@jbrowse/plugin-linear-genome-view 1.5.9 → 1.6.0

package/dist/plugin-linear-genome-view.cjs.production.min.js

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e.preventDefault()}},n.createElement(b.Grid,{container:!0,spacing:1,justifyContent:"center",alignItems:"center"},n.createElement(b.Grid,{item:!0},n.createElement(ce,{onChange:function(e){k(void 0),h(e)},session:i,selected:g})),n.createElement(b.Grid,{item:!0},g?C?n.createElement(Y,{style:{color:"red"}}):R?n.createElement(jt,{fetchResults:N,model:o,assemblyName:x?void 0:g,value:R,minWidth:270,onSelect:function(e){return T(e)},TextFieldProps:{margin:"normal",variant:"outlined",helperText:"Enter sequence name, feature name, or location"}}):n.createElement(b.CircularProgress,{role:"progressbar",size:20,disableShrink:!0}):null),n.createElement(b.Grid,{item:!0}),n.createElement(b.Grid,{item:!0},n.createElement(b.Button,{type:"submit",disabled:!R,className:a.button,onClick:function(){o.setError(void 0),R&&function(e){L.apply(this,arguments)}(R)},variant:"contained",color:"primary"},"Open"),n.createElement(b.Button,{disabled:!R,className:a.button,onClick:function(){o.setError(void 0),o.showAllRegionsInAssembly(g)},variant:"contained",color:"secondary"},"Show all regions in assembly"))))),f?n.createElement(En,{model:o,optAssemblyName:g,handleClose:function(){return o.setSearchResults(void 0,void 0)}}):null)})),Cn=w.observer((function(e){var r=e.model,o=r.bpPerPx,a=r.maxBpPerPx,i=r.minBpPerPx,l=r.scaleFactor,c=Te(t.useState(),2),s=c[0],u=c[1];return n.createElement(n.Fragment,null,n.createElement(te,{style:{background:"#aaa7"}},n.createElement(Q,{color:"secondary",onClick:function(e){u(e.currentTarget)}},n.createElement(ue,null)),n.createElement(Q,{"data-testid":"zoom_out",onClick:function(){r.zoom(2*o)},disabled:o>=a-1e-4||1!==l,color:"secondary"},n.createElement(ee,null)),n.createElement(Q,{"data-testid":"zoom_in",onClick:function(){r.zoom(r.bpPerPx/2)},disabled:o<=i+1e-4||1!==l,color:"secondary"},n.createElement(A,null))),n.createElement(de,{anchorEl:s,open:Boolean(s),onMenuItemClick:function(e,t){t(),u(void 0)},onClose:function(){u(void 0)},menuItems:r.menuItems()}))})),Pn=b.makeStyles((function(e){return{loadingMessage:{padding:e.spacing(5)},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]},dialogContent:{width:"80em"},textAreaFont:{fontFamily:"Courier New"}}}));function Tn(e,t,n){return Bn.apply(this,arguments)}function Bn(){return(Bn=be(Oe.mark((function e(t,n,o){var a,i,l,c,u,d,f;return Oe.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(a=s.getSession(t),l=t.rightOffset,(i=t.leftOffset)&&l){e.next=4;break}throw new Error("no offsets on model to use for range");case 4:if(i.assemblyName===l.assemblyName){e.next=6;break}throw new Error("not able to fetch sequences from multiple assemblies");case 6:if(c=a.rpcManager,d=a.assemblyManager.get(u=i.assemblyName||l.assemblyName||"")){e.next=11;break}throw new Error("assembly ".concat(u," not found"));case 11:return f=r.getConf(d,["sequence","adapter"]),e.next=15,Promise.all(n.map((function(e){return c.call("getSequence","CoreGetFeatures",{adapterConfig:f,region:e,sessionId:"getSequence",signal:o})})));case 15:return e.abrupt("return",e.sent.map((function(e){return e[0]})));case 17:case"end":return e.stop()}}),e)})))).apply(this,arguments)}function Rn(e){var r=e.model,o=e.handleClose,a=Pn(),i=s.getSession(r),l=Te(t.useState(),2),c=l[0],u=l[1],d=Te(t.useState(),2),f=d[0],m=d[1],p=Boolean(void 0===f),g=r.leftOffset,h=r.rightOffset,v=t.useMemo((function(){return r.getSelectedRegions(g,h)}),[r,g,h]);t.useEffect((function(){var e=!0,t=new AbortController;return be(Oe.mark((function n(){var o;return Oe.wrap((function(n){for(;;)switch(n.prev=n.next){case 0:if(n.prev=0,!(v.length>0)){n.next=8;break}return n.next=4,Tn(r,v,t.signal);case 4:o=n.sent,e&&m(me.formatSeqFasta(o.filter((function(e){return!!e})).map((function(e){var t=e.get("seq"),n=e.get("refName"),r=e.get("start")+1,o=e.get("end"),a="".concat(n,":").concat(r,"-").concat(o);if((null==t?void 0:t.length)!==o-r+1)throw new Error("".concat(a," returned ").concat(t.length.toLocaleString()," bases, but should have returned ").concat((o-r).toLocaleString()));return{header:a,seq:t}})))),n.next=9;break;case 8:throw new Error("Selected region is out of bounds");case 9:n.next=15;break;case 11:n.prev=11,n.t0=n.catch(0),console.error(n.t0),e&&u(n.t0);case 15:case"end":return n.stop()}}),n,null,[[0,11]])})))(),function(){t.abort(),e=!1}}),[r,i,v,m]);var y=!!f&&f.length>1e6;return n.createElement(b.Dialog,{"data-testid":"sequence-dialog",maxWidth:"xl",open:!0,onClose:o,"aria-labelledby":"alert-dialog-title","aria-describedby":"alert-dialog-description"},n.createElement(b.DialogTitle,{id:"alert-dialog-title"},"Reference sequence",o?n.createElement(b.IconButton,{"data-testid":"close-seqDialog",className:a.closeButton,onClick:function(){o(),r.setOffsets(void 0,void 0)}},n.createElement(Y,null)):null),n.createElement(b.Divider,null),n.createElement(b.DialogContent,null,c?n.createElement(b.Typography,{color:"error"},"".concat(c)):null,p&&!c?n.createElement(b.Container,null,"Retrieving reference sequence...",n.createElement(b.CircularProgress,{style:{marginLeft:10},size:20,disableShrink:!0})):null,n.createElement(b.TextField,{"data-testid":"rubberband-sequence",variant:"outlined",multiline:!0,rows:5,disabled:y,className:a.dialogContent,fullWidth:!0,value:y?"Reference sequence too large to display, use the download FASTA button":f,InputProps:{readOnly:!0,classes:{input:a.textAreaFont}}})),n.createElement(b.DialogActions,null,n.createElement(b.Button,{onClick:function(){fe(f||""),i.notify("Copied to clipboard","success")},disabled:p||!!c||y,color:"primary",startIcon:n.createElement(O.ContentCopy,null)},"Copy to clipboard"),n.createElement(b.Button,{onClick:function(){var e=new Blob([f||""],{type:"text/x-fasta;charset=utf-8"});D.saveAs(e,"jbrowse_ref_seq.fa")},disabled:p||!!c,color:"primary",startIcon:n.createElement(pe,null)},"Download FASTA"),n.createElement(b.Button,{onClick:o,color:"primary",autoFocus:!0},"Close")))}var Nn=w.observer(Rn),Mn=b.makeStyles((function(e){return{dialogContent:{width:"80em"},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}}));function Ln(e){var t,r,o=e.model,a=e.optAssemblyName,i=e.handleClose,l=Mn(),c=s.getSession(o),u=y.getEnv(c).pluginManager,d=c.assemblyManager,f=a;if(o.displayedRegions.length>0&&(f=null===(r=o.displayedRegions[0])||void 0===r?void 0:r.assemblyName),!f)throw new Error("Assembly name not found");var m=d.get(f);if(!m)throw new Error("assembly ".concat(f," not found"));if(!m.regions)throw new Error("assembly ".concat(f," regions not loaded"));var p=m.regions;function g(e){if(e){var t,n=u.pluggableConfigSchemaType("track"),r=y.resolveIdentifier(n,y.getRoot(o),e);if(r)return null===(t=r.name)||void 0===t?void 0:t.value}return""}return n.createElement(b.Dialog,{open:!0,maxWidth:"xl",onClose:i},n.createElement(b.DialogTitle,null,"Search results",i?n.createElement(b.IconButton,{"data-testid":"close-resultsDialog",className:l.closeButton,onClick:function(){i()}},n.createElement(Y,null)):null),n.createElement(b.Divider,null),n.createElement(b.DialogContent,null,null!==(t=o.searchResults)&&void 0!==t&&t.length?n.createElement(n.Fragment,null,n.createElement(b.Typography,null,"Showing results for 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e===t.refName}));t?(o.setDisplayedRegions([t]),o.showAllRegions()):o.navToLocString(e,f)}catch(e){console.warn(e),c.notify("".concat(e),"warning")}}(e.getLocation());var t=e.getTrackId();t&&o.showTrack(t),i()},disabled:!g(e.getTrackId()),color:"primary",variant:"contained"},"Go")))})))))):n.createElement(b.Typography,null,"No results found for ",n.createElement("b",null,o.searchQuery))),n.createElement(b.Divider,null),n.createElement(b.DialogActions,null,n.createElement(b.Button,{onClick:function(){return i()},color:"primary"},"Cancel")))}var Dn={__proto__:null,useStyles:Mn,default:Ln},On=b.makeStyles((function(e){return{note:{textAlign:"center",paddingTop:e.spacing(1),paddingBottom:e.spacing(1)},dots:{"&::after":{display:"inline-block",animation:"$ellipsis 1.5s infinite",content:'"."',width:"1em",textAlign:"left"}},"@keyframes ellipsis":{"0%":{content:'"."'},"33%":{content:'".."'},"66%":{content:'"..."'