("path").style("stroke",f).attr("fill","none").style("stroke-dasharray","5, 5").attr("stroke-width","2px").attr("d",this.lineGenerator(h));for(let t=0;t<=10;t++){const e=t*10;p.append("text").attr("transform",`translate(-10, ${-e/100*o+5})`).attr("text-anchor","end").style("font-size","0.8rem").text(`${e}%`).attr("pointer-events","none")}if(!this.settings.comparison){this.legendG.append("text").attr("text-anchor","left").style("font-weight","bold").text(`Legend`);let e=t[t.plot].term1.abbrev?`(${t[t.plot].term1.abbrev})`:"";const s=`${t[t.plot].term1.name} ${e}`;this.addLegendItem(s,m,0,"none");e=t[t.plot].term2.abbrev?`(${t[t.plot].term2.abbrev})`:"";const r=`${t[t.plot].term2.name} ${e}`;this.addLegendItem(r,f,1,"5, 5");if(this.state.dslabel=="ProfileAbbrev")this.addEndUserImpressionNote(this.legendG.append("g").attr("transform",`translate(0, -15)`));else this.addPOCNote(this.legendG.append("g").attr("transform",`translate(0, -15)`))}this.addFilterLegend()}addData(t,e,s,r){const a=this.terms[s];const o=this.getPercentage(a[t]);const n=o/100*this.radius;let i=n*Math.cos(e);let l=n*Math.sin(e);const p=t=="term1"?"blue":"#aaa";const d=this.polarG.append("g").attr("transform",`translate(${i}, ${l})`).append("circle").attr("r",4).attr("fill",p);d.datum({module:a.module,percentage:o}).on("click",(t=>this.onMouseOver(t)));r.push([i,l])}addPoligon(t){const e=[];for(let s=0;s<this.terms.length;s++){const r=s*this.angle-Math.PI/2;const a=t/100*this.radius;const o=a*Math.cos(r);const n=a*Math.sin(r);e.push([o,n])}e.push(e[0]);this.polarG.append("g").append("path").style("stroke","#aaa").attr("fill","none").attr("d",this.lineGenerator(e)).style("opacity","0.5")}addLegendItem(t,e,s,r){const a=25;const o=a+s*a;const n=35;this.legendG.append("path").attr("stroke",e).style("stroke-dasharray",r).attr("stroke-width","2px").attr("d",this.lineGenerator([[0,o-5],[n,o-5]]));this.legendG.append("g").attr("transform",`translate(${0}, ${o-5})`).append("circle").attr("r",4).attr("fill",e);const i=this.legendG.append("text").attr("font-size","0.9em").attr("transform",`translate(${n+5}, ${o})`).attr("text-anchor","left");i.append("tspan").text(t)}onMouseOver(t){if(t.target.tagName=="circle"){const e=t.target;const s=e.__data__;const r=this.tip.clear();const a=s.percentage;r.d.text(`${s.module} ${a}%`);r.show(t.clientX,t.clientY,true,true)}else this.onMouseOut(t)}onMouseOut(t){this.tip.hide()}}async function p(e,o){try{const n=o.vocabApi.termdbConfig?.chartConfigByType?.profileRadar;n.settings={profileRadar:r()};if(!n)throw"default config not found in termdbConfig.chartConfigByType.profileRadar";const i=t(structuredClone(n),e);i.settings.controls={isOpen:false};const l=i[e.plot].terms;const p=[];for(const t of l){t.term1.score.q={mode:"continuous"};p.push(t.term1.score);if(t.term1.maxScore.id){t.term1.maxScore.q={mode:"continuous"};p.push(t.term1.maxScore)}t.term2.score.q={mode:"continuous"};p.push(t.term2.score);if(t.term2.maxScore.id){t.term2.maxScore.q={mode:"continuous"};p.push(t.term2.maxScore)}}await s(p,o.vocabApi);await a(i,o);return i}catch(t){throw`${t} [profileRadar getPlotConfig()]`}}const d=e(l);const c=d;export{c as componentInit,p as getPlotConfig,d as profileRadarInit};

package/dist/profileRadarFacility-bbb1ecd8.js

@@ -0,0 +1 @@
