@figtreejs/core 0.0.1-beta.0 → 0.1.0-beta.2

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Files changed (20) hide show
  1. package/dist/index.cjs +2 -2
  2. package/dist/index.d.ts +452 -235
  3. package/dist/index.mjs +1401 -1429
  4. package/package.json +5 -5
  5. package/src/evo/tree/normalized-tree/immutable-tree.ts +1 -3
  6. package/src/evo/tree/parsers/annotation-parser.ts +6 -0
  7. package/src/evo/tree/parsers/newick-character-parser.ts +8 -0
  8. package/src/evo/tree/parsers/newick-parsing.ts +6 -0
  9. package/src/evo/tree/parsers/nexus-parsing.ts +8 -3
  10. package/src/evo/tree/parsers/stream-reader/nexus-importer.ts +8 -1
  11. package/src/evo/tree/parsers/stream-reader/nexus-tokenizer.ts +5 -0
  12. package/src/evo/tree/taxa/helper-functions.ts +14 -0
  13. package/src/evo/tree/taxa/taxon.ts +40 -1
  14. package/src/evo/tree/traversals/preorder-traversal.ts +5 -0
  15. package/src/evo/tree/traversals/traversal-types.ts +3 -0
  16. package/src/evo/tree/tree-types.ts +259 -20
  17. package/src/layouts/functional/radial-layout.ts +14 -10
  18. package/src/layouts/functional/rectangular-layout.ts +7 -0
  19. package/src/layouts/layout-interface.ts +0 -73
  20. package/src/tests/baubles/__snapshots__/node-labels.test.tsx.snap +12 -12
package/dist/index.cjs CHANGED
@@ -1,2 +1,2 @@
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Object.entries(n))i>0&&(r+=", "),r+=`${a}=${Gu(s)}`,i+=1;return r+="]",r}toNewick(t,n){const r={blFormat:Zt("0.2"),includeAnnotations:!1,...n};return t===void 0&&(t=this.getRoot()),this._toString(t,r)+";"}getMRCA(t,n){if(Array.isArray(t)){const r=t;if(r.length===0)throw new Error("No nodes provided to get MRCA");let i=r[0];for(let a=1;a<r.length;a++)if(i=this.getMRCA(i,r[a]),this.isRoot(i))return i;return i}else{if(n===void 0)throw new Error("No second node provided. 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Has it been copied?`);return J(this,r=>{const i=r.getNode(t.number);i.taxon=n.number,r._data.nodes.byTaxon[n.number]=t.number,r._data.nodeToTaxon[t.number]=n.number})}getAnnotationSummary(t){if(this._data.annotations[t]===void 0)throw new Error(`No annotation with name ${t} found in tree`);return this._data.annotations[t]}getAnnotations(){return Object.values(this._data.annotations)}getAnnotation(t,n,r){const i=mr(this,this.getNode(t.number),n);if(r===void 0){const{value:a}=Zi(i,`Node ${t.number} is not annotated with ${n}`);return a}else switch(i.type){case B.Some:return i.value.value;case B.Nothing:return r}}getFullNodeAnnotation(t,n){const r=mr(this,this.getNode(t.number),n);return Zi(r,`Node ${t.number} is not annotated with ${n}`)}hasAnnotation(t,n){switch(mr(this,this.getNode(t.number),n).type){case B.Some:return!0;case B.Nothing:return!1}}annotateNode(t,n,r){if(typeof n=="string"){const i=n,s=Yu(r),o=this._data.annotations[i];if(o!==void 0&&o.type!==s.type)throw new Error(`Tried annotation ${i} was parsed as ${s.type} - but is ${o.type} in tree.`);return J(this,c=>{const u=o?o.domain:void 0,l=Bl(s,u);c._data.nodes.allNodes[t.number].annotations[i]={id:i,type:s.type,value:s.value},c._data.annotations[i]={id:i,type:s.type,domain:l}})}else{let i=this;for(const[a,s]of Object.entries(n))i=i.annotateNode(t,a,s);return i}}setHeight(t,n){if(!this.hasLengths())throw new Error("Can not set the heights of nodes in a tree without branch lengths");return J(this,r=>{const i=r.getNode(t.number);if(n<0)throw new Error("Height must be non-negative");const s=r.getHeight(t)-n;if(i.length===void 0){if(!r.isRoot(t))throw new Error("Cannot set height on a node without length")}else i.length=i.length+s;for(const o of r.getChildren(t)){const c=r.getNode(o.number),u=r.getLength(c)-s;c.length=u}})}setLength(t,n){return J(this,r=>{const i=r.getNode(t.number);i.length=n,r._data.hasLengths=!0})}deleteLength(t){return J(this,n=>{const r=n.getNode(t.number);r.length=void 0})}setDivergence(t,n){if(!this.hasLengths())throw new Error("Can not set the divergences of nodes in a tree without branch lengths");return J(this,r=>{const i=r.getNode(t.number),a=r.getHeight(t),c=r.getHeight(r.getRoot())-a-n,u=r.getLength(t);i.length=u-c})}setLabel(t,n){if(this._data.nodes.byLabel[n]!