@sjcrh/proteinpaint-client 2.74.2 → 2.76.0

package/dist/{termdb.bins-9faa5170.js → termdb.bins-8b656cc3.js}

@@ -1 +1 @@
-import{V as t,C as s,H as e,W as n}from"./app-a8c4854a.js";function i(t){const s=t;if(!s||typeof s!=="object")throw"bin schema must be an object";if(!("type"in s))s.type="regular-bin";if(s.type=="custom-bin"){if(!Array.isArray(s.lst))throw"binconfig.lst must be an array";if(!s.lst.length)throw"binconfig.lst must have entries";const t=s.lst[0];const n=s.lst[s.lst.length-1];for(const i of s.lst){if(!("startinclusive"in i)&&!("stopinclusive"in i)){throw"custom bin.startinclusive and/or bin.stopinclusive must be defined"}if(i==t){if("startunbounded"in i&&!i.startunbounded){throw`a custom first bin must not set bin.startunbounded to false`}i.startunbounded=true;if("start"in i){throw"a custom first bin must not set a bin.start value"}if("start_percentile"in i){throw"the first bin must not set a bin.start_percentile value"}if(!("stop"in i)){throw`a custom first bin must define a bin.stop value`}if(!e(i.stop)){throw`a custom first bin.stop value should be numeric`}}else if(i==n){if(!("start"in i)){throw`a custom last bin must define a bin.start value`}if(!e(i.start)){throw`a custom last bin.start must be numeric`}if("stopunbounded"in i&&!i.stopunbounded){throw"a custom last bin must not set bin.stopunbounded to false"}i.stopunbounded=true;if("stop"in i){throw"a custom last bin must not set a bin.stop value"}}else{if(!e(i.start))throw"bin.start must be numeric for a non-first bin";if(!e(i.stop))throw"bin.stop must be numeric for a non-last bin"}}}else if(s.type=="regular-bin"){if(!Number.isFinite(s.bin_size))throw"non-numeric bin_size";if(s.bin_size<=0)throw"bin_size must be greater than 0";if(!s.startinclusive&&!s.stopinclusive){s.startinclusive=1;s.stopinclusive=0}if(!s.first_bin)throw"first_bin{} missing";if(typeof s.first_bin!="object")throw"first_bin{} is not an object";if(!Object.keys(s.first_bin).length)throw"first_bin is an empty object";{const t=s.first_bin;t.startunbounded=true;if(t.stop_percentile){if(!Number.isInteger(t.stop_percentile))throw"first_bin.stop_percentile should be integer";if(t.stop_percentile<=0||t.stop_percentile>=100)throw"first_bin.stop_percentile out of bound (0-100)"}else if(!Number.isFinite(t.stop)){throw"first_bin.stop not a number when stop_percentile is not set"}}if(s.last_bin){const t=s.last_bin;if(t.start_percentile){if(!Number.isInteger(t.start_percentile))throw"last_bin.start_percentile should be integer";if(t.start_percentile<=0||t.start_percentile>=100)throw"last_bin.start_percentile out of bound (0-100)"}else if(!Number.isFinite(t.start)){throw"last_bin.start not a number when start_percentile is not set"}t.stopunbounded=true;if("stop"in t){throw"a regular last bin must not set a bin.stop value"}}}else{throw`invalid binconfig.type="${s.type}"`}}function o(t,n,o){const l=t;i(l);if(l.lst){const t=s(l.lst.length);for(const s of l.lst)s.color=t(s.label)}if(l.type=="custom-bin")return JSON.parse(JSON.stringify(l.lst));if(typeof n!="function")throw"summaryfxn required for modules/termdb.bins.js compute_bins()";const b=u(l);const c=n(b);if(!c||typeof c!=="object")throw"invalid returned value by summaryfxn";l.results={summary:c};if(!l.binLabelFormatter)l.binLabelFormatter=r(l);const f=Math.floor(c.min*100)/100;const p=Math.ceil(c.max*100)/100;const _=l.first_bin.startunbounded?f:l.first_bin.start_percentile?c["p"+l.first_bin.start_percentile]:l.first_bin.start;let d=p,m,h;if(l.last_bin){d=l.last_bin.stopunbounded?p:l.last_bin.stop_percentile?c["p"+l.last_bin.stop_percentile]:e(l.last_bin.stop)&&l.last_bin.stop<=c.max?l.last_bin.stop:p;m=e(l.last_bin.start_percentile)?c["p"+l.last_bin.start_percentile]:e(l.last_bin.start)?l.last_bin.start:undefined;h=l.last_bin.stopunbounded?null:l.last_bin.stop_percentile?c["p"+l.last_bin.stop_percentile]:e(l.last_bin.stop)?l.last_bin.stop:null}else if(l.lst){const t=l.lst[l.lst.length-1];m=t.start;h="stop"in t&&!t.stopunbounded?t.stop:p;d=h}else{m=p;h=p}const v=e(d);const g=e(m);const w=e(h);if(!v&&!g)return[];const y=[];let F={startunbounded:l.first_bin.startunbounded,start:l.first_bin.startunbounded?undefined:_,stop:e(l.first_bin.stop_percentile)?+c["p"+l.first_bin.stop_percentile]:e(l.first_bin.stop)?+l.first_bin.stop:_+l.bin_size,startinclusive:l.startinclusive,stopinclusive:l.stopinclusive};if(!e(F.stop))throw"the computed first_bin.stop is non-numeric"+F.stop;const U=100;while(v&&F.stop<=d||F.startunbounded&&!y.length||F.stopunbounded){y.push(F);if(F.stop>=d){F.stopunbounded=true;if(y.length>1){delete F.stop}}F.label=a(F,l,o);if(F.stopunbounded)break;const t=F.stop+l.bin_size;const s=F.stop;F={startinclusive:l.startinclusive,stopinclusive:l.stopinclusive,start:s,stop:w&&(s==m||t>h)?h:g&&t>m&&s!=m?m:t};if(F.stop>=d){F.stop=d;if(l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=1;if(l.last_bin&&l.last_bin.stopinclusive)F.stopinclusive=1}if(g&&F.start==m){if(l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=1}if(F.start>F.stop){if(g&&F.stop==m&&l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=true;else break}if(y.length+1>=U){l.error="max_num_bins_reached";break}}delete l.binLabelFormatter;if(y.length>1){delete y[y.length-1].stop}const L=s(y.length);for(const t of y)t.color=L(t.label);return y}function r(t){return"rounding"in t?n(t.rounding):t=>t}function a(s,e,n){const i=e;if(!i.binLabelFormatter)i.binLabelFormatter=r(i);if(!s.startunbounded&&!s.stopunbounded&&!("startinclusive"in s)&&!("stopinclusive"in s)){if(i.startinclusive)s.startinclusive=true;else if(i.stopinclusive)s.stopinclusive=true}const o=i.use_as=="bins"||s.start;const a=i.use_as=="bins"||s.stop;let l=0;if("label_offset"in i){i.label_offset_ignored="bin_size"in i&&i.bin_size<i.label_offset;if(!i.label_offset_ignored)l=i.label_offset}else if(i.bin_size===1&&i.termtype=="integer"){l=1}if(s.startunbounded){const e=s.stopinclusive?"≤":"<";const o=n?t(a,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(a);return e+o}if(s.stopunbounded||o===a){const e=s.startinclusive?"≥":">";const r=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o);return e+r}if(l&&s.startinclusive&&!s.stopinclusive){if(Number.isInteger(i.bin_size)&&Math.abs(o-a)===l){return""+(n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o))}else{const s=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o);const e=n?t(a-l,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(a-l);return+s>=+e?s.toString():s+" to "+e}}else{const e=s.startinclusive?"":">";const r=s.stopinclusive?"":"<";const l=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):Number.isInteger(o)?o:i.binLabelFormatter(o);const u=n?t(a,n.fromUnit,n.toUnit,n.scaleFactor,true):Number.isInteger(a)?a:i.binLabelFormatter(a);if(+l>=+u){const t=s.startinclusive?"≥":">";return t+l}else{return e+l+" to "+r+u}}}function l(t,s){const e='<span style="font-family:Times;font-style:italic;">x</span>';let n;const i=a(t,s);if(t.startunbounded||t.stopunbounded){n=e+"&nbsp;"+i}else if(t.startinclusive){n=i.replace("to <","≤ "+e+" <")}else if(t.stopinclusive){n=i.replace(">","").replace("to","< "+e+" ≤")}return n}function u(t){const s=[];const n=t.first_bin;if(n&&e(n.start_percentile))s.push(n.start_percentile);if(n&&e(n.stop_percentile))s.push(n.stop_percentile);const i=t.last_bin;if(i&&e(i.start_percentile))s.push(i.start_percentile);if(i&&e(i.stop_percentile))s.push(i.stop_percentile);return s}export{l as a,o as c,a as g};
+import{V as t,C as s,H as e,W as n}from"./app-b369b169.js";function i(t){const s=t;if(!s||typeof s!=="object")throw"bin schema must be an object";if(!("type"in s))s.type="regular-bin";if(s.type=="custom-bin"){if(!Array.isArray(s.lst))throw"binconfig.lst must be an array";if(!s.lst.length)throw"binconfig.lst must have entries";const t=s.lst[0];const n=s.lst[s.lst.length-1];for(const i of s.lst){if(!("startinclusive"in i)&&!("stopinclusive"in i)){throw"custom bin.startinclusive and/or bin.stopinclusive must be defined"}if(i==t){if("startunbounded"in i&&!i.startunbounded){throw`a custom first bin must not set bin.startunbounded to false`}i.startunbounded=true;if("start"in i){throw"a custom first bin must not set a bin.start value"}if("start_percentile"in i){throw"the first bin must not set a bin.start_percentile value"}if(!("stop"in i)){throw`a custom first bin must define a bin.stop value`}if(!e(i.stop)){throw`a custom first bin.stop value should be numeric`}}else 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t=s.first_bin;t.startunbounded=true;if(t.stop_percentile){if(!Number.isInteger(t.stop_percentile))throw"first_bin.stop_percentile should be integer";if(t.stop_percentile<=0||t.stop_percentile>=100)throw"first_bin.stop_percentile out of bound (0-100)"}else if(!Number.isFinite(t.stop)){throw"first_bin.stop not a number when stop_percentile is not set"}}if(s.last_bin){const t=s.last_bin;if(t.start_percentile){if(!Number.isInteger(t.start_percentile))throw"last_bin.start_percentile should be integer";if(t.start_percentile<=0||t.start_percentile>=100)throw"last_bin.start_percentile out of bound (0-100)"}else if(!Number.isFinite(t.start)){throw"last_bin.start not a number when start_percentile is not set"}t.stopunbounded=true;if("stop"in t){throw"a regular last bin must not set a bin.stop value"}}}else{throw`invalid binconfig.type="${s.type}"`}}function o(t,n,o){const l=t;i(l);if(l.lst){const t=s(l.lst.length);for(const s of l.lst)s.color=t(s.label)}if(l.type=="custom-bin")return JSON.parse(JSON.stringify(l.lst));if(typeof n!="function")throw"summaryfxn required for modules/termdb.bins.js compute_bins()";const b=u(l);const c=n(b);if(!c||typeof c!=="object")throw"invalid returned value by summaryfxn";l.results={summary:c};if(!l.binLabelFormatter)l.binLabelFormatter=r(l);const f=Math.floor(c.min*100)/100;const p=Math.ceil(c.max*100)/100;const _=l.first_bin.startunbounded?f:l.first_bin.start_percentile?c["p"+l.first_bin.start_percentile]:l.first_bin.start;let d=p,m,h;if(l.last_bin){d=l.last_bin.stopunbounded?p:l.last_bin.stop_percentile?c["p"+l.last_bin.stop_percentile]:e(l.last_bin.stop)&&l.last_bin.stop<=c.max?l.last_bin.stop:p;m=e(l.last_bin.start_percentile)?c["p"+l.last_bin.start_percentile]:e(l.last_bin.start)?l.last_bin.start:undefined;h=l.last_bin.stopunbounded?null:l.last_bin.stop_percentile?c["p"+l.last_bin.stop_percentile]:e(l.last_bin.stop)?l.last_bin.stop:null}else if(l.lst){const t=l.lst[l.lst.length-1];m=t.start;h="stop"in t&&!t.stopunbounded?t.stop:p;d=h}else{m=p;h=p}const v=e(d);const g=e(m);const w=e(h);if(!v&&!g)return[];const y=[];let F={startunbounded:l.first_bin.startunbounded,start:l.first_bin.startunbounded?undefined:_,stop:e(l.first_bin.stop_percentile)?+c["p"+l.first_bin.stop_percentile]:e(l.first_bin.stop)?+l.first_bin.stop:_+l.bin_size,startinclusive:l.startinclusive,stopinclusive:l.stopinclusive};if(!e(F.stop))throw"the computed first_bin.stop is non-numeric"+F.stop;const U=100;while(v&&F.stop<=d||F.startunbounded&&!y.length||F.stopunbounded){y.push(F);if(F.stop>=d){F.stopunbounded=true;if(y.length>1){delete F.stop}}F.label=a(F,l,o);if(F.stopunbounded)break;const t=F.stop+l.bin_size;const s=F.stop;F={startinclusive:l.startinclusive,stopinclusive:l.stopinclusive,start:s,stop:w&&(s==m||t>h)?h:g&&t>m&&s!