}}}})),In={__proto__:null,default:w.observer((function(e){var t=e.model,r=t.tracks,o=t.error,a=t.hideHeader,i=t.initialized,l=t.hasDisplayedRegions,c=On();return i||o?!l||o?n.createElement(Sn,{model:t}):n.createElement("div",{style:{position:"relative"}},t.seqDialogDisplayed?n.createElement(Nn,{model:t,handleClose:function(){t.setSequenceDialogOpen(!1)}}):null,t.isSearchDialogDisplayed?n.createElement(Ln,{model:t,handleClose:function(){t.setSearchResults(void 0,void 0)}}):null,a?n.createElement("div",{style:{position:"absolute",right:0,zIndex:1001}},n.createElement(Cn,{model:t})):n.createElement(Zt,{model:t}),n.createElement(wn,{model:t},r.length?r.map((function(e){return n.createElement(tn,{key:e.id,model:t,track:e})})):n.createElement(b.Paper,{variant:"outlined",className:c.note},n.createElement(b.Typography,null,"No tracks active."),n.createElement(b.Button,{variant:"contained",color:"primary",onClick:t.activateTrackSelector,style:{zIndex:1e3},startIcon:n.createElement(O.TrackSelector,null)},"Open track selector")))):n.createElement(b.Typography,{className:c.dots,variant:"h5"},"Loading")}))};function Fn(e){if(!e.length)return"";var t=e.every((function(t){return t.assemblyName===e[0].assemblyName}));return e.map((function(e){return s.assembleLocString(he(he({},e),{},{start:Math.round(e.start),end:Math.round(e.end),assemblyName:t?void 0:e.assemblyName}))})).join(";")}var jn=48,zn=20,qn=17,An=3;function Hn(e){return y.types.compose(o.BaseViewModel,y.types.model("LinearGenomeView",{id:C.ElementId,type:y.types.literal("LinearGenomeView"),offsetPx:0,bpPerPx:1,displayedRegions:y.types.array(C.Region),tracks:y.types.array(e.pluggableMstType("track","stateModel")),hideHeader:!1,hideHeaderOverview:!1,trackSelectorType:y.types.optional(y.types.enumeration(["hierarchical"]),"hierarchical"),trackLabels:"overlapping",showCenterLine:!1,showCytobandsSetting:!0})).volatile((function(){return{volatileWidth:void 0,minimumBlockWidth:3,draggingTrackId:void 0,volatileError:void 0,afterDisplayedRegionsSetCallbacks:[],scaleFactor:1,trackRefs:{},coarseDynamicBlocks:[],coarseTotalBp:0,leftOffset:void 0,rightOffset:void 0,searchResults:void 0,searchQuery:void 0,seqDialogDisplayed:!1}})).views((function(e){return{get width(){if(void 0===e.volatileWidth)throw new Error("width undefined, make sure to check for model.initialized");return e.volatileWidth},get interRegionPaddingWidth(){return 2}}})).views((function(e){return{get assemblyErrors(){var t=s.getSession(e).assemblyManager;return this.assemblyNames.map((function(e){var n;return null===(n=t.get(e))||void 0===n?void 0:n.error})).filter((function(e){return!!e})).join(", ")},get assembliesInitialized(){var t=s.getSession(e).assemblyManager;return this.assemblyNames.every((function(e){var n;return null===(n=t.get(e))||void 0===n?void 0:n.initialized}))},get initialized(){return void 0!==e.volatileWidth&&this.assembliesInitialized},get hasDisplayedRegions(){return e.displayedRegions.length>0},get isSearchDialogDisplayed(){return void 0!==e.searchResults},get scaleBarHeight(){return qn+An},get headerHeight(){return e.hideHeader?0:e.hideHeaderOverview?jn:jn+zn},get trackHeights(){return e.tracks.map((function(e){return e.displays[0].height})).reduce((function(e,t){return e+t}),0)},get trackHeightsWithResizeHandles(){return this.trackHeights+e.tracks.length*An},get height(){return this.trackHeightsWithResizeHandles+this.headerHeight+this.scaleBarHeight},get totalBp(){var t=0;return e.displayedRegions.forEach((function(e){t+=e.end-e.start})),t},get maxBpPerPx(){return this.totalBp/(.9*e.width)},get minBpPerPx(){return.02},get error(){return e.volatileError||this.assemblyErrors},get maxOffset(){return this.displayedRegionsTotalPx-10},get minOffset(){return 30-e.width},get displayedRegionsTotalPx(){return this.totalBp/e.bpPerPx},renderProps:function(){return he(he({},m.getParentRenderProps(e)),{},{bpPerPx:e.bpPerPx,highResolutionScaling:r.getConf(s.getSession(e),"highResolutionScaling")})},get assemblyNames(){return Be(new Set(e.displayedRegions.map((function(e){return e.assemblyName}))))},searchScope:function(t){return{assemblyName:t,includeAggregateIndexes:!0,tracks:e.tracks}},bpToPx:function(t){var n=t.refName,r=t.coord,o=t.regionNumber,a=0,i=e.interRegionPaddingWidth*e.bpPerPx,l=e.minimumBlockWidth*e.bpPerPx,c=e.displayedRegions.findIndex((function(t,c){var s=t.end-t.start;return n===t.refName&&r>=t.start&&r<=t.end&&(!o||o===c)?(a+=t.reversed?t.end-r:r-t.start,!0):(a+=s>l&&a/e.bpPerPx>=0&&a/e.bpPerPx<e.width?s+i:s,!1)}));if(e.displayedRegions[c])return{index:c,offsetPx:Math.round(a/e.bpPerPx)}},pxToBp:function(t){var n=0,r=(e.offsetPx+t)*e.bpPerPx,o=e.displayedRegions.length;if(r<0){var a=e.displayedRegions[0],i=r;return he(he({},y.getSnapshot(a)),{},{oob:!0,coord:a.reversed?Math.floor(a.end-i)+1:Math.floor(a.start+i)+1,offset:i,index:0})}for(var l=e.interRegionPaddingWidth*e.bpPerPx,c=e.minimumBlockWidth*e.bpPerPx,s=0;s<e.displayedRegions.length;s+=1){var u=e.displayedRegions[s],d=u.end-u.start,f=r-n;if(d+n>r&&n<=r)return he(he({},y.getSnapshot(u)),{},{oob:!1,offset:f,coord:u.reversed?Math.floor(u.end-f)+1:Math.floor(u.start+f)+1,index:s});n+=u.end-u.start>c&&f/e.bpPerPx>0&&f/e.bpPerPx<e.width?d+l:d}if(r>=n){var m=e.displayedRegions[o-1],p=r-n+(m.end-m.start);return he(he({},y.getSnapshot(m)),{},{oob:!0,offset:p,coord:m.reversed?Math.floor(m.end-p)+1:Math.floor(m.start+p)+1,index:o-1})}return{coord:0,index:0,refName:"",oob:!0,assemblyName:"",offset:0,start:0,end:0,reversed:!1}},getTrack:function(t){return e.tracks.find((function(e){return e.configuration.trackId===t}))},rankSearchResults:function(t){var n=e.tracks.map((function(e){return e.configuration.trackId}));return t.forEach((function(e){n!==[]&&n.includes(e.trackId)&&e.updateScore(e.getScore()+1)})),t},rewriteOnClicks:function(t,n){var r=this;n.forEach((function(n){if("subMenu"in n&&r.rewriteOnClicks(t,n.subMenu),"onClick"in n){var o=n.onClick;n.onClick=function(){for(var n=arguments.length,r=new Array(n),a=0;a<n;a++)r[a]=arguments[a];e.tracks.forEach((function(e){e.type===t&&o.apply(e,[e].concat(r))}))}}}))},get trackTypeActions(){var t=this,n=new Map;return e.tracks.forEach((function(e){if(!n.get(e.type)){var r=L(e.viewMenuActions);t.rewriteOnClicks(e.type,r),n.set(e.type,r)}})),n},get centerLineInfo(){return e.displayedRegions.length?this.pxToBp(e.width/2):void 0}}})).actions((function(t){return{setShowCytobands:function(e){t.showCytobandsSetting=e},setWidth:function(e){t.volatileWidth=e},setError:function(e){t.volatileError=e},toggleHeader:function(){t.hideHeader=!t.hideHeader},toggleHeaderOverview:function(){t.hideHeaderOverview=!t.hideHeaderOverview},scrollTo:function(e){var n=s.clamp(e,t.minOffset,t.maxOffset);return t.offsetPx=n,n},zoomTo:function(e){var n=s.clamp(e,t.minBpPerPx,t.maxBpPerPx);if(n===t.bpPerPx)return n;var r=t.bpPerPx;if(t.bpPerPx=n,Math.abs(r-n)<1e-6)return console.warn("zoomTo bpPerPx rounding error"),r;var o=t.width;return this.scrollTo(Math.round((t.offsetPx+o/2)*r/n-o/2)),n},setOffsets:function(e,n){t.leftOffset=e,t.rightOffset=n},setSearchResults:function(e,n){t.searchResults=e,t.searchQuery=n},setSequenceDialogOpen:function(e){t.seqDialogDisplayed=e},setNewView:function(e,t){this.zoomTo(e),this.scrollTo(t)},horizontallyFlip:function(){t.displayedRegions=y.cast(t.displayedRegions.slice().reverse().map((function(e){return he(he({},e),{},{reversed:!e.reversed})}))),this.scrollTo(t.totalBp/t.bpPerPx-t.offsetPx-t.width)},showTrack:function(n){var r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},o=arguments.length>2&&void 0!==arguments[2]?arguments[2]:{},a=e.pluggableConfigSchemaType("track"),i=y.resolveIdentifier(a,y.getRoot(t),n);if(!i)throw new Error("Could not resolve identifier");var l=e.getTrackType(null==i?void 0:i.type);if(!l)throw new Error("unknown track type ".concat(i.type));var c=e.getViewType(t.type),s=c.displayTypes.map((function(e){return e.name})),u=i.displays.find((function(e){return s.includes(e.type)}));if(!u)throw new Error("could not find a compatible display for view type ".concat(t.type));var d=t.tracks.filter((function(e){return e.configuration===i}));if(0===d.length){var f=l.stateModel.create(he(he({},r),{},{type:i.type,configuration:i,displays:[he({type:u.type,configuration:u},o)]}));return t.tracks.push(f),f}return d[0]},hideTrack:function(n){var r=e.pluggableConfigSchemaType("track"),o=y.resolveIdentifier(r,y.getRoot(t),n),a=t.tracks.filter((function(e){return e.configuration===o}));return v.transaction((function(){return a.forEach((function(e){return t.tracks.remove(e)}))})),a.length}}})).actions((function(e){return{moveTrack:function(t,n){var r=e.tracks.findIndex((function(e){return e.id===t}));if(-1===r)throw new Error("Track ID ".concat(t," not found"));var o=e.tracks.findIndex((function(e){return e.id===n}));if(-1===o)throw new Error("Track ID ".concat(n," not found"));var a=y.getSnapshot(e.tracks[r]);e.tracks.splice(r,1),e.tracks.splice(o,0,a)},closeView:function(){var t=s.getContainingView(e);t?s.isViewContainer(t)&&t.removeView(e):s.getSession(e).removeView(e)},toggleTrack:function(t){e.hideTrack(t)||e.showTrack(t)},setTrackLabels:function(t){e.trackLabels=t},toggleCenterLine:function(){e.showCenterLine=!e.showCenterLine},setDisplayedRegions:function(t){e.displayedRegions=y.cast(t),e.zoomTo(e.bpPerPx)},activateTrackSelector:function(){if("hierarchical"===e.trackSelectorType){var t=s.getSession(e);if(s.isSessionModelWithWidgets(t)){var n=t.addWidget("HierarchicalTrackSelectorWidget","hierarchicalTrackSelector",{view:e});return t.showWidget(n),n}}throw new Error("invalid track selector type ".concat(e.trackSelectorType))},navToLocString:function(t,n){var r=s.getSession(e).assemblyManager,o=r.isValidRefName,a=t.split(";");if(e.displayedRegions.length>1){var i=a.map((function(e){return s.parseLocString(e,o)}));this.navToMultiple(i)}else{var l=n,c="";0!==e.displayedRegions.length&&(l=e.displayedRegions[0].assemblyName,c=e.displayedRegions[0].refName);var u=l&&r.get(l);if(!u)throw new Error("Could not find assembly ".concat(l));var d=u.regions;if(!d)throw new Error("Regions for assembly ".concat(l," not yet loaded"));if(a.length>1)throw new Error("Navigating to multiple locations is not allowed when viewing a whole chromosome");var f=s.parseLocString(a[0],(function(e){return o(e,l)})),m=!1;if(f.assemblyName&&f.assemblyName!