gensplore 0.0.10 → 0.0.11

package/dist/gensplore.cjs

@@ -49,4 +49,4 @@ ${e.sequence}
 `,f+=(u.match(/.{1,80}/g)||[]).join(`
 `),f}X(QS,`jsonToFasta`);function $S(e,t={}){let{name:n,features:r,size:i,description:a,circular:o}=t.featuresOnly?e:z_(e),s=``;s+=`${n||`Untitled Sequence`}|`,s+=`|`+i,s+=a?`|`+a:``,s+=`|`+(o?`circular`:`linear`);let c=t.sequenceName||s,l=``;return l+=`track name="${c}" description="${n} Annotations" itemRgb="On"
 `,r.forEach(function(e){let{start:t,end:n,name:r,type:i,forward:a,strand:o}=e,s=r||i,u;u=a||o===1?`+`:!a||o===-1?`-`:`.`;let d=i===`CDS`?`230,88,0`:``;l+=`${c}	${t}	${n+1}	${s}		${u}			${d}
-`}),l}X($S,`jsonToBed`);function eC(e){let t=wm(e);return t&&(delete t.cutsites,delete t.orfs,Bh(t.translations,e=>{delete e.aminoAcids}),t)}X(eC,`cleanUpTeselagenJsonForExport`);function tC(e,t=[]){return e.replace(/u/gi,(e,n)=>(t.push({type:`misc_feature`,name:`tg_uracil`,strand:1,start:n,end:n}),e===`U`?`T`:`t`))}X(tC,`parseUracilFeatures`);function nC(e){return JSON.stringify(ig(eC(z_(e,{annotationsAsObjects:!1})),[`sequenceFragments`,`sequenceFeatures`,`cutsites`,`orfs`,`filteredParts`,`filteredFeatures`]))}X(nC,`jsonToJsonString`);var rC=function(){},iC=typeof window<`u`,aC=iC?l.useLayoutEffect:l.useEffect,oC={x:0,y:0,width:0,height:0,top:0,left:0,bottom:0,right:0};function sC(){var e=(0,l.useState)(null),t=e[0],n=e[1],r=(0,l.useState)(oC),i=r[0],a=r[1],o=(0,l.useMemo)(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;a({x:n,y:r,width:i,height:o,top:s,left:c,bottom:l,right:u})}})},[]);return aC(function(){if(t)return o.observe(t),function(){o.disconnect()}},[t]),[n,i]}var cC=iC&&window.ResizeObserver!==void 0?sC:(function(){return[rC,oC]});function lC(e){return T({tag:`svg`,attr:{fill:`currentColor`,viewBox:`0 0 16 16`},child:[{tag:`path`,attr:{d:`M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0M4.5 7.5a.5.5 0 0 0 0 1h5.793l-2.147 2.146a.5.5 0 0 0 .708.708l3-3a.5.5 0 0 0 0-.708l-3-3a.5.5 0 1 0-.708.708L10.293 7.5z`},child:[]}]})(e)}function uC(e){return T({tag:`svg`,attr:{fill:`currentColor`,viewBox:`0 0 16 16`},child:[{tag:`path`,attr:{d:`M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0m3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5z`},child:[]}]})(e)}function dC({value:e,onChange:t,...n}){let[r,i]=(0,u.useState)(e??``),a=(0,u.useRef)();return(0,u.useEffect)(()=>{clearTimeout(a.current),i(e??``)},[e]),(0,u.useEffect)(()=>()=>clearTimeout(a.current),[]),(0,d.jsx)(`input`,{...n,value:r,onChange:e=>{let n=e.target.value;i(n),clearTimeout(a.current),a.current=setTimeout(()=>t({target:{value:n}}),300)}})}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(0,d.jsxs)(`div`,{className:`bg-white p-1 text-sm shadow rounded `,children:[(0,d.jsx)(`div`,{className:`flex items-center`,children:e?(0,d.jsxs)(d.Fragment,{children:[(0,d.jsx)(`select`,{value:i,onChange:e=>a(e.target.value),className:`bg-gray-100 hover:bg-gray-200 text-gray-800 font-semibold py-2 px-2 rounded inline-flex items-center`,children:[{value:`nuc`,label:`nuc. index`},{value:`annot`,label:`annotation`},{value:`sequence`,label:`sequence`}].map(e=>(0,d.jsx)(`option`,{value:e.value,children:e.label},e.value))}),(0,d.jsx)(dC,{type:`text`,value:n,onChange:e=>{c(0),r(e.target.value),/^[0-9]+$/.test(e.target.value)?a(`nuc`):/^[ACGTacgt]+$/.test(e.target.value)?a(`sequence`):/^[^0-9]+$/.test(e.target.value)&&a(`annot`)},className:`mx-2 bg-white focus:outline-hidden focus:shadow-outline border border-gray-300 rounded-lg py-2 px-4 block w-full appearance-none leading-normal`,placeholder:i===`nuc`?`nuc. index`:i===`annot`?`gene name`:`ATGGC..