=m?m:t};if(F.stop>=d){F.stop=d;if(l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=1;if(l.last_bin&&l.last_bin.stopinclusive)F.stopinclusive=1}if(g&&F.start==m){if(l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=1}if(F.start>F.stop){if(g&&F.stop==m&&l.last_bin&&l.last_bin.stopunbounded)F.stopunbounded=true;else break}if(y.length+1>=U){l.error="max_num_bins_reached";break}}delete l.binLabelFormatter;if(y.length>1){delete y[y.length-1].stop}const L=s(y.length);for(const t of y)t.color=L(t.label);return y}function r(t){return"rounding"in t?n(t.rounding):t=>t}function a(s,e,n){const i=e;if(!i.binLabelFormatter)i.binLabelFormatter=r(i);if(!s.startunbounded&&!s.stopunbounded&&!("startinclusive"in s)&&!("stopinclusive"in s)){if(i.startinclusive)s.startinclusive=true;else if(i.stopinclusive)s.stopinclusive=true}const o=i.use_as=="bins"||s.start;const a=i.use_as=="bins"||s.stop;let l=0;if("label_offset"in i){i.label_offset_ignored="bin_size"in i&&i.bin_size<i.label_offset;if(!i.label_offset_ignored)l=i.label_offset}else if(i.bin_size===1&&i.termtype=="integer"){l=1}if(s.startunbounded){const e=s.stopinclusive?"≤":"<";const o=n?t(a,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(a);return e+o}if(s.stopunbounded||o===a){const e=s.startinclusive?"≥":">";const r=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o);return e+r}if(l&&s.startinclusive&&!s.stopinclusive){if(Number.isInteger(i.bin_size)&&Math.abs(o-a)===l){return""+(n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o))}else{const s=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(o);const e=n?t(a-l,n.fromUnit,n.toUnit,n.scaleFactor,true):i.binLabelFormatter(a-l);return+s>=+e?s.toString():s+" to "+e}}else{const e=s.startinclusive?"":">";const r=s.stopinclusive?"":"<";const l=n?t(o,n.fromUnit,n.toUnit,n.scaleFactor,true):Number.isInteger(o)?o:i.binLabelFormatter(o);const u=n?t(a,n.fromUnit,n.toUnit,n.scaleFactor,true):Number.isInteger(a)?a:i.binLabelFormatter(a);if(+l>=+u){const t=s.startinclusive?"≥":">";return t+l}else{return e+l+" to "+r+u}}}function l(t,s){const e='<span style="font-family:Times;font-style:italic;">x</span>';let n;const i=a(t,s);if(t.startunbounded||t.stopunbounded){n=e+"&nbsp;"+i}else if(t.startinclusive){n=i.replace("to <","≤ "+e+" <")}else if(t.stopinclusive){n=i.replace(">","").replace("to","< "+e+" ≤")}return n}function u(t){const s=[];const n=t.first_bin;if(n&&e(n.start_percentile))s.push(n.start_percentile);if(n&&e(n.stop_percentile))s.push(n.stop_percentile);const i=t.last_bin;if(i&&e(i.start_percentile))s.push(i.start_percentile);if(i&&e(i.stop_percentile))s.push(i.stop_percentile);return s}export{l as a,o as c,a as g};

package/dist/termsetting-33ea66f1.js

@@ -0,0 +1 @@
+import{a as e,b as t,_ as i}from"./tslib.es6-c3c2d88f.js";import{R as n,S as r,T as s,P as o,H as a,i as l,M as p,F as d,d as u}from"./app-b369b169.js";import c from"path";const f=1;const h={continuous:"continuous",discrete:"discrete"};const m={GENE_VARIANT:"geneVariant",GENE_EXPRESSION:"geneExpression",CATEGORICAL:"categorical",INTEGER:"integer",FLOAT:"float",SNP:"snp",SNP_LIST:"snplst",SNP_LOCUS:"snplocus",CONDITION:"condition",SURVIVAL:"survival",SAMPLELST:"samplelst",METABOLITE_INTENSITY:"metaboliteIntensity",SINGLECELL_GENE_EXPRESSION:"singleCellGeneExpression",SINGLECELL_CELLTYPE:"singleCellCellType"};const y={[m.GENE_EXPRESSION]:n,[m.METABOLITE_INTENSITY]:r};const g={[m.CATEGORICAL]:s.DICTIONARY_VARIABLES,[m.CONDITION]:s.DICTIONARY_VARIABLES,[m.FLOAT]:s.DICTIONARY_VARIABLES,[m.INTEGER]:s.DICTIONARY_VARIABLES,[m.SAMPLELST]:s.DICTIONARY_VARIABLES,[m.SURVIVAL]:s.DICTIONARY_VARIABLES,[m.GENE_VARIANT]:s.MUTATION_CNV_FUSION,[m.SNP]:s.SNP,[m.SNP_LIST]:s.SNP_LIST,[m.SNP_LOCUS]:s.SNP_LOCUS,[m.GENE_EXPRESSION]:s.GENE_EXPRESSION,[m.METABOLITE_INTENSITY]:s.METABOLITE_INTENSITY};const v=new Set([m.SNP,m.SNP_LIST,m.SNP_LOCUS,m.GENE_EXPRESSION,m.GENE_VARIANT,m.METABOLITE_INTENSITY,m.SINGLECELL_GENE_EXPRESSION,m.SINGLECELL_CELLTYPE]);const b=new Set([m.INTEGER,m.FLOAT,m.GENE_EXPRESSION,m.METABOLITE_INTENSITY,m.SINGLECELL_GENE_EXPRESSION]);const w=new Set([m.CATEGORICAL,m.SNP]);function q(e){if(!e)return false;return b.has(e.type)}function T(e){if(!e)return false;return w.has(e.type)}function x(e){return!E(e)}function E(e){if(!e)throw new Error("Type is not defined");return v.has(e)}function S(e,t){if(!e)throw new Error("First term is not defined ");if(!t)throw 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s=r.predefined_groupset_idx;if(s!==undefined&&!Number.isInteger(s))throw`missing or invalid tw.q.predefined_groupset_idx='${s}'`;r.predefined_groupset_idx=s||0;const o=e.term.groupsetting;if(!o)throw"no term.groupsetting";if(!((t=o.lst)===null||t===void 0?void 0:t.length))throw"term.groupsetting.lst is empty";const a=(i=o.lst)===null||i===void 0?void 0:i[r.predefined_groupset_idx];if(!a)throw`no groupset entry for groupsetting.lst?.[predefined_groupset_idx=${s}]`;if(r.mode=="binary"){if(a.groups.length!=2)throw"there must be exactly two groups"}vt(r,n);return e}}Te=new WeakMap,xe=new WeakMap;class Ie extends _e{constructor(t,i={}){super(t,i);Ee.set(this,void 0);Se.set(this,void 0);this.q=t.q;Object.defineProperty(this,"groupset",{value:this.q.customset});e(this,Ee,t,"f");e(this,Se,i,"f")}getTw(){return t(this,Ee,"f")}static fill(e){if(!e.type)e.type="CatTWCustomGS";else if(e.type!="CatTWCustomGS")throw`expecting tw.type='CatTWCustomGS', got 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supported by NumericBase.fill()`}}))}}Ge.termTypes=new Set(["integer","float","geneExpression","metaboliteIntensity"]);class Ve extends Ge{constructor(t,i={}){super(t,i);ke.set(this,void 0);Pe.set(this,void 0);this.q=t.q;e(this,ke,t,"f");e(this,Pe,i,"f")}getTw(){return t(this,ke,"f")}static fill(e){var t;return i(this,void 0,void 0,(function*(){if(!e.type)e.type="NumTWRegularBin";else if(e.type!="NumTWRegularBin")throw`expecting tw.type='NumTWRegularBin', got '${e.type}'`;if(!e.q.mode)e.q.mode="discrete";else if(e.q.mode!="discrete"&&e.q.mode!="binary"&&e.q.mode!="continuous")throw`expecting tw.q.mode='discrete'|'binary'|'continous', got '${e.q.mode}'`;if(e.q.type&&e.q.type!="regular-bin")throw`expecting tw.q.type='regular-bin', got '${e.q.type}'`;if(!e.q.first_bin||!a(e.q.bin_size))He(e);if(!a(e.q.bin_size))throw`tw.q.bin_size=${e.q.bin_size} is not numeric`;if(!e.q.first_bin)throw`missing tw.q.first_bin`;if(!a((t=e.q.first_bin)===null||t===void 0?void 0:t.stop))throw`tw.q.first_bin.stop is not numeric`;be.setHiddenValues(e.q,e.term);return e}))}}ke=new WeakMap,Pe=new WeakMap;class De extends Ge{constructor(t,i={}){super(t,i);$e.set(this,void 0);Me.set(this,void 0);this.q=t.q;e(this,$e,t,"f");e(this,Me,i,"f")}getTw(){return t(this,$e,"f")}static fill(e,t={}){return i(this,void 0,void 0,(function*(){if(!e.type)e.type="NumTWCustomBin";else if(e.type!="NumTWCustomBin")throw`expecting tw.type='NumTWCustomBin', got '${e.type}'`;if(!e.q.mode)e.q.mode="discrete";else if(e.q.mode!="discrete"&&e.q.mode!="binary")throw`expecting tw.q.mode='discrete'|binary', got '${e.q.mode}'`;if(e.q.mode=="binary"&&!e.q.preferredBins)e.q.preferredBins="median";if(e.q.preferredBins=="median"){const i=yield t.vocabApi.getPercentile(e.term.id,[50]);if(!i.values)throw".values[] missing from vocab.getPercentile()";const n=Oe(i.values[0]);if(!a(n))throw"median value not a number";e.q.type="custom-bin";e.q.lst=[{startunbounded:true,stop:n,stopinclusive:false,label:"<"+n},{start:n,startinclusive:true,stopunbounded:true,label:"≥"+n}];delete e.q.preferredBins}else if(e.q.type!="custom-bin")throw`expecting tw.q.type='custom-bin', got '${e.q.type}'`;if(!Array.isArray(e.q.lst))He(e);if(!e.q.lst||!e.q.lst.length)throw`missing or empty q.lst[] for custom-bin`;if(e.q.mode=="binary"&&e.q.lst.length!=2)throw`numeric q.mode='binary' requires exactly 2 bins`;be.setHiddenValues(e.q,e.term);e.type="NumTWCustomBin";return e}))}}$e=new WeakMap,Me=new WeakMap;class Qe extends Ge{constructor(t,i={}){super(t,i);Le.set(this,void 0);Re.set(this,void 0);this.q=t.q;e(this,Le,t,"f");e(this,Re,i,"f")}getTw(){return t(this,Le,"f")}static fill(e){return i(this,void 0,void 0,(function*(){if(!e.type)e.type="NumTWCont";else if(e.type!="NumTWCont")throw`expecting tw.type='NumTWCont', got '${e.type}'`;if(e.q.mode!="continuous")throw`tw.q.mode='${e.q.mode}', expecting 'continuous'`;be.setHiddenValues(e.q,e.term);e.type="NumTWCont";return e}))}}Le=new WeakMap,Re=new WeakMap;class Ue extends Ge{constructor(t,i={}){super(t,i);We.set(this,void 0);Be.set(this,void 0);this.q=t.q;e(this,We,t,"f");e(this,Be,i,"f")}static fill(e){return i(this,void 0,void 0,(function*(){if(!e.type)e.type="NumTWSpline";else if(e.type!="NumTWSpline")throw`expecting tw.type='NumTWSpline', got '${e.type}'`;if(e.q.mode!="spline")throw`tw.q.mode='${e.q.mode}', expecting 'spline'`;if(!e.q.knots)throw`missing tw.q.knots`;if(!e.q.knots.length)throw`empty tw.q.knots[]`;be.setHiddenValues(e.q,e.term);e.type="NumTWSpline";return e}))}}We=new WeakMap,Be=new WeakMap;const Ye=new Set(["default","less","median"]);function He(e){if(!e.term.bins)throw`missing tw.term.bins`;const t=e.q.preferredBins||"default";if(!Ye.has(t))throw`invalid preferredBins='${t}'`;if(t!="median"){if(!Object.keys(e.term.bins).includes(t));const i=e.term.bins[t];if(e.q.type&&e.q.type!=i.type)throw`mismatched tw.q.type and term.bins[preferredBins].type`;const n=Object.keys(e.q);for(const[t,r]of Object.entries(i)){if(!n.includes(t))e.q[t]=r}delete e.q.preferredBins}}class Xe{constructor(e){this.opts=e}static init(e,t={}){switch(e.type){case"CatTWValues":return new Ne(e,t);case"CatTWPredefinedGS":return new Ae(e,t);case"CatTWCustomGS":return new Ie(e,t);case"NumTWRegularBin":return new Ve(e,t);case"NumTWCustomBin":return new De(e,t);case"NumTWCont":return new Qe(e,t);default:throw`unable to init(tw)`}}static initRaw(e,t={}){return i(this,void 0,void 0,(function*(){const i=yield Xe.fill(e,t);return Xe.init(i,t)}))}static fill(e,t={}){var n,r;return i(this,void 0,void 0,(function*(){yield Xe.preprocess(e,t===null||t===void 0?void 0:t.vocabApi);const i=e.term.type=="float"||e.term.type=="integer"?"numeric":e.term.type;t.defaultQ=((n=t.defaultQByTsHandler)===null||n===void 0?void 0:n[i])||null;switch(e.term.type){case"categorical":{return yield _e.fill(e,t)}case"integer":case"float":return yield Ge.fill(e,t);default:throw`unrecognized tw.term?.type='${(r=e.term)===null||r===void 0?void 0:r.type}'`}}))}static preprocess(e,t){return i(this,void 0,void 0,(function*(){const i=Object.keys(e);if(!i.length)throw`empty tw object`;if(e.id&&!e.term){yield ct([e],t);delete e.id}if(!e.q)e.q={};e.q.isAtomic=true;Xe.reshapeLegacyTw(e)}))}static reshapeLegacyTw(e){if(Object.keys(e.q).includes("groupsetting")){if(!e.q.groupsetting.inuse){e.q.type="values"}else if(e.q.type=="predefined-groupset"){e.q.predefined_groupset_idx=e.q.groupsetting.predefined_groupset_idx}else if(e.q.type=="custom-groupset"){e.q.customset=e.q.groupsetting.customset}else{throw"invalid q.type"}delete e.q["groupsetting"]}}}function Fe(e){switch(e){case"./handlers/categorical.ts":return import("./categorical-a52014a1.js");case"./handlers/condition.ts":return import("./condition-c646e357.js");case"./handlers/density.ts":return import("./density-a82a8b1c.js");case"./handlers/geneExpression.ts":return import("./geneExpression-7d14983f.js");case"./handlers/geneVariant.ts":return import("./geneVariant-92c4e870.js");case"./handlers/groupsetting.ts":return import("./groupsetting-b4416a96.js");case"./handlers/metaboliteIntensity.ts":return import("./metaboliteIntensity-fac92f8b.js");case"./handlers/numeric.binary.ts":return import("./numeric.binary-1f9e93f2.js");case"./handlers/numeric.continuous.ts":return import("./numeric.continuous-ebcd0567.js");case"./handlers/numeric.discrete.ts":return import("./numeric.discrete-7b97044a.js");case"./handlers/numeric.spline.ts":return import("./numeric.spline-1be88f3d.js");case"./handlers/numeric.toggle.ts":return import("./numeric.toggle-7fa2a770.js");case"./handlers/numeric.ts":return import("./numeric-b0b17185.js");case"./handlers/samplelst.ts":return import("./samplelst-689796e6.js");case"./handlers/singleCellCellType.ts":return import("./singleCellCellType-5db730bb.js");case"./handlers/singleCellGeneExpression.ts":return import("./singleCellGeneExpression-7147a2d0.js");case"./handlers/snp.ts":return import("./snp-a8388ce4.js");case"./handlers/snplocus.ts":return import("./snplocus-7a1ea8c9.js");case"./handlers/snplst.sampleSum.ts":return import("./snplst.sampleSum-e47d05f0.js");case"./handlers/snplst.ts":return import("./snplst-6865d7c7.js");case"./handlers/survival.ts":return import("./survival-e16e068f.js");default:return new Promise((function(t,i){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(i.