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forester.js
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/**
* Copyright (C) 2023 Christian M. Zmasek
* Copyright (C) 2023 Yun Zhang
* Copyright (C) 2023 J. Craig Venter Institute
* All rights reserved
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*
*/
// v 2.1.0.a2
// 2024-06-05
//
// forester.js is a general suite for dealing with phylogenetic trees.
//
// forester.js is used by Archaeopteryx.js:
// https://github.com/cmzmasek/archaeopteryx-js
// https://www.npmjs.com/package/archaeopteryx
//
// Availability:
// https://github.com/cmzmasek/archaeopteryx-js
// https://www.npmjs.com/package/archaeopteryx
//
// Dependencies: none
//
//
// In the following is a basic example shows how to parse a New Hampshire formatted String
// into to a object representing a phylogenetic tree.
// Followed by pre- and post-order traversal,
// and writing back to a New Hampshire formatted String.
//
// Change './forester' to 'forester' if you use this code outside of this package
//
// let forester = require('./forester').forester;
//
// let newHampshireFormattedString = "(((a:1,b:1,c:1)N:2,(d:1,e:1)M:4)O:4,f:1)R:1;";
// let phylogeneticTree = forester.parseNewHampshire(newHampshireFormattedString);
//
// console.log('Pre-order traversal:');
// forester.preOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
// console.log(n.name + ':' + n.branch_length);
// });
//
// console.log('Post-order traversal:');
// forester.postOrderTraversalAll(forester.getTreeRoot(phylogeneticTree), function (n) {
// console.log(n.name + ':' + n.branch_length);
// });
//
// console.log('In New Hampshire format:');
// let nh = forester.toNewHampshire(phylogeneticTree);
// console.log(nh);
(function forester() {
"use strict";
const BRANCH_EVENT_REF = 'aptx:branch_event';
const BRANCH_EVENT_DATATYPE = 'xsd:string';
const BRANCH_EVENT_APPLIES_TO = 'parent_branch';
const NH_FORMAT_ERR = 'New Hampshire (Newick) format error: ';
const NUMBERS_ONLY_PATTERN = /^[-+]?[0-9\\.]+$/;
const MSA_RESIDUE_SORT_MAP = new Map();
MSA_RESIDUE_SORT_MAP.set('A', 0);
MSA_RESIDUE_SORT_MAP.set('C', 1);
MSA_RESIDUE_SORT_MAP.set('D', 2);
MSA_RESIDUE_SORT_MAP.set('E', 3);
MSA_RESIDUE_SORT_MAP.set('F', 4);
MSA_RESIDUE_SORT_MAP.set('G', 5);
MSA_RESIDUE_SORT_MAP.set('H', 6);
MSA_RESIDUE_SORT_MAP.set('I', 7);
MSA_RESIDUE_SORT_MAP.set('K', 8);
MSA_RESIDUE_SORT_MAP.set('L', 9);
MSA_RESIDUE_SORT_MAP.set('M', 10);
MSA_RESIDUE_SORT_MAP.set('N', 11);
MSA_RESIDUE_SORT_MAP.set('P', 12);
MSA_RESIDUE_SORT_MAP.set('Q', 13);
MSA_RESIDUE_SORT_MAP.set('R', 14);
MSA_RESIDUE_SORT_MAP.set('S', 15);
MSA_RESIDUE_SORT_MAP.set('T', 16);
MSA_RESIDUE_SORT_MAP.set('U', 17);// Uracil
MSA_RESIDUE_SORT_MAP.set('V', 18);
MSA_RESIDUE_SORT_MAP.set('W', 19);
MSA_RESIDUE_SORT_MAP.set('Y', 20);
MSA_RESIDUE_SORT_MAP.set('B', 21);// Asparagine or aspartic acid
MSA_RESIDUE_SORT_MAP.set('Z', 22);// Glutamine or glutamic acid
MSA_RESIDUE_SORT_MAP.set('X', 23);
MSA_RESIDUE_SORT_MAP.set('?', 24);
MSA_RESIDUE_SORT_MAP.set('-', 25);
MSA_RESIDUE_SORT_MAP.set('.', 26);
/**
* Sets links to parent nodes for all nodes in a
* phyloXML-based tree object
*
* @param phy - A phyloXML-based tree object.
*/
forester.addParents = function (phy) {
if (phy.children) {
for (let i = phy.children.length - 1; i >= 0; --i) {
let c = phy.children[i];
c.parent = phy;
forester.addParents(c);
}
}
};
/**
* Returns the real root node of a
* phyloXML-based tree object.
* Precondition: needs to have parents set.
*
* @param phy - A phyloXML-based tree object or node.
