gensplore 0.0.13 → 0.0.15

package/dist/gensplore.js

@@ -187,7 +187,7 @@ var ue = ({ isOpen: e, onClose: t, children: n }) => /* @__PURE__ */ x("div", {
 			})
 		})]
 	})
-}), de = ({ x: e, y: t, onClose: n, onCopy: r, onCopyRC: i }) => e === null || t === null ? null : /* @__PURE__ */ S("div", {
+}), de = ({ x: e, y: t, onClose: n, onCopy: r, onCopyRC: i, isComparison: a = !1 }) => e === null || t === null ? null : /* @__PURE__ */ S("div", {
 	className: "fixed bg-white shadow-lg border border-gray-200 rounded-md py-1 z-50",
 	style: {
 		left: e,
@@ -196,11 +196,11 @@ var ue = ({ isOpen: e, onClose: t, children: n }) => /* @__PURE__ */ x("div", {
 	children: [/* @__PURE__ */ x("button", {
 		className: "block w-full text-left px-4 py-2 text-sm text-gray-700 hover:bg-gray-100",
 		onClick: r,
-		children: "Copy Selection"
+		children: a ? "Copy sample selection" : "Copy Selection"
 	}), /* @__PURE__ */ x("button", {
 		className: "block w-full text-left px-4 py-2 text-sm text-gray-700 hover:bg-gray-100",
 		onClick: i,
-		children: "Copy as Reverse Complement"
+		children: a ? "Copy sample as reverse complement" : "Copy as Reverse Complement"
 	})]
 });
 //#endregion
@@ -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{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" });
+}), 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=0,i=n.length;for(;r<i&&n[r]===`N`;)r++;for(;i>r&&n[i-1]===`N`;)i--;let a=r===i?{start:0,end:0}:{start:r,end:i},o=[],s=0;for(let t=a.start;t<a.end;){if(n[t]===e[t]){t++;continue}let r=n[t]===`-`?`Deletion`:/[^ACGT]/.test(n[t]+e[t])?`Ambiguous`:`Substitution`,i=t+1;if(r===`Deletion`||r===`Ambiguous`)for(;i<a.end&&n[i]!==e[i]&&(r===`Deletion`?n[i]===`-`:n[i]!==`-`&&/[^ACGT]/.test(n[i]+e[i]));)i++;o.push({type:r,start:t,end:i,reference:e.slice(t,i),alternative:r===`Deletion`?``:n.slice(t,i)}),s+=i-t,t=i}let c=new Set;for(let n of t.insertions||[]){let t=n.position,r=typeof n.sequence==`string`?n.sequence.toUpperCase():``;if(!Number.isInteger(t)||t<0||t>e.length||c.has(t))throw Error(`Insertions need unique integer positions from 0 to the reference length.`);if(!r||/[^ACGTRYSWKMBDHVN]/.test(r))throw Error(`Insertions must contain ungapped IUPAC DNA bases.`);c.add(t),o.push({type:`Insertion`,start:t,end:t,reference:``,alternative:r}),s+=r.length}return o.sort((e,t)=>e.start-t.start||e.end-t.end),{name:t.name||`Alternative`,distance:s,differences:o,coverage:a}}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=`N`,r=256,{leading:a=1/0,trailing:o=1/0}={}){if(!e.length||!t.length)throw Error(`Both sequences must contain bases.`);if(Math.max(e.length,t.length)>1e5)throw Error(`Comparison supports sequences up to 100,000 bases.`);let s=0,c=0;for(;s<t.length&&s<a&&t[s]===n;)s++;if(s===t.length)return{distance:0,differences:[],coverage:{start:0,end:0}};for(;c<t.length-s&&c<o&&t[t.length-c-1]===n;)c++;let l=e.length-c;if(s>=l)throw Error(`Terminal padding leaves no comparable reference span.`);let u=i(e.slice(s,l),t.slice(s,t.length-c),r);return{...u,coverage:{start:s,end:l},differences:u.differences.map(e=>({...e,start:e.start+s,end:e.end+s}))}}function i(e,t,n=256){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 a(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 o={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`},s=e=>[...e].reverse().map(e=>o[e]||`N`).join(``),c=e=>{let n=``;for(let r=0;r+2<e.length;r+=3)n+=t(e.slice(r,r+3));return n},l=(e,t,n)=>{let r=e.notes?.