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}function ze(e){switch(e){case"./handlers/categorical.ts":return import("./categorical-a52014a1.js");case"./handlers/condition.ts":return import("./condition-c646e357.js");case"./handlers/density.ts":return import("./density-a82a8b1c.js");case"./handlers/geneExpression.ts":return import("./geneExpression-7d14983f.js");case"./handlers/geneVariant.ts":return import("./geneVariant-92c4e870.js");case"./handlers/groupsetting.ts":return import("./groupsetting-b4416a96.js");case"./handlers/metaboliteIntensity.ts":return import("./metaboliteIntensity-fac92f8b.js");case"./handlers/numeric.binary.ts":return import("./numeric.binary-1f9e93f2.js");case"./handlers/numeric.continuous.ts":return import("./numeric.continuous-ebcd0567.js");case"./handlers/numeric.discrete.ts":return import("./numeric.discrete-7b97044a.js");case"./handlers/numeric.spline.ts":return import("./numeric.spline-1be88f3d.js");case"./handlers/numeric.toggle.ts":return import("./numeric.toggle-7fa2a770.js");case"./handlers/numeric.ts":return import("./numeric-b0b17185.js");case"./handlers/samplelst.ts":return import("./samplelst-689796e6.js");case"./handlers/singleCellCellType.ts":return import("./singleCellCellType-5db730bb.js");case"./handlers/singleCellGeneExpression.ts":return import("./singleCellGeneExpression-7147a2d0.js");case"./handlers/snp.ts":return import("./snp-a8388ce4.js");case"./handlers/snplocus.ts":return import("./snplocus-7a1ea8c9.js");case"./handlers/snplst.sampleSum.ts":return import("./snplst.sampleSum-e47d05f0.js");case"./handlers/snplst.ts":return import("./snplst-6865d7c7.js");case"./handlers/survival.ts":return import("./survival-e16e068f.js");default:return new Promise((function(t,i){(typeof queueMicrotask==="function"?queueMicrotask:setTimeout)(i.bind(null,new Error("Unknown variable dynamic import: "+e)))}))}}const Je=`_ts_${(+new Date).toString().slice(-8)}`;let Ze=0;function Ke(e){return i(this,void 0,void 0,(function*(){if(!e)return`${Ze++}${Je}`;delete e.$id;return yield tt(JSON.stringify(e))}))}const et=new TextEncoder;function tt(e){return i(this,void 0,void 0,(function*(){const t=et.encode(e);const i=yield crypto.subtle.digest("SHA-1",t);const n=Array.from(new Uint8Array(i));const r=n.map((e=>e.toString(16).padStart(2,"0"))).join("");return it(r).replace("=","-")}))}function it(e){return btoa([...e].reduce(((t,i,n)=>t+=!(n-1&1)?String.fromCharCode(parseInt(e.substring(n-1,n+1),16)):""),""))}const nt={menuOptions:"edit",menuLayout:"vertical"};class rt{constructor(e){this.opts=this.validateOpts(e);this.vocabApi=e.vocabApi;this.activeCohort=e.activeCohort;this.placeholder=e.placeholder;this.durations={exit:0};this.disable_terms=e.disable_terms;this.usecase=e.usecase;this.abbrCutoff=e.abbrCutoff;this.numqByTermIdModeType={};this.dom={holder:e.holder,tip:e.tip||new p({padding:"0px",parent_menu:this.opts.holder&&this.opts.holder.node()&&this.opts.holder.node().closest(".sja_menu_div")})};this.dom.tip2=new p({padding:"0px",parent_menu:this.dom.tip.d.node()});at(this);ot(this);this.initUI();const t=pt(this);this.handlerByType={default:t};this.handler=t;this.hasError=false;this.api={main:this.main.bind(this),runCallback:this.runCallback.bind(this),showTree:this.showTree,showMenu:this.showMenu.bind(this),showGeneSearch:this.showGeneSearch,hasError:()=>this.hasError,validateQ:e=>{if(!this.handler||!this.handler.validateQ)return;try{this.handler.validateQ(e)}catch(e){this.hasError=true;throw e}}}}runCallback(e=null){var t,i;const n=this.term?{term:this.term,q:this.q,isAtomic:true}:{};if("$id"in this)n.$id=this.$id;if(((t=n.q)===null||t===void 0?void 0:t.reuseId)&&n.q.reuseId===((i=this.data.q)===null||i===void 0?void 0:i.reuseId)){if(!d(n.q,this.data.q)){delete n.q.reuseId;delete n.q.name}}const r=e?JSON.parse(JSON.stringify(e)):{};if(this.opts.callback)this.opts.callback(e?o(JSON.stringify(n),r):n)}validateOpts(e){const t=Object.assign({},nt,e);if(!t.holder&&t.renderAs!="none")throw".holder missing";if(typeof t.callback!="function")throw".callback() is not a function";if(!t.vocabApi)throw".vocabApi missing";if(typeof t.vocabApi!="object");if("placeholder"in t&&!t.placeholder&&"placeholderIcon"in t&&!t.placeholderIcon)throw"must specify a non-empty opts.placeholder and/or .placeholderIcon";if(!("placeholder"in t))t.placeholder="Select term&nbsp;";if(!("placeholderIcon"in t))t.placeholderIcon="+";if(!Number.isInteger(t.abbrCutoff))t.abbrCutoff=18;this.validateMenuOptions(t);if(!t.numericEditMenuVersion)t.numericEditMenuVersion=["discrete"];this.mayValidate_noTermPromptOptions(t);return t}main(e={}){return i(this,void 0,void 0,(function*(){try{if(this.doNotHideTipInMain){delete this.doNotHideTipInMain}else{this.dom.tip.hide()}this.hasError=false;delete this.error;this.validateMainData(e);this.data=e;this.term=e.term;this.q=JSON.parse(JSON.stringify(e.q));if("$id"in e)this.$id=e.$id;if("disable_terms"in e)this.disable_terms=e.disable_terms;if("filter"in e)this.filter=e.filter;if("activeCohort"in e)this.activeCohort=e.activeCohort;if("sampleCounts"in e)this.sampleCounts=e.sampleCounts;if("menuOptions"in e)this.opts.menuOptions=e.menuOptions;yield this.setHandler(this.term?this.term.type:null);if(e.term&&this.handler&&this.handler.validateQ)this.handler.validateQ(e);if(this.handler.postMain)yield this.handler.postMain();if(this.opts.renderAs!="none")this.updateUI()}catch(e){this.hasError=true;throw e}}))}validateMainData(e){if(e.term){if(!e.term.type)throw"data.term.type missing";if(x(e.term.type)){if(!e.term.id&&e.term.type!=m.SAMPLELST)throw"data.term.id missing";if(!e.term.name)throw"data.term.name missing"}}if(!e.q)e.q={};if(typeof e.q!="object")throw"data.q{} is not object";if(e.disable_terms){if(!Array.isArray(e.disable_terms))throw"data.disable_terms[] is not array"}this.mayValidate_noTermPromptOptions(e)}validateMenuOptions(e){if(!e.menuOptions)e.menuOptions=nt.menuOptions;if(e.menuOptions=="all")e.menuOptions="*";for(const t of["edit","replace","remove"]){if(X(t,e.menuOptions))return}throw`no matches found for termsetting opts.menuOptions='${e.menuOptions}'`}mayValidate_noTermPromptOptions(e){if(!e.noTermPromptOptions)return;if(!Array.isArray(e.noTermPromptOptions))throw"noTermPromptOptions[] is not array";for(const t of e.noTermPromptOptions){if(t.isDictionary);else{if(!t.termtype)throw"element of noTermPromptOptions[] missing both isDictionary=true and .termtype"}if(!t.text&&!t.html)throw"element of noTermPromptOptions[] missing both .text and .html";if(t.q&&typeof t.q!="object")throw"type.q{} is not object"}this.noTermPromptOptions=e.noTermPromptOptions}setHandler(e){return i(this,void 0,void 0,(function*(){if(!e){this.handler=this.handlerByType.default;return}const t=e=="integer"||e=="float"?"numeric":e;if(!this.handlerByType[t]){try{const e=yield ze(`./handlers/${t}.ts`);this.handlerByType[t]=yield e.getHandler(this)}catch(e){throw`error with handler='./handlers/${t}.ts': ${e}`}}this.handler=this.handlerByType[t]}))}}const st=l(rt);function ot(e){e.initUI=()=>{if(e.opts.$id){e.dom.tip.d.attr("id",e.opts.$id+"-ts-tip")}if(!e.dom.holder)return;e.dom.nopilldiv=e.dom.holder.append("div").style("cursor","pointer").on("click",e.clickNoPillDiv).on(`keyup.sjpp-termdb`,(t=>{if(t.key=="Enter")e.showTree(t)}));e.dom.pilldiv=e.dom.holder.append("div");if(e.opts.placeholder){e.dom.nopilldiv.append("div").html(e.placeholder).attr("class","sja_clbtext2").style("padding","3px 6px 3px 6px").style("display","inline-block")}if(e.opts.placeholderIcon){e.dom.nopilldiv.append("div").attr("class","sja_filter_tag_btn add_term_btn").style("padding","3px 6px 3px 6px").style("display","inline-block").style("border-radius","6px").style("background-color","#4888BF").text(e.opts.placeholderIcon)}e.dom.btnDiv=e.dom.holder.append("div");e.dom.content_holder=u(e.dom.holder.node().parentNode).append("div")};e.updateUI=()=>i(this,void 0,void 0,(function*(){e.dom.btnDiv.selectAll("*").remove();e.dom.content_holder.selectAll("*").remove();if(!e.term){e.dom.nopilldiv.style("display","block");e.dom.pilldiv.style("display","none");e.dom.btnDiv.style("display","none");return}if(e.term.hashtmldetail){if(e.opts.buttons&&!e.opts.buttons.includes("info"))e.opts.buttons.unshift("info");else e.opts.buttons=["info"]}else{e.opts.buttons=[]}if(e.opts.buttons.length){e.dom.btnDiv.selectAll("div").data(e.opts.buttons).enter().append("div").style("display","inline-block").style("padding","0px 5px").style("cursor","pointer").style("color","#999").style("font-size",".8em").html((e=>e.toUpperCase())).on("click",((t,i)=>{if(i=="delete")e.removeTerm();else if(i=="replace"){e.showTree(t.target)}else throw"unknown button"}));if(e.term.hashtmldetail){const t=e.dom.btnDiv.selectAll("div").filter((function(){return u(this).text()==="INFO"}));const i=yield import("./termInfo-bf99a37e.js");i.termInfoInit({vocabApi:e.opts.vocabApi,icon_holder:t,content_holder:e.dom.content_holder,id:e.term.id,state:{term:e.term}})}}e.dom.nopilldiv.style("display","none");e.dom.pilldiv.style("display",e.opts.buttons?"inline-block":"block");e.dom.btnDiv.style("display",e.opts.buttons?"inline-block":"none");const t=e.dom.pilldiv.selectAll(".ts_pill").data([e.term],(e=>e.id));t.exit().each(e.exitPill);t.transition().duration(200).each(e.updatePill);t.enter().append("div").attr("class","ts_pill").style("display","grid").style("grid-template-columns","auto").style("grid-template-areas",'"left right"').style("cursor","pointer").style("margin","2px").on("click",e.showMenu).transition().duration(200).each(e.enterPill)}));e.enterPill=function(){return i(this,void 0,void 0,(function*(){const t=u(this);e.dom.pill_termname=t.append("div").attr("class","term_name_btn  sja_filter_tag_btn").attr("tabindex",0).style("display","flex").style("grid-area","left").style("position","relative").style("align-items","center").style("padding","3px 6px 3px 6px").style("border-radius","6px").html(e.handler.getPillName).on(`keyup.sjpp-termdb`,(e=>{if(e.key=="Enter")e.target.click()}));e.updatePill.call(this)}))};e.updatePill=function(){return i(this,void 0,void 0,(function*(){const t=u(this);const i=e.handler.getPillStatus()||{};e.dom.pill_termname.style("border-radius",i.text?"6px 0 0 6px":"6px").html(e.handler.getPillName);const n=t.selectAll(".ts_summary_btn").data(i.text?