npm - jbrowse-plugin-msaview - Versions diffs - 1.0.18 → 2.0.1 - Mend

jbrowse-plugin-msaview 1.0.18 → 2.0.1

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Files changed (147) hide show

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

@@ -1,2 +1,94 @@
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Redistributions of source code must retain the above copyright notice, this\nlist of conditions and the following disclaimer.\n\n2. Redistributions in binary form must reproduce the above copyright notice,\nthis list of conditions and the following disclaimer in the documentation and/or\nother materials provided with the distribution.\n\n3. Neither the name of the copyright holder nor the names of its contributors\nmay be used to endorse or promote products derived from this software without\nspecific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND\nANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\nWARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. 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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
+UniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM
+UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM
+UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------
+UniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS
+UniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV
+UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP
+UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
+UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
+UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
+`,mm=`CLUSTAL O(1.2.4) multiple sequence alignment
+sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
+sp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG	60
+sp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG	60
+                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**
+sp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP	120
+sp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP	120
+sp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA	120
+                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**
+sp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR	142
+sp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR	142
+sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
+                           .**: ****: ** ***.***`,vm="(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)"});var Fe,ra,bm,Vt,L2,gm,ym=C(()=>{Fe=x(R()),ra=x(B()),bm=x(D());_m();Xc();Vt=({onClick:e,model:t,children:r})=>Fe.default.createElement("li",null,Fe.default.createElement(ra.Link,{onClick:n=>{t.setError(void 0),n.preventDefault(),e()},href:"#"},Fe.default.createElement(ra.Typography,{display:"inline"},r))),L2=(0,bm.observer)(function({model:e}){return Fe.default.createElement("ul",null,Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,void 0,{uri:"https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh",locationType:"UriLocation"})},"230k COVID-19 samples (tree only)"),Fe.default.createElement(Vt,{model:e,onClick:()=>{e.setData({msa:hm,tree:vm})}},"Small protein MSA+tree"),Fe.default.createElement(Vt,{model:e,onClick:()=>{e.setData({msa:mm})}},"Small MSA only"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/pfam-cov2.stock",locationType:"UriLocation"})},"PFAM SARS-CoV2 multi-stockholm"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock",locationType:"UriLocation"})},"Lysine stockholm file"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt",locationType:"UriLocation"})},"PF01601 stockholm file (SARS-CoV2 spike protein)"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa",locationType:"UriLocation"})},"Europe COVID full genomes (LR883044.1 and 199 other sequences)"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.fa",locationType:"UriLocation"},{uri:"https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh",locationType:"UriLocation"})},"MAFFT+VeryFastTree(17.9k samples)"),Fe.default.createElement(Vt,{model:e,onClick:()=>wt(e,{uri:"https://jbrowse.org/demos/ttc39a.mfa",locationType:"UriLocation"})},"Human BLAST results mfa"))}),gm=L2});var se,wm,Me,Zc,Sm,xm=C(()=>{se=x(R()),wm=x(D()),Me=x(B()),Zc=x(Te());Xc();ym();Sm=(0,wm.observer)(({model:e})=>{let[t,r]=(0,se.useState)(),[n,i]=(0,se.useState)(),{error:o}=e;return se.default.createElement(Me.Container,null,se.default.createElement("div",{style:{width:"50%"}},o?se.default.createElement("div",{style:{padding:20}},se.default.createElement(Me.Typography,{color:"error"},"Error: ",`${o}`)):null,se.default.createElement(Me.Typography,null,"Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),se.default.createElement(Me.Typography,{color:"error"},"Note: you can open up just an MSA or just a tree, both are not required. 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r=t.dyn_tree,n=t.max_code,i=t.stat_desc.static_tree,o=t.stat_desc.has_stree,a=t.stat_desc.extra_bits,u=t.stat_desc.extra_base,p=t.stat_desc.max_length,l,d,s,c,f,m,v=0;for(c=0;c<=pn;c++)e.bl_count[c]=0;for(r[e.heap[e.heap_max]*2+1]=0,l=e.heap_max+1;l<xO;l++)d=e.heap[l],c=r[r[d*2+1]*2+1]+1,c>p&&(c=p,v++),r[d*2+1]=c,!(d>n)&&(e.bl_count[c]++,f=0,d>=u&&(f=a[d-u]),m=r[d*2],e.opt_len+=m*(c+f),o&&(e.static_len+=m*(i[d*2+1]+f)));if(v!==0){do{for(c=p-1;e.bl_count[c]===0;)c--;e.bl_count[c]--,e.bl_count[c+1]+=2,e.bl_count[p]--,v-=2}while(v>0);for(c=p;c!==0;c--)for(d=e.bl_count[c];d!==0;)s=e.heap[--l],!(s>n)&&(r[s*2+1]!==c&&(e.opt_len+=(c-r[s*2+1])*r[s*2],r[s*2+1]=c),d--)}},jO=(e,t,r)=>{let n=new Array(pn+1),i=0,o,a;for(o=1;o<=pn;o++)i=i+r[o-1]<<1,n[o]=i;for(a=0;a<=t;a++){let u=e[a*2+1];u!