==l){var p=r.get(f.assemblyName);if(!p)throw new Error("Could not find assembly 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c=s.getSession(e).assemblyManager.get(l);if(c){var u=c.getCanonicalRefName(r);u&&(r=u)}for(var d,f=o,m=a,p=!1,g=function(e){if(r===e.refName){if(p=!0,void 0===f&&(f=e.start),void 0===m&&(m=e.end),f>=e.start&&f<=e.end&&m<=e.end&&m>=e.start)return!0;f=o,m=a}return!1},h=s.findLastIndex(e.displayedRegions,g);d!==h;)try{var v=d;if(d=e.displayedRegions.slice(void 0===v?0:v+1).findIndex(g),void 0!==v&&(d+=v+1),!p)throw new Error('could not find a region with refName "'.concat(r,'"'));if(void 0===f)throw new Error('could not find a region with refName "'.concat(r,'" that contained an end position ').concat(m));if(void 0===m)throw new Error('could not find a region with refName "'.concat(r,'" that contained a start position ').concat(f+1));if(-1===d)throw new Error('could not find a region that completely contained "'.concat(s.assembleLocString(n),'"'));if(1===t.length){var y=e.displayedRegions[d];return void this.moveTo({index:d,offset:y.reversed?y.end-m:f-y.start},{index:d,offset:y.reversed?y.end-f:m-y.start})}for(var b=0,k=0,w=0;b<t.length;b++){var E=t[b],x=e.displayedRegions[d+b];if(k=E.start||x.start,w=E.end||x.end,E.refName!==x.refName)throw new Error("Entered location ".concat(s.assembleLocString(E)," does not match with displayed regions"));if(b>0&&!(x.reversed?w===x.end:k===x.start))throw new Error("".concat(x.reversed?"End":"Start"," of region ").concat(s.assembleLocString(E)," should be ").concat((x.reversed?x.end:x.start+1).toLocaleString("en-US"),", but it is not"));if(b!==t.length-1&&!(x.reversed?k===x.start:w===x.end))throw new Error("".concat(x.reversed?"Start":"End"," of region ").concat(s.assembleLocString(E)," should be ").concat((x.reversed?x.start+1:x.end).toLocaleString("en-US"),", but it is not"))}var S=e.displayedRegions[d],C=e.displayedRegions[d+(b-=1)];return void this.moveTo({index:d,offset:S.reversed?S.end-m:f-S.start},{index:d+b,offset:C.reversed?C.end-k:w-C.start})}catch(e){if(d===h)throw e}},zoomToDisplayedRegions:function(t,n){if(void 0!==t&&void 0!==n){if(t.refName===n.refName&&t.index===n.index&&n.offset<t.offset||t.index>n.index){var r=[n,t];t=r[0],n=r[1]}var o={start:t.start,end:t.end,index:t.index,offset:t.offset},a={start:n.start,end:n.end,index:n.index,offset:n.offset};o&&a?this.moveTo(o,a):s.getSession(e).notify("No regions found to navigate to","warning")}},getSelectedRegions:function(t,n){var r=M.create(he(he({},y.getSnapshot(e)),{},{interRegionPaddingWidth:e.interRegionPaddingWidth}));return r.setVolatileWidth(e.width),r.zoomToDisplayedRegions(t,n),r.dynamicBlocks.contentBlocks.map((function(e){return he(he({},e),{},{start:Math.floor(e.start),end:Math.ceil(e.end)})}))},afterDisplayedRegionsSet:function(t){e.afterDisplayedRegionsSetCallbacks.push(t)},moveTo:function(t,n){var r=0;if(t.index===n.index)r+=n.offset-t.offset;else{var o=e.displayedRegions[t.index];if(r+=o.end-o.start-t.offset,n.index-t.index>=2)for(var a=t.index+1;a<n.index;a+=1)r+=e.displayedRegions[a].end-e.displayedRegions[a].start;r+=n.offset}var i=r/(e.width-e.interRegionPaddingWidth*(n.index-t.index)),l=e.zoomTo(i),c=0;i<l&&(c=(l-i)*e.width/2);for(var s=-c,u=0;u<e.displayedRegions.length;u+=1){var d=e.displayedRegions[u];if(t.index===u){s+=t.offset;break}s+=d.end-d.start}e.scrollTo(Math.round(s/e.bpPerPx)+e.interRegionPaddingWidth*t.index)},horizontalScroll:function(t){var n=e.offsetPx;return e.scrollTo(e.offsetPx+t)-n},centerAt:function(t,n,r){var o=e.bpToPx({refName:n,coord:t,regionNumber:r});o&&e.scrollTo(Math.round(o.offsetPx-e.width/2))},center:function(){e.scrollTo(Math.round(e.totalBp/2/e.bpPerPx-e.width/2))},showAllRegions:function(){e.zoomTo(e.maxBpPerPx),this.center()},showAllRegionsInAssembly:function(t){var n=s.getSession(e),r=n.assemblyManager;if(!t){var o=Be(new Set(e.displayedRegions.map((function(e){return e.assemblyName}))));if(o.length>1)return void n.notify("Can't perform this with multiple assemblies currently");t=Te(o,1)[0]}var a=r.get(t);if(a){var i=a.regions;i&&(this.setDisplayedRegions(i),e.zoomTo(e.maxBpPerPx),this.center())}},setDraggingTrackId:function(t){e.draggingTrackId=t},setScaleFactor:function(t){e.scaleFactor=t}}})).actions((function(e){var t=function(){};return{slide:function(n){var r=Te(s.springAnimate(e.offsetPx,e.offsetPx+e.width*n,e.scrollTo),2),o=r[0],a=r[1];t(),t=a,o()}}})).actions((function(e){var t=function(){};return{zoom:function(n){if(e.zoomTo(e.bpPerPx),!(n<e.bpPerPx&&e.bpPerPx===e.minBpPerPx||n>e.bpPerPx&&e.bpPerPx===e.maxBpPerPx)){var r=Te(s.springAnimate(1,e.bpPerPx/n,e.setScaleFactor,(function(){e.zoomTo(n),e.setScaleFactor(1)})),2),o=r[0],a=r[1];t(),t=a,o()}}}})).views((function(e){return{get canShowCytobands(){return 1===e.displayedRegions.length&&this.anyCytobandsExist},get showCytobands(){return this.canShowCytobands&&e.showCytobandsSetting},get anyCytobandsExist(){var t=s.getSession(e).assemblyManager;return e.assemblyNames.some((function(e){var n,r;return null===(n=t.get(e))||void 0===n||null===(r=n.cytobands)||void 0===r?void 0:r.length}))},get cytobandOffset(){return this.showCytobands?s.measureText(e.displayedRegions[0].refName,12)+15:0}}})).views((function(e){var t,n="";return{menuItems:function(){var t,n=e.showCytobands,r=[{label:"Return to import form",onClick:function(){s.getSession(e).queueDialog((function(t){return[Wt,{model:e,handleClose:t}]}))},icon:z},{label:"Export SVG",icon:q,onClick:function(){s.getSession(e).queueDialog((function(t){return[qt,{model:e,handleClose:t}]}))}},{label:"Open track selector",onClick:e.activateTrackSelector,icon:O.TrackSelector},{label:"Horizontally flip",icon:I,onClick:e.horizontallyFlip},{type:"divider"},{label:"Show all regions in assembly",icon:F,onClick:e.showAllRegionsInAssembly},{label:"Show center line",icon:F,type:"checkbox",checked:e.showCenterLine,onClick:e.toggleCenterLine},{label:"Show header",icon:F,type:"checkbox",checked:!e.hideHeader,onClick:e.toggleHeader},{label:"Show header overview",icon:F,type:"checkbox",checked:!e.hideHeaderOverview,onClick:e.toggleHeaderOverview,disabled:e.hideHeader},{label:"Track labels",icon:j,subMenu:[{label:"Overlapping",icon:F,type:"radio",checked:"overlapping"===e.trackLabels,onClick:function(){return e.setTrackLabels("overlapping")}},{label:"Offset",icon:F,type:"radio",checked:"offset"===e.trackLabels,onClick:function(){return e.setTrackLabels("offset")}},{label:"Hidden",icon:F,type:"radio",checked:"hidden"===e.trackLabels,onClick:function(){return e.setTrackLabels("hidden")}}]}].concat(Be(e.canShowCytobands?[{label:n?"Hide ideogram":"Show ideograms",onClick:function(){e.setShowCytobands(!n)}}]:[])),o=Me(e.trackTypeActions.entries());try{for(o.s();!(t=o.n()).done;){var a=Te(t.value,2),i=a[1];i.length&&(r.push({type:"divider"},{type:"subHeader",label:a[0]}),i.forEach((function(e){r.push(e)})))}}catch(e){o.e(e)}finally{o.f()}return r},get staticBlocks(){var r=N(e),o=JSON.stringify(r);return n!==o&&(t=r,n=o),t},get dynamicBlocks(){return R(e)},get roundedDynamicBlocks(){return this.dynamicBlocks.contentBlocks.map((function(e){return he(he({},e),{},{start:Math.floor(e.start),end:Math.ceil(e.end)})}))},get visibleLocStrings(){return Fn(this.dynamicBlocks.contentBlocks)},get coarseVisibleLocStrings(){return Fn(e.coarseDynamicBlocks)}}})).actions((function(e){return{clearView:function(){e.setDisplayedRegions([]),e.tracks.clear(),e.scrollTo(0),e.zoomTo(10)},setCoarseDynamicBlocks:function(t){e.coarseDynamicBlocks=t.contentBlocks,e.coarseTotalBp=t.totalBp},afterAttach:function(){var t=this;y.addDisposer(e,v.autorun((function(){e.initialized&&t.setCoarseDynamicBlocks(e.dynamicBlocks)}),{delay:150}))}}})).actions((function(e){return{exportSvg:function(){var t=arguments;return be(Oe.mark((function n(){var r,o;return Oe.wrap((function(n){for(;;)switch(n.prev=n.next){case 0:return r=t.length>0&&void 0!==t[0]?t[0]:{},n.next=3,Mt(e,r);case 3:o=new Blob([n.sent],{type:"image/svg+xml"}),D.saveAs(o,"image.svg");case 6:case"end":return n.stop()}}),n)})))()}}})).views((function(e){return{rubberBandMenuItems:function(){return[{label:"Zoom to region",icon:A,onClick:function(){var t=e.leftOffset,n=e.rightOffset;t&&n&&e.moveTo(t,n)}},{label:"Get sequence",icon:h,onClick:function(){e.setSequenceDialogOpen(!0)}}]}}}))}var Wn=t.lazy((function(){return Promise.resolve().then((function(){return Zn}))})),_n=function(e){return y.types.compose("LinearBasicDisplay",ot,y.types.model({type:y.types.literal("LinearBasicDisplay"),trackShowLabels:y.types.maybe(y.types.boolean),trackShowDescriptions:y.types.maybe(y.types.boolean),trackDisplayMode:y.types.maybe(y.types.string),trackMaxHeight:y.types.maybe(y.types.number),configuration:r.ConfigurationReference(e)})).views((function(e){return{get rendererTypeName(){return r.getConf(e,["renderer","type"])},get showLabels(){var t=r.getConf(e,["renderer","showLabels"]);return void 0!==e.trackShowLabels?e.trackShowLabels:t},get showDescriptions(){var t=r.getConf(e,["renderer","showLabels"]);return void 0!==e.trackShowDescriptions?e.trackShowDescriptions:t},get maxHeight(){var t=r.getConf(e,["renderer","maxHeight"]);return void 0!