gensplore 0.0.10 → 0.0.12

package/dist/gensplore.js

@@ -2907,7 +2907,7 @@ var Pi = Re(ji), Fi = Object.assign(Mi, {
 	Panel: Ni,
 	Title: Pi,
 	Description: dt
-}), Ii = "function e(e,t){if(!t||typeof t.sequence!=`string`)throw Error(`Expected an aligned DNA sequence.`);let n=t.sequence.toUpperCase();if(!e.length||n.length!==e.length)throw Error(`Aligned sequence length must match the reference.`);if(/[^ACGTRYSWKMBDHVN-]/.test(n))throw Error(`Aligned sequences must contain IUPAC DNA bases or deletion gaps (-).`);let r=[],i=0;for(let t=0;t<n.length;){if(n[t]===e[t]){t++;continue}let a=n[t]===`-`?`Deletion`:/[^ACGT]/.test(n[t]+e[t])?`Ambiguous`:`Substitution`,o=t+1;if(a===`Deletion`||a===`Ambiguous`)for(;o<n.length&&n[o]!==e[o]&&(a===`Deletion`?n[o]===`-`:n[o]!==`-`&&/[^ACGT]/.test(n[o]+e[o]));)o++;r.push({type:a,start:t,end:o,reference:e.slice(t,o),alternative:a===`Deletion`?``:n.slice(t,o)}),i+=o-t,t=o}let a=new Set;for(let n of t.insertions||[]){let t=n.position,o=typeof n.sequence==`string`?n.sequence.toUpperCase():``;if(!Number.isInteger(t)||t<0||t>e.length||a.has(t))throw Error(`Insertions need unique integer positions from 0 to the reference length.`);if(!o||/[^ACGTRYSWKMBDHVN]/.test(o))throw Error(`Insertions must contain ungapped IUPAC DNA bases.`);a.add(t),r.push({type:`Insertion`,start:t,end:t,reference:``,alternative:o}),i+=o.length}return r.sort((e,t)=>e.start-t.start||e.end-t.end),{name:t.name||`Alternative`,distance:i,differences:r}}const t=e=>{switch(e){case`TTT`:case`TTC`:return`F`;case`TTA`:case`TTG`:case`CTT`:case`CTC`:case`CTA`:case`CTG`:return`L`;case`ATT`:case`ATC`:case`ATA`:return`I`;case`ATG`:return`M`;case`GTT`:case`GTC`:case`GTA`:case`GTG`:return`V`;case`TCT`:case`TCC`:case`TCA`:case`TCG`:case`AGT`:case`AGC`:return`S`;case`CCT`:case`CCC`:case`CCA`:case`CCG`:return`P`;case`ACT`:case`ACC`:case`ACA`:case`ACG`:return`T`;case`GCT`:case`GCC`:case`GCA`:case`GCG`:return`A`;case`TAT`:case`TAC`:return`Y`;case`TAA`:case`TAG`:case`TGA`:return`*`;case`CAT`:case`CAC`:return`H`;case`CAA`:case`CAG`:return`Q`;case`AAT`:case`AAC`:return`N`;case`AAA`:case`AAG`:return`K`;case`GAT`:case`GAC`:return`D`;case`GAA`:case`GAG`:return`E`;case`TGT`:case`TGC`:return`C`;case`TGG`:return`W`;case`CGT`:case`CGC`:case`CGA`:case`CGG`:case`AGA`:case`AGG`:return`R`;case`GGT`:case`GGC`:case`GGA`:case`GGG`:return`G`;default:return`X`}};function n(e){let t=e.trim().split(/\\r?\\n/);if(!t[0]?.startsWith(`>`))throw Error(`Expected a FASTA header starting with >.`);if(t.slice(1).some(e=>e.startsWith(`>`)))throw Error(`Please supply exactly one FASTA record.`);let n=t.slice(1).join(``).replace(/\\s/g,``).toUpperCase();if(!n||/[^ACGTRYSWKMBDHVN]/.test(n))throw Error(`Expected an ungapped DNA sequence (IUPAC bases).`);return{name:t[0].slice(1).trim()||`Alternative`,sequence:n}}function r(e,t,n=128){let r=e.length,i=t.length;if(!r||!i)throw Error(`Both sequences must contain bases.`);if(Math.max(r,i)>1e5)throw Error(`Comparison supports sequences up to 100,000 bases.`);let a=()=>Error(`Sequences exceed the ${n}-edit comparison limit. Use complete sequences in the same orientation and with the same starting point.