==void 0)throw new Error(`Duplicate node label ${n}`);return J(this,r=>{const i=r.getNode(t.number);i.label=n,r._data.nodes.byLabel[n]=t.number})}insertNode(t,n=.5){return J(this,r=>{const i={number:r._data.nodes.allNodes.length,children:[],parent:void 0,label:"",length:void 0,taxon:void 0,annotations:{},_id:dn()};r._data.nodes.allNodes.push(i),r._data.nodes.byTaxon.length+=1;const a=r.getNode(t.number),s=r.getParent(a),o=s.children.indexOf(a.number);s.children.splice(o,1,i.number),i.parent=s.number;const u=r.getLength(a);a.length=u*(1-n),i.length=u*n,i.children=[a.number],a.parent=i.number})}unroot(t){throw new Error("unroot not implemented in immutable tree")}deleteNode(t){throw new Error("deleteNode not implemented in immutable tree")}deleteClade(t){throw new Error("deleteClade not implemented in immutable tree")}orderNodesByDensity(t,n){return J(this,r=>{n===void 0&&(n=r._data.nodes.allNodes[r._data.rootNode]);const i=t?1:-1;Os(r._data,n,(a,s,o,c)=>(s-c)*i)})}rotate(t,n=!1){return J(this,r=>{const i=r.getNode(t.number);if(i.children=i.children.reverse(),n)for(const a of i.children.map(s=>r.getNode(s)))r.rotate(a,n)})}reroot(t,n=.5){return J(this,r=>{if(t.number===r._data.rootNode)return;const i=r.getRoot();i.children.length!==2&&console.warn("Root node has more than two children and we are rerooting! There be dragons!");let a=0;if(i.children.length==2)a=i.children.map(o=>r.getNode(o)).map(o=>r.getLength(o)).reduce((o,c)=>c+o,0);else{const o=[...r.getPathToRoot(t)],c=o[o.length-2];if(Z(c,"Index error when looking for the root child"),!i.children.includes(c.number))throw new Error("Root child not in path to root - likely an internal error");a=r.getLength(c)}const s=r.getNode(t.number);if(r.getParent(t)!==i){let o=s,c=r.getParent(s);const u=r.getChild(c,0).number===t.number,l=s,h=c;let f=r.getLength(c);for(;!r.isRoot(c);){if(c.children=c.children.filter(m=>m!==o.number),r.getParent(c).number===i.number)if(i.children.length==2){if(!r.hasLeftSibling(c)&&!r.hasRightSibling(c))throw new Error("no sibling in rerooting");const g=r.hasLeftSibling(c)?r.getLeftSibling(c):r.getRightSibling(c);c.children.push(g.number),g.parent=c.number,g.length=a}else{const m={number:r._data.nodes.allNodes.length,children:[],parent:void 0,label:"",length:void 0,taxon:void 0,annotations:{},_id:dn()};r._data.nodes.allNodes.push(m),m.length=a,c.children.push(m.number),m.parent=c.number;for(const g of i.children){const x=r.getNode(g);x.number!==c.number&&(x.parent=m.number,m.children.push(x.number))}}else{const m=r.getParent(c),g=r.getLength(m);m.length=f,f=g,c.children.push(m.number)}o=c,c=r.getParent(c)}l.parent=i.number,h.parent=i.number,i.children=[l.number,h.number],u||(i.children=i.children.reverse()),this.getInternalNodes().forEach(m=>{for(const g of r.getChildren(m))g.parent=m.number});const d=r.getLength(l)*n;h.length=d,Z(l.length,"Expected the root's new child to have a length"),l.length-=d}else{const o=r.getLength(t)*(1-n);s.length=o;const c=r.getNextSibling(t);c.length=a-o}})}removeChild(t,n){return J(this,r=>{r._data.nodes.allNodes[t.number].children=r._data.nodes.allNodes[t.number].children.filter(i=>i!==n.number),r._data.nodes.allNodes[n.number].parent=-1})}sortChildren(t,n){return J(this,r=>{r._data.nodes.allNodes[t.number].children=this._data.nodes.allNodes[t.number].children.map(i=>r.getNode(i)).sort(n).map(i=>i.number)})}addChild(t,n){return J(this,r=>{const i=r.getNode(n.number);r.getNode(t.number).children.push(i.number),i.parent=t.number})}setRoot(t){return J(this,n=>{n._data.rootNode=t.number})}}function Os(e,t,n){let r=0;if(e.nodes.allNodes[t.number].children.length>0){const i=new Map;for(const o of e.nodes.allNodes[t.number].children.map(c=>e.nodes.allNodes[c])){const c=Os(e,o,n);i.set(o.number,c),r+=c}const a=e.nodes.allNodes[t.number].children.slice().sort((o,c)=>n(e.nodes.allNodes[o],pe(i.get(o),"Internal error when ordering. Counts not defined."),e.nodes.allNodes[c],pe(i.get(c),"Internal error when ordering. Counts not defined.")));a.reduce((o,c,u)=>o||c!