`,id:`search-input`,autoComplete:`off`}),(0,d.jsx)(`button`,{className:`bg-gray-200 hover:bg-gray-300 text-gray-800 font-semibold py-2 px-4 rounded inline-flex items-center`,onClick:()=>{t(!1),r(null)},children:(0,d.jsx)(D,{className:`mr-2`})})]}):(0,d.jsx)(`button`,{className:`bg-gray-100 hover:bg-gray-200 text-gray-800 font-semibold py-2 px-4 rounded inline-flex items-center`,onClick:()=>t(!0),children:(0,d.jsx)(O,{className:`mr-2`})})}),i===`sequence`&&n&&n.length>0&&(0,d.jsxs)(`div`,{className:`my-2 text-gray-400 text-left px-3`,children:[(0,d.jsxs)(`label`,{className:`text-gray-900`,children:[` `,(0,d.jsx)(`input`,{type:`checkbox`,value:l,onChange:()=>{u(!l),c(0)}}),`\xA0Include reverse complement`]}),s.length>0&&(0,d.jsxs)(d.Fragment,{children:[(0,d.jsx)(`button`,{children:(0,d.jsx)(uC,{onClick:()=>c(e=>e==0?s.length-1:e-1),className:`mx-3 text-gray-600 hover:text-gray-800`})}),`Hit `,o+1,` of `,s.length,(0,d.jsx)(`button`,{children:(0,d.jsx)(lC,{onClick:()=>c(e=>e==s.length-1?0:e+1),className:`mx-3 text-gray-600  hover:text-gray-800`})})]}),s.length===0&&(0,d.jsx)(d.Fragment,{children:`No hits found`})]})]})}function pC({genbankString:e,searchInput:t,setSearchInput:n,setTitleCallback:r,fastaUrl:i,alignedSequence:a}){let[o,s]=(0,u.useState)(``),c=t===void 0?o:t,l=(0,u.useCallback)(e=>{s(e),n?.(e)},[n]),[f,p]=(0,u.useState)(null),[m,h]=(0,u.useState)(!1),[g,_]=(0,u.useState)({busy:!1,error:``}),[v,y]=(0,u.useState)(!1),[b,x]=(0,u.useState)(0),[S,C]=(0,u.useState)(null),[w,T]=(0,u.useState)(null),[E,D]=(0,u.useState)(null),[O,k]=(0,u.useState)(`nuc`),[N,{width:P}]=cC(),[F,I]=(0,u.useState)(null),[L,R]=(0,u.useState)({x:null,y:null}),[z,ee]=(0,u.useState)(null),[te,ne]=(0,u.useState)([]),[re,ie]=(0,u.useState)(0),[ae,oe]=(0,u.useState)(!1),se=O===`nuc`?parseInt(c):null,B=O===`annot`?c:null,ce=O===`sequence`&&c?c.toUpperCase():null,[le,ue]=(0,u.useState)(0);function de(){var e=document;return Math.max(Math.max(e.body.scrollHeight,e.documentElement.scrollHeight),Math.max(e.body.offsetHeight,e.documentElement.offsetHeight),Math.max(e.body.clientHeight,e.documentElement.clientHeight))}(0,u.useEffect)(()=>{let e=()=>{let e=window.pageYOffset,t=window.innerHeight,n=e/(de()-t);Math.abs(n-le)>.05&&ue(n)};return window.addEventListener(`scroll`,e),()=>{window.removeEventListener(`scroll`,e)}},[le]),(0,u.useEffect)(()=>{let t=!1;return ee(null),p(null),ne([]),ie(0),(async()=>{try{let n=await av(e);if(t)return;n[0].parsedSequence.sequence=n[0].parsedSequence.sequence.toUpperCase(),ee(n[0])}catch(e){console.error(`Error loading GenBank file:`,e)}})(),()=>{t=!0}},[e]),(0,u.useEffect)(()=>{let e=z?.parsedSequence.name;e&&r&&r(f?`${f.name} vs ${e} | Gensplore`:`${e} | Gensplore`)},[z,f,r]),(0,u.useEffect)(()=>{let e=e=>{(e.ctrlKey||e.metaKey)&&e.keyCode===70&&(e.preventDefault(),y(!0),setTimeout(()=>{document.getElementById(`search-input`).focus(),document.getElementById(`search-input`).select()},100))};return window.addEventListener(`keydown`,e),()=>{window.removeEventListener(`keydown`,e)}},[]),(0,u.useEffect)(()=>{let e=e=>{(e.ctrlKey||e.metaKey)&&e.keyCode===67&&S!==null&&w!==null&&(Ie(e.shiftKey),e.preventDefault())};return window.addEventListener(`keydown`,e),()=>{window.removeEventListener(`keydown`,e)}},[z,S,w]);let V=Math.floor(P*.0965/2**b);V<30&&(V=30);let fe,pe;z&&(fe=z.parsedSequence.sequence,pe=fe.length);let H=(0,u.useMemo)(()=>{if(!fe)return[];let e=[];for(let t=0;t<pe;t+=V)e.push({rowStart:t,rowEnd:t+V>pe?pe:t+V});return e},[fe,V,pe]),me=(0,u.useRef)(null),[he,ge]=(0,u.useState)(0);(0,u.useLayoutEffect)(()=>{let e=me.current;if(!e)return;let t=()=>ge(e.getBoundingClientRect().top+window.scrollY);t();let n=new ResizeObserver(t);return n.observe(e.parentElement),()=>n.disconnect()},[z,P]);let _e=_t({count:H.length,estimateSize:()=>90,scrollMargin:he}),ve=_e.getVirtualItems(),[ye,be]=(0,u.useState)(null),xe=e=>{let t=ve[Math.floor(ve.length/2)].index,n=H[t].rowStart,r=H[t].rowEnd,i=Math.floor((n+r)/2);be(i),console.log(`middleRowMiddle`,i),x(e)};(0,u.useEffect)(()=>{if(!ye)return;if(S&&w){let e=Math.floor((S+w)/2);_e.scrollToIndex(3+Math.floor(e/V),{align:`center`,smoothScroll:!1}),be(null);return}let e=Math.floor(ye/V);_e.scrollToIndex(e,{align:`center`,smoothScroll:!1}),be(null),console.log(`scrolling to`,ye)},[ye,b]);let[Se,Ce]=(0,u.useState)(null),[we,Te]=(0,u.useState)(!1),[Ee,De]=(0,u.useState)(!1),[Oe,ke]=(0,u.useState)(null);(0,u.useEffect)(()=>{if(!se)return;let e=Math.floor(se/V);se!