jbrowse-plugin-msaview 2.0.3 → 2.0.4

package/dist/jbrowse-plugin-msaview.umd.production.min.js

@@ -1,4 +1,4 @@
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 UniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
 UniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
 UniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
@@ -11,7 +11,7 @@ UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP----------------
 UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
 UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
 UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
-`,Om=`CLUSTAL O(1.2.4) multiple sequence alignment
+`,yv=`CLUSTAL O(1.2.4) multiple sequence alignment
 
 
 sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
@@ -27,35 +27,35 @@ sp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHF
 sp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR	142
 sp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR	142
 sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
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Uint8Array([0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0]),qc=new Uint8Array([0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13]),eU=new Uint8Array([0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7]),YE=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]),tU=512,fr=new Array((Lo+2)*2);Ei(fr);Co=new Array(wi*2);Ei(Co);Ro=new Array(tU);Ei(Ro);Fo=new Array(JV-KV+1);Ei(Fo);Op=new Array(xp);Ei(Op);kc=new Array(wi);Ei(kc);JE=e=>e<256?Ro[e]:Ro[256+(e>>>7)],Do=(e,t)=>{e.pending_buf[e.pending++]=t&255,e.pending_buf[e.pending++]=t>>>8&255},Ge=(e,t,r)=>{e.bi_valid>ep-r?(e.bi_buf|=t<<e.bi_valid&65535,Do(e,e.bi_buf),e.bi_buf=t>>ep-e.bi_valid,e.bi_valid+=r-ep):(e.bi_buf|=t<<e.bi_valid&65535,e.bi_valid+=r)},zt=(e,t,r)=>{Ge(e,r[t*2],r[t*2+1])},QE=(e,t)=>{let r=0;do r|=e&1,e>>>=1,r<<=1;while(--t>0);return r>>>1},rU=e=>{e.bi_valid===16?(Do(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=e.bi_buf&255,e.bi_buf>>=8,e.bi_valid-=8)},nU=(e,t)=>{let r=t.dyn_tree,n=t.max_code,i=t.stat_desc.static_tree,o=t.stat_desc.has_stree,a=t.stat_desc.extra_bits,u=t.stat_desc.extra_base,f=t.stat_desc.max_length,l,d,s,c,h,m,v=0;for(c=0;c<=vn;c++)e.bl_count[c]=0;for(r[e.heap[e.heap_max]*2+1]=0,l=e.heap_max+1;l<UE;l++)d=e.heap[l],c=r[r[d*2+1]*2+1]+1,c>f&&(c=f,v++),r[d*2+1]=c,!(d>n)&&(e.bl_count[c]++,h=0,d>=u&&(h=a[d-u]),m=r[d*2],e.opt_len+=m*(c+h),o&&(e.static_len+=m*(i[d*2+1]+h)));if(v!==0){do{for(c=f-1;e.bl_count[c]===0;)c--;e.bl_count[c]--,e.bl_count[c+1]+=2,e.bl_count[f]--,v-=2}while(v>0);for(c=f;c!==0;c--)for(d=e.bl_count[c];d!==0;)s=e.heap[--l],!(s>n)&&(r[s*2+1]!==c&&(e.opt_len+=(c-r[s*2+1])*r[s*2],r[s*2+1]=c),d--)}},eM=(e,t,r)=>{let n=new Array(vn+1),i=0,o,a;for(o=1;o<=vn;o++)i=i+r[o-1]<<1,n[o]=i;for(a=0;a<=t;a++){let u=e[a*2+1];u!==0&&(e[a*2]=QE(n[u]++,u))}},iU=()=>{let e,t,r,n,i,o=new Array(vn+1);for(r=0,n=0;n<xp-1;n++)for(Op[n]=r,e=0;e<1<<pp[n];e++)Fo[r++]=n;for(Fo[r-1]=n,i=0,n=0;n<16;n++)for(kc[n]=i,e=0;e<1<<qc[n];e++)Ro[i++]=n;for(i>>=7;n<wi;n++)for(kc[n]=i<<7,e=0;e<1<<qc[n]-7;e++)Ro[256+i++]=n;for(t=0;t<=vn;t++)o[t]=0;for(e=0;e<=143;)fr[e*2+1]=8,e++,o[8]++;for(;e<=255;)fr[e*2+1]=9,e++,o[9]++;for(;e<=279;)fr[e*2+1]=7,e++,o[7]++;for(;e<=287;)fr[e*2+1]=8,e++,o[8]++;for(eM(fr,Lo+1,o),e=0;e<wi;e++)Co[e*2+1]=5,Co[e*2]=QE(e,5);XE=new tp(fr,pp,Vo+1,Lo,vn),ZE=new tp(Co,qc,0,wi,vn),KE=new tp(new Array(0),eU,0,Ep,QV)},tM=e=>{let t;for(t=0;t<Lo;t++)e.dyn_ltree[t*2]=0;for(t=0;t<wi;t++)e.dyn_dtree[t*2]=0;for(t=0;t<Ep;t++)e.bl_tree[t*2]=0;e.dyn_ltree[Mp*2]=1,e.opt_len=e.static_len=0,e.sym_next=e.matches=0},rM=e=>{e.bi_valid>8?Do(e,e.bi_buf):e.bi_valid>0&&(e.pending_buf[e.pending++]=e.bi_buf),e.bi_buf=0,e.bi_valid=0},oE=(e,t,r,n)=>{let i=t*2,o=r*2;return e[i]<e[o]||e[i]===e[o]&&n[t]<=n[r]},np=(e,t,r)=>{let n=e.heap[r],i=r<<1;for(;i<=e.heap_len&&(i<e.heap_len&&oE(t,e.heap[i+1],e.heap[i],e.depth)&&i++,!oE(t,n,e.heap[i],e.depth));)e.heap[r]=e.heap[i],r=i,i<<=1;e.heap[r]=n},aE=(e,t,r)=>{let n,i,o=0,a,u;if(e.sym_next!==0)do n=e.pending_buf[e.sym_buf+o++]&255,n+=(e.pending_buf[e.sym_buf+o++]&255)<<8,i=e.pending_buf[e.sym_buf+o++],n===0?zt(e,i,t):(a=Fo[i],zt(e,a+Vo+1,t),u=pp[a],u!==0&&(i-=Op[a],Ge(e,i,u)),n--,a=JE(n),zt(e,a,r),u=qc[a],u!==0&&(n-=kc[a],Ge(e,n,u)));while(o<e.sym_next);zt(e,Mp,t)},mp=(e,t)=>{let r=t.dyn_tree,n=t.stat_desc.static_tree,i=t.stat_desc.has_stree,o=t.stat_desc.elems,a,u,f=-1,l;for(e.heap_len=0,e.heap_max=UE,a=0;a<o;a++)r[a*2]!==0?(e.heap[++e.heap_len]=f=a,e.depth[a]=0):r[a*2+1]=0;for(;e.heap_len<2;)l=e.heap[++e.heap_len]=f<2?++f:0,r[l*2]=1,e.depth[l]=0,e.opt_len--,i&&(e.static_len-=n[l*2+1]);for(t.max_code=f,a=e.heap_len>>1;a>=1;a--)np(e,r,a);l=o;do a=e.heap[1],e.heap[1]=e.heap[e.heap_len--],np(e,r,1),u=e.heap[1],e.heap[--e.heap_max]=a,e.heap[--e.heap_max]=u,r[l*2]=r[a*2]+r[u*2],e.depth[l]=(e.depth[a]>=e.depth[u]?e.depth[a]:e.depth[u])+1,r[a*2+1]=r[u*2+1]=l,e.heap[1]=l++,np(e,r,1);while(e.heap_len>=2);e.heap[--e.heap_max]=e.heap[1],nU(e,t),eM(r,f,e.bl_count)},uE=(e,t,r)=>{let n,i=-1,o,a=t[0*2+1],u=0,f=7,l=4;for(a===0&&(f=138,l=3),t[(r+1)*2+1]=65535,n=0;n<=r;n++)o=a,a=t[(n+1)*2+1],!