@jbrowse/plugin-linear-genome-view 1.4.4 → 1.5.0

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

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r.createElement(r.Fragment,null,r.createElement("line",{x1:s,x2:u,y1:10,y2:10,stroke:"black"}),r.createElement("line",{x1:s,x2:s,y1:5,y2:15,stroke:"black"}),r.createElement("line",{x1:u,x2:u,y1:5,y2:15,stroke:"black"}),r.createElement("text",{x:s+(u-s)/2,y:2*o,textAnchor:"middle",fontSize:o},t))}function gr(e){var t=e.model,n=e.fontSize,o=t.dynamicBlocks.contentBlocks,a=t.offsetPx,i=t.bpPerPx,l=o.length<5;return r.createElement(r.Fragment,null,r.createElement("defs",null,r.createElement("clipPath",{id:"clip-ruler"},r.createElement("rect",{x:0,y:0,width:e.width,height:20}))),o.map((function(e){var t=e.offsetPx-a;return r.createElement("g",{key:"".concat(e.key),transform:"translate(".concat(t," 0)")},r.createElement("text",{x:t/i,y:n,fontSize:n},e.refName),l?r.createElement("g",{transform:"translate(0 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t=e.model,o=e.offset;return r.createElement(r.Fragment,null,e.displayResults.map((function(e){var a=e.track,i=e.result,l=o,c=n.getConf(a,"name")||"Reference sequence (".concat(n.readConfObject(y.getParent(a.configuration),"name"),")");return o+=a.displays[0].height+20+20,r.createElement("g",{key:a.configuration.trackId,transform:"translate(0 ".concat(l,")")},r.createElement("text",{fontSize:15,x:Math.max(-t.offsetPx,0)},c),r.createElement("g",{transform:"translate(0 ".concat(20,")")},i))})))}function kr(e,t){return wr.apply(this,arguments)}function wr(){return(wr=ye(Ie.mark((function e(t,n){var o,a,i,l,c,s;return Ie.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,v.when((function(){return t.initialized}));case 2:return o=t.width,i=50,l=110,c=hr(a=t.tracks)+l,e.next=8,Promise.all(a.map(function(){var e=ye(Ie.mark((function e(t){var r;return Ie.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return r=t.displays[0],e.next=3,v.when((function(){return void 0===r.ready||r.ready}));case 3:return e.next=5,r.renderSvg(n);case 5:return e.abrupt("return",{track:t,result:e.sent});case 7:case"end":return e.stop()}}),e)})));return function(t){return e.apply(this,arguments)}}()));case 8:return s=e.sent,e.abrupt("return",A.renderToStaticMarkup(r.createElement("svg",{width:o,height:c,xmlns:"http://www.w3.org/2000/svg",xmlnsXlink:"http://www.w3.org/1999/xlink",viewBox:[0,0,o+2*i,c].toString()},r.createElement("rect",{width:o+2*i,height:c,fill:"white"}),r.createElement("g",{stroke:"none",transform:"translate(".concat(i," ").concat(15,")")},r.createElement(vr,{model:t}),r.createElement(br,{model:t,displayResults:s,offset:l}),r.createElement(yr,{model:t})))));case 10:case"end":return e.stop()}}),e)})))).apply(this,arguments)}var xr={__proto__:null,default:w.observer((function(e){var t=e.model,n=t.tracks,o=t.error,a=t.hideHeader,i=t.initialized,l=t.hasDisplayedRegions,c=mr();return i||o?!l||o?r.createElement(nr,{model:t}):r.createElement("div",{style:{position:"relative"}},t.seqDialogDisplayed?r.createElement(sr,{model:t,handleClose:function(){t.setSequenceDialogOpen(!1)}}):null,t.isSearchDialogDisplayed?r.createElement(er,{model:t,handleClose:function(){t.setSearchResults(void 0,void 0)}}):null,a?r.createElement("div",{style:{position:"absolute",right:0,zIndex:1001}},r.createElement(or,{model:t})):r.createElement(Bt,{model:t}),r.createElement(Qt,{model:t},n.length?n.map((function(e){return r.createElement(It,{key:e.id,model:t,track:e})})):r.createElement(b.Paper,{variant:"outlined",className:c.errorMessage},r.createElement(b.Typography,null,"No tracks active."),r.createElement(b.Button,{variant:"contained",color:"primary",onClick:t.activateTrackSelector,style:{zIndex:1e3}},r.createElement(M.TrackSelector,{className:c.spacer}),"Open track selector")))):null})),renderToSvg:kr},Er=E.makeStyles((function(e){return{closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}}));function Sr(e){var n,o=e.model,a=e.handleClose,i=Pe(t.useState("undefined"!