==0&&(e[a*2]=CO(n[u]++,u))}},AU=()=>{let e,t,r,n,i,o=new Array(pn+1);for(r=0,n=0;n<Fh-1;n++)for(Bh[n]=r,e=0;e<1<<Ph[n];e++)zo[r++]=n;for(zo[r-1]=n,i=0,n=0;n<16;n++)for(Lc[n]=i,e=0;e<1<<Rc[n];e++)Bo[i++]=n;for(i>>=7;n<yi;n++)for(Lc[n]=i<<7,e=0;e<1<<Rc[n]-7;e++)Bo[256+i++]=n;for(t=0;t<=pn;t++)o[t]=0;for(e=0;e<=143;)ar[e*2+1]=8,e++,o[8]++;for(;e<=255;)ar[e*2+1]=9,e++,o[9]++;for(;e<=279;)ar[e*2+1]=7,e++,o[7]++;for(;e<=287;)ar[e*2+1]=8,e++,o[8]++;for(jO(ar,No+1,o),e=0;e<yi;e++)Lo[e*2+1]=5,Lo[e*2]=CO(e,5);PO=new mh(ar,Ph,$o+1,No,pn),qO=new mh(Lo,Rc,0,yi,pn),kO=new mh(new Array(0),xU,0,Dh,SU)},IO=e=>{let t;for(t=0;t<No;t++)e.dyn_ltree[t*2]=0;for(t=0;t<yi;t++)e.dyn_dtree[t*2]=0;for(t=0;t<Dh;t++)e.bl_tree[t*2]=0;e.dyn_ltree[Nh*2]=1,e.opt_len=e.static_len=0,e.sym_next=e.matches=0},RO=e=>{e.bi_valid>8?Ho(e,e.bi_buf):e.bi_valid>0&&(e.pending_buf[e.pending++]=e.bi_buf),e.bi_buf=0,e.bi_valid=0},DM=(e,t,r,n)=>{let i=t*2,o=r*2;return e[i]<e[o]||e[i]===e[o]&&n[t]<=n[r]},_h=(e,t,r)=>{let n=e.heap[r],i=r<<1;for(;i<=e.heap_len&&(i<e.heap_len&&DM(t,e.heap[i+1],e.heap[i],e.depth)&&i++,!DM(t,n,e.heap[i],e.depth));)e.heap[r]=e.heap[i],r=i,i<<=1;e.heap[r]=n},NM=(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?Dt(e,i,t):(a=zo[i],Dt(e,a+$o+1,t),u=Ph[a],u!==0&&(i-=Bh[a],We(e,i,u)),n--,a=TO(n),Dt(e,a,r),u=Rc[a],u!==0&&(n-=Lc[a],We(e,n,u)));while(o<e.sym_next);Dt(e,Nh,t)},qh=(e,t)=>{let r=t.dyn_tree,n=t.stat_desc.static_tree,i=t.stat_desc.has_stree,o=t.stat_desc.elems,a,u,p=-1,l;for(e.heap_len=0,e.heap_max=xO,a=0;a<o;a++)r[a*2]!==0?(e.heap[++e.heap_len]=p=a,e.depth[a]=0):r[a*2+1]=0;for(;e.heap_len<2;)l=e.heap[++e.heap_len]=p<2?++p:0,r[l*2]=1,e.depth[l]=0,e.opt_len--,i&&(e.static_len-=n[l*2+1]);for(t.max_code=p,a=e.heap_len>>1;a>=1;a--)_h(e,r,a);l=o;do 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o!==0?(o!==i&&(Dt(e,o,e.bl_tree),u--),Dt(e,EO,e.bl_tree),We(e,u-3,2)):u<=10?(Dt(e,MO,e.bl_tree),We(e,u-3,3)):(Dt(e,OO,e.bl_tree),We(e,u-11,7));u=0,i=o,a===0?(p=138,l=3):o===a?(p=6,l=3):(p=7,l=4)}},PU=e=>{let t;for(BM(e,e.dyn_ltree,e.l_desc.max_code),BM(e,e.dyn_dtree,e.d_desc.max_code),qh(e,e.bl_desc),t=Dh-1;t>=3&&e.bl_tree[AO[t]*2+1]===0;t--);return e.opt_len+=3*(t+1)+5+5+4,t},qU=(e,t,r,n)=>{let i;for(We(e,t-257,5),We(e,r-1,5),We(e,n-4,4),i=0;i<n;i++)We(e,e.bl_tree[AO[i]*2+1],3);zM(e,e.dyn_ltree,t-1),zM(e,e.dyn_dtree,r-1)},kU=e=>{let t=4093624447,r;for(r=0;r<=31;r++,t>>>=1)if(t&1&&e.dyn_ltree[r*2]!==0)return 0;if(e.dyn_ltree[9*2]!==0||e.dyn_ltree[10*2]!==0||e.dyn_ltree[13*2]!==0)return 1;for(r=32;r<$o;r++)if(e.dyn_ltree[r*2]!==0)return 1;return 0},HM=!1,TU=e=>{HM||(AU(),HM=!0),e.l_desc=new vh(e.dyn_ltree,PO),e.d_desc=new vh(e.dyn_dtree,qO),e.bl_desc=new vh(e.bl_tree,kO),e.bi_buf=0,e.bi_valid=0,IO(e)},LO=(e,t,r,n)=>{We(e,(bU<<1)+(n?1:0),3),RO(e),Ho(e,r),Ho(e,~r),r&&e.pending_buf.set(e.window.subarray(t,t+r),e.pending),e.pending+=r},CU=e=>{We(e,SO<<1,3),Dt(e,Nh,ar),MU(e)},jU=(e,t,r,n)=>{let i,o,a=0;e.level>0?