(++u<f&&o===a)&&(u<l?e.bl_tree[o*2]+=u:o!==0?(o!==i&&e.bl_tree[o*2]++,e.bl_tree[WE*2]++):u<=10?e.bl_tree[GE*2]++:e.bl_tree[$E*2]++,u=0,i=o,a===0?(f=138,l=3):o===a?(f=6,l=3):(f=7,l=4))},sE=(e,t,r)=>{let n,i=-1,o,a=t[0*2+1],u=0,f=7,l=4;for(a===0&&(f=138,l=3),n=0;n<=r;n++)if(o=a,a=t[(n+1)*2+1],!(++u<f&&o===a)){if(u<l)do zt(e,o,e.bl_tree);while(--u!==0);else o!==0?(o!==i&&(zt(e,o,e.bl_tree),u--),zt(e,WE,e.bl_tree),Ge(e,u-3,2)):u<=10?(zt(e,GE,e.bl_tree),Ge(e,u-3,3)):(zt(e,$E,e.bl_tree),Ge(e,u-11,7));u=0,i=o,a===0?(f=138,l=3):o===a?(f=6,l=3):(f=7,l=4)}},oU=e=>{let t;for(uE(e,e.dyn_ltree,e.l_desc.max_code),uE(e,e.dyn_dtree,e.d_desc.max_code),mp(e,e.bl_desc),t=Ep-1;t>=3&&e.bl_tree[YE[t]*2+1]===0;t--);return e.opt_len+=3*(t+1)+5+5+4,t},aU=(e,t,r,n)=>{let i;for(Ge(e,t-257,5),Ge(e,r-1,5),Ge(e,n-4,4),i=0;i<n;i++)Ge(e,e.bl_tree[YE[i]*2+1],3);sE(e,e.dyn_ltree,t-1),sE(e,e.dyn_dtree,r-1)},uU=e=>{let t=4093624447,r;for(r=0;r<=31;r++,t>>>=1)if(t&1&&e.dyn_ltree[r*2]!==0)return 0;if(e.dyn_ltree[9*2]!==0||e.dyn_ltree[10*2]!==0||e.dyn_ltree[13*2]!==0)return 1;for(r=32;r<Vo;r++)if(e.dyn_ltree[r*2]!==0)return 1;return 0},lE=!1,sU=e=>{lE||(iU(),lE=!0),e.l_desc=new rp(e.dyn_ltree,XE),e.d_desc=new rp(e.dyn_dtree,ZE),e.bl_desc=new rp(e.bl_tree,KE),e.bi_buf=0,e.bi_valid=0,tM(e)},nM=(e,t,r,n)=>{Ge(e,(XV<<1)+(n?1:0),3),rM(e),Do(e,r),Do(e,~r),r&&e.pending_buf.set(e.window.subarray(t,t+r),e.pending),e.pending+=r},lU=e=>{Ge(e,VE<<1,3),zt(e,Mp,fr),rU(e)},cU=(e,t,r,n)=>{let i,o,a=0;e.level>0?(e.strm.data_type===2&&(e.strm.data_type=uU(e)),mp(e,e.l_desc),mp(e,e.d_desc),a=oU(e),i=e.opt_len+3+7>>>3,o=e.static_len+3+7>>>3,o<=i&&(i=o)):i=o=r+5,r+4<=i&&t!==-1?nM(e,t,r,n):e.strategy===4||o===i?(Ge(e,(VE<<1)+(n?1:0),3),aE(e,fr,Co)):(Ge(e,(ZV<<1)+(n?1:0),3),aU(e,e.l_desc.max_code+1,e.d_desc.max_code+1,a+1),aE(e,e.dyn_ltree,e.dyn_dtree)),tM(e),n&&rM(e)},fU=(e,t,r)=>(e.pending_buf[e.sym_buf+e.sym_next++]=t,e.pending_buf[e.sym_buf+e.sym_next++]=t>>8,e.pending_buf[e.sym_buf+e.sym_next++]=r,t===0?e.dyn_ltree[r*2]++:(e.matches++,t--,e.dyn_ltree[(Fo[r]+Vo+1)*2]++,e.dyn_dtree[JE(t)*2]++),e.sym_next===e.sym_end),dU=sU,hU=nM,pU=cU,mU=fU,vU=lU,_U={_tr_init:dU,_tr_stored_block:hU,_tr_flush_block:pU,_tr_tally:mU,_tr_align:vU},bU=(e,t,r,n)=>{let i=e&65535|0,o=e>>>16&65535|0,a=0;for(;r!==0;){a=r>2e3?2e3:r,r-=a;do i=i+t[n++]|0,o=o+i|0;while(--a);i%=65521,o%=65521}return i|o<<16|0},No=bU,gU=()=>{let e,t=[];for(var r=0;r<256;r++){e=r;for(var n=0;n<8;n++)e=e&1?3988292384^e>>>1:e>>>1;t[r]=e}return t},yU=new Uint32Array(gU()),wU=(e,t,r,n)=>{let i=yU,o=n+r;e^=-1;for(let a=n;a<o;a++)e=e>>>8^i[(e^t[a])&255];return e^-1},ye=wU,gn={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"},Mi={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,Z_OK:0,Z_STREAM_END:1,Z_NEED_DICT:2,Z_ERRNO:-1,Z_STREAM_ERROR:-2,Z_DATA_ERROR:-3,Z_MEM_ERROR:-4,Z_BUF_ERROR:-5,Z_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8},{_tr_init:SU,_tr_stored_block:vp,_tr_flush_block:xU,_tr_tally:Ur,_tr_align:EU}=_U,{Z_NO_FLUSH:Wr,Z_PARTIAL_FLUSH:MU,Z_FULL_FLUSH:OU,Z_FINISH:dt,Z_BLOCK:cE,Z_OK:Ae,Z_STREAM_END:fE,Z_STREAM_ERROR:Ht,Z_DATA_ERROR:AU,Z_BUF_ERROR:ip,Z_DEFAULT_COMPRESSION:PU,Z_FILTERED:qU,Z_HUFFMAN_ONLY:Ec,Z_RLE:kU,Z_FIXED:TU,Z_DEFAULT_STRATEGY:CU,Z_UNKNOWN:jU,Z_DEFLATED:jc}=Mi,IU=9,LU=15,RU=8,FU=29,DU=256,_p=DU+1+FU,NU=30,BU=19,zU=2*_p+1,HU=15,W=3,Vr=258,Vt=Vr+W+1,VU=32,Si=42,Ap=57,bp=69,gp=73,yp=91,wp=103,_n=113,ko=666,Be=1,Oi=2,yn=3,Ai=4,UU=3,bn=(e,t)=>(e.msg=gn[t],t),dE=e=>e*2-(e>4?9:0),Hr=e=>{let t=e.length;for(;--t>=0;)e[t]=0},WU=e=>{let t,r,n,i=e.w_size;t=e.hash_size,n=t;do r=e.head[--n],e.head[n]=r>=i?r-i:0;while(--t);t=i,n=t;do r=e.prev[--n],e.prev[n]=r>=i?r-i:0;while(--t)},GU=(e,t,r)=>(t<<e.hash_shift^r)&e.hash_mask,Gr=GU,rt=e=>{let t=e.state,r=t.pending;r>e.avail_out&&(r=e.avail_out),r!==0&&(e.output.set(t.pending_buf.subarray(t.pending_out,t.pending_out+r),e.next_out),e.next_out+=r,t.pending_out+=r,e.total_out+=r,e.avail_out-=r,t.pending-=r,t.pending===0&&(t.pending_out=0))},nt=(e,t)=>{xU(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,rt(e.strm)},Y=(e,t)=>{e.pending_buf[e.pending++]=t},qo=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=t&255},Sp=(e,t,r,n)=>{let i=e.avail_in;return i>n&&(i=n),i===0?0:(e.avail_in-=i,t.set(e.input.subarray(e.next_in,e.next_in+i),r),e.state.wrap===1?e.adler=No(e.adler,t,i,r):e.state.wrap===2&&(e.adler=ye(e.adler,t,i,r)),e.next_in+=i,e.total_in+=i,i)},iM=(e,t)=>{let r=e.max_chain_length,n=e.strstart,i,o,a=e.prev_length,u=e.nice_match,f=e.strstart>e.w_size-Vt?e.strstart-(e.w_size-Vt):0,l=e.window,d=e.w_mask,s=e.prev,c=e.strstart+Vr,h=l[n+a-1],m=l[n+a];e.prev_length>=e.good_match&&(r>>=2),u>e.lookahead&&(u=e.lookahead);do if(i=t,!(l[i+a]!==m||l[i+a-1]!==h||l[i]!==l[n]||l[++i]!==l[n+1])){n+=2,i++;do;while(l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&n<c);if(o=Vr-(c-n),n=c-Vr,o>a){if(e.match_start=t,a=o,o>=u)break;h=l[n+a-1],m=l[n+a]}}while((t=s[t&d])>f&&--r!