=typeof OffscreenCanvas),2),l=i[0],c=i[1],s=Pe(t.useState(!1),2),u=s[0],d=s[1],f=Pe(t.useState(),2),m=f[0],p=f[1],g=Er();return r.createElement(b.Dialog,{open:!0,onClose:a},r.createElement(b.DialogTitle,null,"Export SVG",r.createElement(b.IconButton,{className:g.closeButton,onClick:a},r.createElement(ne,null))),r.createElement(b.DialogContent,null,m?r.createElement("div",{style:{color:"red"}},"".concat(m)):u?r.createElement("div",null,r.createElement(b.CircularProgress,{size:20,style:{marginRight:20}}),r.createElement(b.Typography,{display:"inline"},"Creating SVG")):null,"undefined"!=typeof OffscreenCanvas?r.createElement(b.FormControlLabel,{control:r.createElement(b.Checkbox,{checked:l,onChange:function(){return c((function(e){return!e}))}}),label:"Rasterize canvas based tracks? File may be much larger if this is turned off"}):r.createElement(b.Typography,null,"Note: rasterizing layers not yet supported in this browser, so SVG size may be large")),r.createElement(b.DialogActions,null,r.createElement(b.Button,{variant:"contained",color:"secondary",onClick:function(){return a()}},"Cancel"),r.createElement(b.Button,{variant:"contained",color:"primary",type:"submit",onClick:(n=ye(Ie.mark((function e(){return Ie.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return d(!0),p(void 0),e.prev=2,e.next=5,o.exportSvg({rasterizeLayers:l});case 5:a(),e.next=11;break;case 8:e.prev=8,e.t0=e.catch(2),p(e.t0);case 11:return e.prev=11,d(!1),e.finish(11);case 14:case"end":return e.stop()}}),e,null,[[2,8,11,14]])}))),function(){return n.apply(this,arguments)})},"Submit")))}var Cr=E.makeStyles((function(e){return{closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}}));function Pr(e){var t=e.model,n=e.handleClose,o=Cr();return r.createElement(b.Dialog,{maxWidth:"xl",open:!0,onClose:n},r.createElement(b.DialogTitle,null,"Reference sequence",n?r.createElement(b.IconButton,{className:o.closeButton,onClick:function(){n()}},r.createElement(ne,null)):null),r.createElement(b.Divider,null),r.createElement(b.DialogContent,null,r.createElement(b.Typography,null,"Are you sure you want to return to the import form? 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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})).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 r;return null===(r=t.get(e))||void 0===r?void 0:r.error})).filter((function(e){return!!e})).join(", ")},get assembliesInitialized(){var t=s.getSession(e).assemblyManager;return this.assemblyNames.every((function(e){var r;return null===(r=t.get(e))||void 0===r?void 0:r.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 Mr+Lr},get headerHeight(){return e.hideHeader?0:e.hideHeaderOverview?Rr:Rr+Nr},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*Lr},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 ge(ge({},m.getParentRenderProps(e)),{},{bpPerPx:e.bpPerPx,highResolutionScaling:n.getConf(s.