* @returns {*} - The real tree root node.
*/
forester.getTreeRoot = function (phy) {
let root = phy;
if (!root.parent && root.children && root.children.length === 1) {
root = root.children[0];
}
while (root.parent && root.parent.parent) {
root = root.parent;
}
return root;
};
/**
* Visits all non-collapsed child nodes of a node
* while applying a function in pre-order.
*
* @param node - The root of the subtree to traverse.
* @param fn - The function to apply.
*/
forester.preOrderTraversal = function (node, fn) {
fn(node);
if (node.children) {
for (let i = node.children.length - 1; i >= 0; --i) {
forester.preOrderTraversal(node.children[i], fn);
}
}
};
/**
* Visits all child nodes of a node
* while applying a function in pre-order.
*
* @param node - The root of the subtree to traverse.
* @param fn - The function to apply.
*/
forester.preOrderTraversalAll = function (node, fn) {
fn(node);
if (node.children) {
for (let i = node.children.length - 1; i >= 0; --i) {
forester.preOrderTraversalAll(node.children[i], fn);
}
} else if (node._children) {
for (let ii = node._children.length - 1; ii >= 0; --ii) {
forester.preOrderTraversalAll(node._children[ii], fn);
}
}
};
forester.postOrderTraversalAll = function (node, fn) {
if (node.children) {
let l = node.children.length;
for (let i = 0; i < l; ++i) {
forester.postOrderTraversalAll(node.children[i], fn);
}
} else if (node._children) {
let ll = node._children.length;
for (let ii = 0; ii < ll; ++ii) {
forester.postOrderTraversalAll(node._children[ii], fn);
}
}
fn(node);
};
forester.findByNodeName = function (node, name) {
let found = [];
forester.preOrderTraversalAll(node, function (n) {
if (n.name === name) {
found.push(n);
}
});
return found;
};
forester.findByTaxonomyCode = function (node, code) {
let found = [];
forester.preOrderTraversalAll(node, function (n) {
if (n.taxonomies && n.taxonomies.length > 0 && n.taxonomies[0].code === code) {
found.push(n);
}
});
return found;
};
forester.findByTaxonomyScientificName = function (node, scientificName) {
let found = [];
forester.preOrderTraversalAll(node, function (n) {
if (n.taxonomies && n.taxonomies.length > 0 && n.taxonomies[0].scientific_name === scientificName) {
found.push(n);
}
});
return found;
};
forester.filterByNodeProperty = function (positive, phy, propertyMap) {
if (!phy) {
throw ("cannot delete null tree");
}
if (!propertyMap) {
throw ("property list is null");
}
const toDelete = [];
forester.preOrderTraversalAll(phy, function (n) {
if (!n.children && !n._children) {
if (n.properties && n.properties.length > 0) {
const propertiesLength = n.properties.length;
for (let i = 0; i < propertiesLength; ++i) {
const property = n.properties[i];
if (property.ref && property.value && property.applies_to === 'node') {
if (positive) {
if (property.ref in propertyMap && !propertyMap[property.ref].includes(property.value)) {
toDelete.push(n);
}
} else {
if (property.ref in propertyMap && propertyMap[property.ref].includes(property.value)) {
toDelete.push(n);
}
}
}
}
}
}
});
const l = toDelete.length;
console.log(toDelete);
for (let i = 0; i < l; ++i) {
forester.deleteSubtree(phy, toDelete[i]);
}
};
/**
* To delete a sub-tree or external node.
*
* @param phy
* @param nodeToDelete
*/
forester.deleteSubtree = function (phy, nodeToDelete) {
if (!phy) {
throw ("cannot delete null tree");
}
if (!nodeToDelete) {
throw ("cannot delete null node");
}
if (!nodeToDelete.parent || !nodeToDelete.parent.parent) {
throw ("cannot delete root");
}
if (!nodeToDelete.parent.parent.parent) {
throw ("cannot delete direct child of root");
}
let p = nodeToDelete.parent;
if ((p.children) && (p.children.length > 1)) {
let i = p.children.indexOf(nodeToDelete);
if (i !== -1) {
p.children.splice(i, 1);
}
}
if ((p._children) && (p._children.length > 1)) {
let ii = p._children.indexOf(nodeToDelete);
if (ii !== -1) {
p._children.splice(ii, 1);
}
}
if (p.children.length === 1) {
let pp = p.parent;
let cni = forester.getChildNodeIndex(pp, p);
if ((cni < 0) || (cni > (pp.children.length - 1))) {
throw ("this should never have happened, child node index = " + cni);
}
let x = p.children[0];
let nbl = undefined;
if (x.branch_length || p.branch_length) {
nbl = (x.branch_length > 0 ? x.branch_length : 0) + (p.branch_length > 0 ? p.branch_length : 0);
}
x.parent = pp;
pp.children[cni] = x;
x.branch_length = nbl;
}
};
/**
* To re-root a tree object.