==0);return a<=e.lookahead?a:e.lookahead},xi=e=>{let t=e.w_size,r,n,i;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-Vt)&&(e.window.set(e.window.subarray(t,t+t-n),0),e.match_start-=t,e.strstart-=t,e.block_start-=t,e.insert>e.strstart&&(e.insert=e.strstart),WU(e),n+=t),e.strm.avail_in===0)break;if(r=Sp(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=r,e.lookahead+e.insert>=W)for(i=e.strstart-e.insert,e.ins_h=e.window[i],e.ins_h=Gr(e,e.ins_h,e.window[i+1]);e.insert&&(e.ins_h=Gr(e,e.ins_h,e.window[i+W-1]),e.prev[i&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=i,i++,e.insert--,!(e.lookahead+e.insert<W)););}while(e.lookahead<Vt&&e.strm.avail_in!==0)},oM=(e,t)=>{let r=e.pending_buf_size-5>e.w_size?e.w_size:e.pending_buf_size-5,n,i,o,a=0,u=e.strm.avail_in;do{if(n=65535,o=e.bi_valid+42>>3,e.strm.avail_out<o||(o=e.strm.avail_out-o,i=e.strstart-e.block_start,n>i+e.strm.avail_in&&(n=i+e.strm.avail_in),n>o&&(n=o),n<r&&(n===0&&t!==dt||t===Wr||n!==i+e.strm.avail_in)))break;a=t===dt&&n===i+e.strm.avail_in?1:0,vp(e,0,0,a),e.pending_buf[e.pending-4]=n,e.pending_buf[e.pending-3]=n>>8,e.pending_buf[e.pending-2]=~n,e.pending_buf[e.pending-1]=~n>>8,rt(e.strm),i&&(i>n&&(i=n),e.strm.output.set(e.window.subarray(e.block_start,e.block_start+i),e.strm.next_out),e.strm.next_out+=i,e.strm.avail_out-=i,e.strm.total_out+=i,e.block_start+=i,n-=i),n&&(Sp(e.strm,e.strm.output,e.strm.next_out,n),e.strm.next_out+=n,e.strm.avail_out-=n,e.strm.total_out+=n)}while(a===0);return 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Pe(e,t){return(await OO(e,t)).text()}async function AO(e,t){return(await OO(e,t)).json()}function Nc(e){return new Promise(t=>setTimeout(t,e))}var Vp=C(()=>{"use strict"});async function qO({query:e,blastDatabase:t,blastProgram:r,onProgress:n,onRid:i}){n("Submitting to NCBI BLAST...");let{rid:o}=await ZG({query:e,blastDatabase:t,blastProgram:r});i(o),await KG({rid:o,onProgress:n});let u=(await AO(`${Ko}?CMD=Get&RID=${o}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`)).BlastOutput2[0].report.results.search.hits;return{rid:o,hits:u}}async function ZG({query:e,blastProgram:t,blastDatabase:r}){let n=await Pe(Ko,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental Databases"}:{}})}),i=/^    RID = (.*$)/m.exec(n)?.[1],o=/^    RTOE = (.*$)/m.exec(n)?.[1];if(!i)throw new Error("Failed to get RID from BLAST request");return{rid:i,rtoe:o}}async function KG({rid:e,onProgress:t}){for(;;){for(let 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t$({rid:e,progress:t}){let{classes:r}=UO();return pt.default.createElement("div",{className:r.loading},e?pt.default.createElement($p,{rid:e}):null,pt.default.createElement(Yp.Typography,null,t))}var pt,Yp,HO,VO,Yc,UO,r$,WO,GO=C(()=>{"use strict";pt=S(I()),Yp=S(z()),HO=S(N()),VO=S(Ot()),Yc=S(Se());zO();UO=(0,VO.makeStyles)()(e=>({margin:{padding:20},loading:{background:e.palette.background.paper}}));r$=(0,HO.observer)(function({model:t}){let{progress:r,rid:n,error:i,processing:o}=t,{classes:a}=UO();return pt.default.createElement("div",{className:a.margin},pt.default.createElement(Yc.LoadingEllipses,{message:"Running NCBI BLAST",variant:"h5"}),i?pt.default.createElement(e$,{rid:n,error:i}):n?pt.default.createElement(t$,{rid:n,progress:r}):null,pt.default.createElement(Yp.Typography,null,o||"Initializing BLAST query"))}),WO=r$});var YO={};at(YO,{default:()=>i$});var Xc,$O,n$,i$,XO=C(()=>{"use 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Bc({jobId:r,algorithm:"clustalo",onProgress:t}),{msa:await Pe(`${it}/clustalo/result/${r}/aln-clustal_num`),tree:await Pe(`${it}/clustalo/result/${r}/phylotree`)}}async function $G({sequence:e,onProgress:t}){let r=await Pe(`${it}/muscle/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",format:"clw",tree:"tree1",sequence:e})});return await Bc({jobId:r,algorithm:"muscle",onProgress:t}),{msa:await Pe(`${it}/muscle/result/${r}/fa`),tree:await Pe(`${it}/muscle/result/${r}/phylotree`)}}async function YG({sequence:e,onProgress:t}){let r=await Pe(`${it}/kalign/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Bc({jobId:r,algorithm:"kalign",onProgress:t}),{msa:await Pe(`${it}/kalign/result/${r}/fa`),tree:await Pe(`${it}/kalign/result/${r}/phylotree`)}}async function XG({sequence:e,onProgress:t}){let r=await Pe(`${it}/mafft/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await Bc({jobId:r,algorithm:"mafft",onProgress:t}),{msa:await Pe(`${it}/mafft/result/${r}/fa`),tree:await Pe(`${it}/mafft/result/${r}/phylotree`)}}async function Bc({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let i=0;i<10;i++)await Nc(1e3),e(`Re-checking MSA status in... ${10-i}`);if(await Pe(`${it}/${r}/status/${t}`)==="FINISHED")break}}async function PO({algorithm:e,sequence:t,onProgress:r}){switch(r(`Launching ${e} MSA...`),e){case"clustalo":return GG({sequence:t,onProgress:r});case"muscle":return $G({sequence:t,onProgress:r});case"kalign":return YG({sequence:t,onProgress:r});case"mafft":return XG({sequence:t,onProgress:r});default:throw new Error("unknown algorithm")}}Up();function kO(e){return`${e.accession}-${e.sciname.replaceAll(" ","_")}`}function TO(e){return e.replace("-","")}async function CO({self:e}){let{blastDatabase:t,blastProgram:r,msaAlgorithm:n,proteinSequence:i}=e.blastParams,o=i.replaceAll("*","").replaceAll("&",""),{hits:a}=await qO({query:o,blastDatabase:t,blastProgram:r,onProgress:l=>e.setProgress(l),onRid:l=>e.setRid(l)}),u=[`>QUERY
