@datagrok/bio 2.27.1 → 2.27.2

package/dist/422.js

@@ -1,2 +1,2 @@
-"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[422],{9422(e,t,i){i.d(t,{showLiabilityScannerDialog:()=>c});var n=i(4328),a=i(7389),o=i(6082),l=i(8012),r=i(4517),d=i(3736);const s=[{id:"deamid-ng",name:"Deamidation (NG)",pattern:/NG/g,length:2,severity:r.Hq.High,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"deamid-ns",name:"Deamidation (NS)",pattern:/NS/g,length:2,severity:r.Hq.Medium,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"deamid-na",name:"Deamidation (NA)",pattern:/NA/g,length:2,severity:r.Hq.Low,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"deamid-nd",name:"Deamidation (ND)",pattern:/ND/g,length:2,severity:r.Hq.Low,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"deamid-nt",name:"Deamidation (NT)",pattern:/NT/g,length:2,severity:r.Hq.Low,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"isom-dg",name:"Isomerization (DG)",pattern:/DG/g,length:2,severity:r.Hq.High,ruleCategory:"isomerization",color:r.D5.liability.isomerization,enabled:!0},{id:"isom-ds",name:"Isomerization (DS)",pattern:/DS/g,length:2,severity:r.Hq.Medium,ruleCategory:"isomerization",color:r.D5.liability.isomerization,enabled:!0},{id:"oxid-m",name:"Oxidation (Met)",pattern:/M/g,length:1,severity:r.Hq.Medium,ruleCategory:"oxidation",color:r.D5.liability.oxidation,enabled:!0},{id:"oxid-w",name:"Oxidation (Trp)",pattern:/W/g,length:1,severity:r.Hq.Low,ruleCategory:"oxidation",color:r.D5.liability.oxidation,enabled:!0},{id:"glyco-nxst",name:"N-glycosylation",pattern:/N[^P][ST]/g,length:3,severity:r.Hq.High,ruleCategory:"glycosylation",color:r.D5.liability.glycosylation,enabled:!0},{id:"free-cys",name:"Free Cysteine",pattern:/C/g,length:1,severity:r.Hq.Info,ruleCategory:"freeCysteine",color:r.D5.liability.freeCysteine,enabled:!1}];function u(e,t){const i=e.getSplitted(t),n=new Array(i.length);for(let e=0;e<i.length;e++)n[e]=i.getOriginal(e);return n.join("")}const g={[r.Hq.High]:"High",[r.Hq.Medium]:"Medium",[r.Hq.Low]:"Low",[r.Hq.Info]:"Info"};function c(){const e=n.shell.tv?.dataFrame;if(!e)return void n.shell.warning("No table open");const t=e.columns.bySemTypeAll(o.SEMTYPE.MACROMOLECULE);if(0===t.length)return void n.shell.warning("No macromolecule columns found");const i=s.map(e=>({...e,pattern:new RegExp(e.pattern.source,"g")})),c=a.input.table("Table",{value:e}),m=a.input.column("Sequence",{table:e,value:t[0],filter:e=>e.semType===o.SEMTYPE.MACROMOLECULE}),y=[],p=a.divV([]);for(const e of i){const t=a.input.bool(e.name,{value:e.enabled,tooltipText:`Severity: ${g[e.severity]??e.severity}`});y.push({rule:e,input:t}),p.append(t.root)}const h=a.input.bool("Highlight in cell renderer",{value:!0}),b=a.input.bool("Create annotation column",{value:!0}),f=a.input.bool("Create summary count column",{value:!1}),v=a.dialog({title:"Scan Sequence Liabilities"}).add(a.inputs([c,m])).add(a.h3("Rules")).add(p).add(a.h3("Output")).add(a.inputs([h,b,f])).onOK(()=>{try{const t=m.value,a=l._package.seqHelper.getSeqHandler(t);for(const{rule:e,input:t}of y)e.enabled=t.value;const o=function(e,t,i){const n=i.filter(e=>e.enabled),a=t.posList,o=new Map,l=new Array(e.length);let d=0;for(let i=0;i<e.length;i++){const e=u(t,i),r=[];for(const t of n){let i;for(t.pattern.lastIndex=0;null!