`);if(Math.abs(r-i)>n)throw a();let o=2*n+1,s=n+1,c=s*s,l=new Uint8Array((r+1)*o),u=(e,t,n)=>e<=t&&e<=n?0:t<=n?1:2,d=new Uint32Array(o*3).fill(c);d[n*3]=0;for(let e=1;e<=Math.min(i,n);e++)d[(e+n)*3+2]=e*s+1,l[e+n]=(e===1?0:2)<<4;for(let a=1;a<=r;a++){let r=new Uint32Array(o*3).fill(c);for(let f=Math.max(0,a-n);f<=Math.min(i,a+n);f++){let i=f-a+n,p=i*3;if(f===0){r[p+1]=a*s+1,l[a*o+i]=(a===1?0:1)<<2;continue}let m=u(d[p],d[p+1],d[p+2]);r[p]=Math.min(c,d[p+m]+(e[a-1]===t[f-1]?0:s));let h=0,g=0;if(i+1<o){let e=p+3,t=d[e]+s+1,n=d[e+1]+s,i=d[e+2]+s+1;h=u(t,n,i),r[p+1]=Math.min(c,t,n,i)}if(i>0){let e=p-3,t=r[e]+s+1,n=r[e+1]+s+1,i=r[e+2]+s;g=u(t,n,i),r[p+2]=Math.min(c,t,n,i)}l[a*o+i]=m|h<<2|g<<4}d=r}let f=(i-r+n)*3,p=u(d[f],d[f+1],d[f+2]),m=Math.floor(d[f+p]/s);if(m>n)throw a();let h=r,g=i,_=[];for(;h||g;){let r=l[h*o+g-h+n]>>p*2&3;p===0?_.push([e[--h],t[--g]]):p===1?_.push([e[--h],`-`]):_.push([`-`,t[--g]]),p=r}_.reverse();let v=[],y=0;for(let[e,t]of _){if(e!==t){let n=e===`-`?`Insertion`:t===`-`?`Deletion`:/[^ACGT]/.test(e+t)?`Ambiguous`:`Substitution`,r=v.at(-1);r&&r.type===n&&n!==`Substitution`&&n!==`Ambiguous`&&r.end===y?(r.reference+=e===`-`?``:e,r.alternative+=t===`-`?``:t,r.end+=e===`-`?0:1):v.push({type:n,start:y,end:y+(e===`-`?0:1),reference:e===`-`?``:e,alternative:t===`-`?``:t})}e!==`-`&&y++}return{distance:m,differences:v}}function i(e,t){return e.locations?.length?e.locations:e.start>e.end?[{start:e.start,end:t-1},{start:0,end:e.end}]:[{start:e.start,end:e.end}]}const a={A:`T`,T:`A`,C:`G`,G:`C`,R:`Y`,Y:`R`,S:`S`,W:`W`,K:`M`,M:`K`,B:`V`,V:`B`,D:`H`,H:`D`,N:`N`},o=e=>[...e].reverse().map(e=>a[e]||`N`).join(``),s=e=>{let n=``;for(let r=0;r+2<e.length;r+=3)n+=t(e.slice(r,r+3));return n},c=(e,t,n)=>{let r=e.notes?.[t];return(Array.isArray(r)?r[0]:r)??n};function l(e,t,n){if(![`CDS`,`mat_peptide`].includes(t.type))return null;let a=i(t,e.length),l=[];for(let t of a){if(!Number.isInteger(t.start)||!Number.isInteger(t.end)||t.start<0||t.end>=e.length||t.end<t.start)return{warning:`Unsupported coding location`,codons:[],changes:[]};for(let e=t.start;e<=t.end;e++)l.push(e)}t.strand<0&&l.reverse();let u=Number(c(t,`codon_start`,1))-1;if(![0,1,2].includes(u))return{warning:`Unsupported codon_start`,codons:[],changes:[]};l.splice(0,u);let d=Number(c(t,`transl_table`,1));if(![1,11].includes(d)||[`transl_except`,`ribosomal_slippage`,`exception`].some(e=>t.notes?.[e]))return{warning:`AA comparison unavailable for this translation table or exception`,codons:[],changes:[]};let f=new Map(l.map((e,t)=>[e,t])),p=e=>t.strand<0?o(e):e,m=l.map(t=>p(e[t])).join(``),h=s(m),g=[...h].map((e,t)=>({positions:l.slice(t*3,t*3+3),aminoAcid:e,codonIndex:t})),_=new Set,v=new Map,y=new Map,b=1/0,x=!1;for(let e of n)if(e.type===`Insertion`){let n=t.strand<0?e.start-1:e.start,r=f.get(n),i=t.strand<0?e.start:e.start-1;r>0&&l[r-1]===i?(y.set(r,p(e.alternative)),e.alternative.length%3&&(b=Math.min(b,r))):(f.has(n)||f.has(i))&&(x=!0)}else if(e.type===`Deletion`){let t=[];for(let n=e.start;n<e.end;n++){let e=f.get(n);e!