==e.trackMaxHeight?e.trackMaxHeight:t},get displayMode(){var t=r.getConf(e,["renderer","displayMode"]);return void 0!==e.trackDisplayMode?e.trackDisplayMode:t},get rendererConfig(){var t=r.getConf(e,["renderer"])||{};return e.rendererType.configSchema.create(he(he({},t),{},{showLabels:this.showLabels,showDescriptions:this.showDescriptions,displayMode:this.displayMode,maxHeight:this.maxHeight}),y.getEnv(e))}}})).actions((function(e){return{toggleShowLabels:function(){e.trackShowLabels=!e.showLabels},toggleShowDescriptions:function(){e.trackShowDescriptions=!e.showDescriptions},setDisplayMode:function(t){e.trackDisplayMode=t},setMaxHeight:function(t){e.trackMaxHeight=t}}})).views((function(e){var t=e.trackMenuItems,n=e.renderProps;return{renderProps:function(){var t=e.rendererConfig;return he(he({},n()),{},{config:t})},trackMenuItems:function(){return[].concat(Be(t()),[{label:"Show labels",icon:F,type:"checkbox",checked:e.showLabels,onClick:function(){e.toggleShowLabels()}},{label:"Show descriptions",icon:F,type:"checkbox",checked:e.showDescriptions,onClick:function(){e.toggleShowDescriptions()}},{label:"Display mode",icon:F,subMenu:["compact","reducedRepresentation","normal","collapse"].map((function(t){return{label:t,onClick:function(){e.setDisplayMode(t)}}}))},{label:"Set max height",onClick:function(){s.getSession(e).queueDialog((function(t){return[Wn,{model:e,handleClose:t}]}))}}])}}}))};function Vn(e){return r.ConfigurationSchema("LinearBasicDisplay",{mouseover:{type:"string",description:"what to display in a given mouseover",defaultValue:"jexl:get(feature,'name')",contextVariable:["feature"]},renderer:e.pluggableConfigSchemaType("renderer"),maxDisplayedBpPerPx:{type:"number",description:"maximum bpPerPx that is displayed in the view",defaultValue:1e3}},{baseConfiguration:Le,explicitlyTyped:!0})}var Gn=function(e){!function(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function");Object.defineProperty(e,"prototype",{value:Object.create(t&&t.prototype,{constructor:{value:e,writable:!0,configurable:!0}}),writable:!1}),t&&xe(e,t)}(m,c);var n,d,f=Pe(m);function m(){var e;return ke(this,m),(e=f.apply(this,arguments)).name="LinearGenomeViewPlugin",e.exports={BaseLinearDisplayComponent:Xe,BaseLinearDisplay:ot,baseLinearDisplayConfigSchema:Le},e}return n=m,(d=[{key:"install",value:function(e){e.addTrackType((function(){var t=r.ConfigurationSchema("FeatureTrack",{},{baseConfiguration:o.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new a({name:"FeatureTrack",configSchema:t,stateModel:o.createBaseTrackModel(e,"FeatureTrack",t)})})),e.addTrackType((function(){var t=r.ConfigurationSchema("BasicTrack",{},{baseConfiguration:o.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new a({name:"BasicTrack",configSchema:t,stateModel:o.createBaseTrackModel(e,"BasicTrack",t)})})),e.addDisplayType((function(){var t=at(e);return new i({name:"LinearBareDisplay",configSchema:t,stateModel:it(t),trackType:"BasicTrack",viewType:"LinearGenomeView",ReactComponent:Xe})})),e.addDisplayType((function(){var t=Vn(e);return new i({name:"LinearBasicDisplay",configSchema:t,stateModel:_n(t),trackType:"FeatureTrack",viewType:"LinearGenomeView",ReactComponent:Xe})})),e.addViewType((function(){return new l({name:"LinearGenomeView",stateModel:Hn(e),ReactComponent:t.lazy((function(){return Promise.resolve().then((function(){return In}))}))})}))}},{key:"configure",value:function(e){s.isAbstractMenuManager(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Linear genome view",icon:u,onClick:function(e){e.addView("LinearGenomeView",{})}})}}])&&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)}}(n.prototype,d),Object.defineProperty(n,"prototype",{writable:!1}),m}(),Xn=b.makeStyles((function(e){return{closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}})),Un={__proto__:null,useStyles:Xn,default:function(e){var t=e.handleClose,r=Xn();return n.createElement(b.Dialog,{open:!0,maxWidth:"xl",onClose:t},n.createElement(b.DialogTitle,null,"Using the search box",t?n.createElement(b.IconButton,{"data-testid":"close-resultsDialog",className:r.closeButton,onClick:function(){t()}},n.createElement(Y,null)):null),n.createElement(b.Divider,null),n.createElement(b.DialogContent,null,n.createElement("h3",null,"Searching"),n.createElement("ul",null,n.createElement("li",null,"Jump to a feature or reference sequence by typing its name in the location box and pressing Enter."),n.createElement("li",null,"Jump to a specific region by typing the region into the location box as: ",n.createElement("code",null,"ref:start..end")," or ",n.createElement("code",null,"ref:start-end"),". Commas are allowed in the start and end coordinates.")),n.createElement("h3",null,"Example Searches"),n.createElement("ul",null,n.createElement("li",null,n.createElement("code",null,"BRCA")," - searches for the feature named BRCA"),n.createElement("li",null,n.createElement("code",null,"chr4")," - jumps to chromosome 4"),n.createElement("li",null,n.createElement("code",null,"chr4:79,500,000..80,000,000")," - jumps the region on chromosome 4 between 79.5Mb and 80Mb."))),n.createElement(b.Divider,null),n.createElement(b.DialogActions,null,n.createElement(b.Button,{onClick:function(){return t()},color:"primary"},"Close")))}},Jn=b.makeStyles((function(e){return{root:{width:500},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]},field:{margin:e.spacing(2)}}}));function Yn(e){var r=e.model,o=e.handleClose,a=Jn(),i=r.maxHeight,l=Te(t.useState("".concat(void 0===i?"":i)),2),c=l[0],s=l[1];return n.createElement(b.Dialog,{open:!0,onClose:o,"aria-labelledby":"alert-dialog-title","aria-describedby":"alert-dialog-description"},n.createElement(b.DialogTitle,{id:"alert-dialog-title"},"Filter options",n.createElement(b.IconButton,{"aria-label":"close",className:a.closeButton,onClick:o},n.createElement(Y,null))),n.createElement(b.DialogContent,null,n.createElement("div",{className:a.root},n.createElement(b.Typography,null,"Set max height for the track"),n.createElement(b.TextField,{value:c,onChange:function(e){s(e.target.value)},placeholder:"Enter max score"}),n.createElement(b.Button,{variant:"contained",color:"primary",type:"submit",style:{marginLeft:20},onClick:function(){r.setMaxHeight(""===c||Number.isNaN(+c)?void 0:+c),o()}},"Submit"))))}var Zn={__proto__:null,default:w.observer(Yn)};exports.BaseLinearDisplay=ot,exports.BaseLinearDisplayComponent=Xe,exports.RefNameAutocomplete=jt,exports.baseLinearDisplayConfigSchema=Le,exports.default=Gn,exports.linearBareDisplayConfigSchemaFactory=at,exports.linearBasicDisplayConfigSchemaFactory=Vn,exports.linearBasicDisplayModelFactory=_n,exports.renderToSvg=Mt;
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t=oe(e);!0===e.ctrlKey?(e.preventDefault(),i.current+=t.pixelY/500,o.setScaleFactor(i.current<0?1-i.current:1/(1+i.current)),c.current&&clearTimeout(c.current),c.current=setTimeout((function(){o.setScaleFactor(1),o.zoomTo(i.current>0?o.bpPerPx*(1+i.current):o.bpPerPx/(1-i.current)),i.current=0}),300)):(Math.abs(t.pixelX)>Math.abs(2*t.pixelY)&&e.preventDefault(),i.current+=t.pixelX,l.current||(l.current=!0,window.requestAnimationFrame((function(){o.horizontalScroll(i.current),i.current=0,l.current=!1}))))}return e?(e.addEventListener("wheel",t),function(){e.removeEventListener("wheel",t)}):function(){}}),[o]),n.createElement("div",{ref:s,role:"presentation",className:a.tracksContainer,onMouseDown:function(e){var t=e.target;t.draggable||t.dataset.resizer||0===e.button&&(u.current=e.clientX,m(!0))},onMouseUp:function(e){e.preventDefault(),m(!1)},onMouseLeave:function(e){e.preventDefault()}},n.createElement(wn,{model:o}),o.showCenterLine?n.createElement(xn,{model:o}):null,n.createElement(dn,{model:o,ControlComponent:n.createElement(hn,{model:o,style:{height:Vn,boxSizing:"border-box"}})}),n.createElement("div",{className:a.spacer}),r)}var Pn=b.observer(Cn),Bn=t.lazy((function(){return Promise.resolve().then((function(){return jn}))})),Tn=f.makeStyles((function(e){return{importFormContainer:{padding:e.spacing(2)},button:{margin:e.spacing(2)}}})),Rn=b.observer((function(e){var r,o=e.model,a=Tn(),i=u.getSession(o),l=i.assemblyNames,c=i.assemblyManager,s=i.textSearchManager,d=o.rankSearchResults,m=o.isSearchDialogDisplayed,p=o.error,g=Be(t.useState(l[0]),2),h=g[0],v=g[1],y=Be(t.useState(p),2),b=y[0],w=y[1],k=o.searchScope(h),E=c.get(h),x=l.length?null==E?void 0:E.error:"No configured assemblies",S=(null==E?void 0:E.regions)||[],C=x||b,P=Be(t.useState(),2),B=P[1],T=P[0]||new G({label:null===(r=S[0])||void 0===r?void 0:r.refName}),R=null==T?void 0:T.getLocation();function N(e,t){return M.apply(this,arguments)}function M(){return(M=be(De.mark((function e(t,n){var r,o,a;return De.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return s||console.warn("No text search manager"),e.next=3,null==s?void 0:s.search({queryString:t,searchType:n},k,d);case 3:return o=e.sent,a=null==E||null===(r=E.allRefNames)||void 0===r?void 0:r.filter((function(e){return e.startsWith(t)})).map((function(e){return new G({label:e})})).slice(0,10),e.abrupt("return",[].concat(Te(a||[]),Te(o||[])));case 6:case"end":return e.stop()}}),e)})))).apply(this,arguments)}function L(){return(L=be(De.mark((function e(t){var n,r,a,l;return De.