(e.strm.data_type===2&&(e.strm.data_type=kU(e)),qh(e,e.l_desc),qh(e,e.d_desc),a=PU(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?LO(e,t,r,n):e.strategy===4||o===i?(We(e,(SO<<1)+(n?1:0),3),NM(e,ar,Lo)):(We(e,(gU<<1)+(n?1:0),3),qU(e,e.l_desc.max_code+1,e.d_desc.max_code+1,a+1),NM(e,e.dyn_ltree,e.dyn_dtree)),IO(e),n&&RO(e)},IU=(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[(zo[r]+$o+1)*2]++,e.dyn_dtree[TO(t)*2]++),e.sym_next===e.sym_end),RU=TU,LU=LO,FU=jU,DU=IU,NU=CU,BU={_tr_init:RU,_tr_stored_block:LU,_tr_flush_block:FU,_tr_tally:DU,_tr_align:NU},zU=(e,t,r,n)=>{let i=e&65535|0,o=e>>>16&65535|0,a=0;for(;r!==0;){a=r>2e3?2e3:r,r-=a;do i=i+t[n++]|0,o=o+i|0;while(--a);i%=65521,o%=65521}return i|o<<16|0},Vo=zU,HU=()=>{let e,t=[];for(var r=0;r<256;r++){e=r;for(var n=0;n<8;n++)e=e&1?3988292384^e>>>1:e>>>1;t[r]=e}return t},VU=new Uint32Array(HU()),UU=(e,t,r,n)=>{let i=VU,o=n+r;e^=-1;for(let a=n;a<o;a++)e=e>>>8^i[(e^t[a])&255];return e^-1},ge=UU,vn={2:"need dictionary",1:"stream end",0:"","-1":"file error","-2":"stream error","-3":"data error","-4":"insufficient memory","-5":"buffer error","-6":"incompatible version"},Ei={Z_NO_FLUSH:0,Z_PARTIAL_FLUSH:1,Z_SYNC_FLUSH:2,Z_FULL_FLUSH:3,Z_FINISH:4,Z_BLOCK:5,Z_TREES:6,Z_OK:0,Z_STREAM_END:1,Z_NEED_DICT:2,Z_ERRNO:-1,Z_STREAM_ERROR:-2,Z_DATA_ERROR:-3,Z_MEM_ERROR:-4,Z_BUF_ERROR:-5,Z_NO_COMPRESSION:0,Z_BEST_SPEED:1,Z_BEST_COMPRESSION:9,Z_DEFAULT_COMPRESSION:-1,Z_FILTERED:1,Z_HUFFMAN_ONLY:2,Z_RLE:3,Z_FIXED:4,Z_DEFAULT_STRATEGY:0,Z_BINARY:0,Z_TEXT:1,Z_UNKNOWN:2,Z_DEFLATED:8},{_tr_init:WU,_tr_stored_block:kh,_tr_flush_block:GU,_tr_tally:Nr,_tr_align:$U}=BU,{Z_NO_FLUSH:Br,Z_PARTIAL_FLUSH:YU,Z_FULL_FLUSH:XU,Z_FINISH:lt,Z_BLOCK:VM,Z_OK:Ee,Z_STREAM_END:UM,Z_STREAM_ERROR:Nt,Z_DATA_ERROR:ZU,Z_BUF_ERROR:bh,Z_DEFAULT_COMPRESSION:KU,Z_FILTERED:JU,Z_HUFFMAN_ONLY:kc,Z_RLE:QU,Z_FIXED:eW,Z_DEFAULT_STRATEGY:tW,Z_UNKNOWN:rW,Z_DEFLATED:Nc}=Ei,nW=9,iW=15,oW=8,aW=29,uW=256,Th=uW+1+aW,sW=30,lW=19,cW=2*Th+1,fW=15,V=3,Dr=258,Bt=Dr+V+1,dW=32,wi=42,zh=57,Ch=69,jh=73,Ih=91,Rh=103,hn=113,Io=666,Ie=1,Mi=2,_n=3,Oi=4,pW=3,mn=(e,t)=>(e.msg=vn[t],t),WM=e=>e*2-(e>4?9:0),Fr=e=>{let t=e.length;for(;--t>=0;)e[t]=0},hW=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)},mW=(e,t,r)=>(t<<e.hash_shift^r)&e.hash_mask,zr=mW,tt=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))},rt=(e,t)=>{GU(e,e.block_start>=0?e.block_start:-1,e.strstart-e.block_start,t),e.block_start=e.strstart,tt(e.strm)},Y=(e,t)=>{e.pending_buf[e.pending++]=t},jo=(e,t)=>{e.pending_buf[e.pending++]=t>>>8&255,e.pending_buf[e.pending++]=t&255},Lh=(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=Vo(e.adler,t,i,r):e.state.wrap===2&&(e.adler=ge(e.adler,t,i,r)),e.next_in+=i,e.total_in+=i,i)},FO=(e,t)=>{let r=e.max_chain_length,n=e.strstart,i,o,a=e.prev_length,u=e.nice_match,p=e.strstart>e.w_size-Bt?e.strstart-(e.w_size-Bt):0,l=e.window,d=e.w_mask,s=e.prev,c=e.strstart+Dr,f=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]!