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){var r=t.refName,n=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 r===t.refName&&n>=t.start&&n<=t.end&&(!o||o===c)?(a+=t.reversed?t.end-n:n-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 r=0,n=(e.offsetPx+t)*e.bpPerPx,o=e.displayedRegions.length;if(n<0){var a=e.displayedRegions[0],i=n;return ge(ge({},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=n-r;if(d+r>n&&r<=n)return ge(ge({},y.getSnapshot(u)),{},{oob:!1,offset:f,coord:u.reversed?Math.floor(u.end-f)+1:Math.floor(u.start+f)+1,index:s});r+=u.end-u.start>c&&f/e.bpPerPx>0&&f/e.bpPerPx<e.width?d+l:d}if(n>=r){var m=e.displayedRegions[o-1],p=n-r+(m.end-m.start);return ge(ge({},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 r=e.tracks.map((function(e){return e.configuration.trackId}));return t.forEach((function(e){r!==[]&&r.includes(e.trackId)&&e.updateScore(e.getScore()+1)})),t},rewriteOnClicks:function(t,r){var n=this;r.forEach((function(r){if("subMenu"in r&&n.rewriteOnClicks(t,r.subMenu),"onClick"in r){var o=r.onClick;r.onClick=function(){for(var r=arguments.length,n=new Array(r),a=0;a<r;a++)n[a]=arguments[a];e.tracks.forEach((function(e){e.type===t&&o.apply(e,[e].concat(n))}))}}}))},get trackTypeActions(){var t=this,r=new Map;return e.tracks.forEach((function(e){if(!r.get(e.type)){var n=z(e.viewMenuActions);t.rewriteOnClicks(e.type,n),r.set(e.type,n)}})),r},get centerLineInfo(){return e.displayedRegions.length?this.pxToBp(e.width/2):void 0}}})).actions((function(t){return{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 r=s.clamp(e,t.minOffset,t.maxOffset);return t.offsetPx=r,r},zoomTo:function(e){var r=s.clamp(e,t.minBpPerPx,t.maxBpPerPx);if(r===t.bpPerPx)return r;var n=t.bpPerPx;if(t.bpPerPx=r,Math.abs(n-r)<1e-6)return console.warn("zoomTo bpPerPx rounding error"),n;var o=t.width;return this.scrollTo(Math.round((t.offsetPx+o/2)*n/r-o/2)),r},setOffsets:function(e,r){t.leftOffset=e,t.rightOffset=r},setSearchResults:function(e,r){t.searchResults=e,t.searchQuery=r},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 ge(ge({},e),{},{reversed:!e.reversed})}))),this.scrollTo(t.totalBp/t.bpPerPx-t.offsetPx-t.width)},showTrack:function(r){var n=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),r);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(ge(ge({},n),{},{type:i.type,configuration:i,displays:[ge({type:u.type,configuration:u},o)]}));return t.tracks.push(f),f}return d[0]},hideTrack:function(r){var n=e.pluggableConfigSchemaType("track"),o=y.resolveIdentifier(n,y.getRoot(t),r),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,r){var n=e.tracks.findIndex((function(e){return e.id===t}));if(-1===n)throw new Error("Track ID ".concat(t," not found"));var o=e.tracks.findIndex((function(e){return e.id===r}));if(-1===o)throw new Error("Track ID ".concat(r," not found"));var a=y.getSnapshot(e.tracks[n]);e.tracks.splice(n,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 r=t.addWidget("HierarchicalTrackSelectorWidget","hierarchicalTrackSelector",{view:e});return t.showWidget(r),r}}throw new Error("invalid track selector type ".concat(e.trackSelectorType))},navToLocString:function(t,r){var n=s.getSession(e).assemblyManager,o=n.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=r,c="";0!==e.displayedRegions.length&&(l=e.displayedRegions[0].assemblyName,c=e.displayedRegions[0].refName);var u=l&&n.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=n.get(f.assemblyName);if(!p)throw new Error("Could not find assembly ".concat(f.assemblyName));u=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=u.getCanonicalRefName(f.refName);if(!h)throw new Error("Could not find refName ".concat(f.refName," in ").concat(u.