-${o}`,...a.map(l=>[kO(l.description[0]),TO(l.hsps[0].hseq)]).map(([l,d])=>`>${l}
-${d}`)].join(`
-`);return await PO({algorithm:n,sequence:u,onProgress:l=>e.setProgress(l)})}var IO=S(we());function jO(e){return!!e&&typeof e=="object"&&"hoverFeature"in e&&"hoverPosition"in e}function LO({model:e}){let{hovered:t}=(0,IO.getSession)(e),{transcriptToMsaMap:r,connectedView:n}=e;if(n?.initialized&&r&&jO(t)){let{coord:i}=t.hoverPosition,{g2p:o}=r,a=o[i];if(a!==void 0)return e.seqCoordToRowSpecificGlobalCoord("QUERY",a+1)}}function zc({model:e,coord:t}){let{transcriptToMsaMap:r}=e;if(t===void 0||r===void 0)return;let n=t-1,i=e.globalCoordToRowSpecificSeqCoord("QUERY",n)||0,o=e.globalCoordToRowSpecificSeqCoord("QUERY",n+1)||0,{refName:a,p2g:u}=r,f=u[i],l=u[o];return f!==void 0&&l!==void 0?{refName:a,start:Math.min(f,l),end:Math.max(f,l)}:void 0}var DO=S(RO());function Wp(){return 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Error(Cn[r]);if(t.header&&na.deflateSetHeader(this.strm,t.header),t.dictionary){let n;if(typeof t.dictionary=="string"?n=fa.string2buf(t.dictionary):XM.call(t.dictionary)==="[object ArrayBuffer]"?n=new Uint8Array(t.dictionary):n=t.dictionary,r=na.deflateSetDictionary(this.strm,n),r!==sf)throw new Error(Cn[r]);this._dict_set=!0}}function xm(e,t){let r=new ma(t);if(r.push(e,!0),r.err)throw r.msg||Cn[r.err];return r.result}function QY(e,t){return t=t||{},t.raw=!0,xm(e,t)}function eX(e,t){return t=t||{},t.gzip=!0,xm(e,t)}function xX(){this.strm=null,this.mode=0,this.last=!1,this.wrap=0,this.havedict=!1,this.flags=0,this.dmax=0,this.check=0,this.total=0,this.head=null,this.wbits=0,this.wsize=0,this.whave=0,this.wnext=0,this.window=null,this.hold=0,this.bits=0,this.length=0,this.offset=0,this.extra=0,this.lencode=null,this.distcode=null,this.lenbits=0,this.distbits=0,this.ncode=0,this.nlen=0,this.ndist=0,this.have=0,this.next=null,this.lens=new Uint16Array(320),this.work=new 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w$,AM,S$,x$,E$,bm,pa,oa,Di,gm,PM,qn,Xh,O$,ym,qM,TM,kM,lm,af,M$,CM,A$,br,ra,aa,ua,wm,uf,jM,IM,RM,FM,sa,et,Kt,LM,P$,q$,DM,T$,NM,BM,VO,Jh,WO,cm,UO,GO,k$,C$,j$,$O,I$,zM,R$,F$,L$,D$,N$,B$,z$,H$,V$,W$,la,U$,G$,$$,Oe,Cn,Hi,Y$,fm,X$,tn,Z$,rn,K$,J$,gt,YO,Ce,XO,Jt,Q$,Qh,eY,tY,ef,rY,nY,iY,oY,cf,aY,uY,sY,lY,cY,dm,fY,dY,pY,hY,U,en,Qt,mY,Ni,Sm,pm,hm,mm,vm,Tn,ea,Ue,Vi,jn,Wi,vY,kn,ZO,Qr,_Y,bY,nn,st,lt,X,Qo,_m,HM,Bi,VM,em,Fi,gY,yY,ta,wY,ha,WM,UM,xY,GM,EY,OY,MY,AY,PY,qY,TY,kY,CY,jY,IY,RY,FY,na,LY,DY,NY,ff,$M,ca,BY,zY,HY,VY,fa,YM,XM,UY,GY,$Y,YY,sf,XY,ZY,KY,JY,tX,rX,nX,iX,oX,aX,tf,uX,sX,Li,KO,JO,QO,tm,eM,lX,cX,fX,dX,pX,ia,hX,ZM,KM,tM,mX,rf,In,vX,_X,yt,JM,QM,bX,rM,df,nM,iM,oM,aM,uM,sM,lM,cM,fM,lf,_r,rm,dM,nm,pM,hM,mM,vM,nf,of,_M,bM,gM,yM,wM,im,SM,xM,ue,eA,tA,gX,yX,wX,SX,EM,Rn,rA,nA,iA,oA,EX,OM,om,am,OX,aA,MX,AX,PX,qX,TX,kX,CX,jX,IX,RX,FX,LX,DX,NX,gr,zX,uA,HX,VX,da,um,sm,WX,MM,UX,$X,YX,XX,ZX,KX,JX,Goe,$oe,Yoe,Xoe,Zoe,Koe,Joe,QX,pf,Om=C(()=>{w$=0,AM=1,S$=2,x$=3,E$=258,bm=29,pa=256,oa=pa+1+bm,Di=30,gm=19,PM=2*oa+1,qn=15,Xh=16,O$=7,ym=256,qM=16,TM=17,kM=18,lm=new Uint8Array([0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0]),af=new Uint8Array([0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13]),M$=new Uint8Array([0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7]),CM=new Uint8Array([16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15]),A$=512,br=new Array((oa+2)*2);zi(br);ra=new Array(Di*2);zi(ra);aa=new Array(A$);zi(aa);ua=new Array(E$-x$+1);zi(ua);wm=new Array(bm);zi(wm);uf=new Array(Di);zi(uf);FM=e=>e<256?aa[e]:aa[256+(e>>>7)],sa=(e,t)=>{e.pending_buf[e.pending++]=t&255,e.pending_buf[e.pending++]=t>>>8&255},et=(e,t,r)=>{e.bi_valid>Xh-r?(e.bi_buf|=t<<e.bi_valid&65535,sa(e,e.bi_buf),e.bi_buf=t>>Xh-e.bi_valid,e.bi_valid+=r-Xh):(e.bi_buf|=t<<e.bi_valid&65535,e.bi_valid+=r)},Kt=(e,t,r)=>{et(e,r[t*2],r[t*2+1])},LM=(e,t)=>{let r=0;do r|=e&1,e>>>=1,r<<=1;while(--t>0);return r>>>1},P$=e=>{e.bi_valid===16?(sa(e,e.bi_buf),e.bi_buf=0,e.bi_valid=0):e.bi_valid>=8&&(e.pending_buf[e.pending++]=e.bi_buf&255,e.bi_buf>>=8,e.bi_valid-=8)},q$=(e,t)=>{let r=t.dyn_tree,n=t.max_code,i=t.stat_desc.static_tree,o=t.stat_desc.has_stree,a=t.stat_desc.extra_bits,u=t.stat_desc.extra_base,d=t.stat_desc.max_length,l,f,s,c,p,m,v=0;for(c=0;c<=qn;c++)e.bl_count[c]=0;for(r[e.heap[e.heap_max]*2+1]=0,l=e.heap_max+1;l<PM;l++)f=e.heap[l],c=r[r[f*2+1]*2+1]+1,c>d&&(c=d,v++),r[f*2+1]=c,!(f>n)&&(e.bl_count[c]++,p=0,f>=u&&(p=a[f-u]),m=r[f*2],e.opt_len+=m*(c+p),o&&(e.static_len+=m*(i[f*2+1]+p)));if(v!==0){do{for(c=d-1;e.bl_count[c]===0;)c--;e.bl_count[c]--,e.bl_count[c+1]+=2,e.bl_count[d]--,v-=2}while(v>0);for(c=d;c!