==f||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=Dr-(c-n),n=c-Dr,o>a){if(e.match_start=t,a=o,o>=u)break;f=l[n+a-1],m=l[n+a]}}while((t=s[t&d])>p&&--r!==0);return a<=e.lookahead?a:e.lookahead},Si=e=>{let t=e.w_size,r,n,i;do{if(n=e.window_size-e.lookahead-e.strstart,e.strstart>=t+(t-Bt)&&(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),hW(e),n+=t),e.strm.avail_in===0)break;if(r=Lh(e.strm,e.window,e.strstart+e.lookahead,n),e.lookahead+=r,e.lookahead+e.insert>=V)for(i=e.strstart-e.insert,e.ins_h=e.window[i],e.ins_h=zr(e,e.ins_h,e.window[i+1]);e.insert&&(e.ins_h=zr(e,e.ins_h,e.window[i+V-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<V)););}while(e.lookahead<Bt&&e.strm.avail_in!==0)},DO=(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!==lt||t===Br||n!==i+e.strm.avail_in)))break;a=t===lt&&n===i+e.strm.avail_in?1:0,kh(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,tt(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&&(Lh(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?Oi:t!==Br&&t!==lt&&e.strm.avail_in===0&&e.strstart===e.block_start?Mi:(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&&(Lh(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===lt)&&t!==Br&&e.strm.avail_in===0&&i<=o)&&(n=i>o?o:i,a=t===lt&&e.strm.avail_in===0&&n===i?1:0,kh(e,e.block_start,n,a),e.block_start+=n,tt(e.strm)),a?_n:Ie)},gh=(e,t)=>{let r,n;for(;;){if(e.lookahead<Bt){if(Si(e),e.lookahead<Bt&&t===Br)return Ie;if(e.lookahead===0)break}if(r=0,e.lookahead>=V&&(e.ins_h=zr(e,e.ins_h,e.window[e.strstart+V-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-Bt&&(e.match_length=FO(e,r)),e.match_length>=V)if(n=Nr(e,e.strstart-e.match_start,e.match_length-V),e.lookahead-=e.match_length,e.match_length<=e.max_lazy_match&&e.lookahead>=V){e.match_length--;do e.strstart++,e.ins_h=zr(e,e.ins_h,e.window[e.strstart+V-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=zr(e,e.ins_h,e.window[e.strstart+1]);else n=Nr(e,0,e.window[e.strstart]),e.lookahead--,e.strstart++;if(n&&(rt(e,!1),e.strm.avail_out===0))return Ie}return e.insert=e.strstart<V-1?e.strstart:V-1,t===lt?(rt(e,!0),e.strm.avail_out===0?_n:Oi):e.sym_next&&(rt(e,!1),e.strm.avail_out===0)?Ie:Mi},bi=(e,t)=>{let r,n,i;for(;;){if(e.lookahead<Bt){if(Si(e),e.lookahead<Bt&&t===Br)return 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e.insert=0,t===lt?(rt(e,!0),e.strm.avail_out===0?