==void 0&&(_.add(e),t.push(e))}t.length%3&&(b=Math.min(b,...t))}else for(let t=e.start;t<e.end;t++){let n=f.get(t);n!==void 0&&v.set(n,p(e.alternative[t-e.start]))}let S=``,C=[];for(let e=0;e<l.length;e++)C[e]=S.length,S+=y.get(e)||``,_.has(e)||(S+=v.get(e)??m[e]);let w=Math.floor(b/3),T=Number.isFinite(b)?h.slice(0,w):h,E=s(Number.isFinite(b)?S.slice(0,C[w*3]):S),D=[],O=e=>{let n=Math.min(e.start,Math.max(0,g.length-1)),r=g[n],i=e.start<g.length?(r?.positions[0]??l[0])+(t.strand<0?.5:-.5):(r?.positions[2]??l[0])+(t.strand<0?-.5:.5);return{...e,anchor:r?.positions[1]??l[0],...e.type===`Insertion`?{pointerPosition:i}:{},aaPosition:e.type===`Insertion`?e.start:e.start+1}};try{T&&E?D=r(T,E).differences.map(e=>O({...e,type:e.type===`Ambiguous`?/X/.test(e.reference+e.alternative)?`Ambiguous`:`Substitution`:e.type})):(T||E)&&(D=[O({type:T?`Deletion`:`Insertion`,start:0,end:T.length,reference:T,alternative:E})])}catch{return{codons:g,changes:[],warning:`AA comparison exceeds the alignment limit`}}return Number.isFinite(b)&&D.push(O({type:`Frameshift`,start:w,end:w+1,reference:``,alternative:``})),{codons:g,changes:D,warning:x?`Insertion at a coding boundary: AA assignment is uncertain`:void 0}}function u(e,t,n){return t.map(t=>l(e,t,n))}self.onmessage=({data:t})=>{try{let i=t.alignedSequence||n(t.fasta),a=t.alignedSequence?e(t.reference,i):r(t.reference,i.sequence);self.postMessage({...a,name:i.name,proteins:u(t.reference,t.features||[],a.differences)})}catch(e){self.postMessage({error:e.message})}};", Li = typeof self < "u" && self.Blob && new Blob(["URL.revokeObjectURL(import.meta.url);", Ii], { type: "text/javascript;charset=utf-8" });
+}), Ii = "function e(e,t){if(!t||typeof t.sequence!=`string`)throw Error(`Expected an aligned DNA sequence.`);let n=t.sequence.toUpperCase();if(!e.length||n.length!==e.length)throw Error(`Aligned sequence length must match the reference.`);if(/[^ACGTRYSWKMBDHVN-]/.test(n))throw Error(`Aligned sequences must contain IUPAC DNA bases or deletion gaps (-).`);let r=[],i=0;for(let t=0;t<n.length;){if(n[t]===e[t]){t++;continue}let a=n[t]===`-`?`Deletion`:/[^ACGT]/.test(n[t]+e[t])?`Ambiguous`:`Substitution`,o=t+1;if(a===`Deletion`||a===`Ambiguous`)for(;o<n.length&&n[o]!==e[o]&&(a===`Deletion`?n[o]===`-`:n[o]!==`-`&&/[^ACGT]/.test(n[o]+e[o]));)o++;r.push({type:a,start:t,end:o,reference:e.slice(t,o),alternative:a===`Deletion`?``:n.slice(t,o)}),i+=o-t,t=o}let a=new Set;for(let n of t.insertions||[]){let t=n.position,o=typeof n.sequence==`string`?n.sequence.toUpperCase():``;if(!Number.isInteger(t)||t<0||t>e.length||a.has(t))throw Error(`Insertions need unique integer positions from 0 to the reference length.`);if(!o||/[^ACGTRYSWKMBDHVN]/.test(o))throw Error(`Insertions must contain ungapped IUPAC DNA bases.