==0;c--)for(f=e.bl_count[c];f!==0;)s=e.heap[--l],!(s>n)&&(r[s*2+1]!==c&&(e.opt_len+=(c-r[s*2+1])*r[s*2],r[s*2+1]=c),f--)}},DM=(e,t,r)=>{let n=new Array(qn+1),i=0,o,a;for(o=1;o<=qn;o++)i=i+r[o-1]<<1,n[o]=i;for(a=0;a<=t;a++){let u=e[a*2+1];u!==0&&(e[a*2]=LM(n[u]++,u))}},T$=()=>{let e,t,r,n,i,o=new Array(qn+1);for(r=0,n=0;n<bm-1;n++)for(wm[n]=r,e=0;e<1<<lm[n];e++)ua[r++]=n;for(ua[r-1]=n,i=0,n=0;n<16;n++)for(uf[n]=i,e=0;e<1<<af[n];e++)aa[i++]=n;for(i>>=7;n<Di;n++)for(uf[n]=i<<7,e=0;e<1<<af[n]-7;e++)aa[256+i++]=n;for(t=0;t<=qn;t++)o[t]=0;for(e=0;e<=143;)br[e*2+1]=8,e++,o[8]++;for(;e<=255;)br[e*2+1]=9,e++,o[9]++;for(;e<=279;)br[e*2+1]=7,e++,o[7]++;for(;e<=287;)br[e*2+1]=8,e++,o[8]++;for(DM(br,oa+1,o),e=0;e<Di;e++)ra[e*2+1]=5,ra[e*2]=LM(e,5);jM=new Zh(br,lm,pa+1,oa,qn),IM=new Zh(ra,af,0,Di,qn),RM=new Zh(new Array(0),M$,0,gm,O$)},NM=e=>{let t;for(t=0;t<oa;t++)e.dyn_ltree[t*2]=0;for(t=0;t<Di;t++)e.dyn_dtree[t*2]=0;for(t=0;t<gm;t++)e.bl_tree[t*2]=0;e.dyn_ltree[ym*2]=1,e.opt_len=e.static_len=0,e.sym_next=e.matches=0},BM=e=>{e.bi_valid>8?sa(e,e.bi_buf):e.bi_valid>0&&(e.pending_buf[e.pending++]=e.bi_buf),e.bi_buf=0,e.bi_valid=0},VO=(e,t,r,n)=>{let i=t*2,o=r*2;return e[i]<e[o]||e[i]===e[o]&&n[t]<=n[r]},Jh=(e,t,r)=>{let n=e.heap[r],i=r<<1;for(;i<=e.heap_len&&(i<e.heap_len&&VO(t,e.heap[i+1],e.heap[i],e.depth)&&i++,!VO(t,n,e.heap[i],e.depth));)e.heap[r]=e.heap[i],r=i,i<<=1;e.heap[r]=n},WO=(e,t,r)=>{let n,i,o=0,a,u;if(e.sym_next!==0)do n=e.pending_buf[e.sym_buf+o++]&255,n+=(e.pending_buf[e.sym_buf+o++]&255)<<8,i=e.pending_buf[e.sym_buf+o++],n===0?Kt(e,i,t):(a=ua[i],Kt(e,a+pa+1,t),u=lm[a],u!==0&&(i-=wm[a],et(e,i,u)),n--,a=FM(n),Kt(e,a,r),u=af[a],u!==0&&(n-=uf[a],et(e,n,u)));while(o<e.sym_next);Kt(e,ym,t)},cm=(e,t)=>{let r=t.dyn_tree,n=t.stat_desc.static_tree,i=t.stat_desc.has_stree,o=t.stat_desc.elems,a,u,d=-1,l;for(e.heap_len=0,e.heap_max=PM,a=0;a<o;a++)r[a*2]!==0?(e.heap[++e.heap_len]=d=a,e.depth[a]=0):r[a*2+1]=0;for(;e.heap_len<2;)l=e.heap[++e.heap_len]=d<2?++d:0,r[l*2]=1,e.depth[l]=0,e.opt_len--,i&&(e.static_len-=n[l*2+1]);for(t.max_code=d,a=e.heap_len>>1;a>=1;a--)Jh(e,r,a);l=o;do 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o!==0?(o!==i&&(Kt(e,o,e.bl_tree),u--),Kt(e,qM,e.bl_tree),et(e,u-3,2)):u<=10?(Kt(e,TM,e.bl_tree),et(e,u-3,3)):(Kt(e,kM,e.bl_tree),et(e,u-11,7));u=0,i=o,a===0?(d=138,l=3):o===a?(d=6,l=3):(d=7,l=4)}},k$=e=>{let t;for(UO(e,e.dyn_ltree,e.l_desc.max_code),UO(e,e.dyn_dtree,e.d_desc.max_code),cm(e,e.bl_desc),t=gm-1;t>=3&&e.bl_tree[CM[t]*2+1]===0;t--);return e.opt_len+=3*(t+1)+5+5+4,t},C$=(e,t,r,n)=>{let i;for(et(e,t-257,5),et(e,r-1,5),et(e,n-4,4),i=0;i<n;i++)et(e,e.bl_tree[CM[i]*2+1],3);GO(e,e.dyn_ltree,t-1),GO(e,e.dyn_dtree,r-1)},j$=e=>{let t=4093624447,r;for(r=0;r<=31;r++,t>>>=1)if(t&1&&e.dyn_ltree[r*2]!==0)return 0;if(e.dyn_ltree[9*2]!==0||e.dyn_ltree[10*2]!==0||e.dyn_ltree[13*2]!==0)return 1;for(r=32;r<pa;r++)if(e.dyn_ltree[r*2]!==0)return 1;return 0},$O=!1,I$=e=>{$O||(T$(),$O=!0),e.l_desc=new Kh(e.dyn_ltree,jM),e.d_desc=new Kh(e.dyn_dtree,IM),e.bl_desc=new 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r=e.max_chain_length,n=e.strstart,i,o,a=e.prev_length,u=e.nice_match,d=e.strstart>e.w_size-Qt?e.strstart-(e.w_size-Qt):0,l=e.window,f=e.w_mask,s=e.prev,c=e.strstart+en,p=l[n+a-1],m=l[n+a];e.prev_length>=e.good_match&&(r>>=2),u>e.lookahead&&(u=e.lookahead);do if(i=t,!(l[i+a]!==m||l[i+a-1]!==p||l[i]!==l[n]||l[++i]!==l[n+1])){n+=2,i++;do;while(l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&l[++n]===l[++i]&&n<c);if(o=en-(c-n),n=c-en,o>a){if(e.match_start=t,a=o,o>=u)break;p=l[n+a-1],m=l[n+a]}}while((t=s[t&f])>d&&--r!==0);return a<=e.lookahead?a:e.lookahead},Bi=e=>{let t=e.w_size,r,n,i;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-Qt)&&(e.window.set(e.window.subarray(t,t+t-n),0),e.match_start-=t,e.strstart-=t,e.block_start-=t,e.insert>e.strstart&&(e.insert=e.strstart),_Y(e),n+=t),e.strm.avail_in===0)break;if(r=_m(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=r,e.lookahead+e.insert>=U)for(i=e.strstart-e.insert,e.ins_h=e.window[i],e.ins_h=nn(e,e.ins_h,e.window[i+1]);e.insert&&(e.ins_h=nn(e,e.ins_h,e.window[i+U-1]),e.prev[i&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=i,i++,e.insert--,!(e.lookahead+e.insert<U)););}while(e.lookahead<Qt&&e.strm.avail_in!==0)},VM=(e,t)=>{let r=e.pending_buf_size-5>e.w_size?e.w_size:e.pending_buf_size-5,n,i,o,a=0,u=e.strm.avail_in;do{if(n=65535,o=e.bi_valid+42>>3,e.strm.avail_out<o||(o=e.strm.avail_out-o,i=e.strstart-e.block_start,n>i+e.strm.avail_in&&(n=i+e.strm.avail_in),n>o&&(n=o),n<r&&(n===0&&t!==gt||t===rn||n!==i+e.strm.avail_in)))break;a=t===gt&&n===i+e.strm.avail_in?1:0,fm(e,0,0,a),e.pending_buf[e.pending-4]=n,e.pending_buf[e.pending-3]=n>>8,e.pending_buf[e.pending-2]=~n,e.pending_buf[e.pending-1]=~n>>8,st(e.strm),i&&(i>n&&(i=n),e.strm.output.set(e.window.subarray(e.block_start,e.block_start+i),e.strm.next_out),e.strm.next_out+=i,e.strm.avail_out-=i,e.strm.total_out+=i,e.block_start+=i,n-=i),n&&(_m(e.strm,e.strm.output,e.strm.next_out,n),e.strm.next_out+=n,e.strm.avail_out-=n,e.strm.total_out+=n)}while(a===0);return u-=e.strm.avail_in,u&&(u>=e.w_size?