==e.nodes.allNodes[t.number].children[u],!0)&&(e.nodes.allNodes[t.number].children=a)}else r=1;return r}function*js(e,t=void 0){const n=function*(r){yield e.getNode(r.number);const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}};t===void 0&&(t=e.getRoot()),yield*n(t)}function*Ol(e,t=void 0,n=(r,i)=>r.number-i.number){const r=function*(i,a=void 0){yield e.getNode(i.number);const s=[...e.getChildren(i),e.getParent(i)].filter(o=>o.number!==a);s.sort(n);for(const o of s)yield*r(o,i.number)};t===void 0&&(t=e.getRoot()),yield*r(t)}function*jl(e,t=void 0,n=(r,i)=>r.number-i.number){const r=function*(i,a=void 0){const s=[...e.getChildren(i),e.getParent(i)].filter(o=>o.number!==a);s.sort(n);for(const o of s)yield*r(o,i.number);yield e.getNode(i.number)};t===void 0&&(t=e.getRoot()),yield*r(t)}function*zs(e,t=void 0){const n=function*(r){const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}yield r};t===void 0&&(t=e.getRoot()),yield*n(t)}function*er(e,t){t===void 0&&(t=e.getRoot());const n=function*(r){const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}else yield r};yield*n(t)}function*zl(e,t){let n=t;for(;!e.isRoot(n);)yield n,n=e.getParent(n);yield n}function Bl(e,t){switch(e.type){case V.BOOLEAN:return[!0,!1];case V.DISCRETE:{const n=e.value;if(t!==void 0){const r=t;return[...new Set([...r,n])].sort()}else return[n]}case V.NUMERICAL:{const n=e.value;return lt([...t||[],n])}case V.DISCRETE_SET:{const n=e.value,r=t||[];return[...new Set([...r,...n])].sort()}case V.NUMERICAL_SET:{const n=e.value;return lt([...t||[],...n])}case V.DENSITIES:if(t!==void 0){const n=t;return[...new Set([...n,...Object.keys(e.value)])].sort()}else return[...new Set(Object.keys(e.value))].sort().filter(n=>n);case V.MARKOV_JUMPS:{const n=e.value.reduce((i,a)=>i.concat([a.to,a.from]),[]),r=t||[];return[...new Set([...r,...n])].sort()}default:throw new Error("Unrecognized type when updating domain")}}function Vl(){return{lastChunk:"",status:"parsing",end:"",start(){},transform(e,t){const n=this.lastChunk+e;let r="";for(let i=0;i<n.length;i++){const a=n[i];Z(a,"Internal Error. Hit empty character in array"),this.status==="parsing"?([this.status,this.end]=ql(a),this.status==="in comment"&&(r.length>0&&t.enqueue(r),r="")):a===this.end&&(this.status="parsing",this.end=""),this.status==="parsing"&&/\s|;|\]/.test(a)?(r.length>0&&(/\]/.test(a)&&(r+=a),t.enqueue(r),r=""),/;/.test(a)&&t.enqueue(a)):r+=a}this.lastChunk=r},flush(e){this.lastChunk&&e.enqueue(this.lastChunk)}}}function ql(e){return e==="'"?["in single quote","'"]:e==='"'?["in double quote",'"']:e==="["?["in comment","]"]:["parsing",""]}const xa=/\s*('[^']+'|"[^"]+"|\[&[^[]+]|,|:|\)|\(|;)\s*/;class Hl{reader;taxonSet;currentBlock;hasTree;options;translateTaxonMap;constructor(t,n={}){const r=new TransformStream(Vl());this.reader=t.pipeThrough(new TextDecoderStream).pipeThrough(r).getReader(),this.taxonSet=new sn,this.currentBlock=void 0,this.options=n}async*getTrees(){for(;this.currentBlock!=="trees";)await this.parseNextBlock(),this.hasTree=!0;yield*this.parseTreesBlock()}async parseNextBlock(){const t=await this.getNextBlockName();switch(t){case"taxa":this.currentBlock="taxa",await this.parseTaxaBlock();break;case"trees":this.currentBlock="trees";break;default:console.log(`skipping block ${t}. Only parsing blocks are taxa and trees for now.`),await this.readToEndOfBlock()}}async nextToken(){const{done:t,value:n}=await this.reader.read();if(t)throw new Error("unexpectedly hit the end of the stream");return n}async skipSemiColon(){const{done:t,value:n}=await this.reader.read();if(t)throw new Error("unexpectedly hit the end of the stream");if(!n.match(/;$/))throw new Error(`expected ";" got ${n}`)}async getNextBlockName(){let t=!0,n;for(;t;)(await this.nextToken()).match(/\bbegin/i)&&(n=await this.nextToken(),await this.skipSemiColon(),t=!1);return n}async readToEndOfBlock(){let t=!0;for(;t;)(await this.nextToken()).match(/\bend;/i)&&(t=!1)}async skipUntil(t){let n,r=!0;for(;r;)n=await