==Se&&(e>H.length||(_e.scrollToIndex(e+1,{align:`center`}),Ce(se)))},[se,V]),(0,u.useEffect)(()=>{if(!Oe)return;let e=Math.floor(Oe.start/V);_e.scrollToIndex(e+1,{align:`center`}),ke(null)},[Oe,V]),(0,u.useEffect)(()=>{if(!B)return;let e=B.replace(/\s/g,``);if(e===``)return;let t=Si(z.parsedSequence.features,e);if(t.length===0){q.error(`No matching features found`);return}let n=t[0],r=Math.floor(n.start/V);_e.scrollToIndex(r+1,{align:`center`}),Ce(B)},[B]),(0,u.useEffect)(()=>{if(!fe||!ce){ne([]);return}let e=ce.replace(/\s/g,``);if(e===``){ne([]);return}console.log(`strippedSequenceInput`,e);let t=[],n=0,r=xi(e);for(console.log(`rc`,r);;){let i=fe.indexOf(e,n),a=ae?fe.indexOf(r,n):-1,o;if(o=i===-1?a:a===-1?i:Math.min(i,a),o===-1)break;t.push([o,o+e.length]),n=o+1}if(ne(t),console.log(`length`,t.length),t.length==0)return;let i=Math.min(re,t.length-1);i!==re&&ie(i);let a=Math.floor(t[i][0]/V);console.log(`row`,a),_e.scrollToIndex(a+1,{align:`center`}),Ce(ce)},[ce,re,ae,fe]);let[Ae,je]=(0,u.useState)(!1),[Me,U]=(0,u.useState)({}),Ne=(0,u.useMemo)(()=>{if(!z)return[];let e=[];return z.parsedSequence.features.forEach((t,n)=>{Me[n]&&e.push(t)}),e},[Me,z]);(0,u.useEffect)(()=>{if(!z)return;let e={};z.parsedSequence.features.forEach((t,n)=>{e[n]=t.type!==`source`&&t.type!==`gene`&&t.type!==`mRNA`}),U(e)},[z]);let Pe=e=>{e.preventDefault(),R({x:e.clientX,y:e.clientY})},Fe=()=>{R({x:null,y:null})},Ie=(e=!1)=>{if(S===null||w===null)return;let t=Math.min(S,w),n=Math.max(S,w),r=z.parsedSequence.sequence.substring(t,n);e&&(r=xi(r)),navigator.clipboard.writeText(r),q.success(`Copied ${e?`reverse complement `:``}to clipboard`)};return(0,u.useEffect)(()=>(document.addEventListener(`click`,Fe),()=>{document.removeEventListener(`click`,Fe)}),[]),z?P?(0,d.jsx)(d.Fragment,{children:(0,d.jsxs)(`div`,{className:`gensplore`,onContextMenu:Pe,children:[(0,d.jsx)(mi,{open:Ee,onClose:()=>De(!1),className:`gensplore fixed z-50 max-w-2xl px-4 py-6 bg-white rounded-lg shadow-xl sm:px-6 sm:py-8 sm:pb-4 sm:pt-6`,children:(0,d.jsx)(fi,{className:`fixed inset-0 flex items-center justify-center bg-gray-500/75 transition-opacity`,style:{zIndex:1e3},children:(0,d.jsxs)(`div`,{className:`bg-white rounded-lg px-4 py-4 sm:px-6 sm:py-6 shadow-md max-w-md mx-auto`,children:[(0,d.jsx)(pi,{as:`h3`,className:`text-lg font-medium leading-6 text-gray-900 mb-4`,children:`Settings`}),(0,d.jsx)(Ge,{className:`text-base text-gray-600 mb-4`,children:`Customize appearance`}),(0,d.jsx)(`p`,{className:`text-sm text-gray-500`,children:(0,d.jsxs)(`label`,{children:[(0,d.jsx)(`input`,{type:`checkbox`,checked:we,onChange:e=>Te(e.target.checked)}),(0,d.jsx)(`span`,{className:`ml-2`,children:`Display antisense strand`})]})}),(0,d.jsx)(`div`,{className:`mt-4 flex justify-end`,children:(0,d.jsx)(`button`,{type:`button`,className:`inline-flex justify-center px-4 py-2 text-sm font-medium text-gray-700 bg-gray-100 border border-transparent rounded-md hover:bg-gray-200 focus:outline-hidden focus-visible:ring-2 focus-visible:ring-offset-2 focus-visible:ring-blue-500`,onClick:()=>De(!1),children:`Close`})})]})})}),(0,d.jsxs)(`div`,{className:`w-full p-5 pl-0`,children:[(0,d.jsx)(no,{}),(0,d.jsx)(`div`,{className:`fixed top-0 right-0 z-10`,children:(0,d.jsx)(fC,{searchInput:c,setSearchInput:l,searchPanelOpen:v,setSearchPanelOpen:y,searchType:O,setSearchType:k,curSeqHitIndex:re,setCurSeqHitIndex:ie,sequenceHits:te,includeRC:ae,setIncludeRC:oe})}),(0,d.jsx)(`div`,{className:`fixed bottom-0 right-0 z-10 p-2 rounded shadow bg-white comparison-toolbar`,children:(0,d.jsx)(bs,{zoomLevel:b,setZoomLevel:xe,configModalOpen:Ee,setConfigModalOpen:De,setFeatureOffcanvasOpen:je,comparisonPanelOpen:m,setComparisonPanelOpen:h,comparisonCount:f?.differences.length,comparisonStatus:g})}),(0,d.jsxs)(`div`,{className:`w-full`,children:[(0,d.jsx)(yi,{hoveredInfo:F}),z&&(0,d.jsxs)(`div`,{ref:N,children:[S!==null&&(w!==null||E!