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 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n=N.create(ge(ge({},y.getSnapshot(e)),{},{interRegionPaddingWidth:e.interRegionPaddingWidth}));return n.setVolatileWidth(e.width),n.zoomToDisplayedRegions(t,r),n.dynamicBlocks.contentBlocks.map((function(e){return ge(ge({},e),{},{start:Math.floor(e.start),end:Math.ceil(e.end)})}))},afterDisplayedRegionsSet:function(t){e.afterDisplayedRegionsSetCallbacks.push(t)},moveTo:function(t,r){var n=0;if(t.index===r.index)n+=r.offset-t.offset;else{var o=e.displayedRegions[t.index];if(n+=o.end-o.start-t.offset,r.index-t.index>=2)for(var a=t.index+1;a<r.index;a+=1)n+=e.displayedRegions[a].end-e.displayedRegions[a].start;n+=r.offset}var i=n/(e.width-e.interRegionPaddingWidth*(r.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 r=e.offsetPx;return 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0!==e.trackMaxHeight?e.trackMaxHeight:t},get displayMode(){var t=n.getConf(e,["renderer","displayMode"]);return void 0!==e.trackDisplayMode?e.trackDisplayMode:t},get rendererConfig(){var t=n.getConf(e,["renderer"])||{};return e.rendererType.configSchema.create(ge(ge({},t),{},{showLabels:this.showLabels,displayMode:this.displayMode,maxHeight:this.maxHeight}),y.getEnv(e))}}})).actions((function(e){return{toggleShowLabels:function(){e.trackShowLabels=!e.showLabels},setDisplayMode:function(t){e.trackDisplayMode=t},setMaxHeight:function(t){e.trackMaxHeight=t}}})).views((function(e){var t=e.trackMenuItems,r=e.renderProps;return{renderProps:function(){var t=e.rendererConfig;return ge(ge({},r()),{},{config:t})},trackMenuItems:function(){return[].concat(Te(t()),[{label:"Show labels",icon:I,type:"checkbox",checked:e.showLabels,onClick:function(){e.toggleShowLabels()}},{label:"Display 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t=s.getSession(e).assemblyManager;return this.assemblyNames.map((function(e){var r;return null===(r=t.get(e))||void 0===r?void 0:r.error})).filter((function(e){return!!e})).join(", ")},get assembliesInitialized(){var t=s.getSession(e).assemblyManager;return this.assemblyNames.every((function(e){var r;return null===(r=t.get(e))||void 0===r?void 0:r.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 Lr+Dr},get headerHeight(){return e.hideHeader?0:e.hideHeaderOverview?Nr:Nr+Mr},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*Dr},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 ge(ge({},p.getParentRenderProps(e)),{},{bpPerPx:e.bpPerPx,highResolutionScaling:n.getConf(s.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){var r=t.refName,n=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 r===t.refName&&n>=t.start&&n<=t.end&&(!o||o===c)?(a+=t.reversed?t.end-n:n-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 r=0,n=(e.offsetPx+t)*e.bpPerPx,o=e.displayedRegions.length;if(n<0){var a=e.displayedRegions[0],i=n;return ge(ge({},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=n-r;if(d+r>n&&r<=n)return ge(ge({},y.getSnapshot(u)),{},{oob:!1,offset:f,coord:u.reversed?Math.floor(u.end-f)+1:Math.floor(u.start+f)+1,index:s});r+=u.end-u.start>c&&f/e.bpPerPx>0&&f/e.bpPerPx<e.width?d+l:d}if(n>=r){var p=e.displayedRegions[o-1],m=n-r+(p.end-p.start);return ge(ge({},y.getSnapshot(p)),{},{oob:!0,offset:m,coord:p.reversed?Math.floor(p.end-m)+1:Math.floor(p.start+m)+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 r=e.tracks.map((function(e){return e.configuration.trackId}));return t.forEach((function(e){r!