*
* @param phy - The tree to be re-rooted.
* @param node - The node on where to place the new root (on its parent branch).
* @param branchLength - The branch length to use if new root is not placed in the middle (if
* non-negative).
*/
forester.reRoot = function (phy, node, branchLength) {
if (!phy) {
throw ("cannot re-root null tree");
}
if (!node) {
throw ("cannot re-root on null node");
}
if (!branchLength) {
branchLength = -1;
}
if (forester.isString(node)) {
let nodes = forester.findByNodeName(phy, node);
if (nodes.length > 1) {
throw ("node name '" + node + "' is not unique");
} else if (nodes.length < 1) {
throw ("node name '" + node + "' is not found");
}
node = nodes[0];
}
phy.rooted = true;
let root = forester.getTreeRoot(phy);
if (!node.parent || !node.parent.parent) {
//do noting
} else if (!node.parent.parent.parent) {
if ((node.parent.children.length === 2) && (branchLength >= 0)) {
let d = node.parent.children[0].branch_length + node.parent.children[1].branch_length;
let other;
if (node.parent.children[0] === node) {
other = node.parent.children[1];
} else {
other = node.parent.children[0];
}
node.branch_length = branchLength;
let dm = d - branchLength;
if (dm >= 0) {
other.branch_length = dm;
} else {
other.branch_length = 0;
}
}
if (node.parent.children.length > 2) {
let index = forester.getChildNodeIndex(node.parent, node);
let dn = node.branch_length;
let prev_root = root;
prev_root.children.splice(index, 1);
let nr = {};
nr.children = [];
forester.setChildNode(nr, 0, node);
forester.setChildNode(nr, 1, prev_root);
forester.copyBranchData(node, prev_root);
phy.children[0] = nr;
nr.parent = phy;
if (branchLength >= 0) {
node.branch_length = branchLength;
let dnmp = dn - branchLength;
if (dnmp >= 0) {
prev_root.branch_length = dnmp;
} else {
prev_root.branch_length = 0;
}
} else {
if (dn >= 0) {
let dn2 = dn / 2.0;
node.branch_length = dn2;
prev_root.branch_length = dn2;
}
}
}
} else {
let a = node;
let new_root = {};
let distance1;
let distance2 = 0.0;
let branch_data_1;
let branch_data_2 = null;
let b = a.parent;
let c = b.parent;
new_root.children = [];
forester.setChildNode(new_root, 0, a);
forester.setChildNode(new_root, 1, b);
distance1 = c.branch_length;
branch_data_1 = forester.getBranchData(c);
c.branch_length = b.branch_length;
forester.copyBranchData(b, c);
forester.copyBranchData(a, b);
// New root is always placed in the middle of the branch:
if (!a.branch_length) {
b.branch_length = undefined;
} else {
if (branchLength >= 0.0) {
let diff = a.branch_length - branchLength;
a.branch_length = branchLength;
b.branch_length = (diff >= 0.0 ? diff : 0.0);
} else {
let d2 = a.branch_length / 2.0;
a.branch_length = d2;
b.branch_length = d2;
}
}
setChildNodeOnly(b, forester.getChildNodeIndex(b, a), c);
// moving to the old root, swapping references:
while (c.parent.parent) {
a = b;
b = c;
c = c.parent;
setChildNodeOnly(b, forester.getChildNodeIndex(b, a), c);
b.parent = a;
distance2 = c.branch_length;
branch_data_2 = forester.getBranchData(c);
c.branch_length = distance1;
forester.setBranchData(c, branch_data_1);
distance1 = distance2;
branch_data_1 = branch_data_2;
}
// removing the old root:
if (c.children.length === 2) {
let node2 = c.children[1 - forester.getChildNodeIndex(c, b)];
node2.parent = b;
if ((!c.branch_length) && (!node2.branch_length)) {
node2.branch_length = undefined;
} else {
node2.branch_length = (c.branch_length >= 0.0 ? c.branch_length : 0.0) + (node2.branch_length >= 0.0 ? node2.branch_length : 0.0);
}
let cbd = forester.getBranchData(c);
if (cbd) {
forester.setBranchData(node2, cbd);
}
let l = b.children.length;
for (let i = 0; i < l; ++i) {
if (b.children[i] === c) {
setChildNodeOnly(b, i, node2);
break;
}
}
} else {
c.parent = b;
forester.removeChildNode(c, forester.getChildNodeIndex(c, b));
}
phy.children[0] = new_root;
new_root.parent = phy;
forester.addParents(phy);
}
function setChildNodeOnly(parentNode, i, node) {
if (parentNode.children.length <= i) {
parentNode.children.push(node);
} else {