`);a.add(t),r.push({type:`Insertion`,start:t,end:t,reference:``,alternative:o}),i+=o.length}return r.sort((e,t)=>e.start-t.start||e.end-t.end),{name:t.name||`Alternative`,distance:i,differences:r}}const t=e=>{switch(e){case`TTT`:case`TTC`:return`F`;case`TTA`:case`TTG`:case`CTT`:case`CTC`:case`CTA`:case`CTG`:return`L`;case`ATT`:case`ATC`:case`ATA`:return`I`;case`ATG`:return`M`;case`GTT`:case`GTC`:case`GTA`:case`GTG`:return`V`;case`TCT`:case`TCC`:case`TCA`:case`TCG`:case`AGT`:case`AGC`:return`S`;case`CCT`:case`CCC`:case`CCA`:case`CCG`:return`P`;case`ACT`:case`ACC`:case`ACA`:case`ACG`:return`T`;case`GCT`:case`GCC`:case`GCA`:case`GCG`:return`A`;case`TAT`:case`TAC`:return`Y`;case`TAA`:case`TAG`:case`TGA`:return`*`;case`CAT`:case`CAC`:return`H`;case`CAA`:case`CAG`:return`Q`;case`AAT`:case`AAC`:return`N`;case`AAA`:case`AAG`:return`K`;case`GAT`:case`GAC`:return`D`;case`GAA`:case`GAG`:return`E`;case`TGT`:case`TGC`:return`C`;case`TGG`:return`W`;case`CGT`:case`CGC`:case`CGA`:case`CGG`:case`AGA`:case`AGG`:return`R`;case`GGT`:case`GGC`:case`GGA`:case`GGG`:return`G`;default:return`X`}};function n(e){let t=e.trim().split(/\\r?\\n/);if(!t[0]?.startsWith(`>`))throw Error(`Expected a FASTA header starting with >.`);if(t.slice(1).some(e=>e.startsWith(`>`)))throw Error(`Please supply exactly one FASTA record.`);let n=t.slice(1).join(``).replace(/\\s/g,``).toUpperCase();if(!n||/[^ACGTRYSWKMBDHVN]/.test(n))throw Error(`Expected an ungapped DNA sequence (IUPAC bases).`);return{name:t[0].slice(1).trim()||`Alternative`,sequence:n}}function r(e,t,n=128){let r=e.length,i=t.length;if(!r||!i)throw Error(`Both sequences must contain bases.`);if(Math.max(r,i)>1e5)throw Error(`Comparison supports sequences up to 100,000 bases.`);let a=()=>Error(`Sequences exceed the ${n}-edit comparison limit. Use complete sequences in the same orientation and with the same starting point.`);if(Math.abs(r-i)>n)throw a();let o=2*n+1,s=n+1,c=s*s,l=new Uint8Array((r+1)*o),u=(e,t,n)=>e<=t&&e<=n?0:t<=n?1:2,d=new Uint32Array(o*3).fill(c);d[n*3]=0;for(let e=1;e<=Math.min(i,n);e++)d[(e+n)*3+2]=e*s+1,l[e+n]=(e===1?0:2)<<4;for(let a=1;a<=r;a++){let r=new Uint32Array(o*3).fill(c);for(let f=Math.max(0,a-n);f<=Math.min(i,a+n);f++){let i=f-a+n,p=i*3;if(f===0){r[p+1]=a*s+1,l[a*o+i]=(a===1?0:1)<<2;continue}let m=u(d[p],d[p+1],d[p+2]);r[p]=Math.min(c,d[p+m]+(e[a-1]===t[f-1]?0:s));let h=0,g=0;if(i+1<o){let e=p+3,t=d[e]+s+1,n=d[e+1]+s,i=d[e+2]+s+1;h=u(t,n,i),r[p+1]=Math.min(c,t,n,i)}if(i>0){let e=p-3,t=r[e]+s+1,n=r[e+1]+s+1,i=r[e+2]+s;g=u(t,n,i),r[p+2]=Math.min(c,t,n,i)}l[a*o+i]=m|h<<2|g<<4}d=r}let f=(i-r+n)*3,p=u(d[f],d[f+1],d[f+2]),m=Math.floor(d[f+p]/s);if(m>n)throw a();let h=r,g=i,_=[];for(;h||g;){let r=l[h*o+g-h+n]>>p*2&3;p===0?_.push([e[--h],t[--g]]):p===1?_.push([e[--h],`-`]):_.push([`-`,t[--g]]),p=r}_.reverse();let v=[],y=0;for(let[e,t]of _){if(e!==t){let n=e===`-`?`Insertion`:t===`-`?`Deletion`:/[^ACGT]/.test(e+t)?`Ambiguous`:`Substitution`,r=v.at(-1);r&&r.type===n&&n!==`Substitution`&&n!==`Ambiguous`&&r.end===y?(r.reference+=e===`-`?``:e,r.alternative+=t===`-`?``:t,r.end+=e===`-`?0:1):v.push({type:n,start:y,end:y+(e===`-`?0:1),reference:e===`-`?``:e,alternative:t===`-`?``:t})}e!==`-`&&y++}return{distance:m,differences:v}}function i(e,t){return e.locations?.length?e.locations:e.start>e.end?[{start:e.start,end:t-1},{start:0,end:e.end}]:[{start:e.start,end:e.end}]}const a={A:`T`,T:`A`,C:`G`,G:`C`,R:`Y`,Y:`R`,S:`S`,W:`W`,K:`M`,M:`K`,B:`V`,V:`B`,D:`H`,H:`D`,N:`N`},o=e=>[...e].reverse().map(e=>a[e]||`N`).join(``),s=e=>{let n=``;for(let r=0;r+2<e.length;r+=3)n+=t(e.slice(r,r+3));return n},c=(e,t,n)=>{let r=e.notes?.