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(T){e.next=2;break}return e.abrupt("return");case 2:if(n=T.getTrackId(),r=t||T.getLocation()||"",e.prev=4,null==E||null===(a=E.allRefNames)||void 0===a||!a.includes(r)){e.next=9;break}o.navToLocString(r,h),e.next=20;break;case 9:return e.next=11,N(t,"exact");case 11:if(!((l=e.sent)&&l.length>1)){e.next=17;break}return o.setSearchResults(l,t.toLowerCase()),e.abrupt("return");case 17:1===(null==l?void 0:l.length)&&(r=l[0].getLocation(),n=l[0].getTrackId());case 18:o.navToLocString(r,h),n&&o.showTrack(n);case 20:e.next=26;break;case 22:e.prev=22,e.t0=e.catch(4),console.error(e.t0),i.notify("".concat(e.t0),"warning");case 26:case"end":return e.stop()}}),e,null,[[4,22]])})))).apply(this,arguments)}return n.createElement("div",null,C?n.createElement(ce,{error:C}):null,n.createElement(f.Container,{className:a.importFormContainer},n.createElement("form",{onSubmit:function(e){return e.preventDefault()}},n.createElement(f.Grid,{container:!0,spacing:1,justifyContent:"center",alignItems:"center"},n.createElement(f.Grid,{item:!0},n.createElement(se,{onChange:function(e){w(void 0),v(e)},session:i,selected:h})),n.createElement(f.Grid,{item:!0},h?C?n.createElement(Y,{style:{color:"red"}}):R?n.createElement(jt,{fetchResults:N,model:o,assemblyName:x?void 0:h,value:R,minWidth:270,onSelect:function(e){return B(e)},TextFieldProps:{margin:"normal",variant:"outlined",helperText:"Enter sequence name, feature name, or location"}}):n.createElement(f.CircularProgress,{role:"progressbar",size:20,disableShrink:!0}):null),n.createElement(f.Grid,{item:!0}),n.createElement(f.Grid,{item:!0},n.createElement(f.Button,{type:"submit",disabled:!R,className:a.button,onClick:function(){o.setError(void 0),R&&function(e){L.apply(this,arguments)}(R)},variant:"contained",color:"primary"},"Open"),n.createElement(f.Button,{disabled:!R,className:a.button,onClick:function(){o.setError(void 0),o.showAllRegionsInAssembly(h)},variant:"contained",color:"secondary"},"Show all regions in assembly"))))),m?n.createElement(Bn,{model:o,optAssemblyName:h,handleClose:function(){return o.setSearchResults(void 0,void 0)}}):null)})),Nn=b.observer((function(e){var r=e.model,o=r.bpPerPx,a=r.maxBpPerPx,i=r.minBpPerPx,l=r.scaleFactor,c=Be(t.useState(),2),s=c[0],u=c[1];return n.createElement(n.Fragment,null,n.createElement(te,{style:{background:"#aaa7"}},n.createElement(Q,{color:"secondary",onClick:function(e){u(e.currentTarget)}},n.createElement(ue,null)),n.createElement(Q,{"data-testid":"zoom_out",onClick:function(){r.zoom(2*o)},disabled:o>=a-1e-4||1!==l,color:"secondary"},n.createElement(ee,null)),n.createElement(Q,{"data-testid":"zoom_in",onClick:function(){r.zoom(r.bpPerPx/2)},disabled:o<=i+1e-4||1!==l,color:"secondary"},n.createElement(A,null))),n.createElement(de,{anchorEl:s,open:Boolean(s),onMenuItemClick:function(e,t){t(),u(void 0)},onClose:function(){u(void 0)},menuItems:r.menuItems()}))})),Mn=f.makeStyles((function(e){return{loadingMessage:{padding:e.spacing(5)},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]},dialogContent:{width:"80em"},textAreaFont:{fontFamily:"Courier New"}}}));function Ln(e,t,n){return Dn.apply(this,arguments)}function Dn(){return(Dn=be(De.mark((function e(t,n,r){var a,i,l,c,s,d,f;return De.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(a=u.getSession(t),l=t.rightOffset,(i=t.leftOffset)&&l){e.next=4;break}throw new Error("no offsets on model to use for range");case 4:if(i.assemblyName===l.assemblyName){e.next=6;break}throw new Error("not able to fetch sequences from multiple assemblies");case 6:if(c=a.rpcManager,d=a.assemblyManager.get(s=i.assemblyName||l.assemblyName||"")){e.next=11;break}throw new Error("assembly ".concat(s," not found"));case 11:return f=o.getConf(d,["sequence","adapter"]),e.next=15,Promise.all(n.map((function(e){return c.call("getSequence","CoreGetFeatures",{adapterConfig:f,region:e,sessionId:"getSequence",signal:r})})));case 15:return e.abrupt("return",e.sent.map((function(e){return e[0]})));case 17:case"end":return e.stop()}}),e)})))).apply(this,arguments)}function In(e){var r=e.model,o=e.handleClose,a=Mn(),i=u.getSession(r),l=Be(t.useState(),2),c=l[0],s=l[1],d=Be(t.useState(),2),m=d[0],p=d[1],g=Boolean(void 0===m),h=r.leftOffset,v=r.rightOffset,y=t.useMemo((function(){return r.getSelectedRegions(h,v)}),[r,h,v]);t.useEffect((function(){var e=!0,t=new AbortController;return be(De.mark((function n(){var o;return De.wrap((function(n){for(;;)switch(n.prev=n.next){case 0:if(n.prev=0,!(y.length>0)){n.next=8;break}return n.next=4,Ln(r,y,t.signal);case 4:o=n.sent,e&&p(me.formatSeqFasta(o.filter((function(e){return!!e})).map((function(e){var t=e.get("seq"),n=e.get("refName"),r=e.get("start")+1,o=e.get("end"),a="".concat(n,":").concat(r,"-").concat(o);if((null==t?void 0:t.length)!==o-r+1)throw new Error("".concat(a," returned ").concat(t.length.toLocaleString()," bases, but should have returned ").concat((o-r).toLocaleString()));return{header:a,seq:t}})))),n.next=9;break;case 8:throw new Error("Selected region is out of bounds");case 9:n.next=15;break;case 11:n.prev=11,n.t0=n.catch(0),console.error(n.t0),e&&s(n.t0);case 15:case"end":return n.stop()}}),n,null,[[0,11]])})))(),function(){t.abort(),e=!1}}),[r,i,y,p]);var b=!!m&&m.length>1e6;return n.createElement(f.Dialog,{"data-testid":"sequence-dialog",maxWidth:"xl",open:!0,onClose:o,"aria-labelledby":"alert-dialog-title","aria-describedby":"alert-dialog-description"},n.createElement(f.DialogTitle,{id:"alert-dialog-title"},"Reference sequence",o?n.createElement(f.IconButton,{"data-testid":"close-seqDialog",className:a.closeButton,onClick:function(){o(),r.setOffsets(void 0,void 0)}},n.createElement(Y,null)):null),n.createElement(f.Divider,null),n.createElement(f.DialogContent,null,c?n.createElement(f.Typography,{color:"error"},"".concat(c)):null,g&&!c?n.createElement(f.Container,null,"Retrieving reference sequence...",n.createElement(f.CircularProgress,{style:{marginLeft:10},size:20,disableShrink:!0})):null,n.createElement(f.TextField,{"data-testid":"rubberband-sequence",variant:"outlined",multiline:!0,rows:5,disabled:b,className:a.dialogContent,fullWidth:!0,value:b?"Reference sequence too large to display, use the download FASTA button":m,InputProps:{readOnly:!0,classes:{input:a.textAreaFont}}})),n.createElement(f.DialogActions,null,n.createElement(f.Button,{onClick:function(){fe(m||""),i.notify("Copied to clipboard","success")},disabled:g||!!c||b,color:"primary",startIcon:n.createElement(I.ContentCopy,null)},"Copy to clipboard"),n.createElement(f.Button,{onClick:function(){var e=new Blob([m||""],{type:"text/x-fasta;charset=utf-8"});D.saveAs(e,"jbrowse_ref_seq.fa")},disabled:g||!!c,color:"primary",startIcon:n.createElement(pe,null)},"Download FASTA"),n.createElement(f.Button,{onClick:o,color:"primary",autoFocus:!0},"Close")))}var On=b.observer(In),Fn=f.makeStyles((function(e){return{dialogContent:{width:"80em"},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}}));function zn(e){var t,r,o=e.model,a=e.optAssemblyName,i=e.handleClose,l=Fn(),c=u.getSession(o),s=h.getEnv(c).pluginManager,d=c.assemblyManager,m=a;if(o.displayedRegions.length>0&&(m=null===(r=o.displayedRegions[0])||void 0===r?void 0:r.assemblyName),!m)throw new Error("Assembly name not found");var p=d.get(m);if(!p)throw new Error("assembly ".concat(m," not found"));if(!p.regions)throw new Error("assembly ".concat(m," regions not loaded"));var g=p.regions;function v(e){if(e){var t,n=s.pluggableConfigSchemaType("track"),r=h.resolveIdentifier(n,h.getRoot(o),e);if(r)return null===(t=r.name)||void 0===t?void 0:t.value}return""}return n.createElement(f.Dialog,{open:!0,maxWidth:"xl",onClose:i},n.createElement(f.DialogTitle,null,"Search results",i?n.createElement(f.IconButton,{"data-testid":"close-resultsDialog",className:l.closeButton,onClick:function(){i()}},n.createElement(Y,null)):null),n.createElement(f.Divider,null),n.createElement(f.DialogContent,null,null!==(t=o.searchResults)&&void 0!==t&&t.length?n.createElement(n.Fragment,null,n.createElement(f.Typography,null,"Showing results for 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e===t.refName}));t?(o.setDisplayedRegions([t]),o.showAllRegions()):o.navToLocString(e,m)}catch(e){console.warn(e),c.notify("".concat(e),"warning")}}(e.getLocation());var t=e.getTrackId();t&&o.showTrack(t),i()},disabled:!v(e.getTrackId()),color:"primary",variant:"contained"},"Go")))})))))):n.createElement(f.Typography,null,"No results found for ",n.createElement("b",null,o.searchQuery))),n.createElement(f.Divider,null),n.createElement(f.DialogActions,null,n.createElement(f.Button,{onClick:function(){return i()},color:"primary"},"Cancel")))}var jn={__proto__:null,useStyles:Fn,default:zn},qn=f.makeStyles((function(e){return{note:{textAlign:"center",paddingTop:e.spacing(1),paddingBottom:e.spacing(1)},dots:{"&::after":{display:"inline-block",animation:"$ellipsis 1.5s infinite",content:'"."',width:"1em",textAlign:"left"}},"@keyframes ellipsis":{"0%":{content:'"."'},"33%":{content:'".."'},"66%":{content:'"..."'