==(i=t.pattern.exec(e));)r.push({annotationId:t.id,positionIndex:i.index,positionName:i.index<a.length?a[i.index]:void 0,matchedMonomers:i[0]}),o.set(t.id,(o.get(t.id)??0)+1),d++}l[i]=r}return{annotations:n.filter(e=>o.has(e.id)).map(e=>({id:e.id,name:e.name,description:`${e.ruleCategory} liability pattern (${o.get(e.id)} hits)`,start:null,end:null,visualType:1===e.length?r.ao.Point:r.ao.Motif,category:r.eI.Liability,color:e.color,severity:e.severity,motifPattern:e.pattern.source,autoGenerated:!0})),rowData:l,totalHits:d}}(t,a,i);(b.value||h.value)&&function(e,t,i){const n=(0,d.Ln)(t).filter(e=>e.category!==r.eI.Liability);(0,d.fh)(t,[...n,...i.annotations]);const a=(0,d.Lz)(e,t);for(let e=0;e<i.rowData.length;e++){const t=(0,d.JG)(a,e)??[];(0,d.z5)(a,e,(0,d.bq)(t,i.rowData[e],!1,!0))}}(e,t,o),f.value&&function(e,t,i){const n=`${t.name}_liability_count`,a=i.rowData.map(e=>e.length),o=e.columns.addNewInt(n);for(let e=0;e<a.length;e++)o.set(e,a[e])}(e,t,o),n.shell.info(`Liability scan: ${o.totalHits} hits found across ${o.annotations.length} rules`),e.fireValuesChanged()}catch(e){n.shell.error(`Liability scan failed: ${e.message??e}`),console.error(e)}});v.show()}}}]);
+"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[422],{9422(e,t,i){i.d(t,{showLiabilityScannerDialog:()=>c});var n=i(4328),a=i(7389),o=i(6082),l=i(9462),r=i(4517),d=i(3736);const s=[{id:"deamid-ng",name:"Deamidation (NG)",pattern:/NG/g,length:2,severity:r.Hq.High,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"deamid-ns",name:"Deamidation (NS)",pattern:/NS/g,length:2,severity:r.Hq.Medium,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"deamid-na",name:"Deamidation (NA)",pattern:/NA/g,length:2,severity:r.Hq.Low,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"deamid-nd",name:"Deamidation (ND)",pattern:/ND/g,length:2,severity:r.Hq.Low,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"deamid-nt",name:"Deamidation (NT)",pattern:/NT/g,length:2,severity:r.Hq.Low,ruleCategory:"deamidation",color:r.D5.liability.deamidation,enabled:!0},{id:"isom-dg",name:"Isomerization (DG)",pattern:/DG/g,length:2,severity:r.Hq.High,ruleCategory:"isomerization",color:r.D5.liability.isomerization,enabled:!0},{id:"isom-ds",name:"Isomerization (DS)",pattern:/DS/g,length:2,severity:r.Hq.Medium,ruleCategory:"isomerization",color:r.D5.liability.isomerization,enabled:!0},{id:"oxid-m",name:"Oxidation (Met)",pattern:/M/g,length:1,severity:r.Hq.Medium,ruleCategory:"oxidation",color:r.D5.liability.oxidation,enabled:!0},{id:"oxid-w",name:"Oxidation (Trp)",pattern:/W/g,length:1,severity:r.Hq.Low,ruleCategory:"oxidation",color:r.D5.liability.oxidation,enabled:!0},{id:"glyco-nxst",name:"N-glycosylation",pattern:/N[^P][ST]/g,length:3,severity:r.Hq.High,ruleCategory:"glycosylation",color:r.D5.liability.glycosylation,enabled:!0},{id:"free-cys",name:"Free Cysteine",pattern:/C/g,length:1,severity:r.Hq.Info,ruleCategory:"freeCysteine",color:r.D5.liability.freeCysteine,enabled:!1}];function u(e,t){const i=e.getSplitted(t),n=new Array(i.length);for(let e=0;e<i.length;e++)n[e]=i.getOriginal(e);return n.join("")}const g={[r.Hq.High]:"High",[r.Hq.Medium]:"Medium",[r.Hq.Low]:"Low",[r.Hq.Info]:"Info"};function c(){const e=n.shell.tv?.dataFrame;if(!e)return void n.shell.warning("No table open");const t=e.columns.bySemTypeAll(o.SEMTYPE.MACROMOLECULE);if(0===t.length)return void n.shell.warning("No macromolecule columns found");const i=s.map(e=>({...e,pattern:new RegExp(e.pattern.source,"g")})),c=a.input.table("Table",{value:e}),m=a.input.column("Sequence",{table:e,value:t[0],filter:e=>e.semType===o.SEMTYPE.MACROMOLECULE}),y=[],p=a.divV([]);for(const e of i){const t=a.input.bool(e.name,{value:e.enabled,tooltipText:`Severity: ${g[e.severity]??e.severity}`});y.push({rule:e,input:t}),p.append(t.root)}const h=a.input.bool("Highlight in cell renderer",{value:!0}),b=a.input.bool("Create annotation column",{value:!0}),f=a.input.bool("Create summary count column",{value:!1}),v=a.dialog({title:"Scan Sequence Liabilities"}).add(a.inputs([c,m])).add(a.h3("Rules")).add(p).add(a.h3("Output")).add(a.inputs([h,b,f])).onOK(()=>{try{const t=m.value,a=l._package.seqHelper.getSeqHandler(t);for(const{rule:e,input:t}of y)e.enabled=t.value;const o=function(e,t,i){const n=i.filter(e=>e.enabled),a=t.posList,o=new Map,l=new Array(e.length);let d=0;for(let i=0;i<e.length;i++){const e=u(t,i),r=[];for(const t of n){let i;for(t.pattern.lastIndex=0;null!==(i=t.pattern.exec(e));)r.push({annotationId:t.id,positionIndex:i.index,positionName:i.index<a.length?a[i.index]:void 0,matchedMonomers:i[0]}),o.set(t.id,(o.get(t.id)??0)+1),d++}l[i]=r}return{annotations:n.filter(e=>o.has(e.id)).map(e=>({id:e.id,name:e.name,description:`${e.ruleCategory} liability pattern (${o.get(e.id)} hits)`,start:null,end:null,visualType:1===e.length?r.ao.Point:r.ao.Motif,category:r.eI.Liability,color:e.color,severity:e.severity,motifPattern:e.pattern.source,autoGenerated:!0})),rowData:l,totalHits:d}}(t,a,i);(b.value||h.value)&&function(e,t,i){const n=(0,d.Ln)(t).filter(e=>e.category!==r.eI.Liability);(0,d.fh)(t,[...n,...i.annotations]);const a=(0,d.Lz)(e,t);for(let e=0;e<i.rowData.length;e++){const t=(0,d.JG)(a,e)??[];(0,d.z5)(a,e,(0,d.bq)(t,i.rowData[e],!1,!0))}}(e,t,o),f.value&&function(e,t,i){const n=`${t.name}_liability_count`,a=i.rowData.map(e=>e.length),o=e.columns.addNewInt(n);for(let e=0;e<a.length;e++)o.set(e,a[e])}(e,t,o),n.shell.info(`Liability scan: ${o.totalHits} hits found across ${o.annotations.length} rules`),e.fireValuesChanged()}catch(e){n.shell.error(`Liability scan failed: ${e.message??e}`),console.error(e)}});v.show()}}}]);
 //# sourceMappingURL=422.js.map