==[]&&r.includes(e.trackId)&&e.updateScore(e.getScore()+1)})),t},rewriteOnClicks:function(t,r){var n=this;r.forEach((function(r){if("subMenu"in r&&n.rewriteOnClicks(t,r.subMenu),"onClick"in r){var o=r.onClick;r.onClick=function(){for(var r=arguments.length,n=new Array(r),a=0;a<r;a++)n[a]=arguments[a];e.tracks.forEach((function(e){e.type===t&&o.apply(e,[e].concat(n))}))}}}))},get trackTypeActions(){var t=this,r=new Map;return e.tracks.forEach((function(e){if(!r.get(e.type)){var n=q(e.viewMenuActions);t.rewriteOnClicks(e.type,n),r.set(e.type,n)}})),r},get centerLineInfo(){return e.displayedRegions.length?this.pxToBp(e.width/2):void 0}}})).actions((function(t){return{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 r=s.clamp(e,t.minOffset,t.maxOffset);return t.offsetPx=r,r},zoomTo:function(e){var r=s.clamp(e,t.minBpPerPx,t.maxBpPerPx);if(r===t.bpPerPx)return r;var n=t.bpPerPx;if(t.bpPerPx=r,Math.abs(n-r)<1e-6)return console.warn("zoomTo bpPerPx rounding error"),n;var o=t.width;return this.scrollTo(Math.round((t.offsetPx+o/2)*n/r-o/2)),r},setOffsets:function(e,r){t.leftOffset=e,t.rightOffset=r},setSearchResults:function(e,r){t.searchResults=e,t.searchQuery=r},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 ge(ge({},e),{},{reversed:!e.reversed})}))),this.scrollTo(t.totalBp/t.bpPerPx-t.offsetPx-t.width)},showTrack:function(r){var n=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),r);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(ge(ge({},n),{},{type:i.type,configuration:i,displays:[ge({type:u.type,configuration:u},o)]}));return t.tracks.push(f),f}return d[0]},hideTrack:function(r){var n=e.pluggableConfigSchemaType("track"),o=y.resolveIdentifier(n,y.getRoot(t),r),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,r){var n=e.tracks.findIndex((function(e){return e.id===t}));if(-1===n)throw new Error("Track ID ".concat(t," not found"));var o=e.tracks.findIndex((function(e){return e.id===r}));if(-1===o)throw new Error("Track ID ".concat(r," not found"));var a=y.getSnapshot(e.tracks[n]);e.tracks.splice(n,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 r=t.addWidget("HierarchicalTrackSelectorWidget","hierarchicalTrackSelector",{view:e});return t.showWidget(r),r}}throw new Error("invalid track selector type ".concat(e.trackSelectorType))},navToLocString:function(t,r){var n=s.getSession(e).assemblyManager,o=n.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=r,c="";0!==e.displayedRegions.length&&(l=e.displayedRegions[0].assemblyName,c=e.displayedRegions[0].refName);var u=l&&n.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)})),p=!1;if(f.assemblyName&&f.assemblyName!==l){var m=n.get(f.assemblyName);if(!m)throw new Error("Could not find assembly ".concat(f.assemblyName));u=m,p=!0;var g=m.regions;if(!g)throw new Error("Regions for assembly ".concat(f.assemblyName," not yet loaded"));d=g}var h=u.getCanonicalRefName(f.refName);if(!h)throw new Error("Could not find refName ".concat(f.refName," in ").concat(u.name));if(p||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(u.name));this.setDisplayedRegions([v])}var y=d.find((function(e){return e.refName===h}));if(y){var b,k,w=s.clamp(null!==(b=null==f?void 0:f.start)&&void 0!==b?b:0,0,y.end),x=s.clamp(null!==(k=null==f?void 0:f.end)&&void 0!