_n:Oi):e.sym_next&&(rt(e,!1),e.strm.avail_out===0)?Ie:Mi};function Ft(e,t,r,n,i){this.good_length=e,this.max_lazy=t,this.nice_length=r,this.max_chain=n,this.func=i}var Ro=[new Ft(0,0,0,0,DO),new Ft(4,4,8,4,gh),new Ft(4,5,16,8,gh),new Ft(4,6,32,32,gh),new Ft(4,4,16,16,bi),new Ft(8,16,32,32,bi),new Ft(8,16,128,128,bi),new Ft(8,32,128,256,bi),new Ft(32,128,258,1024,bi),new Ft(32,258,258,4096,bi)],bW=e=>{e.window_size=2*e.w_size,Fr(e.head),e.max_lazy_match=Ro[e.level].max_lazy,e.good_match=Ro[e.level].good_length,e.nice_match=Ro[e.level].nice_length,e.max_chain_length=Ro[e.level].max_chain,e.strstart=0,e.block_start=0,e.lookahead=0,e.insert=0,e.match_length=e.prev_length=V-1,e.match_available=0,e.ins_h=0};function 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e;u--,l+=n[o++]<<d,d+=8}r.head&&(r.head.time=l),r.flags&512&&r.wrap&4&&(O[0]=l&255,O[1]=l>>>8&255,O[2]=l>>>16&255,O[3]=l>>>24&255,r.check=ge(r.check,O,4,0)),l=0,d=0,r.mode=eO;case eO:for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.head&&(r.head.xflags=l&255,r.head.os=l>>8),r.flags&512&&r.wrap&4&&(O[0]=l&255,O[1]=l>>>8&255,r.check=ge(r.check,O,2,0)),l=0,d=0,r.mode=tO;case tO:if(r.flags&1024){for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.length=l,r.head&&(r.head.extra_len=l),r.flags&512&&r.wrap&4&&(O[0]=l&255,O[1]=l>>>8&255,r.check=ge(r.check,O,2,0)),l=0,d=0}else r.head&&(r.head.extra=null);r.mode=rO;case rO:if(r.flags&1024&&(f=r.length,f>u&&(f=u),f&&(r.head&&(A=r.head.extra_len-r.length,r.head.extra||(r.head.extra=new Uint8Array(r.head.extra_len)),r.head.extra.set(n.subarray(o,o+f),A)),r.flags&512&&r.wrap&4&&(r.check=ge(r.check,n,f,o)),u-=f,o+=f,r.length-=f),r.length))break e;r.length=0,r.mode=nO;case nO:if(r.flags&2048){if(u===0)break e;f=0;do A=n[o+f++],r.head&&A&&r.length<65536&&(r.head.name+=String.fromCharCode(A));while(A&&f<u);if(r.flags&512&&r.wrap&4&&(r.check=ge(r.check,n,f,o)),u-=f,o+=f,A)break e}else r.head&&(r.head.name=null);r.length=0,r.mode=iO;case iO:if(r.flags&4096){if(u===0)break e;f=0;do A=n[o+f++],r.head&&A&&r.length<65536&&(r.head.comment+=String.fromCharCode(A));while(A&&f<u);if(r.flags&512&&r.wrap&4&&(r.check=ge(r.check,n,f,o)),u-=f,o+=f,A)break e}else r.head&&(r.head.comment=null);r.mode=oO;case oO:if(r.flags&512){for(;d<16;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(r.wrap&4&&l!==(r.check&65535)){e.msg="header crc mismatch",r.mode=ne;break}l=0,d=0}r.head&&(r.head.hcrc=r.flags>>9&1,r.head.done=!0),e.adler=r.check=0,r.mode=or;break;case aO:for(;d<32;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}e.adler=r.check=gO(l),l=0,d=0,r.mode=Dc;case Dc:if(r.havedict===0)return e.next_out=a,e.avail_out=p,e.next_in=o,e.avail_in=u,r.hold=l,r.bits=d,hG;e.adler=r.check=1,r.mode=or;case or:if(t===dG||t===Cc)break e;case wh:if(r.last){l>>>=d&7,d-=d&7,r.mode=xh;break}for(;d<3;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}switch(r.last=l&1,l>>>=1,d-=1,l&3){case 0:r.mode=uO;break;case 1:if(SG(r),r.mode=jc,t===Cc){l>>>=2,d-=2;break e}break;case 2:r.mode=lO;break;case 3:e.msg="invalid block type",r.mode=ne}l>>>=2,d-=2;break;case uO:for(l>>>=d&7,d-=d&7;d<32;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if((l&65535)!