this.nextToken(),t.test(n)&&(r=!1);if(n==null)throw new Error(`Internal parsing error: ${t.source} not found `);return n}async readUntil(t){let n="",r=!0;for(;r;){const i=await this.nextToken();t.test(i)&&(n+=i,r=!1),n+=i}return n}async parseTaxaBlock(){let t,n=!0;for(;n;){const r=await this.skipUntil(/dimensions|taxlabels|end/i);switch(!0){case/dimensions/i.test(r):{const i=await this.readUntil(/;/),a=i.match(/ntax=(\d+);/);if(a)Z(a[1],"No number of taxa found despite matching regex"),t=parseInt(a[1]);else throw new Error(`Expected dimension in form of ntax=(\\d+);. Got ${i}`);break}case/taxlabels/i.test(r):{let i=await this.nextToken();for(;i!==";";)this.taxonSet.addTaxon(i),i=await this.nextToken();if(t&&t!=this.taxonSet.getTaxonCount())throw new Error(`found ${this.taxonSet.getTaxonCount()} taxa. Expected: ${t}}`);break}case/end/i.test(r):{if(this.taxonSet.getTaxonCount()===0)throw new Error("hit end of taxa section but didn't find any taxa");this.taxonSet.lockTaxa(),await this.skipSemiColon(),n=!1;break}default:throw new Error(`Reached impossible code looking for dimensions or taxlabels or end in taxa block "${r}"`)}}}async*parseTreesBlock(){let t,n=!0;for(;n;){const r=await this.skipUntil(/translate|tree|end/i);switch(!0){case/translate/i.test(r):{this.translateTaxonMap=new Map;let i=0,a;for(t=await this.nextToken();t!==";";){if(i%2==0)a=t;else{if(t[t.length-1]===","&&(t=t.slice(0,-1)),this.taxonSet.isFinalized){if(!this.taxonSet.hasTaxon(t))throw new Error(`Taxon ${t} not found in taxa block - but found in translate block`)}else this.taxonSet.addTaxon(t);Z(a,"Error parsing nexus. Expected key for taxa but found nothing"),this.translateTaxonMap.set(a,t)}for(t=await this.nextToken();t===",";)t=await this.nextToken();i++}this.taxonSet.lockTaxa();break}case/tree/i.test(r):{await this.nextToken();const i=new ks(this.taxonSet,{translateTaxonNames:this.translateTaxonMap});t=await this.skipUntil(/\(/);let a=t.split(xa).filter(o=>o.length>0).reverse();for(;!i.isDone();){for(;a.length>0;){const o=a.pop();Z(o,"Unexpectedly hit the end of the buffer"),i.parseCharacter(o)}i.isDone()||(t=await this.nextToken(),a=t.split(xa).filter(o=>o.length>0).reverse())}yield i.getTree();break}case/end/i.test(r):await this.skipSemiColon(),this.hasTree=!1,this.reader.releaseLock(),n=!1;break;default:throw new Error(`Reached impossible code in treeblock block "${r}"`)}}}}class Yl{_forwardCache;_reverseCache;constructor(){this._forwardCache=new Map,this._reverseCache=new Map}*traverse(t,n){const r=function*(i){const a=t.getChildCount(i);if(a>0)for(let s=0;s<a;s++){const o=t.getChild(i,s);yield*r(o)}yield i};n===void 0&&(n=t.getRoot()),yield*r(n)}getNext(t,n){const r=this._forwardCache.get(n);if(r!==void 0&&this._forwardCache.get(r)!==void 0)return r;if(t.isRoot(n))return;const i=t.getParent(n);if(t.hasRightSibling(n)){const a=t.getRightSibling(n);this._forwardCache.set(n,a),this._reverseCache.set(a,n)}else this._forwardCache.set(n,i),this._reverseCache.set(i,n);return this._forwardCache.get(n)}getPrevious(t,n){const r=this._reverseCache.get(n);if(r!==void 0&&this._reverseCache.get(r)!==void 0)return r;if(n!==this.traverse(t).next().value){if(t.isInternal(n)){const i=t.getChildCount(n)-1,a=t.getChild(n,i);this._reverseCache.set(n,a),this._forwardCache.set(a,n)}else if(t.hasLeftSibling(n)){const i=t.getLeftSibling(n);this._reverseCache.set(n,i),this._forwardCache.set(i,n)}else{let i=n;for(;!t.hasLeftSibling(i);)i=t.getParent(i);const a=t.getLeftSibling(i);this._reverseCache.set(n,a),this._forwardCache.set(a,n)}return this._reverseCache.get(n)}}}var 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m=Sr(t.to),{config:g}=o,{decay:x,velocity:y}=g;(r||i)&&(g.velocity=0),t.config&&!m&&eu(g,He(t.config,a),t.config!==s.config?He(s.config,a):void 0);let b=Se(this);if(!b||N.und(l))return n(ve(this,!0));const p=N.und(t.reset)?i&&!t.default:!N.und(h)&&Lt(t.reset,a),w=p?h:this.get(),C=Vt(l),k=N.num(C)||N.arr(C)||Bn(C),T=!m&&(!k||Lt(s.immediate||t.immediate,a));if(d){const _=Mr(l);if(_!