==null)&&(0,d.jsx)(`div`,{className:`fixed bottom-1 left-1 z-10 px-3 py-2 text-sm rounded-lg shadow-lg bg-linear-to-r from-gray-50 to-gray-100 border border-gray-200`,children:(0,d.jsxs)(`div`,{className:`flex flex-col `,children:[(0,d.jsxs)(`div`,{className:`flex items-center space-x-2`,children:[(0,d.jsx)(`span`,{className:`font-medium text-gray-700`,children:`Selection:`}),(0,d.jsxs)(`span`,{className:`font-mono text-gray-700`,children:[Math.min(S,w||E)+1,` - `,Math.max(S,w||E)]})]}),(0,d.jsxs)(`div`,{className:`flex items-center space-x-2`,children:[(0,d.jsx)(`span`,{className:`font-medium text-gray-700`,children:`Length:`}),(0,d.jsxs)(`span`,{className:`font-mono text-gray-700 flex items-center`,children:[Math.abs((w||E)-S),` bp`,(0,d.jsx)(`button`,{onClick:()=>Ie(),className:`ml-2 p-1 hover:bg-gray-200 rounded-full`,title:`Copy selection`,children:(0,d.jsx)(A,{className:`h-4 w-4 text-gray-500`})})]})]})]})}),(0,d.jsxs)(`div`,{className:`flex flex-col ml-4 mt-3 text-gray-900`,children:[(0,d.jsx)(`h2`,{className:`text-2xl`,style:{overflowWrap:`anywhere`},children:f?.name||z.parsedSequence.name}),(0,d.jsx)(`div`,{children:(0,d.jsx)(`div`,{className:`flex flex-row`,children:(0,d.jsxs)(`span`,{children:[f&&(0,d.jsxs)(d.Fragment,{children:[`Reference: `,(0,d.jsx)(`strong`,{children:z.parsedSequence.name}),` · `]}),z.parsedSequence.definition]})})})]}),(0,d.jsx)(vi,{open:m,setOpen:h,onStatus:_,reference:fe,features:z.parsedSequence.features,fastaUrl:i,alignedSequence:a,onResult:p,onGoTo:e=>_e.scrollToIndex(Math.floor(e/V),{align:`center`})}),(0,d.jsx)(`div`,{ref:me,className:`mt-5 h-80`,children:(0,d.jsx)(`div`,{style:{height:_e.getTotalSize(),width:`100%`,position:`relative`},className:`stripybg`,children:(0,d.jsx)(`div`,{style:{position:`absolute`,top:0,left:0,width:`100%`,transform:`translateY(${(ve[0]?.start??0)-_e.options.scrollMargin}px)`},className:`whitebg`,children:ve.map(e=>{let t=H[e.index];return(0,d.jsx)(`div`,{ref:_e.measureElement,"data-index":e.index,children:(0,d.jsx)(co,{parsedSequence:z.parsedSequence,visibleFeatures:Ne,differences:f?.differences||[],proteins:f?.proteins,rowStart:t.rowStart,rowEnd:t.rowEnd,rowWidth:V,setHoveredInfo:I,rowId:e.index,intSearchInput:se-1,annotSearchInput:B,renderProperly:!0,zoomLevel:b,whereMouseWentDown:S,setWhereMouseWentDown:C,whereMouseWentUp:w,setWhereMouseWentUp:T,whereMouseCurrentlyIs:E,setWhereMouseCurrentlyIs:D,sequenceHits:te,curSeqHitIndex:re,enableRC:we},e.index)},e.key)})})})})]})]})]}),L.x!==null&&(0,d.jsx)(M,{x:L.x,y:L.y,onClose:Fe,onCopy:()=>{Ie(!1),Fe()},onCopyRC:()=>{Ie(!0),Fe()}}),Ae&&(0,d.jsx)(j,{isOpen:Ae,onClose:()=>je(!1),children:(0,d.jsxs)(`table`,{className:`min-w-full divide-y divide-gray-200`,children:[(0,d.jsx)(`thead`,{children:(0,d.jsxs)(`tr`,{children:[(0,d.jsx)(`th`,{className:`px-6 py-3 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider`,children:`Feature`}),(0,d.jsx)(`th`,{className:`px-6 py-3 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider`,children:`Product`}),(0,d.jsx)(`th`,{className:`px-6 py-3 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider`,children:`Type`}),(0,d.jsx)(`th`,{className:`px-6 py-3 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider`})]})}),(0,d.jsx)(`tbody`,{className:`bg-white divide-y divide-gray-200`,children:z?.parsedSequence.features.map((e,t)=>(0,d.jsxs)(`tr`,{children:[(0,d.jsxs)(`td`,{className:`px-6 py-4 whitespace-nowrap text-sm text-gray-600 font-medium`,children:[(0,d.jsx)(`input`,{type:`checkbox`,className:`focus:ring-indigo-500 text-indigo-600 border-gray-300 rounded mr-2`,checked:!!Me[t],onChange:()=>{let e={...Me};e[t]=!e[t],U(e)}}),e.name]}),(0,d.jsx)(`td`,{className:`px-6 py-4 whitespace-nowrap text-sm text-gray-500`,children:e.notes?.product?.join(`, `)}),(0,d.jsx)(`td`,{className:`px-6 py-4 whitespace-nowrap text-sm text-gray-500`,children:e.type}),(0,d.jsx)(`td`,{children:(0,d.jsx)(`button`,{className:`bg-gray-100 hover:bg-gray-200 text-gray-600 font-semibold py-1 px-1 border border-gray-400 rounded shadow text-sm `,onClick:()=>{je(!1),ke(e)},children:`Go to`})})]},t))})]})})]})}):(0,d.jsx)(`div`,{className:`gensplore w-full h-full p-5`,children:(0,d.jsx)(`div`,{ref:N,className:`w-full h-full`})}):(0,d.jsx)(`div`,{children:`Loading...`})}var mC=pC;module.exports=mC;