(e.matches=2,e.window.set(e.strm.input.subarray(e.strm.next_in-e.w_size,e.strm.next_in),0),e.strstart=e.w_size,e.insert=e.strstart):(e.window_size-e.strstart<=u&&(e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,e.insert>e.strstart&&(e.insert=e.strstart)),e.window.set(e.strm.input.subarray(e.strm.next_in-u,e.strm.next_in),e.strstart),e.strstart+=u,e.insert+=u>e.w_size-e.insert?e.w_size-e.insert:u),e.block_start=e.strstart),e.high_water<e.strstart&&(e.high_water=e.strstart),a?Wi:t!==rn&&t!==gt&&e.strm.avail_in===0&&e.strstart===e.block_start?Vi:(o=e.window_size-e.strstart,e.strm.avail_in>o&&e.block_start>=e.w_size&&(e.block_start-=e.w_size,e.strstart-=e.w_size,e.window.set(e.window.subarray(e.w_size,e.w_size+e.strstart),0),e.matches<2&&e.matches++,o+=e.w_size,e.insert>e.strstart&&(e.insert=e.strstart)),o>e.strm.avail_in&&(o=e.strm.avail_in),o&&(_m(e.strm,e.window,e.strstart,o),e.strstart+=o,e.insert+=o>e.w_size-e.insert?e.w_size-e.insert:o),e.high_water<e.strstart&&(e.high_water=e.strstart),o=e.bi_valid+42>>3,o=e.pending_buf_size-o>65535?65535:e.pending_buf_size-o,r=o>e.w_size?e.w_size:o,i=e.strstart-e.block_start,(i>=r||(i||t===gt)&&t!==rn&&e.strm.avail_in===0&&i<=o)&&(n=i>o?o:i,a=t===gt&&e.strm.avail_in===0&&n===i?1:0,fm(e,e.block_start,n,a),e.block_start+=n,st(e.strm)),a?jn:Ue)},em=(e,t)=>{let r,n;for(;;){if(e.lookahead<Qt){if(Bi(e),e.lookahead<Qt&&t===rn)return Ue;if(e.lookahead===0)break}if(r=0,e.lookahead>=U&&(e.ins_h=nn(e,e.ins_h,e.window[e.strstart+U-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),r!==0&&e.strstart-r<=e.w_size-Qt&&(e.match_length=HM(e,r)),e.match_length>=U)if(n=tn(e,e.strstart-e.match_start,e.match_length-U),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=U){e.match_length--;do e.strstart++,e.ins_h=nn(e,e.ins_h,e.window[e.strstart+U-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart;while(--e.match_length!==0);e.strstart++}else e.strstart+=e.match_length,e.match_length=0,e.ins_h=e.window[e.strstart],e.ins_h=nn(e,e.ins_h,e.window[e.strstart+1]);else n=tn(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(lt(e,!1),e.strm.avail_out===0))return Ue}return e.insert=e.strstart<U-1?e.strstart:U-1,t===gt?(lt(e,!0),e.strm.avail_out===0?jn:Wi):e.sym_next&&(lt(e,!1),e.strm.avail_out===0)?Ue:Vi},Fi=(e,t)=>{let r,n,i;for(;;){if(e.lookahead<Qt){if(Bi(e),e.lookahead<Qt&&t===rn)return Ue;if(e.lookahead===0)break}if(r=0,e.lookahead>=U&&(e.ins_h=nn(e,e.ins_h,e.window[e.strstart+U-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart),e.prev_length=e.match_length,e.prev_match=e.match_start,e.match_length=U-1,r!==0&&e.prev_length<e.max_lazy_match&&e.strstart-r<=e.w_size-Qt&&(e.match_length=HM(e,r),e.match_length<=5&&(e.strategy===tY||e.match_length===U&&e.strstart-e.match_start>4096)&&(e.match_length=U-1)),e.prev_length>=U&&e.match_length<=e.prev_length){i=e.strstart+e.lookahead-U,n=tn(e,e.strstart-1-e.prev_match,e.prev_length-U),e.lookahead-=e.prev_length-1,e.prev_length-=2;do++e.strstart<=i&&(e.ins_h=nn(e,e.ins_h,e.window[e.strstart+U-1]),r=e.prev[e.strstart&e.w_mask]=e.head[e.ins_h],e.head[e.ins_h]=e.strstart);while(--e.prev_length!==0);if(e.match_available=0,e.match_length=U-1,e.strstart++,n&&(lt(e,!1),e.strm.avail_out===0))return Ue}else if(e.match_available){if(n=tn(e,0,e.window[e.strstart-1]),n&&lt(e,!1),e.strstart++,e.lookahead--,e.strm.avail_out===0)return Ue}else e.match_available=1,e.strstart++,e.lookahead--}return e.match_available&&(n=tn(e,0,e.window[e.strstart-1]),e.match_available=0),e.insert=e.strstart<U-1?e.strstart:U-1,t===gt?(lt(e,!0),e.strm.avail_out===0?jn:Wi):e.sym_next&&(lt(e,!1),e.strm.avail_out===0)?Ue:Vi},gY=(e,t)=>{let r,n,i,o,a=e.window;for(;;){if(e.lookahead<=en){if(Bi(e),e.lookahead<=en&&t===rn)return Ue;if(e.lookahead===0)break}if(e.match_length=0,e.lookahead>=U&&e.strstart>0&&(i=e.strstart-1,n=a[i],n===a[++i]&&n===a[++i]&&n===a[++i])){o=e.strstart+en;do;while(n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&n===a[++i]&&i<o);e.match_length=en-(o-i),e.match_length>e.lookahead&&(e.match_length=e.lookahead)}if(e.match_length>=U?(r=tn(e,1,e.match_length-U),e.lookahead-=e.match_length,e.strstart+=e.match_length,e.match_length=0):(r=tn(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++),r&&(lt(e,!1),e.strm.avail_out===0))return Ue}return e.insert=0,t===gt?(lt(e,!0),e.strm.avail_out===0?jn:Wi):e.sym_next&&(lt(e,!1),e.strm.avail_out===0)?Ue:Vi},yY=(e,t)=>{let r;for(;;){if(e.lookahead===0&&(Bi(e),e.lookahead===0)){if(t===rn)return Ue;break}if(e.match_length=0,r=tn(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++,r&&(lt(e,!1),e.strm.avail_out===0))return Ue}return e.insert=0,t===gt?