==(l>>>16^65535)){e.msg="invalid stored block lengths",r.mode=ne;break}if(r.length=l&65535,l=0,d=0,r.mode=Sh,t===Cc)break e;case Sh:r.mode=sO;case sO:if(f=r.length,f){if(f>u&&(f=u),f>p&&(f=p),f===0)break e;i.set(n.subarray(o,o+f),a),u-=f,o+=f,p-=f,a+=f,r.length-=f;break}r.mode=or;break;case lO:for(;d<14;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(r.nlen=(l&31)+257,l>>>=5,d-=5,r.ndist=(l&31)+1,l>>>=5,d-=5,r.ncode=(l&15)+4,l>>>=4,d-=4,r.nlen>286||r.ndist>30){e.msg="too many length or distance symbols",r.mode=ne;break}r.have=0,r.mode=cO;case cO:for(;r.have<r.ncode;){for(;d<3;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.lens[I[r.have++]]=l&7,l>>>=3,d-=3}for(;r.have<19;)r.lens[I[r.have++]]=0;if(r.lencode=r.lendyn,r.lenbits=7,P={bits:r.lenbits},q=Do(fG,r.lens,0,19,r.lencode,0,r.work,P),r.lenbits=P.bits,q){e.msg="invalid code lengths set",r.mode=ne;break}r.have=0,r.mode=fO;case fO:for(;r.have<r.nlen+r.ndist;){for(;h=r.lencode[l&(1<<r.lenbits)-1],_=h>>>24,y=h>>>16&255,w=h&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(w<16)l>>>=_,d-=_,r.lens[r.have++]=w;else{if(w===16){for(k=_+2;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(l>>>=_,d-=_,r.have===0){e.msg="invalid bit length repeat",r.mode=ne;break}A=r.lens[r.have-1],f=3+(l&3),l>>>=2,d-=2}else if(w===17){for(k=_+3;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=_,d-=_,A=0,f=3+(l&7),l>>>=3,d-=3}else{for(k=_+7;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=_,d-=_,A=0,f=11+(l&127),l>>>=7,d-=7}if(r.have+f>r.nlen+r.ndist){e.msg="invalid bit length repeat",r.mode=ne;break}for(;f--;)r.lens[r.have++]=A}}if(r.mode===ne)break;if(r.lens[256]===0){e.msg="invalid code -- missing end-of-block",r.mode=ne;break}if(r.lenbits=9,P={bits:r.lenbits},q=Do(WO,r.lens,0,r.nlen,r.lencode,0,r.work,P),r.lenbits=P.bits,q){e.msg="invalid literal/lengths set",r.mode=ne;break}if(r.distbits=6,r.distcode=r.distdyn,P={bits:r.distbits},q=Do(GO,r.lens,r.nlen,r.ndist,r.distcode,0,r.work,P),r.distbits=P.bits,q){e.msg="invalid distances set",r.mode=ne;break}if(r.mode=jc,t===Cc)break e;case jc:r.mode=Ic;case Ic:if(u>=6&&p>=258){e.next_out=a,e.avail_out=p,e.next_in=o,e.avail_in=u,r.hold=l,r.bits=d,oG(e,c),a=e.next_out,i=e.output,p=e.avail_out,o=e.next_in,n=e.input,u=e.avail_in,l=r.hold,d=r.bits,r.mode===or&&(r.back=-1);break}for(r.back=0;h=r.lencode[l&(1<<r.lenbits)-1],_=h>>>24,y=h>>>16&255,w=h&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(y&&!(y&240)){for(S=_,E=y,M=w;h=r.lencode[M+((l&(1<<S+E)-1)>>S)],_=h>>>24,y=h>>>16&255,w=h&65535,!