[t];return(Array.isArray(r)?r[0]:r)??n};function l(e,t,n){if(![`CDS`,`mat_peptide`].includes(t.type))return null;let a=i(t,e.length),l=[];for(let t of a){if(!Number.isInteger(t.start)||!Number.isInteger(t.end)||t.start<0||t.end>=e.length||t.end<t.start)return{warning:`Unsupported coding location`,codons:[],changes:[]};for(let e=t.start;e<=t.end;e++)l.push(e)}t.strand<0&&l.reverse();let u=Number(c(t,`codon_start`,1))-1;if(![0,1,2].includes(u))return{warning:`Unsupported codon_start`,codons:[],changes:[]};l.splice(0,u);let d=Number(c(t,`transl_table`,1));if(![1,11].includes(d)||[`transl_except`,`ribosomal_slippage`,`exception`].some(e=>t.notes?.[e]))return{warning:`AA comparison unavailable for this translation table or exception`,codons:[],changes:[]};let f=new Map(l.map((e,t)=>[e,t])),p=e=>t.strand<0?o(e):e,m=l.map(t=>p(e[t])).join(``),h=s(m),g=[...h].map((e,t)=>({positions:l.slice(t*3,t*3+3),aminoAcid:e,codonIndex:t})),_=new Set,v=new Map,y=new Map,b=1/0,x=!1;for(let e of n)if(e.type===`Insertion`){let n=t.strand<0?e.start-1:e.start,r=f.get(n),i=t.strand<0?e.start:e.start-1;r>0&&l[r-1]===i?(y.set(r,p(e.alternative)),e.alternative.length%3&&(b=Math.min(b,r))):(f.has(n)||f.has(i))&&(x=!0)}else if(e.type===`Deletion`){let t=[];for(let n=e.start;n<e.end;n++){let e=f.get(n);e!==void 0&&(_.add(e),t.push(e))}t.length%3&&(b=Math.min(b,...t))}else for(let t=e.start;t<e.end;t++){let n=f.get(t);n!==void 0&&v.set(n,p(e.alternative[t-e.start]))}let S=``,C=[];for(let e=0;e<l.length;e++)C[e]=S.length,S+=y.get(e)||``,_.has(e)||(S+=v.get(e)??m[e]);let w=Math.floor(b/3),T=Number.isFinite(b)?h.slice(0,w):h,E=s(Number.isFinite(b)?S.slice(0,C[w*3]):S),D=[],O=e=>{let n=Math.min(e.start,Math.max(0,g.length-1)),r=g[n],i=e.start<g.length?(r?.positions[0]??l[0])+(t.strand<0?.5:-.5):(r?.positions[2]??l[0])+(t.strand<0?-.5:.5);return{...e,anchor:r?.positions[1]??l[0],...e.type===`Insertion`?{pointerPosition:i}:{},aaPosition:e.type===`Insertion`?e.start:e.start+1}};try{if(T&&E){let e=[];for(let t of r(T,E).differences){let n={...t,type:t.type===`Ambiguous`?/X/.test(t.reference+t.alternative)?`Ambiguous`:`Substitution`:t.type},r=e.at(-1);n.type===`Ambiguous`&&r?.type===`Ambiguous`&&r.end===n.start?(r.end=n.end,r.reference+=n.reference,r.alternative+=n.alternative):e.push(n)}D=e.map(O)}else(T||E)&&(D=[O({type:T?`Deletion`:`Insertion`,start:0,end:T.length,reference:T,alternative:E})])}catch{return{codons:g,changes:[],warning:`AA comparison exceeds the alignment limit`}}return Number.isFinite(b)&&D.push(O({type:`Frameshift`,start:w,end:w+1,reference:``,alternative:``})),{codons:g,changes:D,warning:x?`Insertion at a coding boundary: AA assignment is uncertain`:void 0}}function u(e,t,n){return t.map(t=>l(e,t,n))}self.onmessage=({data:t})=>{try{let i=t.alignedSequence||n(t.fasta),a=t.alignedSequence?e(t.reference,i):r(t.reference,i.sequence);self.postMessage({...a,name:i.name,proteins:u(t.reference,t.features||[],a.differences)})}catch(e){self.postMessage({error:e.message})}};", Li = typeof self < "u" && self.Blob && new Blob(["URL.revokeObjectURL(import.meta.url);", Ii], { type: "text/javascript;charset=utf-8" });