[{txt:i.text}]:[],(e=>e.txt));n.exit().remove();const r=n.enter().append("div").attr("class","ts_summary_btn sja_filter_tag_btn").style("display","flex").style("grid-area","right").style("position","relative").style("align-items","center").style("padding","3px 6px 3px 6px").style("border-radius","0 6px 6px 0").style("font-style","italic").html((e=>e.txt)).style("opacity",0).transition().duration(200).style("opacity",1);if(i.bgcolor){r.transition().duration(200).style("background-color",i.bgcolor)}}))};e.exitPill=function(){u(this).style("opacity",1).transition().duration(e.durations.exit).style("opacity",0).remove()}}function at(e){e.removeTerm=()=>{e.opts.callback(null)};e.cancelGroupsetting=()=>{e.opts.callback({id:e.term.id,term:e.term,q:{mode:"discrete",type:"values",isAtomic:true}})};e.clickNoPillDiv=()=>i(this,void 0,void 0,(function*(){if(!e.noTermPromptOptions||e.noTermPromptOptions.length==0){yield e.showTree(e.dom.nopilldiv.node());return}e.dom.tip.clear().showunder(e.dom.nopilldiv.node());for(const t of e.noTermPromptOptions){const n=e.dom.tip.d.append("div").attr("class","sja_menuoption sja_sharp_border").on("click",(()=>i(this,void 0,void 0,(function*(){e.dom.tip.clear();if(t.isDictionary){yield e.showTree(e.dom.tip.d.node())}else if(t.termtype){if(t.q)e.q=structuredClone(t.q);yield e.setHandler(t.termtype);if(q(e.term)&&!e.term.bins&&e.term.type!="survival"){yield e.vocabApi.setTermBins({term:e.term,q:e.q})}e.handler.showEditMenu(e.dom.tip.d)}else{throw"termtype missing"}}))));if(t.text)n.text(t.text);else if(t.html)n.html(t.html)}}));e.showTree=function(t,n){return i(this,void 0,void 0,(function*(){e.dom.tip.clear();if(t)e.dom.tip.showunder(t instanceof Element?t:this instanceof Element?this:e.dom.holder.node());else e.dom.tip.show(n.clientX,n.clientY);if(!e.usecase)e.usecase={target:"default"};const r=yield import("./app-3320ab6f.js");r.appInit({holder:e.dom.tip.d,vocabApi:e.vocabApi,state:{activeCohort:e.activeCohort,tree:{usecase:e.usecase}},tree:{disable_terms:e.disable_terms,click_term:t=>i(this,void 0,void 0,(function*(){e.dom.tip.hide();let i;if(t.term)i=t;else{const e=t;i={term:e,q:{isAtomic:true},isAtomic:true}}if(e.opts.customFillTw)e.opts.customFillTw(i);yield yt(i,e.vocabApi,e.opts.defaultQ4fillTW);e.opts.callback(i)}))}})}))};e.showMenu=(t,n=null,r=null)=>{var s,o,a;const l=e.dom.tip;l.clear();if(e.opts.renderAs=="none"&&n)e.dom.holder=u(n);if(e.dom.holder){const i=(s=e.dom.holder)===null||s===void 0?void 0:s.node();if(i)l.showunder(i);else l.show(t.clientX,t.clientY)}const p=[];if(e.q.type=="predefined-groupset"||e.q.type=="custom-groupset"){if(e.q.mode!="binary"&&e.term.type!="geneVariant"){p.push({label:"Cancel grouping",callback:e.cancelGroupsetting})}}if(e.q&&!((o=e.term.groupsetting)===null||o===void 0?void 0:o.disabled)&&X("edit",e.opts.menuOptions)){p.push({label:"Edit",callback:t=>i(this,void 0,void 0,(function*(){if(e.term&&q(e.term)&&!e.term.bins&&e.term.type!="survival"){yield 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r=e.vocabApi.getCustomTermQLst(e.term);const s=n.append("input").attr("type","text").attr("placeholder",r.nextReuseId).attr("value",e.q.reuseId||r.nextReuseId);n.append("button").style("margin-left","5px").html("Save").on("click",(()=>{const t=s.property("value").trim()||r.nextReuseId;e.q.reuseId=t;e.vocabApi.cacheTermQ(e.term,e.q);e.runCallback();e.dom.tip.hide()}));const o=t.append("div").style("margin","10px");const a={term:e.term,q:{}};yield ht(a,e.vocabApi);a.q.reuseId="Default";r.push(a.q);if(r.length>1){o.append("div").style("color","#aaa").html("Previously saved settings")}o.append("table").selectAll("tr").data(r).enter().append("tr").style("margin","2px 5px").each((function(t){const n=u(this);const r=lt(e.q,t);const s=t.name||t.reuseId;n.append("td").style("min-width","180px").style("text-align","center").html(s);const o=n.append("td").style("text-align","center");if(r){o.html(`In use <span 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Set(["categorical","integer","float"]);function ht(e,t,n){var r;return i(this,void 0,void 0,(function*(){e.isAtomic=true;if(!e.term&&e.id){yield ct([e],t)}if(ft.has((r=e.term)===null||r===void 0?void 0:r.type)){const i=yield Xe.fill(e,{vocabApi:t,defaultQByTsHandler:n});Object.assign(e,i);gt(e);if(!e.$id)e.$id=yield Ke(t.getTwMinCopy(e));if(e.q)e.q.isAtomic=true;return e}delete e.id;if(!e.q)e.q={};e.q.isAtomic=true;mt(e);yield yt(e,t,n);gt(e);if(!e.$id)e.$id=yield Ke(t.getTwMinCopy(e));return e}))}function mt(e){if(Object.keys(e.q).includes("groupsetting")){if(e.q["groupsetting"]["inuse"]){if(e.q.type=="predefined-groupset"){e.q["predefined_groupset_idx"]=e.q["groupsetting"]["predefined_groupset_idx"]}else if(e.q.type=="custom-groupset"){e.q["customset"]=e.q["groupsetting"]["customset"]}else{throw"invalid q.type"}}else{e.q.type="values"}delete e.q["groupsetting"]}}function yt(e,t,n){return i(this,void 0,void 0,(function*(){if(!e.$id)e.$id=yield Ke(t.getTwMinCopy(e));const 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package/dist/tk-071a7550.js

@@ -0,0 +1 @@
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t.color}}if(e.mds.queries?.ld?.mOverlay?.data){const s=e.mds.queries.ld.mOverlay.m;if(t.chr==s.chr&&t.pos==s.pos&&t.ref==s.ref&&t.alt==s.alt){return e.mds.queries.ld.overlay.color_1}for(const s of e.mds.queries.ld.mOverlay.data){if(s.pos==t.pos&&s.alleles==t.ref+"."+t.alt){return e.mds.queries.ld.colorScale(s.r2)}}return e.mds.queries.ld.overlay.color_0}if(e.vcfinfofilter&&e.vcfinfofilter.setidx4mclass!=undefined){const s=e.vcfinfofilter.lst[e.vcfinfofilter.setidx4mclass];const[a,n]=zt(s,t);if(a||n==undefined)return"black";for(const t of n){if(s.categories[t]){return s.categories[t].color}else{return"black"}}}if(i[t.class]){return i[t.class].color}return"black"};gt(e);if(e.hlssmid){e.skewer.hlssmid=new Set(e.hlssmid.split(","));delete e.hlssmid}try{It(e)}catch(t){console.error(t)}}function ht(t,e){return s=>{t.legend?.headTd.text(t.name+(t.filterObj?" - 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skewerModes[] is not object";if(t.type=="skewer"){if(!t.label)t.label="lollipops"}else if(t.type=="numeric"){if(t.byAttribute){if(!t.label)t.label=t.byAttribute}else if(t.byInfo);else{throw"unknown data method for a type=numeric mode"}}else{throw"unknown type from a skewerModes[]"}}if(!e.find((t=>t.inuse)))e[0].inuse=true}function xt(t){if(t.mds.hiddenmclass){for(const e of t.mds.hiddenmclass)t.legend.mclass.hiddenvalues.add(e)}}async function vt(t,e){if(t.dslabel){const s=await u("getDataset",{body:{genome:e.genome.name,dsname:t.dslabel}});if(s.error)throw"Error: "+s.error;if(!s.ds)throw"data.ds{} missing";t.mds=s.ds;t.name=s.ds.label;return}if(!t.name)t.name="Custom data";t.mds={};if(t.bcf){if(!t.bcf.file&&!t.bcf.url)throw"file or url missing for tk.bcf{}";t.mds.has_skewer=true;await Ot(t,e.genome)}else if(t.custom_variants){Lt(t,e);Rt(t)}else{throw"unknown data source for custom track"}yt(t)}function yt(t){if(!t.sampleAnnotation)return;if(!Array.isArray(t.sampleAnnotation.terms))throw"sampleAnnotation.terms is not array";if(!t.mds.termdb)t.mds.termdb={};t.mds.termdb.terms=t.sampleAnnotation.terms;t.mds.termdb.annotations=t.sampleAnnotation.annotations}async function _t(t,e){const s=t.mds.termdb;if(!s)return;{const a={};if(t.mds.label){a.vocab={genome:e.genome.name,dslabel:t.mds.label}}else if(s.terms){a.vocab={terms:s.terms,sampleannotation:s.annotations}}else{throw"do not know how to init vocab"}const n=await import("./FilterRxComp-701a1480.js").then((function(t){return t.k}));s.vocabApi=n.vocabInit(a);if(!s.vocabApi.app){s.vocabApi.app={opts:{genome:e.genome}}}}t.mds.termdbConfig=await s.vocabApi.getTermdbConfig();if(t.mds.termdb.allowCaseDetails){t.mds.termdb.allowCaseDetails.get=async t=>{}}}function jt(t,e){if(!t.mds.queries?.snvindel?.m2csq)return;t.mds.queries.snvindel.m2csq.get=async s=>{const a={genome:e.genome.name,dslabel:t.mds.label,m2csq:1};if(t.mds.queries.snvindel.m2csq.by=="ssm_id"){a.ssm_id=s.ssm_id}else{return{error:"unknown query method"}}const n={"Content-Type":"application/json",Accept:"application/json"};if(t.token)n["X-Auth-Token"]=t.token;return await u("mds3",{body:a,headers:n},{serverData:t.cache})}}function Mt(t,e){if(!t.mds.queries?.singleSampleMutation)return;t.mds.queries.singleSampleMutation.get=async s=>{const a={genome:e.genome.name,dslabel:t.mds.label,sample:s};const n={"Content-Type":"application/json",Accept:"application/json"};if(t.token)n["X-Auth-Token"]=t.token;const i=await u("termdb/singleSampleMutation",{body:a,headers:n});if(i.error)throw i.error;if(!Array.isArray(i.mlst))throw"data.mlst is not array";return i.mlst}}async function At(t,e){if(!t.mds.variant2samples)return;if(t.custom_variants){St(t)}else{qt(t,e)}if(t.mds.variant2samples.twLst){if(!Array.isArray(t.mds.variant2samples.twLst))throw"v2s.twLst[] not 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array from return"}else if(s.querytype==t.mds.variant2samples.type_summary){if(!Array.isArray(o.summary))throw"summary[] not array from return"}else{throw"unknown querytype"}return o};t.mds.getSamples=async(s={})=>{if(s.isSummary){s.querytype=t.mds.variant2samples.type_summary}else{s.querytype=t.mds.variant2samples.type_samples;s.groupSsmBySample=1}Cs(t,e,s);return await t.mds.variant2samples.get(s)}}function Ct(t,e){return async()=>await As(t,e)}function zt(t,e){if(t.altalleleinfo){if(!e.altinfo)return["no .altinfo"];const s=e.altinfo[t.altalleleinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let a=Array.isArray(s)?s:[s];if(t.altalleleinfo.separator){a=a[0].split(t.altalleleinfo.separator)}return[null,a]}if(t.locusinfo){if(!e.info)return["no .info"];const s=e.info[t.locusinfo.key];if(s==undefined){if(t.numericfilter){return[null,[0]]}return[null,undefined]}let a=Array.isArray(s)?s:[s];if(t.locusinfo.separator){a=a[0].split(t.locusinfo.separator)}return[null,a]}return["no trigger"]}function Lt(t,e){for(const a of t.custom_variants){if(a.dt==p){t.mds.has_skewer=true;$t(a);continue}if(a.dt==l||a.dt==r){t.mds.has_skewer=true;Nt(a,e);continue}if(a.dt==s){t.mds.has_cnv=true;a.ssm_id=a.chr+"."+a.start+"."+a.stop+"."+a.class;continue}throw"unknown dt for a custom variant"}}function $t(t){if(!t.chr)throw".chr missing for custom snvindel";if(!Number.isInteger(t.pos))throw".pos not integer for custom snvindel";if(!t.ssm_id){t.ssm_id=t.chr+"."+t.pos+"."+(t.ref&&t.alt?t.ref+"."+t.alt:t.mname)}}function Nt(t,e){if(t.pairlst);else{if(!t.chr1)throw".chr1 missing for custom sv/fusion";if(!Number.isInteger(t.pos1))throw".pos1 not integer for custom svfusion";if(t.strand1!="+"&&t.strand1!="-")throw".strand1 not +/- for custom svfusion";if(!t.chr2)throw".chr1 missing for custom sv/fusion";if(!Number.isInteger(t.pos2))throw".pos1 not integer for custom svfusion";if(t.strand2!="+"&&t.strand2!="-")throw".strand1 not +/- for custom svfusion";t.pairlst=[{a:{chr:t.chr1,pos:t.pos1,strand:t.strand1,name:t.gene1||""},b:{chr:t.chr2,pos:t.pos2,strand:t.strand2,name:t.gene2||""}}];delete t.chr1;delete t.pos1;delete t.strand1;delete t.gene1;delete t.chr2;delete t.pos2;delete t.strand2;delete t.gene2}const s=[t.dt];const a=e.seekcoord(t.pairlst[0].a.chr,t.pairlst[0].a.pos);if(a.length&&a[0].x>0&&a[0].x<e.width){s.push(...