==b.constructor)if(T)b=this._set(C);else throw Error(`Cannot animate between ${b.constructor.name} and ${_.name}, as the "to" prop suggests`)}const L=b.constructor;let I=de(l),D=!1;if(!I){const _=p||!nr(this)&&f;(d||_)&&(D=Re(Vt(w),C),I=!D),(!Re(o.immediate,T)&&!T||!Re(g.decay,x)||!Re(g.velocity,y))&&(I=!0)}if(D&&Le(this)&&(o.changed&&!p?I=!0:I||this._stop(c)),!m&&((I||de(c))&&(o.values=b.getPayload(),o.toValues=de(l)?null:L==Nn?[1]:he(C)),o.immediate!=T&&(o.immediate=T,!T&&!p&&this._set(c)),I)){const{onRest:_}=o;O(iu,M=>Bi(this,t,M));const A=ve(this,St(this,c));Et(this._pendingCalls,A),this._pendingCalls.add(n),o.changed&&R.batchedUpdates(()=>{o.changed=!p,_?.(A,this),p?He(s.onRest,A):o.onStart?.(A,this)})}p&&this._set(w),m?n(is(t.to,t,this._state,this)):I?this._start():Le(this)&&!d?this._pendingCalls.add(n):n(rs(w))}_focus(e){const t=this.animation;e!==t.to&&(Ti(this)&&this._detach(),t.to=e,Ti(this)&&this._attach())}_attach(){let e=0;const{to:t}=this.animation;de(t)&&(xt(t,this),kr(t)&&(e=t.priority+1)),this.priority=e}_detach(){const{to:e}=this.animation;de(e)&&zt(e,this)}_set(e,t=!0){const n=ae(e);if(!N.und(n)){const r=Se(this);if(!r||!Re(n,r.getValue())){const i=Mr(n);!r||r.constructor!=i?ai(this,i.create(n)):r.setValue(n),r&&R.batchedUpdates(()=>{this._onChange(n,t)})}}return Se(this)}_onStart(){const 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Has it been copied?`);return J(this,r=>{const i=r.getNode(t.number);i.taxon=n.number,r._data.nodes.byTaxon[n.number]=t.number,r._data.nodeToTaxon[t.number]=n.number})}getAnnotationSummary(t){if(this._data.annotations[t]===void 0)throw new Error(`No annotation with name ${t} found in tree`);return this._data.annotations[t]}getAnnotations(){return Object.values(this._data.annotations)}getAnnotation(t,n,r){const i=fr(this,this.getNode(t.number),n);if(r===void 0){const{value:a}=Gi(i,`Node ${t.number} is not annotated with ${n}`);return a}else switch(i.type){case B.Some:return i.value.value;case B.Nothing:return r}}getFullNodeAnnotation(t,n){const r=fr(this,this.getNode(t.number),n);return Gi(r,`Node ${t.number} is not annotated with ${n}`)}hasAnnotation(t,n){switch(fr(this,this.getNode(t.number),n).type){case B.Some:return!0;case B.Nothing:return!1}}annotateNode(t,n,r){if(typeof n=="string"){const i=n,s=Hu(r),o=this._data.annotations[i];if(o!==void 0&&o.type!==s.type)throw new Error(`Tried annotation ${i} was parsed as ${s.type} - but is ${o.type} in tree.`);return J(this,c=>{const u=o?o.domain:void 0,l=zl(s,u);c._data.nodes.allNodes[t.number].annotations[i]={id:i,type:s.type,value:s.value},c._data.annotations[i]={id:i,type:s.type,domain:l}})}else{let i=this;for(const[a,s]of Object.entries(n))i=i.annotateNode(t,a,s);return i}}setHeight(t,n){if(!this.hasLengths())throw new Error("Can not set the heights of nodes in a tree without branch lengths");return J(this,r=>{const i=r.getNode(t.number);if(n<0)throw new Error("Height must be non-negative");const s=r.getHeight(t)-n;if(i.length===void 0){if(!r.isRoot(t))throw new Error("Cannot set height on a node without length")}else i.length=i.length+s;for(const o of r.getChildren(t)){const c=r.getNode(o.number),u=r.getLength(c)-s;c.length=u}})}setLength(t,n){return J(this,r=>{const i=r.getNode(t.number);i.length=n,r._data.hasLengths=!0})}deleteLength(t){return J(this,n=>{const r=n.getNode(t.number);r.length=void 0})}setDivergence(t,n){if(!this.hasLengths())throw new Error("Can not set the divergences of nodes in a tree without branch lengths");return J(this,r=>{const i=r.getNode(t.number),a=r.getHeight(t),c=r.getHeight(r.getRoot())-a-n,u=r.getLength(t);i.length=u-c})}setLabel(t,n){if(this._data.nodes.byLabel[n]!