[t];return(Array.isArray(r)?r[0]:r)??n};function u(e,t,n,o){if(![`CDS`,`mat_peptide`].includes(t.type))return null;let u=a(t,e.length),d=[];for(let t of u){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++)d.push(e)}t.strand<0&&d.reverse();let f=Number(l(t,`codon_start`,1))-1;if(![0,1,2].includes(f))return{warning:`Unsupported codon_start`,codons:[],changes:[]};d.splice(0,f);let p=Number(l(t,`transl_table`,1));if(![1,11].includes(p)||[`transl_except`,`ribosomal_slippage`,`exception`].some(e=>t.notes?.[e]))return{warning:`AA comparison unavailable for this translation table or exception`,codons:[],changes:[]};let m=new Map(d.map((e,t)=>[e,t])),h=e=>t.strand<0?s(e):e,g=d.map(t=>h(e[t])).join(``),_=c(g),v=[..._].map((e,t)=>({positions:d.slice(t*3,t*3+3),aminoAcid:e,codonIndex:t})),y=new Set,b=new Map,x=new Map;o&&d.forEach((e,t)=>{(e<o.start||e>=o.end)&&b.set(t,`N`)});let S=1/0,C=!1;for(let e of n)if(e.type===`Insertion`){let n=t.strand<0?e.start-1:e.start,r=m.get(n),i=t.strand<0?e.start:e.start-1;r>0&&d[r-1]===i?(x.set(r,h(e.alternative)),e.alternative.length%3&&(S=Math.min(S,r))):(m.has(n)||m.has(i))&&(C=!0)}else if(e.type===`Deletion`){let t=[];for(let n=e.start;n<e.end;n++){let e=m.get(n);e!==void 0&&(y.add(e),t.push(e))}t.length%3&&(S=Math.min(S,...t))}else for(let t=e.start;t<e.end;t++){let n=m.get(t);n!==void 0&&b.set(n,h(e.alternative[t-e.start]))}let w=``,T=[];for(let e=0;e<d.length;e++)T[e]=w.length,w+=x.get(e)||``,y.has(e)||(w+=b.get(e)??g[e]);let E=Math.floor(S/3),D=Number.isFinite(S)?_.slice(0,E):_,O=c(Number.isFinite(S)?w.slice(0,T[E*3]):w),k=[],A=e=>{let n=Math.min(e.start,Math.max(0,v.length-1)),r=v[n],i=e.start<v.length?(r?.positions[0]??d[0])+(t.strand<0?.5:-.5):(r?.positions[2]??d[0])+(t.strand<0?-.5:.5);return{...e,anchor:r?.positions[1]??d[0],...e.type===`Insertion`?{pointerPosition:i}:{},aaPosition:e.type===`Insertion`?e.start:e.start+1}};try{if(D&&O){let e=e=>v[e].positions.some(e=>e<o.start||e>=o.end),t=0,n=0;if(o){for(;t<D.length&&e(t);)t++;for(;n<D.length-t&&e(D.length-n-1);)n++}let a=o?r(D,O,`X`,256,{leading:t,trailing:n}):i(D,O),s=[];for(let e of a.differences){let t={...e,type:e.type===`Ambiguous`?/X/.test(e.reference+e.alternative)?`Ambiguous`:`Substitution`:e.type},n=s.at(-1);t.type===`Ambiguous`&&n?.type===`Ambiguous`&&n.end===t.start?(n.end=t.end,n.reference+=t.reference,n.alternative+=t.alternative):s.push(t)}k=s.map(A)}else(D||O)&&(k=[A({type:D?`Deletion`:`Insertion`,start:0,end:D.length,reference:D,alternative:O})])}catch{return{codons:v,changes:[],warning:`AA comparison exceeds the alignment limit`}}return Number.isFinite(S)&&k.push(A({type:`Frameshift`,start:E,end:E+1,reference:``,alternative:``})),{codons:v,changes:k,warning:C?`Insertion at a coding boundary: AA assignment is uncertain`:void 0}}function d(e,t,n,r){return t.map(t=>u(e,t,n,r))}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:d(t.reference,t.features||[],a.differences,a.coverage)})}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 {
@@ -3088,6 +3088,7 @@ function zi({ reference: e, features: t, fastaUrl: n, alignedSequence: r, onResu
 								children: D.name
 							})]
 						}),
+						D.coverage && (D.coverage.start > 0 || D.coverage.end < e.length) && /* @__PURE__ */ x("p", { children: D.coverage.end > D.coverage.start ? `Terminal Ns excluded; comparing reference positions ${D.coverage.start + 1}–${D.coverage.end}.` : "No covered bases to compare (the alternative contains only Ns)." }),
 						D.proteins?.some((e) => e?.warning) && /* @__PURE__ */ x("ul", {
 							"aria-label": "Amino-acid comparison notes",