[t.pairlst[0].a.chr,t.pairlst[0].a.pos,t.pairlst[0].a.strand,0,t.pairlst[0].a.name]);t.mname=t.pairlst[0].b.name||"";t.chr=t.pairlst[0].a.chr;t.pos=t.pairlst[0].a.pos;t.pairlstIdx=0}else{const a=e.seekcoord(t.pairlst[0].b.chr,t.pairlst[0].b.pos);if(a.length&&a[0].x>0&&a[0].x<e.width){s.push(...[t.pairlst[0].b.chr,t.pairlst[0].b.pos,t.pairlst[0].b.strand,1,t.pairlst[0].b.name]);t.mname=t.pairlst[0].a.name||"";t.chr=t.pairlst[0].b.chr;t.pos=t.pairlst[0].b.pos;t.pairlstIdx=1}}t.ssm_id=s.join(".")}function Rt(t){if(t.custom_variants.find((t=>t.occurrence!=undefined))){return}for(const e of t.custom_variants){if(e.sample){e.sample_id=e.sample;delete e.sample}}if(!t.custom_variants.find((t=>t.sample_id))){return}const e=[];const s=new Map;for(const a of t.custom_variants){if(a.dt!=p){a.occurrence=1;a.samples=[{sample_id:a.sample_id}];delete a.sample_id;e.push(a);continue}const t=a.mname+"."+a.chr+"."+a.pos+"."+a.ref+"."+a.alt;const n=s.get(t);if(n){n.occurrence++;n.samples.push({sample_id:a.sample_id})}else{a.occurrence=1;a.samples=[{sample_id:a.sample_id}];delete a.sample_id;s.set(t,a)}}t.custom_variants=e;for(const e of s.values())t.custom_variants.push(e);if(!t.mds.variant2samples)t.mds.variant2samples={};const a=t.mds.variant2samples;a.type_samples="samples";a.type_summary="summary";a.type_sunburst="sunburst"}async function Ot(t,e){const s={genome:e.name};if(t.bcf.file){s.file=t.bcf.file}else{s.url=t.bcf.url;if(t.bcf.indexURL)s.indexURL=t.bcf.indexURL}const a=await u("vcfheader",{body:s});if(a.error)throw a.error;const[n,i,o,r]=F(a.metastr.split("\n"));if(r)throw"Error parsing VCF meta lines: "+r.join("; ");t.mds.bcf={info:n,format:i};if(o?.length){t.mds.bcf.samples=o;t.mds.variant2samples={type_samples:"samples",variantkey:"ssm_id"}}if(!t.mds.queries)t.mds.queries={};t.mds.queries.snvindel={forTrack:true}}function It(t){const e=t.allow2selectSamples;if(!e)return;if(!e.buttonText)e.buttonText="Select samples";if(typeof e.buttonText!="string")throw"allow2selectSamples.buttonText value is not string";if(!e.attributes)e.attributes=[{from:"sample_id",to:"sample_id"}];if(!Array.isArray(e.attributes))throw"allow2selectSamples.attributes[] is not array";if(e.attributes.length==0)throw"allow2selectSamples.attributes[] blank array";for(const t of e.attributes){if(typeof t.from!="string"||!t.from)throw"allow2selectSamples.attributes.from is not string";if(typeof t.to!="string"||!t.to)throw"allow2selectSamples.attributes.to is not string"}if(typeof e.callback!="function")throw"allow2selectSamples.callback() is not function";e._cart=[]}async function Dt(t){for(const e of t.mlst){if(e.dt!=p&&e.dt!=l&&e.dt!=r&&e.dt!=s)throw"mlst[] contains unknown dt"}if(t.mlst.length==1){await Bt(t)}else{await Ft(t)}Tt(t)}function Tt(t){if(!t.tipDiv){return}const e=[];for(const s of t.div.selectAll("div").selectAll("table")){if(s)e.push(s)}if(!e.length)return;let s=0;for(const t of e){const e=t.firstChild;if(e.tagName!="THEAD")continue;const a=e.firstChild;if(a.tagName!="TR")continue;s=Math.max(s,a.childNodes?.length)}if(s>5){t.tipDiv.style("left","50px")}}async function Bt(t){const e=h({holder:t.div});const a=t.mlst[0];if(a.dt==p){Ut(t,e)}else if(a.dt==r||a.dt==l){await Wt(t,e)}else if(a.dt==s){Kt(t,e)}else{throw"oneItem: unknown dt"}t.singleSampleDiv=e;if(t.tk.mds.variant2samples){if(a.occurrence){await Zt(t)}}}async function Ft(t){const e=t.div.append("div").style("margin-bottom","10px").style("display","none");e.append("span").html("&#8810; Back to list").attr("class","sja_clbtext").on("click",(()=>{m.style("display","");e.style("display","none");a.style("display","none")}));const a=t.div.append("div").style("display","none");const n=[{label:"Click a variant to see details"}];const o=t.mlst.some((t=>t.occurrence));if(o){n.push({label:"Occurrence"})}let c=null;if(t.tk.mds.bcf?.info){c=[];for(const e in t.tk.mds.bcf.info){if(t.tk.mds.bcf.info[e].categories){c.push(e);n.push({label:t.tk.mds.bcf.info[e].name||e})}}if(c.length==0)c=null}let d;if(t.tk.skewer){d=t.tk.skewer.viewModes.find((t=>t.inuse&&t.type=="numeric"&&t.byAttribute!="occurrence"));if(d){n.push({label:d.label})}}t.mlst.sort(((t,e)=>t.__x-e.__x));const f=[];for(const e of t.mlst){const s=[{}];if(o){s.push({value:"occurrence"in e?e.occurrence:""})}if(c){for(const a of c){const n=e.info[a];if(n==undefined){s.push({})}else{const e=t.tk.mds.bcf.info[a].categories[n];if(e?.color){s.push({html:`<span style="background:${e.color}">&nbsp;&nbsp;</span> 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if(o.dt==s){c.append("span").style("background",t.tk.cnv.colorScale(o.value)).text(o.value).style("font-size",".8em").style("padding","0px 3px");c.append("span").style("margin-left","10px").text(`${o.chr}:${o.start}-${o.stop}`)}else{c.text("error: unknown m.dt")}}if(!t.doNotListSample4multim&&t.tk.mds.variant2samples){const e=t.mlst.reduce(((t,e)=>t+(e.occurrence||0)),0);if(e){t.div.append("div").style("margin-top","10px").append("span").attr("class","sja_clbtext").text("List all samples").on("click",(async e=>{e.target.remove();m.remove();await Zt(t);Tt(t)}))}}}function Ut({mlst:t,tk:e,block:s},a){const n=t[0];{const[t,e]=a.addRow();t.text(s.mclassOverride?s.mclassOverride.className:"Consequence");Ht(e,n)}{const[t,i]=a.addRow();t.text(n.ref&&n.alt?"Mutation":"Position");Vt(i,n,e,s)}if(n.occurrence>1){const[t,e]=a.addRow();t.text("Occurrence");e.text(n.occurrence)}Gt(n,e,a);Pt(n,e,a);Yt(n,e,a);if(n.info){for(const t in n.info){if(t=="CSQ"){continue}const[s,i]=a.addRow();s.text(t);const o=n.info[t];const r=e.mds?.bcf?.info?.[t];if(Array.isArray(o)){for(const t of o){Et(n,r,t,i)}}else{Et(n,r,o,i)}if(r?.Description){i.append("span").style("margin-left","10px").style("font-size",".8em").style("opacity",.6).text(r.Description)}}}}function Gt(t,e,s){const a=e.skewer.viewModes.find((t=>t.inuse));if(a.type!="numeric"||a.byAttribute=="occurrence")return;if(a.tooltipPrintValue){const e=a.tooltipPrintValue(t);if(Array.isArray(e)){for(const t of e){const[e,a]=s.addRow();e.text(t.k);a.text(t.v)}}else{console.log("unknown return value")}return}const[n,i]=s.addRow();n.text(a.label);i.text(t.__value_missing?"NA":t.__value_use)}function Pt(t,e,s){if(!t.htmlSections)return;if(!Array.isArray(t.htmlSections))throw"htmlSections[] is not array";for(const e of t.htmlSections){const[t,a]=s.addRow();if(e.key&&e.html){t.text(e.key);a.html(e.html)}}}function Et(t,e,s,a,n){if(!e){a.append("span").text(s);return}if(e.urlBase){a.append("a").text(s).attr("href",e.urlBase+s).attr("target","_blank");return}const i=a.append("span").text(s);if(e&&e.categories){const t=e.categories[s];if(t){i.style("padding","1px 4px").style("background",t.color);if(t.textcolor){i.style("color",t.textcolor)}}}}function Ht(t,e){t.append("span").text(e.mname);t.append("span").style("margin-left","5px").style("color",i[e.class].color).style("font-size",".8em").text(i[e.class].label.toUpperCase())}function Vt(t,e,s,a){const n=t.append("span").text(`${e.chr}:${e.pos+1} ${e.ref&&e.alt?e.ref+">"+e.alt:""}`);const i=s.mds.termdbConfig?.urlTemplates?.ssm||s.mds.queries?.snvindel?.ssmUrl;if(i){const s=z(i,e,n,a.genome.name);if(s?.length){t.append("span").style("margin-left","10px").html(s.join(" "))}}}async function Wt(t,e){await Xt(t.mlst[0],e.scrollDiv.insert("div",":first-child"),t.block);{const[s,a]=e.addRow();s.text("Data type");a.text(i[t.mlst[0].class].label)}{const[s,a]=e.addRow();s.text("Break points");for(const e of t.mlst[0].pairlst){Qt(e,a.append("div"))}}}function Kt(t,e){const s=t.mlst[0];{const[a,n]=e.addRow();a.text("Copy number change");n.html(`<span style="background:${t.tk.cnv.colorScale(s.value)}">&nbsp;&nbsp;</span> ${s.value}`)}{const[t,a]=e.addRow();t.text("Position");a.text(s.chr+":"+s.start+"-"+s.stop)}if(s.samples){const[t,a]=e.addRow();t.text("Sample");for(const t of s.samples){a.append("div").text(t.sample_id)}}}function Qt(t,e){if(t.a.name)e.append("span").text(t.a.name).style("font-weight","bold").style("margin-right","5px");e.append("span").text(`${t.a.chr}:${t.a.pos} ${t.a.strand=="+"?"forward":"reverse"} > ${t.b.chr}:${t.b.pos} ${t.b.strand=="+"?"forward":"reverse"}`);if(t.b.name)e.append("span").text(t.b.name).style("font-weight","bold").style("margin-left","5px")}async function Xt(t,e,s){const a=e.append("div").text("Loading...");try{if(!t.pairlst)throw".pairlst[] missing";const n={a:{chr:t.pairlst[0].a.chr,position:t.pairlst[0].a.pos,strand:t.pairlst[0].a.strand},b:{chr:t.pairlst[0].b.chr,position:t.pairlst[0].b.pos,strand:t.pairlst[0].b.strand}};await Jt(n.a,s);await Jt(n.b,s);a.remove();const i=await import("./svgraph-6fac8cbc.js");i.default({pairlst:[n],genome:s.genome,holder:e})}catch(t){a.text(t.message||t)}}async function Jt(t,e){const s=await u("isoformbycoord",{body:{genome:e.genome.name,chr:t.chr,pos:t.position}});if(s.error)throw s.error;const a=s.lst.find((t=>t.isdefault))||s.lst[0];if(a){t.name=a.name;t.gm={isoform:a.isoform}}}function Yt(t,e,s){if(!e.mds.queries?.ld)return;const[a,n]=s.addRow();a.text("LD overlay");const i=e.mds.queries.ld.mOverlay?.m;if(i){const s=n.append("div").style("margin-bottom","5px");if(t.ssm_id==i.ssm_id){s.html(e.mds.queries.ld.mOverlay.ldtkname+" r<sup>2</sup> values against this variant are displayed on all the other variants.")}else{let a=null;for(const s of e.mds.queries.ld.mOverlay.data||[]){if(s.pos==t.pos&&s.alleles==t.ref+"."+t.alt){a=s.r2;break}}if(a==null){s.html("No r<sup>2</sup> value is found.")}else{s.html(e.mds.queries.ld.mOverlay.ldtkname+" r<sup>2</sup> = "+a)}}}n.append("div").html("Click a button to overlay LD r<sup>2</sup> values against this variant:").style("font-size",".8em").style("opacity",.5);for(const s of e.mds.queries.ld.tracks){const a=n.append("button").text(s.name);if(i&&i.ssm_id==t.ssm_id){if(s.name==e.mds.queries.ld.mOverlay.ldtkname){a.property("disabled",true);continue}}a.on("click",(()=>{e.itemtip.hide();e.mds.queries.ld.mOverlay={ldtkname:s.name,m:{chr:t.chr,pos:t.pos,ref:t.ref,alt:t.alt,ssm_id:t.ssm_id}};e.load()}))}}async function Zt(t){const e=t.div.append("div").text("Loading...").style("padding","10px").style("color","#8AB1D4").style("font-size","1.25em").style("font-weight","bold");t.tid2value_orig=new Set;if(t.tid2value)Object.keys(t.tid2value).forEach(t.tid2value_orig.add,t.tid2value_orig);try{t.querytype=t.tk.mds.variant2samples.type_samples;const s=await t.tk.mds.variant2samples.get(t);await te(s.samples,t);e.remove()}catch(t){e.text("Error: "+(t.message||t));if(t.stack)console.log(t.stack)}}async function te(t,e){if(t.length==1){return await se(t[0],e)}const[s,a]=await oe(t,e.tk);const n={rows:a,columns:s,div:e.div,resize:a.length>10,dataTestId:"sjpp_mds3tk_sampletable"};n.columnButtons=[];if(e.tk.mds.queries?.singleSampleMutation){const s={text:"Disco",dataTestId:"sja_sample_table_disco_button",callback:async(s,a)=>{e.tk.itemtip.hide();e.tk.menutip.hide();let n;if(t[a].ssm_id_lst?.