}}}})),An={__proto__:null,default:b.observer((function(e){var t=e.model,r=t.tracks,o=t.error,a=t.hideHeader,i=t.initialized,l=t.hasDisplayedRegions,c=qn();return i||o?!l||o?n.createElement(Rn,{model:t}):n.createElement("div",{style:{position:"relative"}},t.seqDialogDisplayed?n.createElement(On,{model:t,handleClose:function(){t.setSequenceDialogOpen(!1)}}):null,t.isSearchDialogDisplayed?n.createElement(zn,{model:t,handleClose:function(){t.setSearchResults(void 0,void 0)}}):null,a?n.createElement("div",{style:{position:"absolute",right:0,zIndex:1001}},n.createElement(Nn,{model:t})):n.createElement(tn,{model:t}),n.createElement(Pn,{model:t},r.length?r.map((function(e){return n.createElement(ln,{key:e.id,model:t,track:e})})):n.createElement(f.Paper,{variant:"outlined",className:c.note},n.createElement(f.Typography,null,"No tracks active."),n.createElement(f.Button,{variant:"contained",color:"primary",onClick:t.activateTrackSelector,style:{zIndex:1e3},startIcon:n.createElement(I.TrackSelector,null)},"Open track selector")))):n.createElement(f.Typography,{className:c.dots,variant:"h5"},"Loading")}))};function Hn(e){if(!e.length)return"";var t=e.every((function(t){return t.assemblyName===e[0].assemblyName}));return e.map((function(e){return u.assembleLocString(he(he({},e),{},{start:Math.round(e.start),end:Math.round(e.end),assemblyName:t?void 0:e.assemblyName}))})).join(";")}var Wn=48,_n=20,Vn=17,Gn=3,Xn=32,Un=7;function Jn(e){return h.types.compose(a.BaseViewModel,h.types.model("LinearGenomeView",{id:x.ElementId,type:h.types.literal("LinearGenomeView"),offsetPx:0,bpPerPx:1,displayedRegions:h.types.array(x.Region),tracks:h.types.array(e.pluggableMstType("track","stateModel")),hideHeader:!1,hideHeaderOverview:!1,trackSelectorType:h.types.optional(h.types.enumeration(["hierarchical"]),"hierarchical"),trackLabels:h.types.optional(h.types.string,(function(){return localStorage.getItem("lgv-trackLabels")||"overlapping"})),showCenterLine:h.types.optional(h.types.boolean,(function(){var e=localStorage.getItem("lgv-showCenterLine");return void 0!==e&&!!e})),showCytobandsSetting:h.types.optional(h.types.boolean,(function(){var e=localStorage.getItem("lgv-showCytobands");return void 0===e||!!e}))})).volatile((function(){return{volatileWidth:void 0,minimumBlockWidth:3,draggingTrackId:void 0,volatileError:void 0,afterDisplayedRegionsSetCallbacks:[],scaleFactor:1,trackRefs:{},coarseDynamicBlocks:[],coarseTotalBp:0,leftOffset:void 0,rightOffset:void 0,searchResults:void 0,searchQuery:void 0,seqDialogDisplayed:!1}})).views((function(e){return{get width(){if(void 0===e.volatileWidth)throw new Error("width undefined, make sure to check for model.initialized");return e.volatileWidth},get interRegionPaddingWidth(){return 2}}})).views((function(e){return{get assemblyErrors(){var t=u.getSession(e).assemblyManager;return this.assemblyNames.map((function(e){var n;return null===(n=t.get(e))||void 0===n?void 0:n.error})).filter((function(e){return!!e})).join(", ")},get assembliesInitialized(){var t=u.getSession(e).assemblyManager;return this.assemblyNames.every((function(e){var n;return null===(n=t.get(e))||void 0===n?void 0:n.initialized}))},get initialized(){return void 0!==e.volatileWidth&&this.assembliesInitialized},get hasDisplayedRegions(){return e.displayedRegions.length>0},get isSearchDialogDisplayed(){return void 0!==e.searchResults},get scaleBarHeight(){return Vn+Gn},get headerHeight(){return e.hideHeader?0:e.hideHeaderOverview?Wn:Wn+_n},get trackHeights(){return e.tracks.map((function(e){return e.displays[0].height})).reduce((function(e,t){return e+t}),0)},get trackHeightsWithResizeHandles(){return this.trackHeights+e.tracks.length*Gn},get height(){return this.trackHeightsWithResizeHandles+this.headerHeight+this.scaleBarHeight},get totalBp(){return e.displayedRegions.reduce((function(e,t){return e+t.end-t.start}),0)},get maxBpPerPx(){return this.totalBp/(.9*e.width)},get minBpPerPx(){return.02},get error(){return e.volatileError||this.assemblyErrors},get maxOffset(){return this.displayedRegionsTotalPx-10},get minOffset(){return 30-e.width},get displayedRegionsTotalPx(){return this.totalBp/e.bpPerPx},renderProps:function(){return he(he({},g.getParentRenderProps(e)),{},{bpPerPx:e.bpPerPx,highResolutionScaling:o.getConf(u.getSession(e),"highResolutionScaling")})},get assemblyNames(){return Te(new Set(e.displayedRegions.map((function(e){return e.assemblyName}))))},searchScope:function(t){return{assemblyName:t,includeAggregateIndexes:!0,tracks:e.tracks}},bpToPx:function(t){return u.viewBpToPx({refName:t.refName,coord:t.coord,regionNumber:t.regionNumber,self:e})},pxToBp:function(t){var n=0,r=(e.offsetPx+t)*e.bpPerPx,o=e.displayedRegions.length;if(r<0){var a=e.displayedRegions[0],i=r;return he(he({},h.getSnapshot(a)),{},{oob:!0,coord:a.reversed?Math.floor(a.end-i)+1:Math.floor(a.start+i)+1,offset:i,index:0})}for(var l=e.interRegionPaddingWidth*e.bpPerPx,c=e.minimumBlockWidth*e.bpPerPx,s=0;s<e.displayedRegions.length;s+=1){var u=e.displayedRegions[s],d=u.end-u.start,f=r-n;if(d+n>r&&n<=r)return he(he({},h.getSnapshot(u)),{},{oob:!1,offset:f,coord:u.reversed?Math.floor(u.end-f)+1:Math.floor(u.start+f)+1,index:s});n+=u.end-u.start>c&&f/e.bpPerPx>0&&f/e.bpPerPx<e.width?d+l:d}if(r>=n){var m=e.displayedRegions[o-1],p=r-n+(m.end-m.start);return he(he({},h.getSnapshot(m)),{},{oob:!0,offset:p,coord:m.reversed?Math.floor(m.end-p)+1:Math.floor(m.start+p)+1,index:o-1})}return{coord:0,index:0,refName:"",oob:!0,assemblyName:"",offset:0,start:0,end:0,reversed:!1}},getTrack:function(t){return e.tracks.find((function(e){return e.configuration.trackId===t}))},rankSearchResults:function(t){var n=e.tracks.map((function(e){return e.configuration.trackId}));return t.forEach((function(e){n!==[]&&n.includes(e.trackId)&&e.updateScore(e.getScore()+1)})),t},rewriteOnClicks:function(t,n){var r=this;n.forEach((function(n){if("subMenu"in n&&r.rewriteOnClicks(t,n.subMenu),"onClick"in n){var o=n.onClick;n.onClick=function(){for(var n=arguments.length,r=new Array(n),a=0;a<n;a++)r[a]=arguments[a];e.tracks.forEach((function(e){e.type===t&&o.apply(e,[e].concat(r))}))}}}))},get trackTypeActions(){var t=this,n=new Map;return e.tracks.forEach((function(e){if(!n.get(e.type)){var r=L(e.viewMenuActions);t.rewriteOnClicks(e.type,r),n.set(e.type,r)}})),n},get centerLineInfo(){return e.displayedRegions.length?this.pxToBp(e.width/2):void 0}}})).actions((function(t){return{setShowCytobands:function(e){t.showCytobandsSetting=e,localStorage.setItem("lgv-showCytobands","".concat(+e))},setWidth:function(e){t.volatileWidth=e},setError:function(e){t.volatileError=e},toggleHeader:function(){t.hideHeader=!t.hideHeader},toggleHeaderOverview:function(){t.hideHeaderOverview=!t.hideHeaderOverview},scrollTo:function(e){var n=u.clamp(e,t.minOffset,t.maxOffset);return t.offsetPx=n,n},zoomTo:function(e){var n=u.clamp(e,t.minBpPerPx,t.maxBpPerPx);if(n===t.bpPerPx)return n;var r=t.bpPerPx;if(t.bpPerPx=n,Math.abs(r-n)<1e-6)return console.warn("zoomTo bpPerPx rounding error"),r;var o=t.width;return this.scrollTo(Math.round((t.offsetPx+o/2)*r/n-o/2)),n},setOffsets:function(e,n){t.leftOffset=e,t.rightOffset=n},setSearchResults:function(e,n){t.searchResults=e,t.searchQuery=n},setSequenceDialogOpen:function(e){t.seqDialogDisplayed=e},setNewView:function(e,t){this.zoomTo(e),this.scrollTo(t)},horizontallyFlip:function(){t.displayedRegions=h.cast(t.displayedRegions.slice().reverse().map((function(e){return he(he({},e),{},{reversed:!e.reversed})}))),this.scrollTo(t.totalBp/t.bpPerPx-t.offsetPx-t.width)},showTrack:function(n){var r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},o=arguments.length>2&&void 0!==arguments[2]?arguments[2]:{},a=e.pluggableConfigSchemaType("track"),i=h.resolveIdentifier(a,h.getRoot(t),n);if(!i)throw new Error('Could not resolve identifier "'.concat(n,'"'));var l=e.getTrackType(null==i?void 0:i.type);if(!l)throw new Error("Unknown track type ".concat(i.type));var c=e.getViewType(t.type),s=c.displayTypes.map((function(e){return e.name})),u=i.displays.find((function(e){return s.includes(e.type)}));if(!u)throw new Error("Could not find a compatible display for view type ".concat(t.type));var d=t.tracks.filter((function(e){return e.configuration===i}));if(0===d.length){var f=l.stateModel.create(he(he({},r),{},{type:i.type,configuration:i,displays:[he({type:u.type,configuration:u},o)]}));return t.tracks.push(f),f}return d[0]},hideTrack:function(n){var o=e.pluggableConfigSchemaType("track"),a=h.resolveIdentifier(o,h.getRoot(t),n),i=t.tracks.filter((function(e){return e.configuration===a}));return r.transaction((function(){return i.forEach((function(e){return t.tracks.remove(e)}))})),i.length}}})).actions((function(e){return{moveTrack:function(t,n){var r=e.tracks.findIndex((function(e){return e.id===t}));if(-1===r)throw new Error("Track ID ".concat(t," not found"));var o=e.tracks.findIndex((function(e){return e.id===n}));if(-1===o)throw new Error("Track ID ".concat(n," not found"));var a=h.getSnapshot(e.tracks[r]);e.tracks.splice(r,1),e.tracks.splice(o,0,a)},closeView:function(){var t=u.getContainingView(e);t?u.isViewContainer(t)&&t.removeView(e):u.getSession(e).removeView(e)},toggleTrack:function(t){e.hideTrack(t)||e.showTrack(t)},setTrackLabels:function(t){e.trackLabels=t,localStorage.setItem("lgv-trackLabels",t)},toggleCenterLine:function(){e.showCenterLine=!e.showCenterLine,localStorage.setItem("lgv-showCenterLine","".concat(+e.showCenterLine))},setDisplayedRegions:function(t){e.displayedRegions=h.cast(t),e.zoomTo(e.bpPerPx)},activateTrackSelector:function(){if("hierarchical"===e.trackSelectorType){var t=u.getSession(e);if(u.isSessionModelWithWidgets(t)){var n=t.addWidget("HierarchicalTrackSelectorWidget","hierarchicalTrackSelector",{view:e});return t.showWidget(n),n}}throw new Error("invalid track selector type ".concat(e.trackSelectorType))},navToLocString:function(t,n){var r=u.getSession(e).assemblyManager,o=r.isValidRefName,a=t.split(";");if(e.displayedRegions.length>1){var i=a.map((function(e){return u.parseLocString(e,o)}));this.navToMultiple(i)}else{var l=n,c="";0!