 function Ri(e) {
 	let t;
 	try {
@@ -4275,18 +4275,18 @@ var Ao = ({ parsedSequence: e, rowStart: t, rowEnd: n, setHoveredInfo: r, rowId:
 			let i = ba(r, e.locations, w.length);
 			return i >= t && i < n;
 		}).sort((e, t) => e.anchor - t.anchor).map((n) => {
-			let r = n.end > n.start + 1 ? `${n.start + 1}–${n.end}` : n.start + 1, i = n.type === "Insertion" ? `AA INS +${n.alternative} · after ${n.aaPosition}` : n.type === "Deletion" ? `AA DEL ${n.reference} · ${r}` : n.type === "Frameshift" ? `Frame shift · AA ${n.aaPosition}` : `AA ${n.reference}${n.aaPosition} → ${n.alternative}`, a = Math.max(8, Math.floor((P - 20) / 7)), o = i.length > a ? `${i.slice(0, a - 1)}…` : i, s = Math.min(P, o.length * 7 + 16), c = ((n.pointerPosition ?? n.anchor) - t) * C, l = Math.max(-C / 2, Math.min(c - s / 2, P - s)), u = R[e.lane], d = u.findIndex((e) => e + 8 <= l);
-			d === -1 && (d = u.length), u[d] = l + s;
-			let f = n.type === "Insertion" ? "#1d4ed8" : n.type === "Deletion" ? "#b91c1c" : ["Frameshift", "Ambiguous"].includes(n.type) ? "#6d28d9" : "#92400e";
+			let r = n.end > n.start + 1 ? `${n.start + 1}–${n.end}` : n.start + 1, i = n.type === "Insertion" ? `AA INS +${n.alternative} · after ${n.aaPosition}` : n.type === "Deletion" ? `AA DEL ${n.reference} · ${r}` : n.type === "Frameshift" ? `Frame shift · AA ${n.aaPosition}` : n.type === "Ambiguous" ? `Coverage gap · AA ${r}` : `AA ${n.reference}${n.aaPosition} → ${n.alternative}`, a = Math.max(8, Math.floor((P - 20) / 7)), o = n.type === "Ambiguous" ? "Coverage gap" : i, s = o.length > a ? `${o.slice(0, a - 1)}…` : o, c = Math.min(P, s.length * 7 + 16), l = ((n.pointerPosition ?? n.anchor) - t) * C, u = Math.max(-C / 2, Math.min(l - c / 2, P - c)), d = R[e.lane], f = d.findIndex((e) => e + 8 <= u);
+			f === -1 && (f = d.length), d[f] = u + c;
+			let p = n.type === "Insertion" ? "#1d4ed8" : n.type === "Deletion" ? "#b91c1c" : ["Frameshift", "Ambiguous"].includes(n.type) ? "#6d28d9" : "#92400e";
 			return {
 				...n,
 				text: i,
-				label: o,
-				labelWidth: s,
-				anchor: c,
-				left: l,
-				lane: d,
-				color: f
+				label: s,
+				labelWidth: c,
+				anchor: l,
+				left: u,
+				lane: f,
+				color: p
 			};
 		});
 	});
@@ -4402,7 +4402,7 @@ var Ao = ({ parsedSequence: e, rowStart: t, rowEnd: n, setHoveredInfo: r, rowId:
 						width: t.labelWidth,
 						height: 20,
 						rx: 4,
-						fill: "white",
+						fill: t.type === "Ambiguous" ? "#f5f3ff" : "white",
 						stroke: t.color
 					}),
 					/* @__PURE__ */ x("text", {
@@ -4482,7 +4482,7 @@ var Ao = ({ parsedSequence: e, rowStart: t, rowEnd: n, setHoveredInfo: r, rowId:
 					locusTag: e.notes?.locus_tag || null
 				}),
 				onMouseLeave: () => r(null),
-				fillOpacity: .75,
+				fillOpacity: e.proteinChanges.some((e) => e.type === "Ambiguous" && t.codonIndex >= e.start && t.codonIndex < e.end) ? .35 : .75,
 				style: { cursor: "pointer" },
 				children: t.aminoAcid