+import{P as t,h as e}from"./app-b369b169.js";import{m as s}from"./termsetting-33ea66f1.js";import{r as a}from"./table-29d5a973.js";import{getDefaultProfilePlotSettings as o,loadFilterTerms as r,profilePlot as i}from"./profilePlot-c7e099e8.js";import{l as n}from"./line-264f8f9e.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./svg.download-35926549.js";import"./FilterRxComp-701a1480.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./controls-287e6efa.js";import"./controls.btns-79b805dd.js";import"./controls.config-28d6d6a8.js";import"./recover-49e09de0.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";import"./constant-426a1483.js";class l extends i{constructor(){super();this.type="profileRadarFacility";this.radius=250}async init(t){await super.init(t);const e=t.plots.find((t=>t.id===this.id));this.twLst=[];this.terms=e[e.plot].terms;for(const t of this.terms){this.rowCount++;this.twLst.push(t.score);this.twLst.push(t.maxScore)}this.lineGenerator=n()}async main(){await super.main();await this.setControls();this.angle=Math.PI*2/this.terms.length;this.plot()}plot(){this.dom.plotDiv.selectAll("*").remove();if(this.data.lst.length==0)return;const t=1300;const e=650;this.svg=this.dom.plotDiv.append("div").style("display","inline-block").append("svg").attr("width",t).attr("height",e);this.tableDiv=this.dom.plotDiv.append("div").style("display","inline-block").style("vertical-align","top").style("margin-top","45px");this.svg.append("text").attr("transform",`translate(110, ${40})`).attr("font-weight","bold").text(this.config[this.config.plot].title);const s=this.radius;const o=370;const r=340;const i=this.svg.append("g").attr("transform",`translate(${o},${r})`);this.polarG=i;this.legendG=this.svg.append("g").attr("transform",`translate(${o+420},${r-180})`);this.filterG=this.svg.append("g").attr("transform",`translate(${o+420},${r+10})`);const n=[];const l=[{label:"Color"},{label:"Module"},{label:`Facility`},{label:"Global"},{label:"Diff"}];for(let t=0;t<=10;t++)this.addPoligon(t*10);let p=0;const c=[],d=[];for(const t of this.terms){const e=p*this.angle-Math.PI/2;this.addData(e,p,d,true);this.addData(e,p,c,false);const a=t.score.term.color;const o=this.getPercentage(t);const r=this.getPercentage(t,true);const l=Math.abs(o-r);const h={value:l};if(l>=20)h.color=r>o?"red":"blue";const f=[{color:a,disabled:true},{value:t.module},{value:o},{value:r},h];n.push(f);p++;const m=e>Math.PI/2&&e<=3/2*Math.PI;let g=s*1.1*Math.cos(e);let u=s*1.1*Math.sin(e)-10;const b=i.append("text").attr("x",`${g}px`).attr("y",`${u}px`);const y=t.module.split(" ");let x;y.forEach(((t,e)=>{if(t!="and"){u+=15;x=b.append("tspan").attr("x",`${g}px`).attr("y",`${u}px`).text(t+"")}else x.append("tspan").text(" and")}));if(m)b.attr("text-anchor","end")}if(this.settings.showTable)a({rows:n,columns:l,div:this.tableDiv,showLines:true,resize:true,maxHeight:"60vh"});c.push(c[0]);d.push(d[0]);const h="gray",f="blue";i.append("g").append("path").style("stroke",h).attr("fill","none").style("stroke-dasharray","5, 5").attr("stroke-width","2px").attr("d",this.lineGenerator(c));if(this.state.logged){i.append("g").append("path").style("stroke",f).attr("fill","none").attr("stroke-width","2px").attr("d",this.lineGenerator(d))}for(let t=0;t<=10;t++){const e=t*10;i.append("text").attr("transform",`translate(-10, ${-e/100*s+5})`).attr("text-anchor","end").style("font-size","0.8rem").text(`${e}%`).attr("pointer-events","none")}this.addFilterLegend();this.legendG.append("text").attr("text-anchor","left").style("font-weight","bold").text("Legend");const m=this.sites.find((t=>t.value==this.settings.site)).label;this.addLegendItem(m,f,0,"none");this.addLegendItem(this.config[this.config.plot].score,h,1,"5, 5")}addData(t,e,s,a){const o=this.terms[e];const r=a?this.getPercentage(o):this.getPercentage(o,true);const i=r/100*this.radius;let n=i*Math.cos(t);let l=i*Math.sin(t);const p=a?"blue":"#aaa";const c=this.polarG.append("g").attr("transform",`translate(${n}, ${l})`).append("circle").attr("r",4).attr("fill",p).on("click",(t=>this.onMouseOver(t)));s.push([n,l]);c.datum({module:o.module,percentage:r})}addPoligon(t){const e=[];for(let s=0;s<this.terms.length;s++){const a=s*this.angle-Math.PI/2;const o=t/100*this.radius;const