 							children: D.proteins.map((e, n) => e?.warning && /* @__PURE__ */ S("li", { children: [
@@ -23762,8 +23763,28 @@ async function kC(e) {
 	return t;
 }
 //#endregion
+//#region src/comparison/selection.mjs
+function AC(e, t, n, r) {
+	if (t = Math.max(0, Math.min(e.length, t)), n = Math.max(0, Math.min(e.length, n)), t >= n) return "";
+	let i = [...e.slice(t, n)];
+	if (!r) return i.join("");
+	let { coverage: a, differences: o } = r;
+	if (a) for (let e = t; e < n; e++) (e < a.start || e >= a.end) && (i[e - t] = "N");
+	let s = /* @__PURE__ */ new Map();
+	for (let e of o) {
+		if (e.type === "Insertion") {
+			(e.start > t && e.start <= n || t === 0 && e.start === 0) && s.set(e.start, e.alternative);
+			continue;
+		}
+		for (let r = Math.max(t, e.start); r < Math.min(n, e.end); r++) i[r - t] = e.type === "Deletion" ? "" : e.alternative[r - e.start];
+	}
+	let c = s.get(t) || "";
+	for (let e = t; e < n; e++) c += i[e - t] + (s.get(e + 1) || "");
+	return c;
+}
+//#endregion
 //#region node_modules/react-use/esm/misc/util.js
-var AC = function() {}, jC = typeof window < "u", MC = jC ? m : d, NC = {
+var jC = function() {}, MC = typeof window < "u", NC = MC ? m : d, PC = {
 	x: 0,
 	y: 0,
 	width: 0,
@@ -23773,8 +23794,8 @@ var AC = function() {}, jC = typeof window < "u", MC = jC ? m : d, NC = {
 	bottom: 0,
 	right: 0
 };
-function PC() {
-	var e = v(null), t = e[0], n = e[1], r = v(NC), i = r[0], a = r[1], o = h(function() {
+function FC() {
+	var e = v(null), t = e[0], n = e[1], r = v(PC), 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;
@@ -23791,18 +23812,18 @@ function PC() {
 			}
 		});
 	}, []);
-	return MC(function() {
+	return NC(function() {
 		if (t) return o.observe(t), function() {
 			o.disconnect();
 		};
 	}, [t]), [n, i];
 }
-var FC = jC && window.ResizeObserver !== void 0 ? PC : (function() {
-	return [AC, NC];
+var IC = MC && window.ResizeObserver !== void 0 ? FC : (function() {
+	return [jC, PC];
 });
 //#endregion
 //#region node_modules/react-icons/bs/index.mjs
-function IC(e) {
+function LC(e) {
 	return ie({
 		tag: "svg",
 		attr: {
@@ -23816,7 +23837,7 @@ function IC(e) {
 		}]
 	})(e);
 }
-function LC(e) {
+function RC(e) {
 	return ie({
 		tag: "svg",
 		attr: {
@@ -23832,7 +23853,7 @@ function LC(e) {
 }
 //#endregion
 //#region src/SearchPanel.jsx
-function RC({ value: e, onChange: t, ...n }) {
+function zC({ value: e, onChange: t, ...n }) {
 	let [r, i] = v(e ?? ""), a = _();
 	return d(() => {
 		clearTimeout(a.current), i(e ?? "");
@@ -23845,7 +23866,7 @@ function RC({ value: e, onChange: t, ...n }) {
 		}
 	});
 }
-function zC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSearchInput: r, searchType: i, setSearchType: a, curSeqHitIndex: o, sequenceHits: s, setCurSeqHitIndex: c, includeRC: l, setIncludeRC: u }) {
+function BC({ 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", {
@@ -23873,7 +23894,7 @@ function zC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSear
 						children: e.label
 					}, e.value))
 				}),
-				/* @__PURE__ */ x(RC, {
+				/* @__PURE__ */ x(zC, {
 					type: "text",
 					value: n,
 					onChange: (e) => {
@@ -23914,7 +23935,7 @@ function zC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSear
 					]
 				}),
 				s.length > 0 && /* @__PURE__ */ S(b, { children: [
-					/* @__PURE__ */ x("button", { children: /* @__PURE__ */ x(LC, {
+					/* @__PURE__ */ x("button", { children: /* @__PURE__ */ x(RC, {
 						onClick: () => c((e) => e == 0 ? s.length - 1 : e - 1),