==void 0)throw new Error(`Duplicate node label ${n}`);return J(this,r=>{const i=r.getNode(t.number);i.label=n,r._data.nodes.byLabel[n]=t.number})}insertNode(t,n=.5){return J(this,r=>{const i={number:r._data.nodes.allNodes.length,children:[],parent:void 0,label:"",length:void 0,taxon:void 0,annotations:{},_id:hn()};r._data.nodes.allNodes.push(i),r._data.nodes.byTaxon.length+=1;const a=r.getNode(t.number),s=r.getParent(a),o=s.children.indexOf(a.number);s.children.splice(o,1,i.number),i.parent=s.number;const u=r.getLength(a);a.length=u*(1-n),i.length=u*n,i.children=[a.number],a.parent=i.number})}unroot(t){throw new Error("unroot not implemented in immutable tree")}deleteNode(t){throw new Error("deleteNode not implemented in immutable tree")}deleteClade(t){throw new Error("deleteClade not implemented in immutable tree")}orderNodesByDensity(t,n){return J(this,r=>{n===void 0&&(n=r._data.nodes.allNodes[r._data.rootNode]);const i=t?1:-1;Us(r._data,n,(a,s,o,c)=>(s-c)*i)})}rotate(t,n=!1){return J(this,r=>{const i=r.getNode(t.number);if(i.children=i.children.reverse(),n)for(const a of i.children.map(s=>r.getNode(s)))r.rotate(a,n)})}reroot(t,n=.5){return J(this,r=>{if(t.number===r._data.rootNode)return;const i=r.getRoot();i.children.length!==2&&console.warn("Root node has more than two children and we are rerooting! There be dragons!");let a=0;if(i.children.length==2)a=i.children.map(o=>r.getNode(o)).map(o=>r.getLength(o)).reduce((o,c)=>c+o,0);else{const o=[...r.getPathToRoot(t)],c=o[o.length-2];if(Z(c,"Index error when looking for the root child"),!i.children.includes(c.number))throw new Error("Root child not in path to root - likely an internal error");a=r.getLength(c)}const s=r.getNode(t.number);if(r.getParent(t)!==i){let o=s,c=r.getParent(s);const u=r.getChild(c,0).number===t.number,l=s,h=c;let f=r.getLength(c);for(;!r.isRoot(c);){if(c.children=c.children.filter(m=>m!==o.number),r.getParent(c).number===i.number)if(i.children.length==2){if(!r.hasLeftSibling(c)&&!r.hasRightSibling(c))throw new Error("no sibling in rerooting");const g=r.hasLeftSibling(c)?r.getLeftSibling(c):r.getRightSibling(c);c.children.push(g.number),g.parent=c.number,g.length=a}else{const m={number:r._data.nodes.allNodes.length,children:[],parent:void 0,label:"",length:void 0,taxon:void 0,annotations:{},_id:hn()};r._data.nodes.allNodes.push(m),m.length=a,c.children.push(m.number),m.parent=c.number;for(const g of i.children){const x=r.getNode(g);x.number!==c.number&&(x.parent=m.number,m.children.push(x.number))}}else{const m=r.getParent(c),g=r.getLength(m);m.length=f,f=g,c.children.push(m.number)}o=c,c=r.getParent(c)}l.parent=i.number,h.parent=i.number,i.children=[l.number,h.number],u||(i.children=i.children.reverse()),this.getInternalNodes().forEach(m=>{for(const g of r.getChildren(m))g.parent=m.number});const d=r.getLength(l)*n;h.length=d,Z(l.length,"Expected the root's new child to have a length"),l.length-=d}else{const o=r.getLength(t)*(1-n);s.length=o;const c=r.getNextSibling(t);c.length=a-o}})}removeChild(t,n){return J(this,r=>{r._data.nodes.allNodes[t.number].children=r._data.nodes.allNodes[t.number].children.filter(i=>i!==n.number),r._data.nodes.allNodes[n.number].parent=-1})}sortChildren(t,n){return J(this,r=>{r._data.nodes.allNodes[t.number].children=this._data.nodes.allNodes[t.number].children.map(i=>r.getNode(i)).sort(n).map(i=>i.number)})}addChild(t,n){return J(this,r=>{const i=r.getNode(n.number);r.getNode(t.number).children.push(i.number),i.parent=t.number})}setRoot(t){return J(this,n=>{n._data.rootNode=t.number})}}function Us(e,t,n){let r=0;if(e.nodes.allNodes[t.number].children.length>0){const i=new Map;for(const o of e.nodes.allNodes[t.number].children.map(c=>e.nodes.allNodes[c])){const c=Us(e,o,n);i.set(o.number,c),r+=c}const a=e.nodes.allNodes[t.number].children.slice().sort((o,c)=>n(e.nodes.allNodes[o],pe(i.get(o),"Internal error when ordering. Counts not defined."),e.nodes.allNodes[c],pe(i.get(c),"Internal error when ordering. Counts not defined.")));a.reduce((o,c,u)=>o||c!==e.nodes.allNodes[t.number].children[u],!0)&&(e.nodes.allNodes[t.number].children=a)}else r=1;return r}function*Os(e,t=void 0){const n=function*(r){yield e.getNode(r.number);const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}};t===void 0&&(t=e.getRoot()),yield*n(t)}function*Ul(e,t=void 0,n=(r,i)=>r.number-i.number){const r=function*(i,a=void 0){yield e.getNode(i.number);const s=[...e.getChildren(i),e.getParent(i)].filter(o=>o.number!