==k?k:y.end,0,y.end);this.navTo(ge(ge({},f),{},{start:w,end:x}))}}},navTo:function(e){this.navToMultiple([e])},navToMultiple:function(t){var r=t[0],n=r.refName,o=r.start,a=r.end,i=r.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=s.getSession(e).assemblyManager.get(l);if(c){var u=c.getCanonicalRefName(n);u&&(n=u)}for(var d,f=o,p=a,m=!1,g=function(e){if(n===e.refName){if(m=!0,void 0===f&&(f=e.start),void 0===p&&(p=e.end),f>=e.start&&f<=e.end&&p<=e.end&&p>=e.start)return!0;f=o,p=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),!m)throw new Error('could not find a region with refName "'.concat(n,'"'));if(void 0===f)throw new Error('could not find a region with refName "'.concat(n,'" that contained an end position ').concat(p));if(void 0===p)throw new Error('could not find a region with refName "'.concat(n,'" 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(r),'"'));if(1===t.length){var y=e.displayedRegions[d];return void this.moveTo({index:d,offset:y.reversed?y.end-p:f-y.start},{index:d,offset:y.reversed?y.end-f:p-y.start})}for(var b=0,k=0,w=0;b<t.length;b++){var x=t[b],E=e.displayedRegions[d+b];if(k=x.start||E.start,w=x.end||E.end,x.refName!==E.refName)throw new Error("Entered location ".concat(s.assembleLocString(x)," does not match with displayed regions"));if(b>0&&!(E.reversed?w===E.end:k===E.start))throw new Error("".concat(E.reversed?"End":"Start"," of region ").concat(s.assembleLocString(x)," should be ").concat((E.reversed?E.end:E.start+1).toLocaleString("en-US"),", but it is not"));if(b!==t.length-1&&!(E.reversed?k===E.start:w===E.end))throw new Error("".concat(E.reversed?"Start":"End"," of region ").concat(s.assembleLocString(x)," should be ").concat((E.reversed?E.start+1:E.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-p: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,r){if(void 0!==t&&void 0!==r){if(t.refName===r.refName&&t.index===r.index&&r.offset<t.offset||t.index>r.index){var n=[r,t];t=n[0],r=n[1]}var o={start:t.start,end:t.end,index:t.index,offset:t.offset},a={start:r.start,end:r.end,index:r.index,offset:r.offset};o&&a?this.moveTo(o,a):s.getSession(e).notify("No regions found to navigate to","warning")}},getSelectedRegions:function(t,r){var n=M.create(ge(ge({},y.getSnapshot(e)),{},{interRegionPaddingWidth:e.interRegionPaddingWidth}));return n.setVolatileWidth(e.width),n.zoomToDisplayedRegions(t,r),n.dynamicBlocks.contentBlocks.map((function(e){return ge(ge({},e),{},{start:Math.floor(e.start),end:Math.ceil(e.end)})}))},afterDisplayedRegionsSet:function(t){e.afterDisplayedRegionsSetCallbacks.push(t)},moveTo:function(t,r){var n=0;if(t.index===r.index)n+=r.offset-t.offset;else{var o=e.displayedRegions[t.index];if(n+=o.end-o.start-t.offset,r.index-t.index>=2)for(var a=t.index+1;a<r.index;a+=1)n+=e.displayedRegions[a].end-e.displayedRegions[a].start;n+=r.offset}var i=n/(e.width-e.interRegionPaddingWidth*(r.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 r=e.offsetPx;return e.scrollTo(e.offsetPx+t)-r},centerAt:function(t,r,n){var o=e.bpToPx({refName:r,coord:t,regionNumber:n});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 r=s.getSession(e),n=r.assemblyManager;if(!t){var o=Te(new Set(e.displayedRegions.map((function(e){return e.assemblyName}))));if(o.length>1)return void r.notify("Can't perform this with multiple assemblies currently");t=Pe(o,1)[0]}var a=n.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(r){var n=Pe(s.springAnimate(e.offsetPx,e.offsetPx+e.width*r,e.scrollTo),2),o=n[0],a=n[1];t(),t=a,o()}}})).actions((function(e){var t=function(){};return{zoom:function(r){if(e.zoomTo(e.bpPerPx),!