(lt(e,!0),e.strm.avail_out===0?jn:Wi):e.sym_next&&(lt(e,!1),e.strm.avail_out===0)?Ue:Vi};ta=[new Zt(0,0,0,0,VM),new Zt(4,4,8,4,em),new Zt(4,5,16,8,em),new Zt(4,6,32,32,em),new Zt(4,4,16,16,Fi),new Zt(8,16,32,32,Fi),new Zt(8,16,128,128,Fi),new Zt(8,32,128,256,Fi),new Zt(32,128,258,1024,Fi),new Zt(32,258,258,4096,Fi)],wY=e=>{e.window_size=2*e.w_size,Qr(e.head),e.max_lazy_match=ta[e.level].max_lazy,e.good_match=ta[e.level].good_length,e.nice_match=ta[e.level].nice_length,e.max_chain_length=ta[e.level].max_chain,e.strstart=0,e.block_start=0,e.lookahead=0,e.insert=0,e.match_length=e.prev_length=U-1,e.match_available=0,e.ins_h=0};ha=e=>{if(!e)return 1;let t=e.state;return!t||t.strm!==e||t.status!==Ni&&t.status!==Sm&&t.status!==pm&&t.status!==hm&&t.status!==mm&&t.status!==vm&&t.status!==Tn&&t.status!==ea?1:0},WM=e=>{if(ha(e))return kn(e,Jt);e.total_in=e.total_out=0,e.data_type=oY;let t=e.state;return t.pending=0,t.pending_out=0,t.wrap<0&&(t.wrap=-t.wrap),t.status=t.wrap===2?Sm:t.wrap?Ni:Tn,e.adler=t.wrap===2?0:1,t.last_flush=-2,Y$(t),Ce},UM=e=>{let t=WM(e);return t===Ce&&wY(e.state),t},xY=(e,t)=>ha(e)||e.state.wrap!==2?Jt:(e.state.gzhead=t,Ce),GM=(e,t,r,n,i,o)=>{if(!e)return Jt;let a=1;if(t===eY&&(t=6),n<0?(a=0,n=-n):n>15&&(a=2,n-=16),i<1||i>aY||r!==cf||n<8||n>15||t<0||t>9||o<0||o>nY||n===8&&a!==1)return kn(e,Jt);n===8&&(n=9);let u=new SY;return e.state=u,u.strm=e,u.status=Ni,u.wrap=a,u.gzhead=null,u.w_bits=n,u.w_size=1<<u.w_bits,u.w_mask=u.w_size-1,u.hash_bits=i+7,u.hash_size=1<<u.hash_bits,u.hash_mask=u.hash_size-1,u.hash_shift=~~((u.hash_bits+U-1)/U),u.window=new Uint8Array(u.w_size*2),u.head=new Uint16Array(u.hash_size),u.prev=new Uint16Array(u.w_size),u.lit_bufsize=1<<i+6,u.pending_buf_size=u.lit_bufsize*4,u.pending_buf=new Uint8Array(u.pending_buf_size),u.sym_buf=u.lit_bufsize,u.sym_end=(u.lit_bufsize-1)*3,u.level=t,u.strategy=o,u.method=r,UM(e)},EY=(e,t)=>GM(e,t,cf,uY,sY,iY),OY=(e,t)=>{if(ha(e)||t>YO||t<0)return e?kn(e,Jt):Jt;let r=e.state;if(!e.output||e.avail_in!==0&&!e.input||r.status===ea&&t!==gt)return kn(e,e.avail_out===0?Qh:Jt);let n=r.last_flush;if(r.last_flush=t,r.pending!==0){if(st(e),e.avail_out===0)return r.last_flush=-1,Ce}else if(e.avail_in===0&&ZO(t)<=ZO(n)&&t!==gt)return kn(e,Qh);if(r.status===ea&&e.avail_in!==0)return kn(e,Qh);if(r.status===Ni&&r.wrap===0&&(r.status=Tn),r.status===Ni){let i=cf+(r.w_bits-8<<4)<<8,o=-1;if(r.strategy>=ef||r.level<2?o=0:r.level<6?o=1:r.level===6?o=2:o=3,i|=o<<6,r.strstart!==0&&(i|=mY),i+=31-i%31,Qo(r,i),r.strstart!==0&&(Qo(r,e.adler>>>16),Qo(r,e.adler&65535)),e.adler=1,r.status=Tn,st(e),r.pending!==0)return r.last_flush=-1,Ce}if(r.status===Sm){if(e.adler=0,X(r,31),X(r,139),X(r,8),r.gzhead)X(r,(r.gzhead.text?1:0)+(r.gzhead.hcrc?2:0)+(r.gzhead.extra?4:0)+(r.gzhead.name?8:0)+(r.gzhead.comment?16:0)),X(r,r.gzhead.time&255),X(r,r.gzhead.time>>8&255),X(r,r.gzhead.time>>16&255),X(r,r.gzhead.time>>24&255),X(r,r.level===9?2:r.strategy>=ef||r.level<2?4:0),X(r,r.gzhead.os&255),r.gzhead.extra&&r.gzhead.extra.length&&(X(r,r.gzhead.extra.length&255),X(r,r.gzhead.extra.length>>8&255)),r.gzhead.hcrc&&(e.adler=Oe(e.adler,r.pending_buf,r.pending,0)),r.gzindex=0,r.status=pm;else if(X(r,0),X(r,0),X(r,0),X(r,0),X(r,0),X(r,r.level===9?2:r.strategy>=ef||r.level<2?4:0),X(r,vY),r.status=Tn,st(e),r.pending!==0)return r.last_flush=-1,Ce}if(r.status===pm){if(r.gzhead.extra){let i=r.pending,o=(r.gzhead.extra.length&65535)-r.gzindex;for(;r.pending+o>r.pending_buf_size;){let 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e.drawLabels&&e.rowHeight>=5}})).actions(e=>({setDrawMsaLetters(t){e.drawMsaLetters=t},zoomOutHorizontal(){e.colWidth=Math.max(1,Math.floor(e.colWidth*.75)),e.scrollX=Ut(e.maxScrollX,e.scrollX,0)},zoomInHorizontal(){e.colWidth=Math.ceil(e.colWidth*1.5),e.scrollX=Ut(e.maxScrollX,e.scrollX,0)},zoomInVertical(){e.rowHeight=Math.ceil(e.rowHeight*1.5)},zoomOutVertical(){e.rowHeight=Math.max(1.5,Math.floor(e.rowHeight*.75))},zoomIn(){(0,Ct.transaction)(()=>{e.colWidth=Math.ceil(e.colWidth*1.5),e.rowHeight=Math.ceil(e.rowHeight*1.5),e.scrollX=Ut(e.maxScrollX,e.scrollX,0)})},zoomOut(){(0,Ct.transaction)(()=>{e.colWidth=Math.max(1,Math.floor(e.colWidth*.75)),e.rowHeight=Math.max(1.5,Math.floor(e.rowHeight*.75)),e.scrollX=Ut(e.maxScrollX,e.scrollX,0)})},setInterProAnnotations(t){e.interProAnnotations=t},doScrollY(t){e.scrollY=Ut(-e.totalHeight+10,e.scrollY+t,0)},doScrollX(t){e.scrollX=Ut(e.maxScrollX,e.scrollX+t,0)},setScrollX(t){e.scrollX=Ut(e.maxScrollX,t,0)},toggleTrack(t){e.turnedOffTracks.has(t)?e.turnedOffTracks.delete(t):e.turnedOffTracks.set(t,!0)},setStatus(t){e.status=t}})).views(e=>({get 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n.get(t)?.[Cm(i,r)]},mouseOverCoordToGapRemovedRowCoord(t,r){let{rowMap:n,blanks:i}=e,o=n.get(t);if(o!==void 0){let a=Cm(i,r),u=WA(o,a);return o[u]==="-"||!o[u]?void 0:u}else return},seqCoordToRowSpecificGlobalCoord(t,r){let{rowNames:n,rows:i}=e,o=n.indexOf(t);if(o!==-1&&i[o]){let a=i[o][1],u=0,d=0;for(;u<r;d++)if(a[d]!