[0]){n=(e.tk.skewer.rawmlst||e.tk.custom_variants).find((e=>e.ssm_id==t[a].ssm_id_lst[0]))}await ie(e.tk,e.block,t[a],n)}};n.columnButtons.push(s)}if(e.tk.mds.queries?.singleSampleGenomeQuantification){for(const s in e.tk.mds.queries.singleSampleGenomeQuantification){const a={text:s,dataTestId:`${s}_button`,callback:async(a,n)=>{const i=g(e.tk.newChartHolder||e.block.holder0);i.header.text(t[n].sample_id);await(await import("./plot.ssgq-5581dc56.js")).plotSingleSampleGenomeQuantification(e.tk.mds,e.tk.mds.label,s,t[n],i.body.append("div").style("margin","20px"),e.block.genome,e.block.usegm?.name)}};n.columnButtons.push(a)}}if(e.tk.allow2selectSamples){n.buttons=[{text:e.tk.allow2selectSamples.buttonText,class:e.tk.allow2selectSamples.class,callback:s=>{ee(e.tk,e.block,t,s);e.tk.itemtip.hide();e.tk.menutip.hide()}}]}return R(n)}async function ee(t,e,s,a){const n=[...s];const i=a.map((t=>n[t]));t.allow2selectSamples.callback({samples:await t.mds.termdb.vocabApi.convertSampleId(i,t.allow2selectSamples.attributes),source:"Samples with "+le(e)})}async function se(t,e){const s=e.singleSampleDiv||h({holder:e.div});if(t.sample_id){const[a,n]=s.addRow();a.text(e.tk.mds.termdbConfig?.lollipop?.sample||"Sample");let i;if(t.ssm_id_lst?.[0]){i=e.tk.skewer.rawmlst.find((e=>e.ssm_id==t.ssm_id_lst[0]))}ne(t,e.tk,n,e.block,i)}if("caseIsOpenAccess"in t){const[e,a]=s.addRow();e.text("Access");a.text(t.caseIsOpenAccess?"Open":"Controlled")}if(e.tk.mds.variant2samples.twLst){for(const a of e.tk.mds.variant2samples.twLst){const[e,n]=s.addRow();e.text(a.term.name).style("text-overflow","ellipsis");n.style("text-overflow","ellipsis");if(a.term.id in t){if(Array.isArray(t[a.term.id])){if(a.baseURL){n.html(t[a.term.id].map((t=>`<a href=${a.baseURL+t} target=_blank>${t}</a>`)).join("<br>"))}else{n.html(t[a.term.id].join("<br>"))}}else{const e=ae(t,a);if(a.baseURL){n.html(`<a href=${a.baseURL+e} target=_blank>${e}</a>`)}else{n.text(e)}}}}}if(t.ssmid2format){for(const a of t.ssm_id_lst){if(t.ssm_id_lst.length>1){const[t,n]=s.addRow();n.style("padding-top","20px");const i=e.tk.skewer.rawmlst.find((t=>t.ssm_id==a));if(i){if(i.dt==p){Vt(n,i,e.tk,e.block)}else if(i.dt==r||i.dt==l){Qt(i.pairlst[0],n)}else{n.text(a)}}else{n.text(a)}}for(const n in t.ssmid2format[a]){const i=t.ssmid2format[a][n];const[o,r]=s.addRow();const l=e.tk.mds?.bcf?.format?.[n];o.text(l&&l.Description||n);r.html(re(l,i))}}}}function ae(t,e){if(!(e.term.id in t))return"";const s=t[e.term.id];if(e.term.values?.[s]?.label)return e.term.values[s].label;const a=e.term.valueConversion;if(a)return f(s,a.fromUnit,a.toUnit,a.scaleFactor);return s}function ne(t,e,s,a,n){const i=e.mds.termdbConfig?.urlTemplates?.sample;if(i){const e=s.append("a");e.attr("href",i.base+(t[i.namekey]||t.sample_id));e.attr("target","_blank");e.text(t.sample_id);e.style("word-break","break-word")}else{s.append("span").attr("class","pp_mds3_singleSampleNameSpan").text(t.sample_id)}const o=s.append("div");if(e.allow2selectSamples){const s=e.allow2selectSamples.buttonText;const n=o.append("button").style("margin-right","10px").text(s.endsWith("s")?s.substring(0,s.length-1):s).on("click",(()=>{ee(e,a,[t],[0]);e.itemtip.hide();e.menutip.hide()}));if(e.allow2selectSamples.class)n.attr("class",e.allow2selectSamples.class)}if(e.mds.queries?.singleSampleMutation){o.append("button").style("margin-right","10px").text("Disco plot").attr("data-testid","proteinpaint_disc_table_disco_button").on("click",(async()=>{e.itemtip.hide();await ie(e,a,t,n)}))}if(e.mds.queries?.singleSampleGenomeQuantification){for(const s in e.mds.queries.singleSampleGenomeQuantification){o.append("button").text(s).on("click",(async()=>{const n=g(e.newChartHolder||a.holder0);n.header.text(t.sample_id);await(await import("./plot.ssgq-5581dc56.js")).plotSingleSampleGenomeQuantification(e.mds,e.mds.label,s,t,n.body.append("div").style("margin","20px"),a.genome,a.usegm?.name)}))}}}async function ie(t,e,s,a){const n=g(t.newChartHolder||e.holder0);const i=[s.sample_id];if(a){i.push(", with 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Map;if(t.skewer){const e=t.skewer.viewModes.find((t=>t.inuse));let s;if(e.type=="skewer"){s=t.skewer.data.filter((t=>t.x>=0&&t.x<=a.width))}else if(e.type=="numeric"){s=e.data}else{throw"unknown mode type"}for(const t of s){for(const e of t.mlst){if(!n.has(e.dt))n.set(e.dt,[]);n.get(e.dt).push(e)}}}if(t.cnv?.cnvLst){n.set(s,t.cnv.cnvLst)}if(n.size==1){const e=t.menutip.d.append("div").style("margin","10px");await Dt({div:e,mlst:n.get([...n.keys()][0]),tk:t,block:a,doNotListSample4multim:true});return}const i=[];for(const[t,s]of n){i.push({label:s.length+" "+e[t]})}new T({holder:t.menutip.d.append("div").attr("class","sja_pp_vlb_dttabdiv").style("margin","10px"),tabs:i}).main();let o=0;for(const[e,s]of n){Dt({div:i[o++].contentHolder.append("div").style("margin-left","10px"),mlst:s,tk:t,block:a,doNotListSample4multim:true})}}function Ie(t,e){if(!t.skewer)return;if(t.skewer.viewModes.length<=1){return}const s=[];for(const[e,a]of t.skewer.viewModes.entries()){const t={label:De(a),value:e};if(a.inuse)t.checked=true;s.push(t)}B({holder:t.menutip.d.append("div").attr("class","sja_pp_vlb_viewmoderadiodiv").style("margin","10px"),options:s,callback:async s=>{for(const e of t.skewer.viewModes)e.inuse=false;t.skewer.viewModes[s].inuse=true;us({skewer:t.skewer.rawmlst},t,e);Pe(t,e);t._finish()}})}function De(t){if(!t)return"MISSING!!";if(t.type=="skewer")return"As lollipops";if(t.type=="numeric")return t.label+" as Y axis";return"unknown mode"}async function Te(t,e){if(!t.mds.variant2samples){console.log("TODO: variant-only");return}const s={querytype:"samples"};Cs(t,e,s);const a=(await t.mds.variant2samples.get(s)).samples;const[n,o]=await oe(a,t);const c=[];for(const t of n){if(t.isSsm){c.push("AAchange");c.push("Consequence");c.push("Mutation");continue}if(t.isMaf){c.push("Alternative allele depth in tumor");c.push("Total depth in tumor");continue}c.push(t.label)}const d=[];for(const[e,s]of a.entries()){let 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a=0;const n=new Map;const i=[];for(const e of t.cnv){if(!e.chr)continue;if(!Number.isFinite(e.value)){if(typeof e.class=="string"){if(e.class==A){e.value=1}else if(e.class==S){e.value=-1}else{continue}}else{continue}}if(!Number.isInteger(e.start)||!Number.isInteger(e.stop))continue;const t=s.seekcoord(e.chr,e.start)[0];if(!t)continue;const o=s.seekcoord(e.chr,e.stop)[0];if(!o)continue;const r=structuredClone(e);if(t.x>o.x){r.x1=o.x;r.x2=t.x}else{r.x1=t.x;r.x2=o.x}a=Math.max(a,Math.abs(e.value));i.push(r);if(Array.isArray(e.samples)){for(const t of e.samples){if(!n.has(t.sample_id))n.set(t.sample_id,[]);n.get(t.sample_id).push(structuredClone(r))}}}let o;if(n.size){o=[];for(const[t,e]of n){e.sort(((t,e)=>t.x1-e.x1));o.push({sample_id:t,cnvs:e,x1:Math.min(...e.map((t=>t.x1))),x2:Math.max(...e.map((t=>t.x2)))})}o.sort(((t,e)=>t.x1-e.x1));for(let t=0;t<o.length;t++)o[t].y=t}else{i.sort(((t,e)=>t.x1-e.x1));Ms(i,0)}return[o,i,Math.min(e.cnv.absoluteValueRenderMax,a)]}const ys=d([40,120],[10,1]);function _s(t){if(t.length>120)return[1,0];if(t.length<40)return[10,1];return[Math.ceil(ys(t.length)),1]}function js(t,e,s,a,n,i){const o=Math.max(0,t.x1),r=Math.min(t.x2,n.width);a.cnv.g.append("rect").attr("x",o).attr("y",e).attr("width",r-o).attr("height",s).attr("fill",a.cnv.colorScale(t.value)).on("mouseover",(e=>{e.target.setAttribute("stroke","black");a.itemtip.clear().show(e.clientX,e.clientY);const s=h({holder:a.itemtip.d});const n=structuredClone(t);if(i){n.samples=[{sample_id:i.sample_id}]}Kt({mlst:[n],tk:a},s)})).on("mouseout",(t=>{t.target.setAttribute("stroke","");a.itemtip.hide()}))}function Ms(t,e){const s=[];for(const a of t){for(let t=0;t<s.length;t++){if(s[t]+e<a.x1){s[t]=a.x2;a.y=t;break}}if(!("y"in a)){a.y=s.length;s.push(a.x2)}}}async function As(t,e){e.tkcloakon(t);e.block_setheight();try{if(!t.mds||t.uninitialized){await pt(t,e)}const s=await qs(t,e);if(t.uninitialized){t.clear();delete t.uninitialized}us(s,t,e);xs(s,t,e);await Ue(s,t,e);t._finish(s)}catch(e){if(t.clear)t.clear();if(t.subtk2height)t.subtk2height.skewer=50;if(t._finish)t._finish({error:e.message||e});if(e.stack)console.log(e.stack);return}}function Ss(t,e){const s={genome:e.genome.name,forTrack:1,skewerRim:t.mds.queries?.snvindel?.skewerRim};const a={"Content-Type":"application/json",Accept:"application/json"};if(t.mds.has_skewer){s.skewer=1}if(t.set_id){s.set_id=t.set_id}if(t.filter0){s.filter0=t.filter0}if(t.filterObj){if(t.filterObj?.lst.length){s.filterObj=t.filterObj}}if(t.token){a["X-Auth-Token"]=t.token}if(t.mds.label){s.dslabel=t.mds.label}else{if(t.bcf){if(t.bcf.file){s.bcffile=t.bcf.file}else if(t.bcf.url){s.bcfurl=t.bcf.url;if(t.bcf.indexURL)s.bcfindexURL=t.bcf.indexURL}else{throw".file and .url missing for tk.bcf{}"}}}Cs(t,e,s);if(t.legend.mclass.hiddenvalues.size){s.hiddenmclasslst=[...t.legend.mclass.hiddenvalues].join(",")}if(t.legend.bcfInfo){const e={};for(const s in t.legend.bcfInfo){if(t.legend.bcfInfo[s].hiddenvalues.size){e[s]=[...t.legend.bcfInfo[s].hiddenvalues]}}if(Object.keys(e).length){s.infoFilter=e}}if(t.legend.formatFilter){const e={};for(const s in t.legend.formatFilter){if(t.legend.formatFilter[s].hiddenvalues.size){e[s]=[...t.legend.formatFilter[s].hiddenvalues]}}if(Object.keys(e).length){s.formatFilter=e}}if(t.cnv){if(t.cnv.cnvMaxLength)s.cnvMaxLength=t.cnv.cnvMaxLength;if(t.cnv.cnvGainCutoff)s.cnvGainCutoff=t.cnv.cnvGainCutoff;if(t.cnv.cnvLossCutoff)s.cnvLossCutoff=t.cnv.cnvLossCutoff}return[s,a]}async function qs(t,e){let s;if(t.custom_variants){s=await zs(t,e)}else{const[a,n]=Ss(t,e);s=await u("mds3",{body:a,headers:n})}if(s.error)throw s.error;return s}function Cs(t,e,s){if(typeof s!="object")throw"par{} is not object";let a=[];if(e.usegm){const t={chr:e.rglst[0].chr,reverse:e.rglst[0].reverse,width:0,start:null,stop:null};for(let s=e.startidx;s<=e.stopidx;s++){const a=e.rglst[s];t.width+=a.width+e.regionspace;t.start=t.start==null?a.start:Math.min(t.start,a.start);t.stop=t.stop==null?a.stop:Math.max(t.stop,a.stop)}a.push(t);if(e.gmmode=="genomic");else{s.isoform=e.usegm.isoform;s.gene=e.usegm.name}}else{a=e.tkarg_rglst(t)}let n=0;for(const t of a){t.xoff=0;n+=t.width+e.regionspace}if(e.subpanels.length==t.subpanels.length){for(const t of e.subpanels){a.push({chr:t.chr,start:t.start,stop:t.stop,width:t.width,exonsf:t.exonsf,xoff:n});n+=t.width+t.leftpad}}s.rglst=a}async function zs(t,e){const a={skewer:[],cnv:[]};let n=null,o;for(let t=e.startidx;t<=e.stopidx;t++){if(n==null){n=e.rglst[t].start;o=e.rglst[t].stop}else{n=Math.min(n,e.rglst[t].start);o=Math.max(o,e.rglst[t].stop)}}const c=new Map;for(const d of t.custom_variants){if(d.dt==s){if(d.chr!=e.rglst[0].chr)continue;if(Math.max(d.start,n)>Math.min(d.stop,o))continue;a.cnv.push(d)}else if(d.dt==p||d.dt==r||d.dt==l){if(d.chr!=e.rglst[0].chr)continue;if(d.pos<=n||d.pos>=o)continue;if(!d.class)d.class="X";if(!i[d.class])d.class="X";if(t.legend.mclass.hiddenvalues.has(d.class))continue;a.skewer.push(d)}else{throw"unknown custom data dt"}c.set(d.class,1+(c.get(d.class)||0))}if(a.cnv.length==0)delete a.cnv;const d=new Set;if(a.skewer?.some((t=>t.samples))){for(const t of a.skewer){if(t.samples){for(const e of t.samples)d.add(e.sample_id)}}}if(a.cnv?.some((t=>t.samples))){for(const t of a.cnv){if(t.samples){for(const e of t.samples)d.add(e.sample_id)}}}if(d.size)a.sampleTotalNumber=d.size;a.mclass2variantcount=[...c];await Ls(t,a.skewer);return a}async function Ls(t){if(!t.mds.queries?.ld?.mOverlay)return;if(!t.mds.termdb?.vocabApi)return;delete t.mds.queries.ld.mOverlay.data;const e=await t.mds.termdb.vocabApi.getLDdata(t.mds.queries.ld.mOverlay.ldtkname,t.mds.queries.ld.mOverlay.m);if(e.error||!Array.isArray(e.lst))return;t.mds.queries.ld.mOverlay.data=e.lst}var $s=Object.freeze({__proto__:null,loadTk:As,rangequery_rglst:Cs});export{te as d,mt as g,Ee as m,$s as t};