+`}),l}X($S,`jsonToBed`);function eC(e){let t=wm(e);return t&&(delete t.cutsites,delete t.orfs,Bh(t.translations,e=>{delete e.aminoAcids}),t)}X(eC,`cleanUpTeselagenJsonForExport`);function tC(e,t=[]){return e.replace(/u/gi,(e,n)=>(t.push({type:`misc_feature`,name:`tg_uracil`,strand:1,start:n,end:n}),e===`U`?`T`:`t`))}X(tC,`parseUracilFeatures`);function nC(e){return JSON.stringify(ig(eC(z_(e,{annotationsAsObjects:!1})),[`sequenceFragments`,`sequenceFeatures`,`cutsites`,`orfs`,`filteredParts`,`filteredFeatures`]))}X(nC,`jsonToJsonString`);async function rC(e){let t=await av(e);for(let e of t)e.parsedSequence?.sequence&&(e.parsedSequence.sequence=e.parsedSequence.sequence.toUpperCase().replace(/U/g,`T`));return t}var iC=function(){},aC=typeof window<`u`,oC=aC?l.useLayoutEffect:l.useEffect,sC={x:0,y:0,width:0,height:0,top:0,left:0,bottom:0,right:0};function cC(){var e=(0,l.useState)(null),t=e[0],n=e[1],r=(0,l.useState)(sC),i=r[0],a=r[1],o=(0,l.useMemo)(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;a({x:n,y:r,width:i,height:o,top:s,left:c,bottom:l,right:u})}})},[]);return oC(function(){if(t)return o.observe(t),function(){o.disconnect()}},[t]),[n,i]}var lC=aC&&window.ResizeObserver!==void 0?cC:(function(){return[iC,sC]});function uC(e){return T({tag:`svg`,attr:{fill:`currentColor`,viewBox:`0 0 16 16`},child:[{tag:`path`,attr:{d:`M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0M4.5 7.5a.5.5 0 0 0 0 1h5.793l-2.147 2.146a.5.5 0 0 0 .708.708l3-3a.5.5 0 0 0 0-.708l-3-3a.5.5 0 1 0-.708.708L10.293 7.5z`},child:[]}]})(e)}function dC(e){return T({tag:`svg`,attr:{fill:`currentColor`,viewBox:`0 0 16 16`},child:[{tag:`path`,attr:{d:`M8 0a8 8 0 1 0 0 16A8 8 0 0 0 8 0m3.5 7.5a.5.5 0 0 1 0 1H5.707l2.147 2.146a.5.5 0 0 1-.708.708l-3-3a.5.5 0 0 1 0-.708l3-3a.5.5 0 1 1 .708.708L5.707 7.5z`},child:[]}]})(e)}function fC({value:e,onChange:t,...n}){let[r,i]=(0,u.useState)(e??``),a=(0,u.useRef)();return(0,u.useEffect)(()=>{clearTimeout(a.current),i(e??``)},[e]),(0,u.useEffect)(()=>()=>clearTimeout(a.current),[]),(0,d.jsx)(`input`,{...n,value:r,onChange:e=>{let n=e.target.value;i(n),clearTimeout(a.current),a.current=setTimeout(()=>t({target:{value:n}}),300)}})}function pC({searchPanelOpen:e,setSearchPanelOpen:t,searchInput:n,setSearchInput:r,searchType:i,setSearchType:a,curSeqHitIndex:o,sequenceHits:s,setCurSeqHitIndex:c,includeRC:l,setIncludeRC:u}){return(0,d.jsxs)(`div`,{className:`bg-white p-1 text-sm shadow rounded `,children:[(0,d.jsx)(`div`,{className:`flex items-center`,children:e?(0,d.jsxs)(d.Fragment,{children:[(0,d.jsx)(`select`,{value:i,onChange:e=>a(e.target.value),className:`bg-gray-100 hover:bg-gray-200 text-gray-800 font-semibold py-2 px-2 rounded inline-flex items-center`,children:[{value:`nuc`,label:`nuc. index`},{value:`annot`,label:`annotation`},{value:`sequence`,label:`sequence`}].map(e=>(0,d.jsx)(`option`,{value:e.value,children:e.label},e.value))}),(0,d.jsx)(fC,{type:`text`,value:n,onChange:e=>{c(0),r(e.target.value),/^[0-9]+$/.test(e.target.value)?a(`nuc`):/^[ACGTacgt]+$/.test(e.target.value)?a(`sequence`):/^[^0-9]+$/.test(e.target.value)&&a(`annot`)},className:`mx-2 bg-white focus:outline-hidden focus:shadow-outline border border-gray-300 rounded-lg py-2 px-4 block w-full appearance-none leading-normal`,placeholder:i===`nuc`?`nuc. index`:i===`annot`?`gene name`:`ATGGC..`,id:`search-input`,autoComplete:`off`}),(0,d.jsx)(`button`,{className:`bg-gray-200 hover:bg-gray-300 text-gray-800 font-semibold py-2 px-4 rounded inline-flex items-center`,onClick:()=>{t(!1),r(null)},children:(0,d.jsx)(D,{className:`mr-2`})})]}):(0,d.jsx)(`button`,{className:`bg-gray-100 hover:bg-gray-200 text-gray-800 font-semibold py-2 px-4 rounded inline-flex items-center`,onClick:()=>t(!0),children:(0,d.jsx)(O,{className:`mr-2`})})}),i===`sequence`&&n&&n.length>0&&(0,d.jsxs)(`div`,{className:`my-2 text-gray-400 text-left px-3`,children:[(0,d.jsxs)(`label`,{className:`text-gray-900`,children:[` `,(0,d.jsx)(`input`,{type:`checkbox`,value:l,onChange:()=>{u(!l),c(0)}}),`\xA0Include reverse complement`]}),s.length>0&&(0,d.jsxs)(d.Fragment,{children:[(0,d.jsx)(`button`,{children:(0,d.jsx)(dC,{onClick:()=>c(e=>e==0?s.length-1:e-1),className:`mx-3 text-gray-600 hover:text-gray-800`})}),`Hit `,o+1,` of `,s.length,(0,d.jsx)(`button`,{children:(0,d.jsx)(uC,{onClick:()=>c(e=>e==s.length-1?0:e+1),className:`mx-3 text-gray-600  hover:text-gray-800`})})]}),s.length===0&&(0,d.jsx)(d.Fragment,{children:`No hits found`})]})]})}function mC({genbankString:e,searchInput:t,setSearchInput:n,setTitleCallback:r,fastaUrl:i,alignedSequence:a}){let[o,s]=(0,u.useState)(``),c=t===void 0?o:t,l=(0,u.useCallback)(e=>{s(e),n?.