r=o*Math.cos(a);const i=o*Math.sin(a);e.push([r,i])}e.push(e[0]);this.polarG.append("g").append("path").style("stroke","#aaa").attr("fill","none").attr("d",this.lineGenerator(e)).style("opacity","0.5")}addLegendItem(t,e,s,a){const o=25;const r=o+s*o;const i=35;this.legendG.append("path").attr("stroke",e).style("stroke-dasharray",a).attr("stroke-width","2px").attr("d",this.lineGenerator([[0,r-5],[i,r-5]]));this.legendG.append("g").attr("transform",`translate(${0}, ${r-5})`).append("circle").attr("r",4).attr("fill",e);const n=this.legendG.append("text").attr("font-size","0.9em").attr("transform",`translate(${i+5}, ${r})`).attr("text-anchor","left");n.append("tspan").text(t)}onMouseOver(t){if(t.target.tagName=="circle"){const e=t.target;const s=e.__data__;const a=this.tip.clear();const o=s.percentage;a.d.text(`${s.module} ${o}%`);a.show(t.clientX,t.clientY,true,true)}else this.onMouseOut(t)}onMouseOut(t){this.tip.hide()}}async function p(e,a){try{const i=a.vocabApi.termdbConfig?.chartConfigByType?.profileRadarFacility;if(!i)throw"default config not found in termdbConfig.chartConfigByType.profileRadarFacility";let n=t(structuredClone(i),e);const l=o();n.settings={profileRadarFacility:l,controls:{isOpen:false}};const p=n[e.plot].terms;const c=[];for(const t of p){t.score.q=t.maxScore.q={mode:"continuous"};c.push(t.score);c.push(t.maxScore)}await s(c,a.vocabApi);await r(n,a);return n}catch(t){throw`${t} [profileRadarFacility getPlotConfig()]`}}const c=e(l);const d=c;export{d as componentInit,p as getPlotConfig,c as profileRadarFacilityInit};

package/dist/profileSummary-b114204f.js

@@ -0,0 +1 @@
+import{P as t,h as s}from"./app-b369b169.js";import"./termsetting-33ea66f1.js";import{getDefaultProfilePlotSettings as o,loadFilterTerms as i,profilePlot as r}from"./profilePlot-c7e099e8.js";import"./tslib.es6-c3c2d88f.js";import"path";import"./svg.download-35926549.js";import"./FilterRxComp-701a1480.js";import"./table-29d5a973.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"./controls-287e6efa.js";import"./controls.btns-79b805dd.js";import"./controls.config-28d6d6a8.js";import"./recover-49e09de0.js";import"./FilterStateless-54c0b763.js";import"./app-3320ab6f.js";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";import"./genesearch-a4e19f0d.js";import"./checkbox-96437f4d.js";import"./rehydrateFilter-12d118cb.js";class e extends r{constructor(){super();this.type="profileSummary";this.twLst=[]}async init(t){await super.init(t);t.plots.find((t=>t.id===this.id))}async main(){await super.main();await this.setControls();this.plot()}plot(){const t=this.config;this.dom.plotDiv.selectAll("*").remove();const s=1100;const o=600;this.svg=this.dom.plotDiv.append("div").style("display","inline-block").append("svg").attr("width",s).attr("height",o);this.dom.tableDiv=this.dom.plotDiv.append("div").style("display","inline-block").style("vertical-align","top").style("margin-top","45px");this.svg.append("text").attr("transform",`translate(150, ${o-40})`).attr("font-weight","bold").text(t.title);const i=300;const r=280;const e=this.svg.append("g").attr("transform",`translate(${i},${r})`);this.mainG=e;this.legendG=this.svg.append("g").attr("transform",`translate(${i+280}, ${r-200})`);this.filterG=this.svg.append("g").attr("transform",`translate(${i+280},${r-80})`)}}async function a(s,r){try{const e=r.vocabApi.termdbConfig?.chartConfigByType?.profileSummary;if(!e)throw"default config not found in termdbConfig.chartConfigByType.profileSummary";const a=t(structuredClone(e),s);const n=o();a.settings={profileSummary:n,controls:{isOpen:false}};await i(a,r);return a}catch(t){throw`${t} [profileSummary getPlotConfig()]`}}const n=s(e);const p=n;export{p as componentInit,a as getPlotConfig,n as profileSummaryInit};