package/dist/{toggleButtons-002aeda1.js → toggleButtons-dbdbad01.js}

@@ -1 +1 @@
-import{_ as t}from"./tslib.es6-1f85f553.js";import{d as i}from"./app-a8c4854a.js";class e{constructor(t){this.opts=this.validateOpts(t);this.tabs=t.tabs;this.dom={holder:t.holder};this.defaultTabWidth=90;o(this)}validateOpts(t){if(!t.holder)throw`missing opts.holder for Tabs()`;if(!Array.isArray(t.tabs))throw`invalid opts.tabs array for Tabs()`;if(!t.linePosition)t.linePosition="bottom";if(t.linePosition!="bottom"&&t.linePosition!="top"&&t.linePosition!="right"&&t.linePosition!="left")throw`Invalid .linePosition arg. Must be either bottom, top, right, or left`;if(!t.tabsPosition)t.tabsPosition="horizontal";if(t.tabsPosition!="horizontal"&&t.tabsPosition!="vertical")throw`Invalid .tabsPosition arg. Must be either vertical or horizontal`;return t}main(){return t(this,void 0,void 0,(function*(){try{yield this.render()}catch(t){if(t.stack)console.log(t.stack);else throw t}}))}}function o(e){e.render=()=>t(this,void 0,void 0,(function*(){const o=e.tabs.find((t=>t.active));if(!o)e.tabs[0].active=true;const s=e.opts.linePosition=="bottom"||e.opts.linePosition=="top"?"center":e.opts.linePosition;e.dom.tabsHolder=e.dom.holder.append("div").style(`border-${e.opts.linePosition}`,"0.5px solid #1575ad");if(!e.opts.contentHolder&&!e.opts.noContent){e.dom.contentHolder=e.dom.holder.append("div")}else e.dom.contentHolder=e.opts.contentHolder;if(e.opts.tabsPosition=="vertical"){e.dom.tabsHolder.style("display","inline-grid").style("align-items","start").style("gap",e.opts.gap||"");e.dom.contentHolder.style("display","inline-block").style("vertical-align","top").style("position","relative")}else e.dom.tabsHolder.style("display","inline-block");yield e.dom.tabsHolder.selectAll("button").data(e.tabs).enter().append("button").attr("data-testid","sja_toggle_button").attr("class","sj-toggle-button").classed("sjpp-active",(t=>t.active)).style("padding","0px").style("width",(t=>t.width?`${t.width}px`:"fit-content")).style("min-width",(t=>t.width?null:Math.max(e.defaultTabWidth))).style("border","none").style("background-color","transparent").style("display",e.opts.tabsPosition=="vertical"?"flex":"inline-grid").property("disabled",(t=>t.disabled?t.disabled():false)).each((function(o){return t(this,void 0,void 0,(function*(){o.wrapper=i(this);if(e.opts.linePosition=="right")o.wrapper.style("justify-self","end");if(e.opts.linePosition=="left")o.wrapper.style("justify-self","start");if(e.opts.linePosition=="top"||e.opts.linePosition=="left"){o.line=o.wrapper.append("div").style("display",e.opts.linePosition=="left"?"inline-flex":"flex");o.tab=o.wrapper.append("div").style("display",e.opts.linePosition=="left"?"inline-block":"block")}else{o.tab=o.wrapper.append("div").style("display",e.opts.linePosition=="right"?"inline-block":"block");o.line=o.wrapper.append("div").style("display",e.opts.linePosition=="right"?"inline-flex":"flex")}if(o.disabled&&o.isVisible){o.wrapper.style("cursor",o.disabled()==true&&o.isVisible()==true?"not-allowed":"pointer")}o.tab.style("color",o.active?"#1575ad":"#757373").style("text-align",s).style("padding","5px").html(o.label);o.line.style("background-color","#1575ad").style("visibility",o.active?"visible":"hidden");if(e.opts.linePosition=="top"||e.opts.linePosition=="bottom"){o.line.style("height","8px").style("padding","0px 5px")}else{o.line.style("align-self","stretch").style("padding","5px 0px").html('<span style="width: 8px";>&nbsp</span>')}if(e.dom.contentHolder){o.contentHolder=e.dom.contentHolder.append("div").style("display",o.active?"block":"none");if(e.opts.tabsPosition=="horizontal"&&!e.opts.noTopContentStyle){o.contentHolder.style("padding-top","10px").style("margin-top","10px")}}if(o.active&&o.callback)yield o.callback(event,o);o.wrapper.on("mouseenter",(()=>{o.tab.style("color",o.active?"#757373":"#1575ad")})).on("mouseleave",(()=>{o.tab.style("color",o.active?"#1575ad":"#757373")}))}))})).on("click",((i,o)=>t(this,void 0,void 0,(function*(){for(const t of e.tabs){t.active=t===o}const t=e.tabs.findIndex((t=>t.active));e.update(t);if(o.callback)yield o.callback(i,o)}))));const l=e.tabs.findIndex((t=>t.active));e.update(l)}));e.update=(t=0,i={})=>{e.tabs.forEach(((i,e)=>{i.active=t===e}));e.dom.tabsHolder.selectAll("button").data(e.tabs).classed("sjpp-active",(t=>t.active)).each((t=>{t.wrapper.classed("sjpp-active",t.active);if(t.isVisible)t.wrapper.style("display",(t=>i&&t.isVisible()?"":"none"));if(t.contentHolder)t.contentHolder.style("display",t.active?"block":"none");t.tab.style("color",t.active?"#1575ad":"#757373");t.line.style("visibility",t.active?"visible":"hidden")}))}}export{e as T};
+import{_ as t}from"./tslib.es6-c3c2d88f.js";import{d as i}from"./app-b369b169.js";class e{constructor(t){this.opts=this.validateOpts(t);this.tabs=t.tabs;this.dom={holder:t.holder};this.defaultTabWidth=90;o(this)}validateOpts(t){if(!t.holder)throw`missing opts.holder for Tabs()`;if(!Array.isArray(t.tabs))throw`invalid opts.tabs array for Tabs()`;if(!t.linePosition)t.linePosition="bottom";if(t.linePosition!="bottom"&&t.linePosition!="top"&&t.linePosition!="right"&&t.linePosition!="left")throw`Invalid .linePosition arg. Must be either bottom, top, right, or left`;if(!t.tabsPosition)t.tabsPosition="horizontal";if(t.tabsPosition!="horizontal"&&t.tabsPosition!="vertical")throw`Invalid .tabsPosition arg. Must be either vertical or horizontal`;return t}main(){return t(this,void 0,void 0,(function*(){try{yield this.render()}catch(t){if(t.stack)console.log(t.stack);else throw t}}))}}function o(e){e.render=()=>t(this,void 0,void 0,(function*(){const o=e.tabs.find((t=>t.active));if(!o)e.tabs[0].active=true;const s=e.opts.linePosition=="bottom"||e.opts.linePosition=="top"?"center":e.opts.linePosition;e.dom.tabsHolder=e.dom.holder.append("div").style(`border-${e.opts.linePosition}`,"0.5px solid #1575ad");if(!e.opts.contentHolder&&!e.opts.noContent){e.dom.contentHolder=e.dom.holder.append("div")}else e.dom.contentHolder=e.opts.contentHolder;if(e.opts.tabsPosition=="vertical"){e.dom.tabsHolder.style("display","inline-grid").style("align-items","start").style("gap",e.opts.gap||"");e.dom.contentHolder.style("display","inline-block").style("vertical-align","top").style("position","relative")}else e.dom.tabsHolder.style("display","inline-block");yield e.dom.tabsHolder.selectAll("button").data(e.tabs).enter().append("button").attr("data-testid","sja_toggle_button").attr("class","sj-toggle-button").classed("sjpp-active",(t=>t.active)).style("padding","0px").style("width",(t=>t.width?`${t.width}px`:"fit-content")).style("min-width",(t=>t.width?null:Math.max(e.defaultTabWidth))).style("border","none").style("background-color","transparent").style("display",e.opts.tabsPosition=="vertical"?"flex":"inline-grid").property("disabled",(t=>t.disabled?t.disabled():false)).each((function(o){return t(this,void 0,void 0,(function*(){o.wrapper=i(this);if(e.opts.linePosition=="right")o.wrapper.style("justify-self","end");if(e.opts.linePosition=="left")o.wrapper.style("justify-self","start");if(e.opts.linePosition=="top"||e.opts.linePosition=="left"){o.line=o.wrapper.append("div").style("display",e.opts.linePosition=="left"?"inline-flex":"flex");o.tab=o.wrapper.append("div").style("display",e.opts.linePosition=="left"?"inline-block":"block")}else{o.tab=o.wrapper.append("div").style("display",e.opts.linePosition=="right"?"inline-block":"block");o.line=o.wrapper.append("div").style("display",e.opts.linePosition=="right"?"inline-flex":"flex")}if(o.disabled&&o.isVisible){o.wrapper.style("cursor",o.disabled()==true&&o.isVisible()==true?"not-allowed":"pointer")}o.tab.style("color",o.active?"#1575ad":"#757373").style("text-align",s).style("padding","5px").html(o.label);o.line.style("background-color","#1575ad").style("visibility",o.active?"visible":"hidden");if(e.opts.linePosition=="top"||e.opts.linePosition=="bottom"){o.line.style("height","8px").style("padding","0px 5px")}else{o.line.style("align-self","stretch").style("padding","5px 0px").html('<span style="width: 8px";>&nbsp</span>')}if(e.dom.contentHolder){o.contentHolder=e.dom.contentHolder.append("div").style("display",o.active?"block":"none");if(e.opts.tabsPosition=="horizontal"&&!e.opts.noTopContentStyle){o.contentHolder.style("padding-top","10px").style("margin-top","10px")}}if(o.active&&o.callback)yield o.callback(event,o);o.wrapper.on("mouseenter",(()=>{o.tab.style("color",o.active?"#757373":"#1575ad")})).on("mouseleave",(()=>{o.tab.style("color",o.active?"#1575ad":"#757373")}))}))})).on("click",((i,o)=>t(this,void 0,void 0,(function*(){for(const t of e.tabs){t.active=t===o}const t=e.tabs.findIndex((t=>t.active));e.update(t);if(o.callback)yield o.callback(i,o)}))));const l=e.tabs.findIndex((t=>t.active));e.update(l)}));e.update=(t=0,i={})=>{e.tabs.forEach(((i,e)=>{i.active=t===e}));e.dom.tabsHolder.selectAll("button").data(e.tabs).classed("sjpp-active",(t=>t.active)).each((t=>{t.wrapper.classed("sjpp-active",t.active);if(t.isVisible)t.wrapper.style("display",(t=>i&&t.isVisible()?"":"none"));if(t.contentHolder)t.contentHolder.style("display",t.active?"block":"none");t.tab.style("color",t.active?"#1575ad":"#757373");t.line.style("visibility",t.active?"visible":"hidden")}))}}export{e as T};

package/dist/tp.ui-9c2e9fc5.js

@@ -0,0 +1 @@
+import{bC as t,bi as e,z as s,ak as n,ar as o,aP as a,aR as l,aQ as r,bD as i,bE as c,Z as p,ac as d,p as f,ab as m,e as u,M as h,bF as g,bG as y,j as b,ah as x,aa as w,bH as k,bI as v,bJ as j,bK as _}from"./app-b369b169.js";import{b as z}from"./block.lazyload-87b12654.js";function E(t){if(!t.ok)throw new Error(t.status+" "+t.statusText);if(t.status===204||t.status===205)return;return t.json()}function R(t,e){return fetch(t,e).then(E)}function S(p,d,f){let m=true;for(const t in p.dsset){m=false}if(m){d.remove();f.remove();return null}const u=new Map;let h=0;for(const s in p.dsset){const n=p.dsset[s].bulkdata;if(!n)continue;const o=new Map;const a=new Set;const l=new Set;for(const s in n){for(const r of n[s]){const s=r.class;if(s==t){a.add((r.sample?r.sample:"")+"."+(r.sampletype?r.sampletype:"")+JSON.stringify(r.pairlst));continue}if(s==e){l.add((r.sample?r.sample:"")+"."