(r<e.bpPerPx&&e.bpPerPx===e.minBpPerPx||r>e.bpPerPx&&e.bpPerPx===e.maxBpPerPx)){var n=Pe(s.springAnimate(1,e.bpPerPx/r,e.setScaleFactor,(function(){e.zoomTo(r),e.setScaleFactor(1)})),2),o=n[0],a=n[1];t(),t=a,o()}}}})).views((function(e){var t,r="";return{menuItems:function(){var t,r=[{label:"Return to import form",onClick:function(){s.getSession(e).queueDialog((function(t){return[Br,{model:e,handleClose:t}]}))},icon:F},{label:"Export SVG",icon:j,onClick:function(){s.getSession(e).queueDialog((function(t){return[Cr,{model:e,handleClose:t}]}))}},{label:"Open track selector",onClick:e.activateTrackSelector,icon:L.TrackSelector},{label:"Horizontally flip",icon:D,onClick:e.horizontallyFlip},{type:"divider"},{label:"Show all regions in assembly",icon:I,onClick:e.showAllRegionsInAssembly},{label:"Show center line",icon:I,type:"checkbox",checked:e.showCenterLine,onClick:e.toggleCenterLine},{label:"Show header",icon:I,type:"checkbox",checked:!e.hideHeader,onClick:e.toggleHeader},{label:"Show header overview",icon:I,type:"checkbox",checked:!e.hideHeaderOverview,onClick:e.toggleHeaderOverview,disabled:e.hideHeader},{label:"Track labels",icon:O,subMenu:[{label:"Overlapping",icon:I,type:"radio",checked:"overlapping"===e.trackLabels,onClick:function(){return e.setTrackLabels("overlapping")}},{label:"Offset",icon:I,type:"radio",checked:"offset"===e.trackLabels,onClick:function(){return e.setTrackLabels("offset")}},{label:"Hidden",icon:I,type:"radio",checked:"hidden"===e.trackLabels,onClick:function(){return e.setTrackLabels("hidden")}}]}],n=Ne(e.trackTypeActions.entries());try{for(n.s();!(t=n.n()).done;){var o=Pe(t.value,2),a=o[1];a.length&&(r.push({type:"divider"},{type:"subHeader",label:o[0]}),a.forEach((function(e){r.push(e)})))}}catch(e){n.e(e)}finally{n.f()}return r},get staticBlocks(){var n=N(e),o=JSON.stringify(n);return r!==o&&(t=n,r=o),t},get dynamicBlocks(){return R(e)},get roundedDynamicBlocks(){return this.dynamicBlocks.contentBlocks.map((function(e){return ge(ge({},e),{},{start:Math.floor(e.start),end:Math.ceil(e.end)})}))},get visibleLocStrings(){return Rr(this.dynamicBlocks.contentBlocks)},get coarseVisibleLocStrings(){return Rr(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 ye(De.mark((function r(){var n,o;return De.wrap((function(r){for(;;)switch(r.prev=r.next){case 0:return n=t.length>0&&void 0!==t[0]?t[0]:{},r.next=3,wr(e,n);case 3:o=new Blob([r.sent],{type:"image/svg+xml"}),A.saveAs(o,"image.svg");case 6:case"end":return r.stop()}}),r)})))()}}})).views((function(e){return{rubberBandMenuItems:function(){return[{label:"Zoom to region",icon:z,onClick:function(){e.leftOffset&&e.rightOffset&&e.moveTo(e.leftOffset,e.rightOffset)}},{label:"Get sequence",icon:h,onClick:function(){e.setSequenceDialogOpen(!0)}}]}}}))}var Or=t.lazy((function(){return Promise.resolve().then((function(){return Hr}))})),Fr=function(e){return y.types.compose("LinearBasicDisplay",nt,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:n.ConfigurationReference(e)})).views((function(e){return{get rendererTypeName(){return n.getConf(e,["renderer","type"])},get showLabels(){var t=n.getConf(e,["renderer","showLabels"]);return void 0!==e.trackShowLabels?e.trackShowLabels:t},get showDescriptions(){var t=n.getConf(e,["renderer","showLabels"]);return void 0!==e.trackShowDescriptions?e.trackShowDescriptions:t},get maxHeight(){var t=n.getConf(e,["renderer","maxHeight"]);return void 0!