 			}), t.middle > 2 && s > -.5 && /* @__PURE__ */ x("text", {
@@ -23728,8 +23728,15 @@ function wC(e) {
 }
 Z(wC, "jsonToJsonString");
 //#endregion
+//#region src/comparison/parseReference.mjs
+async function TC(e) {
+	let t = await Dv(e, { isOligo: !0 });
+	for (let e of t) e.parsedSequence?.sequence && (e.parsedSequence.sequence = e.parsedSequence.sequence.toUpperCase());
+	return t;
+}
+//#endregion
 //#region node_modules/react-use/esm/misc/util.js
-var TC = function() {}, EC = typeof window < "u", DC = EC ? m : d, OC = {
+var EC = function() {}, DC = typeof window < "u", OC = DC ? m : d, kC = {
 	x: 0,
 	y: 0,
 	width: 0,
@@ -23739,8 +23746,8 @@ var TC = function() {}, EC = typeof window < "u", DC = EC ? m : d, OC = {
 	bottom: 0,
 	right: 0
 };
-function kC() {
-	var e = v(null), t = e[0], n = e[1], r = v(OC), i = r[0], a = r[1], o = h(function() {
+function AC() {
+	var e = v(null), t = e[0], n = e[1], r = v(kC), i = r[0], a = r[1], o = h(function() {
 		return new window.ResizeObserver(function(e) {
 			if (e[0]) {
 				var t = e[0].contentRect, n = t.x, r = t.y, i = t.width, o = t.height, s = t.top, c = t.left, l = t.bottom, u = t.right;
@@ -23757,18 +23764,18 @@ function kC() {
 			}
 		});
 	}, []);
-	return DC(function() {
+	return OC(function() {
 		if (t) return o.observe(t), function() {
 			o.disconnect();
 		};
 	}, [t]), [n, i];
 }
-var AC = EC && window.ResizeObserver !== void 0 ? kC : (function() {
-	return [TC, OC];
+var jC = DC && window.ResizeObserver !== void 0 ? AC : (function() {
+	return [EC, kC];
 });
 //#endregion
 //#region node_modules/react-icons/bs/index.mjs
-function jC(e) {
+function MC(e) {
 	return ie({
 		tag: "svg",
 		attr: {
@@ -23782,7 +23789,7 @@ function jC(e) {
 		}]
 	})(e);
 }
-function MC(e) {
+function NC(e) {
 	return ie({
 		tag: "svg",
 		attr: {
@@ -23798,7 +23805,7 @@ function MC(e) {
 }
 //#endregion
 //#region src/SearchPanel.jsx
-function NC({ value: e, onChange: t, ...n }) {
+function PC({ value: e, onChange: t, ...n }) {
 	let [r, i] = v(e ?? ""), a = _();
 	return d(() => {
 		clearTimeout(a.current), i(e ?? "");
@@ -23811,7 +23818,7 @@ function NC({ value: e, onChange: t, ...n }) {
 		}
 	});
 }
-function PC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSearchInput: r, searchType: i, setSearchType: a, curSeqHitIndex: o, sequenceHits: s, setCurSeqHitIndex: c, includeRC: l, setIncludeRC: u }) {
+function FC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSearchInput: r, searchType: i, setSearchType: a, curSeqHitIndex: o, sequenceHits: s, setCurSeqHitIndex: c, includeRC: l, setIncludeRC: u }) {
 	return /* @__PURE__ */ S("div", {
 		className: "bg-white p-1 text-sm shadow rounded ",
 		children: [/* @__PURE__ */ x("div", {
@@ -23839,7 +23846,7 @@ function PC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSear
 						children: e.label
 					}, e.value))
 				}),
-				/* @__PURE__ */ x(NC, {
+				/* @__PURE__ */ x(PC, {
 					type: "text",
 					value: n,
 					onChange: (e) => {
@@ -23880,7 +23887,7 @@ function PC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSear
 					]
 				}),
 				s.length > 0 && /* @__PURE__ */ S(b, { children: [
-					/* @__PURE__ */ x("button", { children: /* @__PURE__ */ x(MC, {
+					/* @__PURE__ */ x("button", { children: /* @__PURE__ */ x(NC, {
 						onClick: () => c((e) => e == 0 ? s.length - 1 : e - 1),
 						className: "mx-3 text-gray-600 hover:text-gray-800"
 					}) }),
@@ -23888,7 +23895,7 @@ function PC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSear
 					o + 1,
 					" of ",
 					s.length,
-					/* @__PURE__ */ x("button", { children: /* @__PURE__ */ x(jC, {
+					/* @__PURE__ */ x("button", { children: /* @__PURE__ */ x(MC, {
 						onClick: () => c((e) => e == s.length - 1 ? 0 : e + 1),
 						className: "mx-3 text-gray-600  hover:text-gray-800"
 					}) })
@@ -23900,13 +23907,13 @@ function PC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSear
 }
 //#endregion
 //#region src/components/GensploreView.jsx
-function FC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallback: r, fastaUrl: i, alignedSequence: a }) {
+function IC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallback: r, fastaUrl: i, alignedSequence: a }) {
 	let [o, s] = v(""), c = t === void 0 ? o : t, u = l((e) => {
 		s(e), n?.(e);
 	}, [n]), [f, p] = v(null), [g, y] = v(!1), [C, w] = v({
 		busy: !1,
 		error: ""
-	}), [T, E] = v(!1), [D, O] = v(0), [k, A] = v(null), [j, M] = v(null), [N, P] = v(null), [F, I] = v("nuc"), [L, { width: R }] = AC(), [z, ee] = v(null), [B, te] = v({
+	}), [T, E] = v(!1), [D, O] = v(0), [k, A] = v(null), [j, M] = v(null), [N, P] = v(null), [F, I] = v("nuc"), [L, { width: R }] = jC(), [z, ee] = v(null), [B, te] = v({
 		x: null,
 		y: null
 	}), [V, ne] = v(null), [re, ie] = v([]), [ae, oe] = v(0), [se, ce] = v(!1), fe = F === "nuc" ? parseInt(c) : null, pe = F === "annot" ? c : null, me = F === "sequence" && c ? c.toUpperCase() : null, [he, ge] = v(0);
@@ -23926,9 +23933,9 @@ function FC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 		let t = !1;
 		return ne(null), p(null), ie([]), oe(0), (async () => {
 			try {
-				let n = await Dv(e);
+				let n = await TC(e);
 				if (t) return;
-				n[0].parsedSequence.sequence = n[0].parsedSequence.sequence.toUpperCase(), ne(n[0]);
+				ne(n[0]);
 			} catch (e) {
 				console.error("Error loading GenBank file:", e);
 			}
@@ -24144,7 +24151,7 @@ function FC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 					/* @__PURE__ */ x(wo, {}),
 					/* @__PURE__ */ x("div", {
 						className: "fixed top-0 right-0 z-10",
-						children: /* @__PURE__ */ x(PC, {
+						children: /* @__PURE__ */ x(FC, {
 							searchInput: c,
 							setSearchInput: u,
 							searchPanelOpen: T,
@@ -24374,6 +24381,6 @@ function FC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 }
 //#endregion
 //#region src/index.js
-var IC = FC;
+var LC = IC;
 //#endregion
-export { IC as default };
+export { LC as default };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gensplore",
-  "version": "0.0.10",
+  "version": "0.0.12",
   "description": "React component for displaying genbank files",
   "keywords": [
     "genbank",