==e.displayedRegions.length&&(l=e.displayedRegions[0].assemblyName,c=e.displayedRegions[0].refName);var s=l&&r.get(l);if(!s)throw new Error("Could not find assembly ".concat(l));var d=s.regions;if(!d)throw new Error("Regions for assembly ".concat(l," not yet loaded"));if(a.length>1)throw new Error("Navigating to multiple locations is not allowed when viewing a whole chromosome");var f=u.parseLocString(a[0],(function(e){return o(e,l)})),m=!1;if(f.assemblyName&&f.assemblyName!==l){var p=r.get(f.assemblyName);if(!p)throw new Error("Could not find assembly ".concat(f.assemblyName));s=p,m=!0;var g=p.regions;if(!g)throw new Error("Regions for assembly ".concat(f.assemblyName," not yet loaded"));d=g}var h=s.getCanonicalRefName(f.refName);if(!h)throw new Error("Could not find refName ".concat(f.refName," in ").concat(s.name));if(m||h!==c){var v=d.find((function(e){return e.refName===h}));if(!v)throw new Error("Could not find refName ".concat(f.refName," in ").concat(s.name));this.setDisplayedRegions([v])}var y=d.find((function(e){return e.refName===h}));if(y){var b,w,k=u.clamp(null!==(b=null==f?void 0:f.start)&&void 0!==b?b:0,0,y.end),E=u.clamp(null!==(w=null==f?void 0:f.end)&&void 0!==w?w:y.end,0,y.end);this.navTo(he(he({},f),{},{start:k,end:E}))}}},navTo:function(e){this.navToMultiple([e])},navToMultiple:function(t){var n=t[0],r=n.refName,o=n.start,a=n.end,i=n.assemblyName,l=void 0===i?e.assemblyNames[0]:i;if(void 0!==o&&void 0!==a&&o>a)throw new Error('start "'.concat(o+1,'" is greater than end "').concat(a,'"'));var c=u.getSession(e).assemblyManager.get(l);if(c){var s=c.getCanonicalRefName(r);s&&(r=s)}for(var d,f=o,m=a,p=!1,g=function(e){if(r===e.refName){if(p=!0,void 0===f&&(f=e.start),void 0===m&&(m=e.end),f>=e.start&&f<=e.end&&m<=e.end&&m>=e.start)return!0;f=o,m=a}return!1},h=u.findLastIndex(e.displayedRegions,g);d!==h;)try{var v=d;if(d=e.displayedRegions.slice(void 0===v?0:v+1).findIndex(g),void 0!==v&&(d+=v+1),!p)throw new Error('could not find a region with refName "'.concat(r,'"'));if(void 0===f)throw new Error('could not find a region with refName "'.concat(r,'" that contained an end position ').concat(m));if(void 0===m)throw new Error('could not find a region with refName "'.concat(r,'" that contained a start position ').concat(f+1));if(-1===d)throw new Error('could not find a region that completely contained "'.concat(u.assembleLocString(n),'"'));if(1===t.length){var y=e.displayedRegions[d];return void this.moveTo({index:d,offset:y.reversed?y.end-m:f-y.start},{index:d,offset:y.reversed?y.end-f:m-y.start})}for(var b=0,w=0,k=0;b<t.length;b++){var E=t[b],x=e.displayedRegions[d+b];if(w=E.start||x.start,k=E.end||x.end,E.refName!==x.refName)throw new Error("Entered location ".concat(u.assembleLocString(E)," does not match with displayed regions"));if(b>0&&!(x.reversed?k===x.end:w===x.start))throw new Error("".concat(x.reversed?"End":"Start"," of region ").concat(u.assembleLocString(E)," should be ").concat((x.reversed?x.end:x.start+1).toLocaleString("en-US"),", but it is not"));if(b!==t.length-1&&!(x.reversed?w===x.start:k===x.end))throw new Error("".concat(x.reversed?"Start":"End"," of region ").concat(u.assembleLocString(E)," should be ").concat((x.reversed?x.start+1:x.end).toLocaleString("en-US"),", but it is not"))}var S=e.displayedRegions[d],C=e.displayedRegions[d+(b-=1)];return void this.moveTo({index:d,offset:S.reversed?S.end-m:f-S.start},{index:d+b,offset:C.reversed?C.end-w:k-C.start})}catch(e){if(d===h)throw e}},zoomToDisplayedRegions:function(t,n){if(void 0!==t&&void 0!==n){if(t.refName===n.refName&&t.index===n.index&&n.offset<t.offset||t.index>n.index){var r=[n,t];t=r[0],n=r[1]}var o={start:t.start,end:t.end,index:t.index,offset:t.offset},a={start:n.start,end:n.end,index:n.index,offset:n.offset};o&&a?this.moveTo(o,a):u.getSession(e).notify("No regions found to navigate to","warning")}},getSelectedRegions:function(t,n){var r=M.create(he(he({},h.getSnapshot(e)),{},{interRegionPaddingWidth:e.interRegionPaddingWidth}));return r.setVolatileWidth(e.width),r.zoomToDisplayedRegions(t,n),r.dynamicBlocks.contentBlocks.map((function(e){return he(he({},e),{},{start:Math.floor(e.start),end:Math.ceil(e.end)})}))},afterDisplayedRegionsSet:function(t){e.afterDisplayedRegionsSetCallbacks.push(t)},moveTo:function(t,n){var r=0;if(t.index===n.index)r+=n.offset-t.offset;else{var o=e.displayedRegions[t.index];if(r+=o.end-o.start-t.offset,n.index-t.index>=2)for(var a=t.index+1;a<n.index;a+=1)r+=e.displayedRegions[a].end-e.displayedRegions[a].start;r+=n.offset}var i=r/(e.width-e.interRegionPaddingWidth*(n.index-t.index)),l=e.zoomTo(i),c=0;i<l&&(c=(l-i)*e.width/2);for(var s=-c,u=0;u<e.displayedRegions.length;u+=1){var d=e.displayedRegions[u];if(t.index===u){s+=t.offset;break}s+=d.end-d.start}e.scrollTo(Math.round(s/e.bpPerPx)+e.interRegionPaddingWidth*t.index)},horizontalScroll:function(t){var n=e.offsetPx;return e.scrollTo(e.offsetPx+t)-n},centerAt:function(t,n,r){var o=e.bpToPx({refName:n,coord:t,regionNumber:r});o&&e.scrollTo(Math.round(o.offsetPx-e.width/2))},center:function(){e.scrollTo(Math.round(e.totalBp/2/e.bpPerPx-e.width/2))},showAllRegions:function(){e.zoomTo(e.maxBpPerPx),this.center()},showAllRegionsInAssembly:function(t){var n=u.getSession(e),r=n.assemblyManager;if(!t){var o=Te(new Set(e.displayedRegions.map((function(e){return e.assemblyName}))));if(o.length>1)return void n.notify("Can't perform this with multiple assemblies currently");t=Be(o,1)[0]}var a=r.get(t);if(a){var i=a.regions;i&&(this.setDisplayedRegions(i),e.zoomTo(e.maxBpPerPx),this.center())}},setDraggingTrackId:function(t){e.draggingTrackId=t},setScaleFactor:function(t){e.scaleFactor=t}}})).actions((function(e){var t=function(){};return{slide:function(n){var r=Be(u.springAnimate(e.offsetPx,e.offsetPx+e.width*n,e.scrollTo),2),o=r[0],a=r[1];t(),t=a,o()}}})).actions((function(e){var t=function(){};return{zoom:function(n){if(e.zoomTo(e.bpPerPx),!(n<e.bpPerPx&&e.bpPerPx===e.minBpPerPx||n>e.bpPerPx&&e.bpPerPx===e.maxBpPerPx)){var r=Be(u.springAnimate(1,e.bpPerPx/n,e.setScaleFactor,(function(){e.zoomTo(n),e.setScaleFactor(1)})),2),o=r[0],a=r[1];t(),t=a,o()}}}})).views((function(e){return{get canShowCytobands(){return 1===e.displayedRegions.length&&this.anyCytobandsExist},get showCytobands(){return this.canShowCytobands&&e.showCytobandsSetting},get anyCytobandsExist(){var t=u.getSession(e).assemblyManager;return e.assemblyNames.some((function(e){var n,r;return null===(n=t.get(e))||void 0===n||null===(r=n.cytobands)||void 0===r?void 0:r.length}))},get cytobandOffset(){return this.showCytobands?u.measureText(e.displayedRegions[0].refName,12)+15:0}}})).views((function(e){var t,n="";return{menuItems:function(){var t,n=e.showCytobands,r=[{label:"Return to import form",onClick:function(){u.getSession(e).queueDialog((function(t){return[Xt,{model:e,handleClose:t}]}))},icon:j},{label:"Export SVG",icon:q,onClick:function(){u.getSession(e).queueDialog((function(t){return[_t,{model:e,handleClose:t}]}))}},{label:"Open track selector",onClick:e.activateTrackSelector,icon:I.TrackSelector},{label:"Horizontally flip",icon:O,onClick:e.horizontallyFlip},{type:"divider"},{label:"Show all regions in assembly",icon:F,onClick:e.showAllRegionsInAssembly},{label:"Show center line",icon:F,type:"checkbox",checked:e.showCenterLine,onClick:e.toggleCenterLine},{label:"Show header",icon:F,type:"checkbox",checked:!e.hideHeader,onClick:e.toggleHeader},{label:"Show header overview",icon:F,type:"checkbox",checked:!e.hideHeaderOverview,onClick:e.toggleHeaderOverview,disabled:e.hideHeader},{label:"Track labels",icon:z,subMenu:[{label:"Overlapping",icon:F,type:"radio",checked:"overlapping"===e.trackLabels,onClick:function(){return e.setTrackLabels("overlapping")}},{label:"Offset",icon:F,type:"radio",checked:"offset"===e.trackLabels,onClick:function(){return e.setTrackLabels("offset")}},{label:"Hidden",icon:F,type:"radio",checked:"hidden"===e.trackLabels,onClick:function(){return e.setTrackLabels("hidden")}}]}].concat(Te(e.canShowCytobands?[{label:n?"Hide ideogram":"Show ideograms",onClick:function(){e.setShowCytobands(!n)}}]:[])),o=Me(e.trackTypeActions.entries());try{for(o.s();!(t=o.n()).done;){var a=Be(t.value,2),i=a[1];i.length&&(r.push({type:"divider"},{type:"subHeader",label:a[0]}),i.forEach((function(e){r.push(e)})))}}catch(e){o.e(e)}finally{o.f()}return r},get staticBlocks(){var r=N(e),o=JSON.stringify(r);return n!