==e.trackMaxHeight?e.trackMaxHeight:t},get displayMode(){var t=n.getConf(e,["renderer","displayMode"]);return void 0!==e.trackDisplayMode?e.trackDisplayMode:t},get rendererConfig(){var t=n.getConf(e,["renderer"])||{};return e.rendererType.configSchema.create(ge(ge({},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,r=e.renderProps;return{renderProps:function(){var t=e.rendererConfig;return ge(ge({},r()),{},{config:t})},trackMenuItems:function(){return[].concat(Te(t()),[{label:"Show labels",icon:I,type:"checkbox",checked:e.showLabels,onClick:function(){e.toggleShowLabels()}},{label:"Show descriptions",icon:I,type:"checkbox",checked:e.showDescriptions,onClick:function(){e.toggleShowDescriptions()}},{label:"Display mode",icon:I,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[Or,{model:e,handleClose:t}]}))}}])}}}))};function jr(e){return n.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:Me,explicitlyTyped:!0})}var zr=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&&xe(e,t)}(f,c);var r,d=Ce(f);function f(){var e;return be(this,f),(e=d.apply(this,arguments)).name="LinearGenomeViewPlugin",e.exports={BaseLinearDisplayComponent:Ge,BaseLinearDisplay:nt,baseLinearDisplayConfigSchema:Me},e}return(r=[{key:"install",value:function(e){e.addTrackType((function(){var t=n.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=n.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=ot(e);return new i({name:"LinearBareDisplay",configSchema:t,stateModel:at(t),trackType:"BasicTrack",viewType:"LinearGenomeView",ReactComponent:Ge})})),e.addDisplayType((function(){var t=jr(e);return new i({name:"LinearBasicDisplay",configSchema:t,stateModel:Fr(t),trackType:"FeatureTrack",viewType:"LinearGenomeView",ReactComponent:Ge})})),e.addViewType((function(){return new l({name:"LinearGenomeView",stateModel:Ir(e),ReactComponent:t.lazy((function(){return Promise.resolve().then((function(){return Er}))}))})}))}},{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 r=0;r<t.length;r++){var n=t[r];n.enumerable=n.enumerable||!1,n.configurable=!0,"value"in n&&(n.writable=!0),Object.defineProperty(e,n.key,n)}}(f.prototype,r),f}(),qr=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 Ar(e){var n=e.model,o=e.handleClose,a=qr(),i=n.maxHeight,l=Pe(t.useState("".concat(void 0===i?"":i)),2),c=l[0],s=l[1];return r.createElement(b.Dialog,{open:!0,onClose:o,"aria-labelledby":"alert-dialog-title","aria-describedby":"alert-dialog-description"},r.createElement(b.DialogTitle,{id:"alert-dialog-title"},"Filter options",r.createElement(b.IconButton,{"aria-label":"close",className:a.closeButton,onClick:o},r.createElement(ne,null))),r.createElement(b.DialogContent,null,r.createElement("div",{className:a.root},r.createElement(b.Typography,null,"Set max height for the track"),r.createElement(b.TextField,{value:c,onChange:function(e){s(e.target.value)},placeholder:"Enter max score"}),r.createElement(b.Button,{variant:"contained",color:"primary",type:"submit",style:{marginLeft:20},onClick:function(){n.setMaxHeight(""===c||Number.isNaN(+c)?void 0:+c),o()}},"Submit"))))}var Hr={__proto__:null,default:w.observer(Ar)};exports.BaseLinearDisplay=nt,exports.BaseLinearDisplayComponent=Ge,exports.RefNameAutocomplete=ut,exports.baseLinearDisplayConfigSchema=Me,exports.default=zr,exports.linearBareDisplayConfigSchemaFactory=ot,exports.linearBasicDisplayConfigSchemaFactory=jr,exports.linearBasicDisplayModelFactory=Fr,exports.renderToSvg=wr;
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