+(r.sampletype?r.sampletype:"")+JSON.stringify(r.pairlst));continue}h++;if(!o.has(s)){o.set(s,0)}o.set(s,o.get(s)+1)}}if(a.size){o.set(t,a.size);h+=a.size}if(l.size){o.set(e,l.size);h+=l.size}u.set(s,o)}d.html(h+' <span style="font-size:.8em">VARIANTS</span>').attr("aria-label","A summary of variant hits from all genes, in descending order.");const g=f.append("table").style("margin-right","20px");const y=g.append("tr");const b=g.append("tr");const x=(t,e,s)=>{e.selectAll("*").remove();for(const n of t){const t=e.append("div").style("margin","10px");t.append("span").attr("class","sja_mcdot").style("background-color",n.color).style("padding","2px 5px").style("margin-right","5px").html(s?n.count:"&nbsp;&nbsp;");t.append("span").style("color",n.color).text(n.label)}};const w={};for(const[d,f]of u){const m=[];for(const[t,e]of f){const i=s[t];if(i.dt==n||i.dt==o||i.dt==a||i.dt==l||i.dt==r){m.push({key:t,label:i.label,color:i.color,count:e})}}m.sort(((t,e)=>e.count-t.count));for(const n of[i,c,t,e]){if(f.has(n)){const t=s[n];m.push({key:n,label:t.label,color:t.color,count:f.get(n)})}}w[d]=m;const u=b.append("td").attr("valign","top").attr("shownumber",0);x(m,u,true);const h=y.append("td").style("border-bottom","solid 1px #ccc").style("padding","5px 10px").style("color","#858585").style("font-size",".8em").text(p.dsset[d].label);h.append("button").style("margin","5px").text("Hide number").on("click",(t=>{const e=u.attr("shownumber")=="1";x(m,u,e);u.attr("shownumber",e?"0":"1");t.target.innerHTML=e?"Hide number":"Show number"}))}return h?w:null}function U(t){Promise.resolve().then((()=>{if(!t.gene)throw{message:"gene name missing"};if(!t.genome)throw{message:"genome name missing"};if(t.hostURL==undefined)throw{message:"no 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a=n[s.key];if(!a)return o;const l=t.patientannotation.mdh[s.key].values[a];if(!l){console.error("invalid value key: "+a+" at term: "+s.key);return o}return l.color}));e.legendholder.selectAll("*").remove();e.legendholder.append("div").style("margin-bottom","5px").text(s.label).style("font-weight","bold");for(const t of s.values){const s=e.legendholder.append("div").style("margin-bottom","3px");s.append("span").attr("class","sja_mcdot").style("background-color",t.color).style("margin-right","5px").html("&nbsp;");s.append("span").text(t.label)}if(e.expressiondata){O(t,e)}}))}}))}async function H(t,e,s,n={callbacks:{sjcharts:{}}}){const o=n.debugmode;if(o){window.cohort=t}if(!("hostURL"in t))t.hostURL=s;if(t.headerhtml){e.append("div").html(t.headerhtml)}let a=0;for(const e in t.p2st){a++;for(const s in t.p2st[e]){const n=t.p2st[e][s];n.sampletype=s;n.patientname=e;n.cohort=t}}const l=e.append("table").style("margin-top","20px");const r=l.append("tr");t.__tdleft=r.append("td").style("vertical-align","top").style("padding-right","20px");t.__tdright=r.append("td").style("vertical-align","top");if(t.hide_navigation){t.__tdleft.style("display","none")}if(!t.hide_addnewfile){const[n,o]=I(t);o.style("background-color","#f4f4f4").style("margin","0px 20px 20px 0px").style("padding","20px");n.html('&#43; <span style="font-size:.8em">NEW FILE</span>');const a=o.append("p");const l=o.append("div");const r=()=>{l.selectAll("*").remove();l.append("span").html("Select data type&nbsp;");const n=k(l).style("margin-right","20px");l.append("input").attr("type","file").on("change",(o=>{a.text("");const l=o.target.files[0];if(!l){r();return}if(l.size==0){a.text("Wrong file: "+l.name);r();return}const i=new FileReader;i.onload=o=>{a.text(l.name+" loaded.");const i=v(t.genome.name);if(!i){a.text("should not happen");r();return}const c=j(o.target.result,n.node().selectedIndex,i);if(c){a.text("Error with "+l.name+": "+c);r();return}let p=null;for(const e in t.dsset){p=t.dsset[e];break}if(!p){a.text("no dataset in cohort, this should not happen");r();return}const d=_({flag:i,cohort:t,flag2thisds:p});if(d){a.text("Error with "+l.name+": "+d);r();return}if(i.good==0){a.text(l.name+": no data loaded");r();return}a.text("");r();e.selectAll("*").remove();H(t,e,s)};i.onerror=function(){a.text("Error reading file "+l.name);r();return};a.text("Parsing file "+l.name+" ...");i.readAsText(l,"utf8")}))};r()}const[i,c]=I(t);const p=S(t,i,c);const m=[];for(const e in t.dsset){const s=t.genome.datasets[e];if(s.hassample){m.push(e)}if(s.hasdisease);}if(p){const[e,n]=I(t,t.show_genetable);L(t,p,e,n,a>0,s)}let h=false;if(m.length||a>0){t.patientset={};for(const e in t.p2st){t.patientset[e]={trlst:[],samples:t.p2st[e]}}if(m.length>0&&!t.hardcodemap){h=true}}if(t.show_heatmap){h=true}if(h){const[e,s]=I(t);e.text("HEATMAP").style("font-size",".8em");const a=await w();const l=(t.name?t.name+".":"")+"hm";a.heatmap({cohort:t,hassamplelst:m,blockinit:u,debugmode:o,dom:{butt:e.node(),holder:s.node()},tp_getgeneexpression:U,show_heatmap:t.show_heatmap,instanceTracker:n.instanceTracker&&n.instanceTracker.sjcharts,callbacks:n.callbacks&&n.callbacks.sjcharts&&(n.callbacks.sjcharts[l]||n.callbacks.sjcharts.hm)})}if(t.hardcodemap){const[e,s]=I(t,t.show_hardcodemap);e.text("HEATMAP").style("font-size",".8em");for(const e of t.hardcodemap){const t=s.append("div").style("display","inline-block").style("margin-bottom","20px");if(e.name){t.append("h3").text(e.name)}T(e,t)}}if(t.survivalJSON){const[e,s]=I(t,t.show_hardcodemap);e.text("SURVIVAL CURVE").style("font-size",".8em").style("border-color","transparent");const o=await w();o.survival({cohort:t,dom:{butt:e.node(),holder:s.node()},instanceTracker:n.instanceTracker&&n.instanceTracker.sjcharts,callbacks:n.callbacks&&n.callbacks.sjcharts&&n.callbacks.sjcharts.sv})}if(t.browserview){const[n,a]=I(t);n.style("font-size",".8em").text("BROWSER");let l=false;n.on("click",(()=>{if(a.style("display")=="none"){n.style("border-color","black");f(a)}else{n.style("border-color","transparent");d(a)}if(l)return;l=true;const r={holder:a,genome:t.genome,debugmode:o,dogtag:t.genome.name,hostURL:s,jwt:t.jwt,cohort:t,nobox:t.browserview.nobox,datasetqueries:t.browserview.datasetqueries,tklst:[]};if(t.browserview.position){r.chr=t.browserview.position.chr;r.start=t.browserview.position.start;r.stop=t.browserview.position.stop}if(t.browserview.nativetracks){r.nativetracks=t.browserview.nativetracks}if(t.browserview.tracks){for(const e of t.browserview.tracks){r.tklst.push(e)}}if(t.browserview.assays){if(!t.assaylst){console.error("assaylst not set!");t.assaylst=[]}for(const e in t.browserview.assays){const s=t.browserview.assays[e];if(!s.assayobj){continue}if(s.combined){if(s.combinetk){r.tklst.push(s.combinetk)}}else{for(const e in t.patientset){for(const n in t.patientset[e].samples){for(const o of t.patientset[e].samples[n].tktemplate){if(o.id==s.assayobj.id){r.tklst.push(o)}}}}}}}if(t.browserview.defaultassaytracks){const[s,n]=J(t);if(s){b(e,"error with .defaultassaytracks: "+s)}else{for(const t of n)r.tklst.push(t)}}for(const t of r.tklst){t.iscustom=true}z(r)}));if(t.show_browser){n.node().click()}}if(t.e2pca){const[e,s]=I(t);e.text(t.e2pca.label).style("font-size",".8em");let n=false;e.on("click",(()=>{if(s.style("display")=="none"){e.style("border-color","black");f(s)}else{e.style("border-color","transparent");d(s)}if(n)return;n=true;C(t,s)}));if(t.show_e2pca){e.node().click()}}}function I(t,e){const s=t.__tdleft.append("div").attr("class","sja_menuoption").style("margin-top","10px").style("white-space","nowrap");const n=t.__tdright.append("div").style("padding-bottom","20px");s.on("click",(()=>{if(n.style("display")=="block"){d(n);s.style("border","solid 1px transparent")}else{s.style("border","solid 1px #545454");f(n)}}));if(e){s.style("border","solid 1px #545454");n.style("display","block")}else{s.style("border","solid 1px transparent");n.style("display","none")}return[s,n]}function J(t){if(!t.browserview)return[null,[]];if(!t.browserview.defaultassaytracks)return[null,[]];const e=[];for(const s of t.browserview.defaultassaytracks){const n=t.p2st[s.level1];if(!n)continue;if(s.level2){const t=n[s.level2];if(!t)continue;if(!t.tktemplate)continue;for(const n of t.tktemplate){if(n.assayname==s.assay){e.push(n);if(s.justone){break}}}}else{for(const t in n){const o=n[t];if(o.tktemplate){for(const t of o.tktemplate){if(t.assayname==s.assay){e.push(t)}}}}}}return[null,e]}var P=Object.freeze({__proto__:null,default:H});export{R as d,P as t};

package/dist/tslib.es6-c3c2d88f.js

@@ -0,0 +1 @@
+function e(e,t){var r={};for(var n in e)if(Object.prototype.hasOwnProperty.call(e,n)&&t.indexOf(n)<0)r[n]=e[n];if(e!=null&&typeof Object.getOwnPropertySymbols==="function")for(var o=0,n=Object.getOwnPropertySymbols(e);o<n.length;o++){if(t.indexOf(n[o])<0&&Object.prototype.propertyIsEnumerable.call(e,n[o]))r[n[o]]=e[n[o]]}return r}function t(e,t,r,n){function o(e){return e instanceof r?e:new r((function(t){t(e)}))}return new(r||(r=Promise))((function(r,a){function i(e){try{f(n.next(e))}catch(e){a(e)}}function c(e){try{f(n["throw"](e))}catch(e){a(e)}}function f(e){e.done?r(e.value):o(e.value).then(i,c)}f((n=n.apply(e,t||[])).next())}))}function r(e,t,r,n){if(r==="a"&&!n)throw new TypeError("Private accessor was defined without a getter");if(typeof t==="function"?e!==t||!n:!t.has(e))throw new TypeError("Cannot read private member from an object whose class did not declare it");return r==="m"?n:r==="a"?n.call(e):n?n.value:t.get(e)}function n(e,t,r,n,o){if(n==="m")throw new TypeError("Private method is not writable");if(n==="a"&&!o)throw new TypeError("Private accessor was defined without a setter");if(typeof t==="function"?e!==t||!o:!t.has(e))throw new TypeError("Cannot write private member to an object whose class did not declare it");return n==="a"?o.call(e,r):o?o.value=r:t.set(e,r),r}export{t as _,n as a,r as b,e as c};

package/dist/tvs.density-f6128793.js

@@ -0,0 +1 @@
+import{b as t}from"./brush-aa175142.js";import{c as n}from"./termsetting-33ea66f1.js";import{d as e}from"./app-b369b169.js";import"./pointer-c7475677.js";import"./nodrag-16ad4b03.js";import"./tslib.es6-c3c2d88f.js";import"path";function s(t,n){const s=t.num_obj.brushes;const r=t.num_obj.density_data.maxvalue;const a=t.num_obj.density_data.minvalue;const i=(r-a)/10;const u=t.tvs.term.type=="integer"?Math.floor(i):i;for(const[e,o]of t.num_obj.ranges.entries()){const t=s.find((t=>t.orig===o));let e;if(!t){e={orig:o,range:JSON.parse(JSON.stringify(o))};s.push(e)}else{e=t}if(o.start===""){if(n=="center")e.range.start=a+u*4;else e.range.start=a+u*8}if(o.stop===""){if(n=="center")e.range.stop=a+u*6;else e.range.stop=Math.floor(r)}}const d=t.num_obj.brush_g.selectAll(".range_brush").data(s,(t=>s.indexOf(t)));d.exit().remove();d.each((function(t,n){e(this).selectAll(".overlay").style("pointer-events","all")}));d.enter().append("g").attr("class","range_brush").each((function(n,e){o(t,this,n)}))}function o(n,s,o){if(!o.elem)o.elem=e(s);const a=o.range;const i=n.num_obj.plot_size;const u=n.num_obj.xscale;const d=n.num_obj.density_data.maxvalue;const l=n.num_obj.density_data.minvalue;o.d3brush=t().extent([[0,0],[i.width,i.height]]).on("brush",(function(t,e){const s=t.selection;if(!s)return;const i=o.rangeInput.getRange();if(i.value!=undefined){o.range=i;return}r(u,s,a,i,l,d,n.tvs.term.type);const c=a.startunbounded?"":i.startinclusive?`${a.start} <=`:`${a.start} <`;const p=a.stopunbounded?"":i.stopinclusive?`<= ${a.stop}`:`< ${a.stop}`;o.rangeInput.getInput().node().value=`${c} x ${p}`})).on("end",(function(){o.elem.selectAll(".overlay").style("pointer-events","none")}));const c=a.startunbounded?l:a.start;const p=a.stopunbounded?d:a.stop;o.init=()=>{if(a.value==undefined)o.elem.call(o.d3brush).call(o.d3brush.move,[c,p].map(u))};if(a.startunbounded)delete a.start;if(a.stopunbounded)delete a.stop;o.elem.selectAll(".selection").style("fill",o.orig.start===""&&o.orig.stop===""||JSON.stringify(a)!=JSON.stringify(o.orig)?"#23cba7":"#777777")}function r(t,e,s,o,r,i,u){s.start=a(t,e[0]);s.stop=a(t,e[1]);const d=n(Number(r));const l=n(Number(i));s.startunbounded=d==s.start&&o.startunbounded;s.stopunbounded=l==s.stop&&o.stopunbounded;if(u=="integer"){s.start=s.startunbounded?"":Math.round(s.start);s.stop=s.stopunbounded?"":Math.round(s.stop)}}function a(t,e){let s=Number(t.invert(e));return n(s)}function i(t,n="end",e){const o={start:"",stop:"",index:t.tvs.ranges.length};t.num_obj.ranges.push(o);const r={orig:o,range:JSON.parse(JSON.stringify(o))};t.num_obj.brushes.push(r);s(t,n);if(e)e();r.init()}export{s as addBrushes,i as addNewBrush,r as updateTempRanges};