(e)},[n]),[f,p]=(0,u.useState)(null),[m,h]=(0,u.useState)(!1),[g,_]=(0,u.useState)({busy:!1,error:``}),[v,y]=(0,u.useState)(!1),[b,x]=(0,u.useState)(0),[S,C]=(0,u.useState)(null),[w,T]=(0,u.useState)(null),[E,D]=(0,u.useState)(null),[O,k]=(0,u.useState)(`nuc`),[N,{width:P}]=lC(),[F,I]=(0,u.useState)(null),[L,R]=(0,u.useState)({x:null,y:null}),[z,ee]=(0,u.useState)(null),[te,ne]=(0,u.useState)([]),[re,ie]=(0,u.useState)(0),[ae,oe]=(0,u.useState)(!1),se=O===`nuc`?parseInt(c):null,B=O===`annot`?c:null,ce=O===`sequence`&&c?c.toUpperCase():null,[le,ue]=(0,u.useState)(0);function de(){var e=document;return Math.max(Math.max(e.body.scrollHeight,e.documentElement.scrollHeight),Math.max(e.body.offsetHeight,e.documentElement.offsetHeight),Math.max(e.body.clientHeight,e.documentElement.clientHeight))}(0,u.useEffect)(()=>{let e=()=>{let e=window.pageYOffset,t=window.innerHeight,n=e/(de()-t);Math.abs(n-le)>.05&&ue(n)};return window.addEventListener(`scroll`,e),()=>{window.removeEventListener(`scroll`,e)}},[le]),(0,u.useEffect)(()=>{let t=!1;return ee(null),p(null),ne([]),ie(0),(async()=>{try{let n=await rC(e);if(t)return;ee(n[0])}catch(e){console.error(`Error loading GenBank file:`,e)}})(),()=>{t=!0}},[e]),(0,u.useEffect)(()=>{let e=z?.parsedSequence.name;e&&r&&r(f?`${f.name} vs ${e} | Gensplore`:`${e} | Gensplore`)},[z,f,r]),(0,u.useEffect)(()=>{let e=e=>{(e.ctrlKey||e.metaKey)&&e.keyCode===70&&(e.preventDefault(),y(!0),setTimeout(()=>{document.getElementById(`search-input`).focus(),document.getElementById(`search-input`).select()},100))};return window.addEventListener(`keydown`,e),()=>{window.removeEventListener(`keydown`,e)}},[]),(0,u.useEffect)(()=>{let e=e=>{(e.ctrlKey||e.metaKey)&&e.keyCode===67&&S!==null&&w!==null&&(Ie(e.shiftKey),e.preventDefault())};return window.addEventListener(`keydown`,e),()=>{window.removeEventListener(`keydown`,e)}},[z,S,w]);let V=Math.floor(P*.0965/2**b);V<30&&(V=30);let fe,pe;z&&(fe=z.parsedSequence.sequence,pe=fe.length);let H=(0,u.useMemo)(()=>{if(!fe)return[];let e=[];for(let t=0;t<pe;t+=V)e.push({rowStart:t,rowEnd:t+V>pe?pe:t+V});return e},[fe,V,pe]),me=(0,u.useRef)(null),[he,ge]=(0,u.useState)(0);(0,u.useLayoutEffect)(()=>{let e=me.current;if(!e)return;let t=()=>ge(e.getBoundingClientRect().top+window.scrollY);t();let n=new ResizeObserver(t);return n.observe(e.parentElement),()=>n.disconnect()},[z,P]);let _e=_t({count:H.length,estimateSize:()=>90,scrollMargin:he}),ve=_e.getVirtualItems(),[ye,be]=(0,u.useState)(null),xe=e=>{let t=ve[Math.floor(ve.length/2)].index,n=H[t].rowStart,r=H[t].rowEnd,i=Math.floor((n+r)/2);be(i),console.log(`middleRowMiddle`,i),x(e)};(0,u.useEffect)(()=>{if(!ye)return;if(S&&w){let e=Math.floor((S+w)/2);_e.scrollToIndex(3+Math.floor(e/V),{align:`center`,smoothScroll:!1}),be(null);return}let e=Math.floor(ye/V);_e.scrollToIndex(e,{align:`center`,smoothScroll:!1}),be(null),console.log(`scrolling to`,ye)},[ye,b]);let[Se,Ce]=(0,u.useState)(null),[we,Te]=(0,u.useState)(!1),[Ee,De]=(0,u.useState)(!1),[Oe,ke]=(0,u.useState)(null);(0,u.useEffect)(()=>{if(!se)return;let e=Math.floor(se/V);se!==Se&&(e>H.length||(_e.scrollToIndex(e+1,{align:`center`}),Ce(se)))},[se,V]),(0,u.useEffect)(()=>{if(!Oe)return;let e=Math.floor(Oe.start/V);_e.scrollToIndex(e+1,{align:`center`}),ke(null)},[Oe,V]),(0,u.useEffect)(()=>{if(!B)return;let e=B.replace(/\s/g,``);if(e===``)return;let t=Si(z.parsedSequence.features,e);if(t.length===0){q.error(`No matching features found`);return}let n=t[0],r=Math.floor(n.start/V);_e.scrollToIndex(r+1,{align:`center`}),Ce(B)},[B]),(0,u.useEffect)(()=>{if(!fe||!ce){ne([]);return}let e=ce.replace(/\s/g,``);if(e===``){ne([]);return}console.log(`strippedSequenceInput`,e);let t=[],n=0,r=xi(e);for(console.log(`rc`,r);;){let i=fe.indexOf(e,n),a=ae?fe.indexOf(r,n):-1,o;if(o=i===-1?a:a===-1?i:Math.min(i,a),o===-1)break;t.push([o,o+e.length]),n=o+1}if(ne(t),console.log(`length`,t.length),t.length==0)return;let i=Math.min(re,t.length-1);i!