 						className: "mx-3 text-gray-600 hover:text-gray-800"
 					}) }),
@@ -23922,7 +23943,7 @@ function zC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSear
 					o + 1,
 					" of ",
 					s.length,
-					/* @__PURE__ */ x("button", { children: /* @__PURE__ */ x(IC, {
+					/* @__PURE__ */ x("button", { children: /* @__PURE__ */ x(LC, {
 						onClick: () => c((e) => e == s.length - 1 ? 0 : e + 1),
 						className: "mx-3 text-gray-600  hover:text-gray-800"
 					}) })
@@ -23934,13 +23955,13 @@ function zC({ searchPanelOpen: e, setSearchPanelOpen: t, searchInput: n, setSear
 }
 //#endregion
 //#region src/components/GensploreView.jsx
-function BC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallback: r, fastaUrl: i, alignedSequence: a }) {
+function VC({ 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 }] = FC(), [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 }] = IC(), [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);
@@ -23995,7 +24016,9 @@ function BC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 	}, [
 		V,
 		k,
-		j
+		j,
+		f,
+		C
 	]);
 	let H = Math.floor(R * .0965 / 2 ** D);
 	H < 30 && (H = 30);
@@ -24120,8 +24143,12 @@ function BC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 		});
 	}, He = (e = !1) => {
 		if (k === null || j === null) return;
-		let t = Math.min(k, j), n = Math.max(k, j), r = V.parsedSequence.sequence.substring(t, n);
-		e && (r = Hi(r)), navigator.clipboard.writeText(r), J.success(`Copied ${e ? "reverse complement " : ""}to clipboard`);
+		if (C.busy || C.error) {
+			J.info("Load a comparison successfully or clear it before copying.");
+			return;
+		}
+		let t = Math.min(k, j), n = Math.max(k, j), r = AC(V.parsedSequence.sequence, t, n, f);
+		e && (r = Hi(r)), navigator.clipboard.writeText(r), J.success(`Copied ${f ? "sample " : ""}${e ? "reverse complement " : ""}to clipboard`);
 	};
 	return d(() => (document.addEventListener("click", Ve), () => {
 		document.removeEventListener("click", Ve);
@@ -24178,7 +24205,7 @@ function BC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 					/* @__PURE__ */ x(Oo, {}),
 					/* @__PURE__ */ x("div", {
 						className: "fixed top-0 right-0 z-10",
-						children: /* @__PURE__ */ x(zC, {
+						children: /* @__PURE__ */ x(BC, {
 							searchInput: c,
 							setSearchInput: u,
 							searchPanelOpen: T,
@@ -24241,7 +24268,7 @@ function BC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 													/* @__PURE__ */ x("button", {
 														onClick: () => He(),
 														className: "ml-2 p-1 hover:bg-gray-200 rounded-full",
-														title: "Copy selection",
+														title: f ? "Copy sample selection" : "Copy selection",
 														children: /* @__PURE__ */ x(le, { className: "h-4 w-4 text-gray-500" })
 													})
 												]
@@ -24342,7 +24369,8 @@ function BC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 				},
 				onCopyRC: () => {
 					He(!0), Ve();
-				}
+				},
+				isComparison: !!f
 			}),
 			Fe && /* @__PURE__ */ x(ue, {
 				isOpen: Fe,
@@ -24408,6 +24436,6 @@ function BC({ genbankString: e, searchInput: t, setSearchInput: n, setTitleCallb
 }
 //#endregion
 //#region src/index.js
-var VC = BC;
+var HC = VC;
 //#endregion
-export { VC as default };
+export { HC as default };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gensplore",
-  "version": "0.0.13",
+  "version": "0.0.15",
   "description": "React component for displaying genbank files",
   "keywords": [
     "genbank",