(S+_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=S,d-=S,r.back+=S}if(l>>>=_,d-=_,r.back+=_,r.length=w,y===0){r.mode=vO;break}if(y&32){r.back=-1,r.mode=or;break}if(y&64){e.msg="invalid literal/length code",r.mode=ne;break}r.extra=y&15,r.mode=dO;case dO:if(r.extra){for(k=r.extra;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.length+=l&(1<<r.extra)-1,l>>>=r.extra,d-=r.extra,r.back+=r.extra}r.was=r.length,r.mode=pO;case pO:for(;h=r.distcode[l&(1<<r.distbits)-1],_=h>>>24,y=h>>>16&255,w=h&65535,!(_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}if(!(y&240)){for(S=_,E=y,M=w;h=r.distcode[M+((l&(1<<S+E)-1)>>S)],_=h>>>24,y=h>>>16&255,w=h&65535,!(S+_<=d);){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}l>>>=S,d-=S,r.back+=S}if(l>>>=_,d-=_,r.back+=_,y&64){e.msg="invalid distance code",r.mode=ne;break}r.offset=w,r.extra=y&15,r.mode=hO;case hO:if(r.extra){for(k=r.extra;d<k;){if(u===0)break e;u--,l+=n[o++]<<d,d+=8}r.offset+=l&(1<<r.extra)-1,l>>>=r.extra,d-=r.extra,r.back+=r.extra}if(r.offset>r.dmax){e.msg="invalid distance too far back",r.mode=ne;break}r.mode=mO;case mO:if(p===0)break e;if(f=c-p,r.offset>f){if(f=r.offset-f,f>r.whave&&r.sane){e.msg="invalid distance too far back",r.mode=ne;break}f>r.wnext?(f-=r.wnext,m=r.wsize-f):m=r.wnext-f,f>r.length&&(f=r.length),v=r.window}else v=i,m=a-r.offset,f=r.length;f>p&&(f=p),p-=f,r.length-=f;do i[a++]=v[m++];while(--f);r.length===0&&(r.mode=Ic);break;case vO:if(p===0)break e;i[a++]=r.length,p--,r.mode=Ic;break;case xh:if(r.wrap){for(;d<32;){if(u===0)break e;u--,l|=n[o++]<<d,d+=8}if(c-=p,e.total_out+=c,r.total+=c,r.wrap&4&&c&&(e.adler=r.check=r.flags?ge(r.check,i,c,a-c):Vo(r.check,i,c,a-c)),c=p,r.wrap&4&&(r.flags?l:gO(l))!==r.check){e.msg="incorrect data check",r.mode=ne;break}l=0,d=0}r.mode=_O;case _O:if(r.wrap&&r.flags){for(;d<32;){if(u===0)break 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+/*! Bundled license information:
+canvas2svg/canvas2svg.js:
+  (*!!
+   *  Canvas 2 Svg v1.0.15
+   *  A low level canvas to SVG converter. Uses a mock canvas context to build an SVG document.
+   *
+   *  Licensed under the MIT license:
+   *  http://www.opensource.org/licenses/mit-license.php
+   *
+   *  Author:
+   *  Kerry Liu
+   *
+   *  Copyright (c) 2014 Gliffy Inc.
+   *)
+svgcanvas/dist/svgcanvas.js:
+  (*!!
+   *  SVGCanvas v2.0.3
+   *  Draw on SVG using Canvas's 2D Context API.
+   *
+   *  Licensed under the MIT license:
+   *  http://www.opensource.org/licenses/mit-license.php
+   *
+   *  Author:
+   *  Kerry Liu
+   *  Zeno Zeng
+   *
+   *  Copyright (c) 2014 Gliffy Inc.
+   *  Copyright (c) 2021 Zeno Zeng
+   *)
+pako/dist/pako.esm.mjs:
+  (*! pako 2.1.0 https://github.com/nodeca/pako @license (MIT AND Zlib) *)
+*/
 //# sourceMappingURL=jbrowse-plugin-msaview.umd.production.min.js.map