=="-")u++;else if(u>=r)break;return d}return 0}})).views(e=>({get msaAreaHeight(){return e.height-(e.showHorizontalScrollbar?e.minimapHeight:0)-e.headerHeight},get totalTrackAreaHeight(){return(0,Ln.sum)(e.turnedOnTracks.map(t=>t.model.height))},get tidyInterProAnnotationTypes(){let t=new Map;for(let r of this.tidyInterProAnnotations)t.set(r.accession,r);return t},get tidyInterProAnnotations(){let t=[],{interProAnnotations:r}=e;if(r)for(let[n,i]of Object.entries(r))for(let{signature:o,locations:a}of i.matches){let{entry:u}=o;if(u){let{name:d,accession:l,description:f}=u;for(let{start:s,end:c}of a)t.push({id:n,name:d,accession:l,description:f,start:s,end:c})}}return 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d2=g((due,f2)=>{f2.exports=JBrowseExports["@jbrowse/core/pluggableElementTypes"]});async function p2(e,t){let r=await fetch(e,t);if(!r.ok)throw new Error(`HTTP ${r.status} fetching ${e} ${await r.text()}`);return r}async function je(e,t){return(await p2(e,t)).text()}async function h2(e,t){return(await p2(e,t)).json()}function _f(e){return new Promise(t=>setTimeout(t,e))}var Lm=C(()=>{"use strict"});async function v2({query:e,blastDatabase:t,blastProgram:r,onProgress:n,onRid:i}){n("Submitting to NCBI BLAST...");let{rid:o}=await bZ({query:e,blastDatabase:t,blastProgram:r});i(o),await gZ({rid:o,onProgress:n});let a=await h2(`${xa}?CMD=Get&RID=${o}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);return{rid:o,hits:a.BlastOutput2[0]?.report.results.search.hits??[]}}async function bZ({query:e,blastProgram:t,blastDatabase:r}){let n=await je(xa,{method:"POST",body:new URLSearchParams({CMD:"Put",PROGRAM:t,DATABASE:r,QUERY:e,...r==="nr_clustered_seq"?{CLUSTERED_DB:"on",DB_TYPE:"Experimental 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strict";Ef=x(R()),Of=x(B());A2();Dm();zm=wZ});function SZ({rid:e,error:t}){return wt.default.createElement("div",null,e?wt.default.createElement(zm,{rid:e}):null,wt.default.createElement(Mf.ErrorMessage,{error:t}))}function xZ({rid:e,progress:t}){let{classes:r}=k2();return wt.default.createElement("div",{className:r.loading},e?wt.default.createElement(zm,{rid:e}):null,wt.default.createElement(Hm.Typography,null,t))}var wt,Hm,q2,T2,Mf,k2,EZ,C2,j2=C(()=>{"use strict";wt=x(R()),Hm=x(B()),q2=x(D()),T2=x(It()),Mf=x(Ae());P2();k2=(0,T2.makeStyles)()(e=>({margin:{padding:20},loading:{background:e.palette.background.paper}}));EZ=(0,q2.observer)(function({model:t}){let{progress:r,rid:n,error:i,processing:o}=t,{classes:a}=k2();return wt.default.createElement("div",{className:a.margin},wt.default.createElement(Mf.LoadingEllipses,{message:"Running NCBI 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Sf=x(Me()),E2=x(d2());Lm();var ct="https://www.ebi.ac.uk/Tools/services/rest";async function hZ({sequence:e,onProgress:t}){let r=await je(`${ct}/clustalo/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",sequence:e})});return await bf({jobId:r,algorithm:"clustalo",onProgress:t}),{msa:await je(`${ct}/clustalo/result/${r}/aln-clustal_num`),tree:await je(`${ct}/clustalo/result/${r}/phylotree`)}}async function mZ({sequence:e,onProgress:t}){let r=await je(`${ct}/muscle/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",format:"clw",tree:"tree1",sequence:e})});return await bf({jobId:r,algorithm:"muscle",onProgress:t}),{msa:await je(`${ct}/muscle/result/${r}/fa`),tree:await je(`${ct}/muscle/result/${r}/phylotree`)}}async function vZ({sequence:e,onProgress:t}){let r=await je(`${ct}/kalign/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await bf({jobId:r,algorithm:"kalign",onProgress:t}),{msa:await je(`${ct}/kalign/result/${r}/fa`),tree:await je(`${ct}/kalign/result/${r}/phylotree`)}}async function _Z({sequence:e,onProgress:t}){let r=await je(`${ct}/mafft/run`,{method:"POST",body:new URLSearchParams({email:"colin.diesh@gmail.com",stype:"protein",sequence:e})});return await bf({jobId:r,algorithm:"mafft",onProgress:t}),{msa:await je(`${ct}/mafft/result/${r}/fa`),tree:await je(`${ct}/mafft/result/${r}/phylotree`)}}async function bf({onProgress:e,jobId:t,algorithm:r}){for(;;){for(let i=0;i<10;i++)await _f(1e3),e(`Re-checking MSA status in... ${10-i}`);let n=await je(`${ct}/${r}/status/${t}`);if(n==="FINISHED")break;if(n.includes("FAILURE"))throw new Error(`Failed to run: jobId ${t}`)}}async function m2({algorithm:e,sequence:t,onProgress:r}){switch(r(`Launching ${e} MSA...`),e){case"clustalo":return hZ({sequence:t,onProgress:r});case"muscle":return mZ({sequence:t,onProgress:r});case"kalign":return vZ({sequence:t,onProgress:r});case"mafft":return _Z({sequence:t,onProgress:r});default:throw new Error("unknown algorithm")}}Dm();function _2(e){return`${e.accession}-${e.sciname.replaceAll(" ","_")}`}function b2(e){return e.replace("-","")}async function g2({self:e}){let{blastDatabase:t,blastProgram:r,msaAlgorithm:n,proteinSequence:i}=e.blastParams,o=i.replaceAll("*","").replaceAll("&",""),{hits:a}=await v2({query:o,blastDatabase:t,blastProgram:r,onProgress:l=>{e.setProgress(l)},onRid:l=>{e.setRid(l)}}),u=[`>QUERY
+${o}`,...a.map(l=>[_2(l.description[0]??{accession:"unknown",id:"unknown",sciname:"unknown"}),b2(l.hsps[0]?.hseq??"")]).map(([l,f])=>`>${l}
+${f}`)].join(`
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 /*! Bundled license information:
 
 canvas2svg/canvas2svg.js: