jbrowse-plugin-msaview 1.0.14 → 1.0.18

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Files changed (14) hide show
  1. package/CHANGELOG.md +16 -0
  2. package/README.md +7 -4
  3. package/dist/jbrowse-plugin-msaview.cjs.development.js +11 -6
  4. package/dist/jbrowse-plugin-msaview.cjs.development.js.map +1 -1
  5. package/dist/jbrowse-plugin-msaview.cjs.production.min.js +1 -1
  6. package/dist/jbrowse-plugin-msaview.cjs.production.min.js.map +1 -1
  7. package/dist/jbrowse-plugin-msaview.esm.js +9 -3
  8. package/dist/jbrowse-plugin-msaview.esm.js.map +1 -1
  9. package/dist/jbrowse-plugin-msaview.umd.development.js +7059 -5440
  10. package/dist/jbrowse-plugin-msaview.umd.development.js.map +1 -1
  11. package/dist/jbrowse-plugin-msaview.umd.production.min.js +1 -1
  12. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +1 -1
  13. package/package.json +2 -3
  14. package/src/index.ts +5 -4
package/dist/jbrowse-plugin-msaview.umd.production.min.js CHANGED
@@ -1,2 +1,2 @@
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t,r=e[0]/255,n=e[1]/255,o=e[2]/255;return[100*((1-r-(t=Math.min(1-r,1-n,1-o)))/(1-t)||0),100*((1-n-t)/(1-t)||0),100*((1-o-t)/(1-t)||0),100*t]},n.rgb.keyword=function(e){var r=t[e];if(r)return r;var n,o,a,i=Infinity;for(var l in I)if(I.hasOwnProperty(l)){var s=(o=e,a=I[l],Math.pow(o[0]-a[0],2)+Math.pow(o[1]-a[1],2)+Math.pow(o[2]-a[2],2));s<i&&(i=s,n=l)}return n},n.keyword.rgb=function(e){return I[e]},n.rgb.xyz=function(e){var t=e[0]/255,r=e[1]/255,n=e[2]/255;return[100*(.4124*(t=t>.04045?Math.pow((t+.055)/1.055,2.4):t/12.92)+.3576*(r=r>.04045?Math.pow((r+.055)/1.055,2.4):r/12.92)+.1805*(n=n>.04045?Math.pow((n+.055)/1.055,2.4):n/12.92)),100*(.2126*t+.7152*r+.0722*n),100*(.0193*t+.1192*r+.9505*n)]},n.rgb.lab=function(e){var t=n.rgb.xyz(e),r=t[0],o=t[1],a=t[2];return o/=100,a/=108.883,r=(r/=95.047)>.008856?Math.pow(r,1/3):7.787*r+16/116,[116*(o=o>.008856?Math.pow(o,1/3):7.787*o+16/116)-16,500*(r-o),200*(o-(a=a>.008856?Math.pow(a,1/3):7.787*a+16/116))]},n.hsl.rgb=function(e){var t,r,n,o,a,i=e[0]/360,l=e[1]/100,s=e[2]/100;if(0===l)return[a=255*s,a,a];t=2*s-(r=s<.5?s*(1+l):s+l-s*l),o=[0,0,0];for(var c=0;c<3;c++)(n=i+1/3*-(c-1))<0&&n++,n>1&&n--,o[c]=255*(a=6*n<1?t+6*(r-t)*n:2*n<1?r:3*n<2?t+(r-t)*(2/3-n)*6:t);return o},n.hsl.hsv=function(e){var t=e[0],r=e[1]/100,n=e[2]/100,o=r,a=Math.max(n,.01);return r*=(n*=2)<=1?n:2-n,o*=a<=1?a:2-a,[t,100*(0===n?2*o/(a+o):2*r/(n+r)),(n+r)/2*100]},n.hsv.rgb=function(e){var t=e[0]/60,r=e[1]/100,n=e[2]/100,o=Math.floor(t)%6,a=t-Math.floor(t),i=255*n*(1-r),l=255*n*(1-r*a),s=255*n*(1-r*(1-a));switch(n*=255,o){case 0:return[n,s,i];case 1:return[l,n,i];case 2:return[i,n,s];case 3:return[i,l,n];case 4:return[s,i,n];case 5:return[n,i,l]}},n.hsv.hsl=function(e){var t,r,n,o=e[0],a=e[1]/100,i=e[2]/100,l=Math.max(i,.01);return n=(2-a)*i,r=a*l,[o,100*(r=(r/=(t=(2-a)*l)<=1?t:2-t)||0),100*(n/=2)]},n.hwb.rgb=function(e){var t,r,n,o,a,i,l,s=e[0]/360,c=e[1]/100,u=e[2]/100,h=c+u;switch(h>1&&(c/=h,u/=h),n=6*s-(t=Math.floor(6*s)),0!=(1&t)&&(n=1-n),o=c+n*((r=1-u)-c),t){default:case 6:case 0:a=r,i=o,l=c;break;case 1:a=o,i=r,l=c;break;case 2:a=c,i=r,l=o;break;case 3:a=c,i=o,l=r;break;case 4:a=o,i=c,l=r;break;case 5:a=r,i=c,l=o}return[255*a,255*i,255*l]},n.cmyk.rgb=function(e){var t=e[1]/100,r=e[2]/100,n=e[3]/100;return[255*(1-Math.min(1,e[0]/100*(1-n)+n)),255*(1-Math.min(1,t*(1-n)+n)),255*(1-Math.min(1,r*(1-n)+n))]},n.xyz.rgb=function(e){var t,r,n,o=e[0]/100,a=e[1]/100,i=e[2]/100;return r=-.9689*o+1.8758*a+.0415*i,n=.0557*o+-.204*a+1.057*i,t=(t=3.2406*o+-1.5372*a+-.4986*i)>.0031308?1.055*Math.pow(t,1/2.4)-.055:12.92*t,r=r>.0031308?1.055*Math.pow(r,1/2.4)-.055:12.92*r,n=n>.0031308?1.055*Math.pow(n,1/2.4)-.055:12.92*n,[255*(t=Math.min(Math.max(0,t),1)),255*(r=Math.min(Math.max(0,r),1)),255*(n=Math.min(Math.max(0,n),1))]},n.xyz.lab=function(e){var t=e[0],r=e[1],n=e[2];return 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t=e[0],r=e[1],n=e[2];return t===r&&r===n?t<8?16:t>248?231:Math.round((t-8)/247*24)+232:16+36*Math.round(t/255*5)+6*Math.round(r/255*5)+Math.round(n/255*5)},n.ansi16.rgb=function(e){var t=e%10;if(0===t||7===t)return e>50&&(t+=3.5),[t=t/10.5*255,t,t];var r=.5*(1+~~(e>50));return[(1&t)*r*255,(t>>1&1)*r*255,(t>>2&1)*r*255]},n.ansi256.rgb=function(e){if(e>=232){var t=10*(e-232)+8;return[t,t,t]}var r;return e-=16,[Math.floor(e/36)/5*255,Math.floor((r=e%36)/6)/5*255,r%6/5*255]},n.rgb.hex=function(e){var t=(((255&Math.round(e[0]))<<16)+((255&Math.round(e[1]))<<8)+(255&Math.round(e[2]))).toString(16).toUpperCase();return"000000".substring(t.length)+t},n.hex.rgb=function(e){var t=e.toString(16).match(/[a-f0-9]{6}|[a-f0-9]{3}/i);if(!t)return[0,0,0];var r=t[0];3===t[0].length&&(r=r.split("").map((function(e){return e+e})).join(""));var n=parseInt(r,16);return[n>>16&255,n>>8&255,255&n]},n.rgb.hcg=function(e){var t,r=e[0]/255,n=e[1]/255,o=e[2]/255,a=Math.max(Math.max(r,n),o),i=Math.min(Math.min(r,n),o),l=a-i;return t=l<=0?0:a===r?(n-o)/l%6:a===n?2+(o-r)/l:4+(r-n)/l+4,t/=6,[360*(t%=1),100*l,100*(l<1?i/(1-l):0)]},n.hsl.hcg=function(e){var t,r=e[1]/100,n=e[2]/100,o=0;return(t=n<.5?2*r*n:2*r*(1-n))<1&&(o=(n-.5*t)/(1-t)),[e[0],100*t,100*o]},n.hsv.hcg=function(e){var t=e[2]/100,r=e[1]/100*t,n=0;return r<1&&(n=(t-r)/(1-r)),[e[0],100*r,100*n]},n.hcg.rgb=function(e){var t=e[1]/100,r=e[2]/100;if(0===t)return[255*r,255*r,255*r];var n,o=[0,0,0],a=e[0]/360%1*6,i=a%1,l=1-i;switch(Math.floor(a)){case 0:o[0]=1,o[1]=i,o[2]=0;break;case 1:o[0]=l,o[1]=1,o[2]=0;break;case 2:o[0]=0,o[1]=1,o[2]=i;break;case 3:o[0]=0,o[1]=l,o[2]=1;break;case 4:o[0]=i,o[1]=0,o[2]=1;break;default:o[0]=1,o[1]=0,o[2]=l}return[255*(t*o[0]+(n=(1-t)*r)),255*(t*o[1]+n),255*(t*o[2]+n)]},n.hcg.hsv=function(e){var t=e[1]/100,r=t+e[2]/100*(1-t),n=0;return r>0&&(n=t/r),[e[0],100*n,100*r]},n.hcg.hsl=function(e){var t=e[1]/100,r=e[2]/100*(1-t)+.5*t,n=0;return r>0&&r<.5?n=t/(2*r):r>=.5&&r<1&&(n=t/(2*(1-r))),[e[0],100*n,100*r]},n.hcg.hwb=function(e){var t=e[1]/100,r=t+e[2]/100*(1-t);return[e[0],100*(r-t),100*(1-r)]},n.hwb.hcg=function(e){var t=1-e[2]/100,r=t-e[1]/100,n=0;return r<1&&(n=(t-r)/(1-r)),[e[0],100*r,100*n]},n.apple.rgb=function(e){return[e[0]/65535*255,e[1]/65535*255,e[2]/65535*255]},n.rgb.apple=function(e){return[e[0]/255*65535,e[1]/255*65535,e[2]/255*65535]},n.gray.rgb=function(e){return[e[0]/100*255,e[0]/100*255,e[0]/100*255]},n.gray.hsl=n.gray.hsv=function(e){return[0,0,e[0]]},n.gray.hwb=function(e){return[0,100,e[0]]},n.gray.cmyk=function(e){return[0,0,0,e[0]]},n.gray.lab=function(e){return[e[0],0,0]},n.gray.hex=function(e){var t=255&Math.round(e[0]/100*255),r=((t<<16)+(t<<8)+t).toString(16).toUpperCase();return"000000".substring(r.length)+r},n.rgb.gray=function(e){return[(e[0]+e[1]+e[2])/3/255*100]}}));function _(e,t){return function(r){return t(e(r))}}function q(e,t){for(var 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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. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR\nANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES\n(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;\nLOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON\nANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT\n(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS\nSOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n ')))}function lt(e){var t=e.onClose,r=e.open,o=n.useState(!1),a=o[1];return g.createElement(g.Fragment,null,g.createElement(it,{onClose:function(){return a(!1)},open:o[0]}),g.createElement(i.Dialog,{onClose:function(){return t()},open:r},g.createElement(i.DialogTitle,null,"About this plugin"),g.createElement(i.DialogContent,null,g.createElement(i.Typography,null,"JBrowse 2 MSAView plugin v1.0.0 (",g.createElement(i.Link,{href:"https://github.com/gmod/jbrowse-plugin-msaview"},"Github"),")"),g.createElement("ul",null,g.createElement("li",null,"We use some color schemes from the"," ",g.createElement(i.Link,{href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",g.createElement(i.Link,{onClick:function(){return a(!0)}},"here")),g.createElement("li",null,"See this page for some information on jalview colorings"," ",g.createElement(i.Link,{href:"https://www.jalview.org/help/html/colourSchemes/"},"here")),g.createElement("li",null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",g.createElement(i.Link,{href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here")),g.createElement("li",null,"See this paper about the flower color scheme"," ",g.createElement(i.Link,{href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}var st=a.observer((function(e){var t=e.onClose,r=e.model.alignmentDetails;return g.createElement(i.Dialog,{onClose:function(){return t()},open:e.open},g.createElement(i.DialogTitle,null,"Metadata"),g.createElement(i.DialogContent,null,g.createElement(l.Attributes,{attributes:r})))})),ct=a.observer((function(e){var t=e.model,r=n.useState(),o=r[0],a=r[1],l=n.useState(),u=l[0],h=l[1];return g.createElement(i.Container,{className:{}.importFormContainer},g.createElement("div",{style:{width:"50%"}},g.createElement(i.Typography,null,"Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),g.createElement(i.Typography,{color:"error"},"Note: you can open up just an MSA or just a tree, both are not required. 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Ln(this,void 0,void 0,(function(){return Tn(this,(function(n){return e.msaFilehandle=t,[2]}))}))},setTreeFilehandle:function(t){return Ln(this,void 0,void 0,(function(){var n;return Tn(this,(function(r){switch(r.label){case 0:return t&&"blobId"in t?[4,h.openLocation(t).readFile("utf8")]:[3,2];case 1:return n=r.sent(),this.setTree(n),[3,3];case 2:e.treeFilehandle=t,r.label=3;case 3:return[2]}}))}))},setMSA:function(t){e.data.setMSA(t)},setTree:function(t){e.data.setTree(t)},afterCreate:function(){var t=this;u.addDisposer(e,i.autorun((function(){return Ln(t,void 0,void 0,(function(){var t,n,r;return Tn(this,(function(o){switch(o.label){case 0:if(!(t=e.treeFilehandle))return[3,4];o.label=1;case 1:return o.trys.push([1,3,,4]),n=this.setTree,[4,h.openLocation(t).readFile("utf8")];case 2:return n.apply(this,[o.sent()]),[3,4];case 3:return r=o.sent(),this.setError(r),[3,4];case 4:return[2]}}))}))}))),u.addDisposer(e,i.autorun((function(){return Ln(t,void 0,void 0,(function(){var t,n,r;return Tn(this,(function(o){switch(o.label){case 0:if(!(t=e.msaFilehandle))return[3,4];o.label=1;case 1:return o.trys.push([1,3,,4]),n=this.setMSA,[4,h.openLocation(t).readFile("utf8")];case 2:return n.apply(this,[o.sent()]),[3,4];case 3:return r=o.sent(),this.setError(r),[3,4];case 4:return[2]}}))}))})))}}})).views((function(e){var t=[],n=[],r=0,o=0;return{get initialized(){return(e.data.msa||e.data.tree||e.msaFilehandle||e.treeFilehandle)&&!e.error},get blocksX(){for(var n=e.blockSize,o=e.colWidth,a=-n*Math.floor(e.scrollX/n)-n,i=[],l=a;l<a+3*n;l+=n)l+n>0&&i.push(l);return JSON.stringify(i)===JSON.stringify(t)&&o===r||(t=i,r=o),t},get blocksY(){for(var t=e.blockSize,r=e.rowHeight,a=-t*Math.floor(e.scrollY/t)-2*t,i=[],l=a;l<a+3*t;l+=t)l+t>0&&i.push(l);return JSON.stringify(i)===JSON.stringify(n)&&r===o||(n=i,o=r),n}}})).views((function(e){return{get blocks2d(){return e.blocksY.map((function(t){return e.blocksX.map((function(e){return[e,t]}))})).flat()},get done(){return e.initialized&&(e.data.msa||e.data.tree)},get colorScheme(){return Je[e.colorSchemeName]},get alignmentDetails(){var e;return(null===(e=this.MSA)||void 0===e?void 0:e.getDetails())||{}},getRowDetails:function(e){var t,n,r=null===(n=null===(t=this.MSA)||void 0===t?void 0:t.getRowDetails)||void 0===n?void 0:n.call(t,e),o=e.match(/\S+\/(\d+)-(\d+)/);return kn(kn({},r),o&&{range:{start:+o[1],end:+o[2]}})},get currentAlignmentName(){return this.alignmentNames[e.currentAlignment]},get alignmentNames(){var e;return(null===(e=this.MSA)||void 0===e?void 0:e.alignmentNames)||[]},get noTree(){return!!this.tree.noTree},get menuItems(){return[]},get MSA(){var t=e.data.msa;return t?dn.sniff(t)?new yn(t,e.currentAlignment):t.startsWith(">")?new wn(t):new vn(t):null},get numColumns(){var t;return(((null===(t=this.MSA)||void 0===t?void 0:t.getWidth())||0)-this.blanks.length)*e.colWidth},get tree(){var t;return e.data.tree?Ke(bn(e.data.tree)):(null===(t=this.MSA)||void 0===t?void 0:t.getTree())||{noTree:!0}},get rowNames(){return this.hierarchy.leaves().map((function(e){return e.data.name}))},get mouseOverRowName(){return void 0!==e.mouseRow?this.rowNames[e.mouseRow]:void 0},getMouseOverResidue:function(e){return this.columns[e]},get root(){var t=Ft(this.tree,(function(e){return e.branchset})).sum((function(e){return e.branchset?0:1})).sort((function(e,t){return function(e,t){return e<t?-1:e>t?1:e>=t?0:NaN}(e.data.length||1,t.data.length||1)}));if(e.showOnly){var n=t.find((function(t){return t.data.id===e.showOnly}));n&&(t=n)}return e.collapsed.length&&e.collapsed.map((function(e){return t.find((function(t){return t.data.id===e}))})).filter((function(e){return!!e})).map((function(e){return Rn(e)})),t},get structures(){var e;return(null===(e=this.MSA)||void 0===e?void 0:e.getStructures())||{}},get inverseStructures(){var e=Object.entries(this.structures).map((function(e){var t=e[0];return e[1].map((function(e){return[e.pdb,{id:t}]}))})).flat();return Object.fromEntries(e)},get msaAreaWidth(){return e.width-e.treeAreaWidth},get blanks(){for(var e,t=this,n=[],r=this.hierarchy.leaves().map((function(e){var n;return null===(n=t.MSA)||void 0===n?void 0:n.getRow(e.data.name)})).filter((function(e){return!!e})),o=0;o<(null===(e=r[0])||void 0===e?void 0:e.length);o++){for(var a=0,i=0;i<r.length;i++)"-"===r[i][o]&&a++;a===r.length&&n.push(o)}return n},get rows(){var e=this;return this.hierarchy.leaves().map((function(t){var n,r=t.data;return[r.name,null===(n=e.MSA)||void 0===n?void 0:n.getRow(r.name)]})).filter((function(e){return!!e[1]}))},get columns(){var e=this.columns2d;return Object.fromEntries(this.rows.map((function(t,n){return[t[0],e[n]]})))},get columns2d(){for(var e=this.rows.map((function(e){return e[1]})),t=[],n=0;n<e.length;n++)t.push(Pn(this.blanks,e[n]));return t},get colStats(){for(var e=[],t=this.columns2d,n=0;n<t.length;n++)for(var r=0;r<t[n].length;r++){var o=e[r]||{};o[t[n][r]]||(o[t[n][r]]=0),o[t[n][r]]++,e[r]=o}return e},get hierarchy(){var t=this.root;return function(){var e=Dt,t=1,n=1,r=!1;function o(o){var a,i=0;o.eachAfter((function(t){var n=t.children;n?(t.x=function(e){return e.reduce(Nt,0)/e.length}(n),t.y=function(e){return 1+e.reduce(jt,0)}(n)):(t.x=a?i+=e(t,a):0,t.y=0,a=t)}));var l=function(e){for(var t;t=e.children;)e=t[0];return e}(o),s=function(e){for(var t;t=e.children;)e=t[t.length-1];return e}(o),c=l.x-e(l,s)/2,u=s.x+e(s,l)/2;return o.eachAfter(r?function(e){e.x=(e.x-o.x)*t,e.y=(o.y-e.y)*n}:function(e){e.x=(e.x-c)/(u-c)*t,e.y=(1-(o.y?e.y/o.y:1))*n})}return o.separation=function(t){return arguments.length?(e=t,o):e},o.size=function(e){return arguments.length?(r=!1,t=+e[0],n=+e[1],o):r?null:[t,n]},o.nodeSize=function(e){return arguments.length?(r=!0,t=+e[0],n=+e[1],o):r?[t,n]:null},o}().size([this.totalHeight,e.treeWidth]).separation((function(){return 1}))(t),function e(t,n,r){var o;t.len=(n+=Math.max(t.data.length||0,0))*r,null===(o=t.children)||void 0===o||o.forEach((function(t){e(t,n,r)}))}(t,t.data.length=0,e.treeWidth/On(t)),t},get totalHeight(){return this.root.leaves().length*e.rowHeight}}})).actions((function(e){return{addUniprotTrack:function(t){e.boxTracks.find((function(e){return e.name===t.name}))?e.turnedOffTracks.has(t.name)&&this.toggleTrack(t.name):e.boxTracks.push(kn(kn({},t),{id:t.name,associatedRowName:t.name}))},doScrollY:function(t){e.scrollY=Dn(10-e.totalHeight,e.scrollY+t,0)},doScrollX:function(t){e.scrollX=Dn(e.msaAreaWidth-100-e.numColumns,e.scrollX+t,0)},setMouseoveredColumn:function(t,n,r){var o,a=0,i=0,l=(e.inverseStructures[r.slice(0,-4)]||{}).id,s=null===(o=e.MSA)||void 0===o?void 0:o.getRow(l);if(s){for(i=0;i<s.length&&a<t;i++)"-"!==s[i]&&a++;e.mouseCol=a+1}else e.mouseCol=void 0},toggleTrack:function(t){e.turnedOffTracks.has(t)?e.turnedOffTracks.delete(t):e.turnedOffTracks.set(t,!0)}}})).views((function(e){return{get secondaryStructureConsensus(){var t;return null===(t=e.MSA)||void 0===t?void 0:t.secondaryStructureConsensus},get seqConsensus(){var t;return null===(t=e.MSA)||void 0===t?void 0:t.seqConsensus},get conservation(){var t=e.columns2d;if(t.length)for(var n=0;n<t[0].length;n++)for(var r=[],o=0;o<t.length;o++)r.push(t[o][n]);return["a"]},get tracks(){var t=e.blanks,n=e.MSA?e.MSA.tracks.map((function(n){var r=n.data;return{model:kn(kn({},n),{data:r?Pn(t,r):void 0,height:e.rowHeight}),ReactComponent:Sn}})):[],r=e.boxTracks.filter((function(t){return!!e.rows.find((function(e){return e[0]===t.name}))})).map((function(e){return{model:e,ReactComponent:An}})),o=e.annotatedRegions.length>0?[{model:{features:e.annotatedRegions,height:100,id:"annotations",name:"User-created annotations",data:e.annotatedRegions.map((function(e){var t=e.attributes?Object.entries(e.attributes).map((function(e){var t=e[1];return"".concat(e[0],"=").concat(t.join(","))})).join(";"):".";return["MSA_refcoord",".",".",e.start,e.end,".",".",".",t].join("\t")})).join("\n")},ReactComponent:An}]:[];return Cn(Cn(Cn([],n,!0),r,!0),o,!0)},get turnedOnTracks(){return this.tracks.filter((function(t){return!e.turnedOffTracks.has(t.model.id)}))},pxToBp:function(t){return Math.floor((t-e.scrollX)/e.colWidth)},rowSpecificBpToPx:function(t,n){var r,o=e.blanks,a=e.rows[e.rowNames.indexOf(t)][1],i=n-((null===(r=e.getRowDetails(t).range)||void 0===r?void 0:r.start)||0);if(i<0)return 0;for(var l=0,s=0;s<a.length&&("-"===a[s]||l++!==i);s++);for(var c=0,u=0;u<a.length;u++)-1!==o.indexOf(u)&&u<s+1&&c++;return s-c},globalBpToPx:function(t){for(var n,r=0,o=0;o<(null===(n=e.rows[0])||void 0===n?void 0:n[1].length);o++)-1!==e.blanks.indexOf(o)&&o<t+1&&r++;return t-r},relativePxToBp:function(t,n){for(var r=e.rows[e.rowNames.indexOf(t)][1],o=0,a=0;a<n;a++)if("-"!==r[a])o++;else if(o>=n)break;return o},getPos:function(t){for(var n=0,r=0,o=0;r<t;r++,n++)for(;n===e.blanks[o];)o++,n++;return n}}})).actions((function(e){return{addAnnotation:function(t,n,r){e.annotatedRegions.push({start:e.getPos(t),end:e.getPos(n),attributes:r})},setOffsets:function(t,n){e.annotPos={left:t,right:n}},clearAnnotPos:function(){e.annotPos=void 0}}})),Fn=u.types.snapshotProcessor(u.types.compose(hn,In),{postProcessor:function(e){var t=e.data,n=t.tree,r=t.msa,o=function(e,t){var n={};for(var r in e)Object.prototype.hasOwnProperty.call(e,r)&&t.indexOf(r)<0&&(n[r]=e[r]);if(null!=e&&"function"==typeof Object.getOwnPropertySymbols){var o=0;for(r=Object.getOwnPropertySymbols(e);o<r.length;o++)t.indexOf(r[o])<0&&Object.prototype.propertyIsEnumerable.call(e,r[o])&&(n[r[o]]=e[r[o]])}return n}(e,["data"]);return kn({data:kn(kn({},!e.treeFilehandle&&{tree:n}),!e.msaFilehandle&&{msa:r})},o)}}),_n={__proto__:null,MSAModel:Fn,MSAView:Rt},Bn=A(k((function(e,t){Object.defineProperty(t,"__esModule",{value:!0}),t.default=void 0;var n=C(p),r=(0,L(P).default)(n.createElement("path",{d:"M20 2H4c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2zM8 20H4v-4h4v4zm0-6H4v-4h4v4zm0-6H4V4h4v4zm6 12h-4v-4h4v4zm0-6h-4v-4h4v4zm0-6h-4V4h4v4zm6 12h-4v-4h4v4zm0-6h-4v-4h4v4zm0-6h-4V4h4v4z"}),"GridOn");t.default=r})));e.default=function(e){!function(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function");e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,writable:!0,configurable:!0}}),t&&w(e,t)}(o,e);var t,r=S(o);function o(){var e;return b(this,o),(e=r.apply(this,arguments)).name="MsaViewPlugin",e.version="1.0.18",e}return(t=[{key:"install",value:function(e){console.log({MSA:_n}),e.addViewType((function(){return new m({name:"MsaView",stateModel:Fn,ReactComponent:Rt})}))}},{key:"configure",value:function(e){n.isAbstractMenuManager(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Bn,onClick:function(e){e.addView("MsaView",{})}})}}])&&function(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}(o.prototype,t),o}(t),Object.defineProperty(e,"__esModule",{value:!0})}));
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