==re&&ie(i);let a=Math.floor(t[i][0]/V);console.log(`row`,a),_e.scrollToIndex(a+1,{align:`center`}),Ce(ce)},[ce,re,ae,fe]);let[Ae,je]=(0,u.useState)(!1),[Me,U]=(0,u.useState)({}),Ne=(0,u.useMemo)(()=>{if(!z)return[];let e=[];return z.parsedSequence.features.forEach((t,n)=>{Me[n]&&e.push(t)}),e},[Me,z]);(0,u.useEffect)(()=>{if(!z)return;let e={};z.parsedSequence.features.forEach((t,n)=>{e[n]=t.type!==`source`&&t.type!==`gene`&&t.type!==`mRNA`}),U(e)},[z]);let Pe=e=>{e.preventDefault(),R({x:e.clientX,y:e.clientY})},Fe=()=>{R({x:null,y:null})},Ie=(e=!1)=>{if(S===null||w===null)return;let t=Math.min(S,w),n=Math.max(S,w),r=z.parsedSequence.sequence.substring(t,n);e&&(r=xi(r)),navigator.clipboard.writeText(r),q.success(`Copied ${e?`reverse complement `:``}to clipboard`)};return(0,u.useEffect)(()=>(document.addEventListener(`click`,Fe),()=>{document.removeEventListener(`click`,Fe)}),[]),z?P?(0,d.jsx)(d.Fragment,{children:(0,d.jsxs)(`div`,{className:`gensplore`,onContextMenu:Pe,children:[(0,d.jsx)(mi,{open:Ee,onClose:()=>De(!1),className:`gensplore fixed z-50 max-w-2xl px-4 py-6 bg-white rounded-lg shadow-xl sm:px-6 sm:py-8 sm:pb-4 sm:pt-6`,children:(0,d.jsx)(fi,{className:`fixed inset-0 flex items-center justify-center bg-gray-500/75 transition-opacity`,style:{zIndex:1e3},children:(0,d.jsxs)(`div`,{className:`bg-white rounded-lg px-4 py-4 sm:px-6 sm:py-6 shadow-md max-w-md mx-auto`,children:[(0,d.jsx)(pi,{as:`h3`,className:`text-lg font-medium leading-6 text-gray-900 mb-4`,children:`Settings`}),(0,d.jsx)(Ge,{className:`text-base text-gray-600 mb-4`,children:`Customize appearance`}),(0,d.jsx)(`p`,{className:`text-sm text-gray-500`,children:(0,d.jsxs)(`label`,{children:[(0,d.jsx)(`input`,{type:`checkbox`,checked:we,onChange:e=>Te(e.target.checked)}),(0,d.jsx)(`span`,{className:`ml-2`,children:`Display antisense strand`})]})}),(0,d.jsx)(`div`,{className:`mt-4 flex justify-end`,children:(0,d.jsx)(`button`,{type:`button`,className:`inline-flex justify-center px-4 py-2 text-sm font-medium text-gray-700 bg-gray-100 border border-transparent rounded-md hover:bg-gray-200 focus:outline-hidden focus-visible:ring-2 focus-visible:ring-offset-2 focus-visible:ring-blue-500`,onClick:()=>De(!1),children:`Close`})})]})})}),(0,d.jsxs)(`div`,{className:`w-full p-5 pl-0`,children:[(0,d.jsx)(no,{}),(0,d.jsx)(`div`,{className:`fixed top-0 right-0 z-10`,children:(0,d.jsx)(pC,{searchInput:c,setSearchInput:l,searchPanelOpen:v,setSearchPanelOpen:y,searchType:O,setSearchType:k,curSeqHitIndex:re,setCurSeqHitIndex:ie,sequenceHits:te,includeRC:ae,setIncludeRC:oe})}),(0,d.jsx)(`div`,{className:`fixed bottom-0 right-0 z-10 p-2 rounded shadow bg-white comparison-toolbar`,children:(0,d.jsx)(bs,{zoomLevel:b,setZoomLevel:xe,configModalOpen:Ee,setConfigModalOpen:De,setFeatureOffcanvasOpen:je,comparisonPanelOpen:m,setComparisonPanelOpen:h,comparisonCount:f?.differences.length,comparisonStatus:g})}),(0,d.jsxs)(`div`,{className:`w-full`,children:[(0,d.jsx)(yi,{hoveredInfo:F}),z&&(0,d.jsxs)(`div`,{ref:N,children:[S!==null&&(w!==null||E!==null)&&(0,d.jsx)(`div`,{className:`fixed bottom-1 left-1 z-10 px-3 py-2 text-sm rounded-lg shadow-lg bg-linear-to-r from-gray-50 to-gray-100 border border-gray-200`,children:(0,d.jsxs)(`div`,{className:`flex flex-col `,children:[(0,d.jsxs)(`div`,{className:`flex items-center space-x-2`,children:[(0,d.jsx)(`span`,{className:`font-medium text-gray-700`,children:`Selection:`}),(0,d.jsxs)(`span`,{className:`font-mono text-gray-700`,children:[Math.min(S,w||E)+1,` - `,Math.max(S,w||E)]})]}),(0,d.jsxs)(`div`,{className:`flex items-center space-x-2`,children:[(0,d.jsx)(`span`,{className:`font-medium text-gray-700`,children:`Length:`}),(0,d.jsxs)(`span`,{className:`font-mono text-gray-700 flex items-center`,children:[Math.abs((w||E)-S),` bp`,(0,d.jsx)(`button`,{onClick:()=>Ie(),className:`ml-2 p-1 hover:bg-gray-200 rounded-full`,title:`Copy selection`,children:(0,d.jsx)(A,{className:`h-4 w-4 text-gray-500`})})]})]})]})}),(0,d.jsxs)(`div`,{className:`flex flex-col ml-4 mt-3 text-gray-900`,children:[(0,d.jsx)(`h2`,{className:`text-2xl`,style:{overflowWrap:`anywhere`},children:f?.name||z.parsedSequence.name}),(0,d.jsx)(`div`,{children:(0,d.jsx)(`div`,{className:`flex flex-row`,children:(0,d.jsxs)(`span`,{children:[f&&(0,d.jsxs)(d.Fragment,{children:[`Reference: `,(0,d.jsx)(`strong`,{children:z.parsedSequence.name}),` · `]}),z.parsedSequence.definition]})})})]}),(0,d.jsx)(vi,{open:m,setOpen:h,onStatus:_,reference:fe,features:z.parsedSequence.features,fastaUrl:i,alignedSequence:a,onResult:p,onGoTo:e=>_e.scrollToIndex(Math.floor(e/V),{align:`center`})}),(0,d.jsx)(`div`,{ref:me,className:`mt-5 h-80`,children:(0,d.jsx)(`div`,{style:{height:_e.getTotalSize(),width:`100%`,position:`relative`},className:`stripybg`,children:(0,d.jsx)(`div`,{style:{position:`absolute`,top:0,left:0,width:`100%`,transform:`translateY(${(ve[0]?.start??0)-_e.options.scrollMargin}px)`},className:`whitebg`,children:ve.map(e=>{let t=H[e.index];return(0,d.jsx)(`div`,{ref:_e.measureElement,"data-index":e.index,children:(0,d.jsx)(co,{parsedSequence:z.parsedSequence,visibleFeatures:Ne,differences:f?.differences||[],proteins:f?.proteins,rowStart:t.rowStart,rowEnd:t.rowEnd,rowWidth:V,setHoveredInfo:I,rowId:e.index,intSearchInput:se-1,annotSearchInput:B,renderProperly:!0,zoomLevel:b,whereMouseWentDown:S,setWhereMouseWentDown:C,whereMouseWentUp:w,setWhereMouseWentUp:T,whereMouseCurrentlyIs:E,setWhereMouseCurrentlyIs:D,sequenceHits:te,curSeqHitIndex:re,enableRC:we},e.index)},e.key)})})})})]})]})]}),L.x!==null&&(0,d.jsx)(M,{x:L.x,y:L.y,onClose:Fe,onCopy:()=>{Ie(!1),Fe()},onCopyRC:()=>{Ie(!0),Fe()}}),Ae&&(0,d.jsx)(j,{isOpen:Ae,onClose:()=>je(!1),children:(0,d.jsxs)(`table`,{className:`min-w-full divide-y divide-gray-200`,children:[(0,d.jsx)(`thead`,{children:(0,d.jsxs)(`tr`,{children:[(0,d.jsx)(`th`,{className:`px-6 py-3 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider`,children:`Feature`}),(0,d.jsx)(`th`,{className:`px-6 py-3 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider`,children:`Product`}),(0,d.jsx)(`th`,{className:`px-6 py-3 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider`,children:`Type`}),(0,d.jsx)(`th`,{className:`px-6 py-3 bg-gray-50 text-left text-xs font-medium text-gray-500 uppercase tracking-wider`})]})}),(0,d.jsx)(`tbody`,{className:`bg-white divide-y divide-gray-200`,children:z?.parsedSequence.features.map((e,t)=>(0,d.jsxs)(`tr`,{children:[(0,d.jsxs)(`td`,{className:`px-6 py-4 whitespace-nowrap text-sm text-gray-600 font-medium`,children:[(0,d.jsx)(`input`,{type:`checkbox`,className:`focus:ring-indigo-500 text-indigo-600 border-gray-300 rounded mr-2`,checked:!!Me[t],onChange:()=>{let e={...Me};e[t]=!e[t],U(e)}}),e.name]}),(0,d.jsx)(`td`,{className:`px-6 py-4 whitespace-nowrap text-sm text-gray-500`,children:e.notes?.product?.join(`, `)}),(0,d.jsx)(`td`,{className:`px-6 py-4 whitespace-nowrap text-sm text-gray-500`,children:e.type}),(0,d.jsx)(`td`,{children:(0,d.jsx)(`button`,{className:`bg-gray-100 hover:bg-gray-200 text-gray-600 font-semibold py-1 px-1 border border-gray-400 rounded shadow text-sm `,onClick:()=>{je(!1),ke(e)},children:`Go to`})})]},t))})]})})]})}):(0,d.jsx)(`div`,{className:`gensplore w-full h-full p-5`,children:(0,d.jsx)(`div`,{ref:N,className:`w-full h-full`})}):(0,d.jsx)(`div`,{children:`Loading...`})}var hC=mC;module.exports=hC;

package/dist/gensplore.js

@@ -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);
+	for (let e of t) e.parsedSequence?.sequence && (e.parsedSequence.sequence = e.parsedSequence.sequence.toUpperCase().replace(/U/g, "T"));
+	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": "0.0.11",
   "description": "React component for displaying genbank files",
   "keywords": [
     "genbank",