==o&&(t=r,n=o),t},get dynamicBlocks(){return R(e)},get roundedDynamicBlocks(){return this.dynamicBlocks.contentBlocks.map((function(e){return he(he({},e),{},{start:Math.floor(e.start),end:Math.ceil(e.end)})}))},get visibleLocStrings(){return Hn(this.dynamicBlocks.contentBlocks)},get coarseVisibleLocStrings(){return Hn(e.coarseDynamicBlocks)}}})).actions((function(e){return{clearView:function(){e.setDisplayedRegions([]),e.tracks.clear(),e.scrollTo(0),e.zoomTo(10)},setCoarseDynamicBlocks:function(t){e.coarseDynamicBlocks=t.contentBlocks,e.coarseTotalBp=t.totalBp},afterAttach:function(){var t=this;h.addDisposer(e,r.autorun((function(){e.initialized&&t.setCoarseDynamicBlocks(e.dynamicBlocks)}),{delay:150}))}}})).actions((function(e){return{exportSvg:function(){var t=arguments;return be(De.mark((function n(){var r,o;return De.wrap((function(n){for(;;)switch(n.prev=n.next){case 0:return r=t.length>0&&void 0!==t[0]?t[0]:{},n.next=3,Lt(e,r);case 3:o=new Blob([n.sent],{type:"image/svg+xml"}),D.saveAs(o,"image.svg");case 6:case"end":return n.stop()}}),n)})))()}}})).views((function(e){return{rubberBandMenuItems:function(){return[{label:"Zoom to region",icon:A,onClick:function(){var t=e.leftOffset,n=e.rightOffset;t&&n&&e.moveTo(t,n)}},{label:"Get sequence",icon:v,onClick:function(){e.setSequenceDialogOpen(!0)}}]}}}))}var Yn=t.lazy((function(){return Promise.resolve().then((function(){return rr}))})),Zn=function(e){return h.types.compose("LinearBasicDisplay",at,h.types.model({type:h.types.literal("LinearBasicDisplay"),trackShowLabels:h.types.maybe(h.types.boolean),trackShowDescriptions:h.types.maybe(h.types.boolean),trackDisplayMode:h.types.maybe(h.types.string),trackMaxHeight:h.types.maybe(h.types.number),configuration:o.ConfigurationReference(e)})).views((function(e){return{get rendererTypeName(){return o.getConf(e,["renderer","type"])},get showLabels(){var t=o.getConf(e,["renderer","showLabels"]);return void 0!==e.trackShowLabels?e.trackShowLabels:t},get showDescriptions(){var t=o.getConf(e,["renderer","showLabels"]);return void 0!==e.trackShowDescriptions?e.trackShowDescriptions:t},get maxHeight(){var t=o.getConf(e,["renderer","maxHeight"]);return void 0!==e.trackMaxHeight?e.trackMaxHeight:t},get displayMode(){var t=o.getConf(e,["renderer","displayMode"]);return void 0!==e.trackDisplayMode?e.trackDisplayMode:t},get rendererConfig(){var t=o.getConf(e,["renderer"])||{};return e.rendererType.configSchema.create(he(he({},t),{},{showLabels:this.showLabels,showDescriptions:this.showDescriptions,displayMode:this.displayMode,maxHeight:this.maxHeight}),h.getEnv(e))}}})).actions((function(e){return{toggleShowLabels:function(){e.trackShowLabels=!e.showLabels},toggleShowDescriptions:function(){e.trackShowDescriptions=!e.showDescriptions},setDisplayMode:function(t){e.trackDisplayMode=t},setMaxHeight:function(t){e.trackMaxHeight=t}}})).views((function(e){var t=e.trackMenuItems,n=e.renderProps;return{renderProps:function(){var t=e.rendererConfig;return he(he({},n()),{},{config:t})},trackMenuItems:function(){return[].concat(Te(t()),[{label:"Show labels",icon:F,type:"checkbox",checked:e.showLabels,onClick:function(){e.toggleShowLabels()}},{label:"Show descriptions",icon:F,type:"checkbox",checked:e.showDescriptions,onClick:function(){e.toggleShowDescriptions()}},{label:"Display mode",icon:F,subMenu:["compact","reducedRepresentation","normal","collapse"].map((function(t){return{label:t,onClick:function(){e.setDisplayMode(t)}}}))},{label:"Set max height",onClick:function(){u.getSession(e).queueDialog((function(t){return[Yn,{model:e,handleClose:t}]}))}}])}}}))};function Kn(e){return o.ConfigurationSchema("LinearBasicDisplay",{mouseover:{type:"string",description:"what to display in a given mouseover",defaultValue:"jexl:get(feature,'name')",contextVariable:["feature"]},renderer:e.pluggableConfigSchemaType("renderer")},{baseConfiguration:Ie,explicitlyTyped:!0})}var Qn=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}}),Object.defineProperty(e,"prototype",{writable:!1}),t&&xe(e,t)}(p,s);var n,f,m=Pe(p);function p(){var e;return we(this,p),(e=m.apply(this,arguments)).name="LinearGenomeViewPlugin",e.exports={BaseLinearDisplayComponent:Xe,BaseLinearDisplay:at,baseLinearDisplayConfigSchema:Ie},e}return n=p,(f=[{key:"install",value:function(e){e.addTrackType((function(){var t=o.ConfigurationSchema("FeatureTrack",{},{baseConfiguration:a.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new i({name:"FeatureTrack",configSchema:t,stateModel:a.createBaseTrackModel(e,"FeatureTrack",t)})})),e.addTrackType((function(){var t=o.ConfigurationSchema("BasicTrack",{},{baseConfiguration:a.createBaseTrackConfig(e),explicitIdentifier:"trackId"});return new i({name:"BasicTrack",configSchema:t,stateModel:a.createBaseTrackModel(e,"BasicTrack",t)})})),e.addDisplayType((function(){var t=it(e);return new l({name:"LinearBareDisplay",configSchema:t,stateModel:lt(t),trackType:"BasicTrack",viewType:"LinearGenomeView",ReactComponent:Xe})})),e.addDisplayType((function(){var t=Kn(e);return new l({name:"LinearBasicDisplay",configSchema:t,stateModel:Zn(t),trackType:"FeatureTrack",viewType:"LinearGenomeView",ReactComponent:Xe})})),e.addViewType((function(){return new c({name:"LinearGenomeView",stateModel:Jn(e),ReactComponent:t.lazy((function(){return Promise.resolve().then((function(){return An}))}))})})),e.addToExtensionPoint("LaunchView-LinearGenomeView",function(){var e=be(De.mark((function e(t){var n,o,a,i,l,c,s,u;return De.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return o=t.assembly,a=t.loc,l=void 0===(i=t.tracks)?[]:i,c=(n=t.session).assemblyManager,s=n.addView("LinearGenomeView",{}),e.next=5,r.when((function(){return!!s.volatileWidth}));case 5:if(o){e.next=7;break}throw new Error("No assembly provided when launching linear genome view");case 7:return e.next=9,c.waitForAssembly(o);case 9:if(e.sent){e.next=12;break}throw new Error('Assembly "'.concat(o,'" not found when launching linear genome view'));case 12:if(s.navToLocString(a,o),u=[],l.forEach((function(e){try{s.showTrack(e)}catch(t){if(!"".concat(t).match("Could not resolve identifier"))throw t;u.push(e)}})),!u.length){e.next=17;break}throw new Error("Could not resolve identifiers: ".concat(u.join(",")));case 17:case"end":return e.stop()}}),e)})));return function(t){return e.apply(this,arguments)}}())}},{key:"configure",value:function(e){u.isAbstractMenuManager(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Linear genome view",icon:d,onClick:function(e){e.addView("LinearGenomeView",{})}})}}])&&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)}}(n.prototype,f),Object.defineProperty(n,"prototype",{writable:!1}),p}(),$n=f.makeStyles((function(e){return{closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}})),er={__proto__:null,useStyles:$n,default:function(e){var t=e.handleClose,r=$n();return n.createElement(f.Dialog,{open:!0,maxWidth:"xl",onClose:t},n.createElement(f.DialogTitle,null,"Using the search box",t?n.createElement(f.IconButton,{"data-testid":"close-resultsDialog",className:r.closeButton,onClick:function(){t()}},n.createElement(Y,null)):null),n.createElement(f.Divider,null),n.createElement(f.DialogContent,null,n.createElement("h3",null,"Searching"),n.createElement("ul",null,n.createElement("li",null,"Jump to a feature or reference sequence by typing its name in the location box and pressing Enter."),n.createElement("li",null,"Jump to a specific region by typing the region into the location box as: ",n.createElement("code",null,"ref:start..end")," or ",n.createElement("code",null,"ref:start-end"),". Commas are allowed in the start and end coordinates.")),n.createElement("h3",null,"Example Searches"),n.createElement("ul",null,n.createElement("li",null,n.createElement("code",null,"BRCA")," - searches for the feature named BRCA"),n.createElement("li",null,n.createElement("code",null,"chr4")," - jumps to chromosome 4"),n.createElement("li",null,n.createElement("code",null,"chr4:79,500,000..80,000,000")," - jumps the region on chromosome 4 between 79.5Mb and 80Mb."))),n.createElement(f.Divider,null),n.createElement(f.DialogActions,null,n.createElement(f.Button,{onClick:function(){return t()},color:"primary"},"Close")))}},tr=f.makeStyles((function(e){return{root:{width:500},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]},field:{margin:e.spacing(2)}}}));function nr(e){var r=e.model,o=e.handleClose,a=tr(),i=r.maxHeight,l=Be(t.useState("".concat(void 0===i?"":i)),2),c=l[0],s=l[1];return n.createElement(f.Dialog,{open:!0,onClose:o,"aria-labelledby":"alert-dialog-title","aria-describedby":"alert-dialog-description"},n.createElement(f.DialogTitle,{id:"alert-dialog-title"},"Filter options",n.createElement(f.IconButton,{"aria-label":"close",className:a.closeButton,onClick:o},n.createElement(Y,null))),n.createElement(f.DialogContent,null,n.createElement("div",{className:a.root},n.createElement(f.Typography,null,"Set max height for the track"),n.createElement(f.TextField,{value:c,onChange:function(e){s(e.target.value)},placeholder:"Enter max score"}),n.createElement(f.Button,{variant:"contained",color:"primary",type:"submit",style:{marginLeft:20},onClick:function(){r.setMaxHeight(""===c||Number.isNaN(+c)?void 0:+c),o()}},"Submit"))))}var rr={__proto__:null,default:b.observer(nr)};exports.BaseLinearDisplay=at,exports.BaseLinearDisplayComponent=Xe,exports.RefNameAutocomplete=jt,exports.SearchBox=Ht,exports.baseLinearDisplayConfigSchema=Ie,exports.default=Qn,exports.linearBareDisplayConfigSchemaFactory=it,exports.linearBasicDisplayConfigSchemaFactory=Kn,exports.linearBasicDisplayModelFactory=Zn,exports.renderToSvg=Lt;
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