==a);s.sort(n);for(const o of s)yield*r(o,i.number)};t===void 0&&(t=e.getRoot()),yield*r(t)}function*Ol(e,t=void 0,n=(r,i)=>r.number-i.number){const r=function*(i,a=void 0){const s=[...e.getChildren(i),e.getParent(i)].filter(o=>o.number!==a);s.sort(n);for(const o of s)yield*r(o,i.number);yield e.getNode(i.number)};t===void 0&&(t=e.getRoot()),yield*r(t)}function*js(e,t=void 0){const n=function*(r){const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}yield r};t===void 0&&(t=e.getRoot()),yield*n(t)}function*Kn(e,t){t===void 0&&(t=e.getRoot());const n=function*(r){const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}else yield r};yield*n(t)}function*jl(e,t){let n=t;for(;!e.isRoot(n);)yield n,n=e.getParent(n);yield n}function zl(e,t){switch(e.type){case V.BOOLEAN:return[!0,!1];case V.DISCRETE:{const n=e.value;if(t!==void 0){const r=t;return[...new Set([...r,n])].sort()}else return[n]}case V.NUMERICAL:{const n=e.value;return lt([...t||[],n])}case V.DISCRETE_SET:{const n=e.value,r=t||[];return[...new Set([...r,...n])].sort()}case V.NUMERICAL_SET:{const n=e.value;return lt([...t||[],...n])}case V.DENSITIES:if(t!==void 0){const n=t;return[...new Set([...n,...Object.keys(e.value)])].sort()}else return[...new Set(Object.keys(e.value))].sort().filter(n=>n);case V.MARKOV_JUMPS:{const n=e.value.reduce((i,a)=>i.concat([a.to,a.from]),[]),r=t||[];return[...new Set([...r,...n])].sort()}default:throw new Error("Unrecognized type when updating domain")}}function Bl(){return{lastChunk:"",status:"parsing",end:"",start(){},transform(e,t){const n=this.lastChunk+e;let r="";for(let i=0;i<n.length;i++){const a=n[i];Z(a,"Internal Error. Hit empty character in array"),this.status==="parsing"?([this.status,this.end]=Vl(a),this.status==="in comment"&&(r.length>0&&t.enqueue(r),r="")):a===this.end&&(this.status="parsing",this.end=""),this.status==="parsing"&&/\s|;|\]/.test(a)?(r.length>0&&(/\]/.test(a)&&(r+=a),t.enqueue(r),r=""),/;/.test(a)&&t.enqueue(a)):r+=a}this.lastChunk=r},flush(e){this.lastChunk&&e.enqueue(this.lastChunk)}}}function Vl(e){return e==="'"?["in single quote","'"]:e==='"'?["in double quote",'"']:e==="["?["in comment","]"]:["parsing",""]}const ga=/\s*('[^']+'|"[^"]+"|\[&[^[]+]|,|:|\)|\(|;)\s*/;class ql{reader;taxonSet;currentBlock;hasTree;options;translateTaxonMap;constructor(t,n={}){const r=new TransformStream(Bl());this.reader=t.pipeThrough(new TextDecoderStream).pipeThrough(r).getReader(),this.taxonSet=new rn,this.currentBlock=void 0,this.options=n}async*getTrees(){for(;this.currentBlock!=="trees";)await this.parseNextBlock(),this.hasTree=!0;yield*this.parseTreesBlock()}async parseNextBlock(){const t=await this.getNextBlockName();switch(t){case"taxa":this.currentBlock="taxa",await this.parseTaxaBlock();break;case"trees":this.currentBlock="trees";break;default:console.log(`skipping block ${t}. Only parsing blocks are taxa and trees for now.`),await this.readToEndOfBlock()}}async nextToken(){const{done:t,value:n}=await this.reader.read();if(t)throw new Error("unexpectedly hit the end of the stream");return n}async skipSemiColon(){const{done:t,value:n}=await this.reader.read();if(t)throw new Error("unexpectedly hit the end of the stream");if(!n.match(/;$/))throw new Error(`expected ";" got ${n}`)}async getNextBlockName(){let t=!0,n;for(;t;)(await this.nextToken()).match(/\bbegin/i)&&(n=await this.nextToken(),await this.skipSemiColon(),t=!1);return n}async readToEndOfBlock(){let t=!0;for(;t;)(await this.nextToken()).match(/\bend;/i)&&(t=!1)}async skipUntil(t){let n,r=!0;for(;r;)n=await this.nextToken(),t.test(n)&&(r=!1);if(n==null)throw new Error(`Internal parsing error: ${t.source} not found `);return n}async readUntil(t){let n="",r=!0;for(;r;){const i=await this.nextToken();t.test(i)&&(n+=i,r=!1),n+=i}return n}async parseTaxaBlock(){let t,n=!0;for(;n;){const r=await this.skipUntil(/dimensions|taxlabels|end/i);switch(!0){case/dimensions/i.test(r):{const i=await this.readUntil(/;/),a=i.match(/ntax=(\d+);/);if(a)Z(a[1],"No number of taxa found despite matching regex"),t=parseInt(a[1]);else throw new Error(`Expected dimension in form of ntax=(\\d+);. Got ${i}`);break}case/taxlabels/i.test(r):{let i=await this.nextToken();for(;i!==";";)this.taxonSet.addTaxon(i),i=await this.nextToken();if(t&&t!=this.taxonSet.getTaxonCount())throw new Error(`found ${this.taxonSet.getTaxonCount()} taxa. Expected: ${t}}`);break}case/end/i.test(r):{if(this.taxonSet.getTaxonCount()===0)throw new Error("hit end of taxa section but didn't find any taxa");this.taxonSet.lockTaxa(),await this.skipSemiColon(),n=!1;break}default:throw new Error(`Reached impossible code looking for dimensions or taxlabels or end in taxa block "${r}"`)}}}async*parseTreesBlock(){let t,n=!0;for(;n;){const r=await this.skipUntil(/translate|tree|end/i);switch(!0){case/translate/i.test(r):{this.translateTaxonMap=new Map;let i=0,a;for(t=await this.nextToken();t!==";";){if(i%2==0)a=t;else{if(t[t.length-1]===","&&(t=t.slice(0,-1)),this.taxonSet.isFinalized){if(!this.taxonSet.hasTaxon(t))throw new Error(`Taxon ${t} not found in taxa block - but found in translate block`)}else this.taxonSet.addTaxon(t);Z(a,"Error parsing nexus. Expected key for taxa but found nothing"),this.translateTaxonMap.set(a,t)}for(t=await this.nextToken();t===",";)t=await this.nextToken();i++}this.taxonSet.lockTaxa();break}case/tree/i.test(r):{await this.nextToken();const i=new $s(this.taxonSet,{translateTaxonNames:this.translateTaxonMap});t=await this.skipUntil(/\(/);let a=t.split(ga).filter(o=>o.length>0).reverse();for(;!i.isDone();){for(;a.length>0;){const o=a.pop();Z(o,"Unexpectedly hit the end of the buffer"),i.parseCharacter(o)}i.isDone()||(t=await this.nextToken(),a=t.split(ga).filter(o=>o.length>0).reverse())}yield i.getTree();break}case/end/i.test(r):await this.skipSemiColon(),this.hasTree=!1,this.reader.releaseLock(),n=!1;break;default:throw new Error(`Reached impossible code in treeblock block "${r}"`)}}}}class Hl{_forwardCache;_reverseCache;constructor(){this._forwardCache=new Map,this._reverseCache=new Map}*traverse(t,n){const r=function*(i){const a=t.getChildCount(i);if(a>0)for(let s=0;s<a;s++){const o=t.getChild(i,s);yield*r(o)}yield i};n===void 0&&(n=t.getRoot()),yield*r(n)}getNext(t,n){const r=this._forwardCache.get(n);if(r!==void 0&&this._forwardCache.get(r)!==void 0)return r;if(t.isRoot(n))return;const i=t.getParent(n);if(t.hasRightSibling(n)){const a=t.getRightSibling(n);this._forwardCache.set(n,a),this._reverseCache.set(a,n)}else this._forwardCache.set(n,i),this._reverseCache.set(i,n);return this._forwardCache.get(n)}getPrevious(t,n){const r=this._reverseCache.get(n);if(r!==void 0&&this._reverseCache.get(r)!==void 0)return r;if(n!==this.traverse(t).next().value){if(t.isInternal(n)){const i=t.getChildCount(n)-1,a=t.getChild(n,i);this._reverseCache.set(n,a),this._forwardCache.set(a,n)}else if(t.hasLeftSibling(n)){const i=t.getLeftSibling(n);this._reverseCache.set(n,i),this._forwardCache.set(i,n)}else{let i=n;for(;!t.hasLeftSibling(i);)i=t.getParent(i);const a=t.getLeftSibling(i);this._reverseCache.set(n,a),this._forwardCache.set(a,n)}return this._reverseCache.get(n)}}}var 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S.jsx("g",{children:S.jsx("g",{transform:`translate(${b},${p})`,children:S.jsx(Ie.Provider,{value:I,children:S.jsx(sn.Provider,{value:L,children:S.jsx(bt.Provider,{value:w,children:S.jsxs(vt.Provider,{value:s,children:[c?S.jsx(Bf,{...c}):null,D.map((_,A)=>S.jsx(cf,{..._},_.id??A))]})})})})})})}exports.BaseAnnotationType=V;exports.BranchLabels=Lf;exports.Branches=to;exports.CartoonClades=Df;exports.CircleNodes=Ef;exports.FigTree=qf;exports.HighlightClades=Ff;exports.ImmutableTree=bi;exports.NexusImporter=ql;exports.NodeLabels=If;exports.PreOrderTraversalCache=Hl;exports.RectangleNodes=Rf;exports.TaxonSet=rn;exports.dateToDecimal=ol;exports.decimalToDate=sl;exports.defaultInternalLayoutOptions=ys;exports.layoutClass=H;exports.leapYear=mi;exports.pathToRootIterator=jl;exports.polarLayout=Yl;exports.postOrderIterator=js;exports.preOrderIterator=Os;exports.psuedoRootPostOrderIterator=Ol;exports.psuedoRootPreOrderIterator=Ul;exports.radialLayout=Wl;exports.rectangularLayout=Bs;exports.tipIterator=Kn;