parentNode.children[i] = node;
}
}
};
forester.midpointRoot = function (phy) {
let root = forester.getTreeRoot(phy);
let extNodes = forester.getAllExternalNodes(root);
if ((extNodes.length < 2) || (forester.calcMaxBranchLength(root) <= 0)) {
return;
}
let counter = 0;
let totalNodes = forester.getAllNodes(phy).length;
while (true) {
if (++counter > (totalNodes + 1)) {
throw('this should not have happened: midpoint rooting does not converge');
}
let a = null;
let da = 0;
let db = 0;
let cl = forester.getTreeRoot(phy).children.length;
for (let i = 0; i < cl; ++i) {
let f = forester.getFurthestDescendant(forester.getTreeRoot(phy).children[i]);
let df = forester.getDistance(f, forester.getTreeRoot(phy));
if (df > 0) {
if (df > da) {
db = da;
da = df;
a = f;
} else if (df > db) {
db = df;
}
}
}
let diff = da - db;
if (diff < 0.0001) {
break;
}
let x = da - (diff / 2.0);
while ((x > a.branch_length) && a.parent) {
x -= (a.branch_length > 0 ? a.branch_length : 0);
a = a.parent;
}
forester.reRoot(phy, a, x);
}
};
forester.getFurthestDescendant = function (node) {
let children = forester.getAllExternalNodes(node);
let farthest = null;
let longest = -1000000;
let l = children.length;
for (let i = 0; i < l; ++i) {
let dist = forester.getDistance(children[i], node);
if (dist > longest) {
farthest = children[i];
longest = dist;
}
}
return farthest;
};
/**
* Calculates the distance between PhylogenyNodes n1 and n2.
* PRECONDITION: n1 is a descendant of n2.
*
* @param n1 a descendant of n2
* @param n2
* @returns {number} distance between n1 and n2
*/
forester.getDistance = function (n1, n2) {
let d = 0.0;
while (n1 !== n2) {
if (n1.branch_length > 0.0) {
d += n1.branch_length;
}
n1 = n1.parent;
}
return d;
};
forester.removeChildNode = function (parentNode, i) {
if (!parentNode.children) {
throw ("cannot remove the child node for a external node");
}
if ((i >= parentNode.children.length) || (i < 0)) {
throw ("attempt to get child node " + i + " of a node with " + parentNode.children.length + " child nodes.");
}
parentNode.children[i].parent = undefined;
parentNode.children.splice(i, 1);
};
/**
* Inserts node node at the specified position i into the list of
* child nodes of parentNode. This does not allow null slots in the list of child nodes:
* If i is larger than the number of child nodes, node is just added to the
* list, not placed at index i.
*/
forester.setChildNode = function (parentNode, i, node) {
node.parent = parentNode;
if (parentNode.children.length <= i) {
parentNode.children.push(node);
} else {
parentNode.children[i] = node;
}
};
forester.getBranchData = function (node) {
let branchData = null;
if (node.width || node.color || node.confidences) {
branchData = {};
branchData.width = node.width;
branchData.color = node.color;
branchData.confidences = node.confidences;
}
return branchData;
};
forester.setBranchData = function (node, branchData) {
if (branchData) {
node.width = branchData.width;
node.color = branchData.color;
node.confidences = branchData.confidences;
}
};
forester.unCollapseAll = function (node) {
forester.preOrderTraversal(node, function (d) {
if (d._children) {
d.children = d._children;
d._children = null;
}
});
};
forester.copyBranchData = function (nodeFrom, nodeTo) {
nodeTo.width = nodeFrom.width;
nodeTo.color = nodeFrom.color;
nodeTo.confidences = nodeFrom.confidences;
};
forester.getChildNodeIndex = function (parentNode, childNode) {
if (!parentNode) {
throw ("cannot get the child index for a root node");
}
let c = parentNode.children.length;
for (let i = 0; i < c; ++i) {
if (parentNode.children[i] === childNode) {
return i;
}
}
throw ("unexpected exception: Could not determine the child index for a node");
};
forester.getChildren = function (node) {
return node._children ? node._children : (node.children ? node.children : []);
};
forester.calcAverageTreeHeight = function (node, externalDescendants) {
let c = externalDescendants ? externalDescendants : forester.getAllExternalNodes(node);
let l = c.length;
let s = 0;
for (let i = 0; i < l; ++i) {
let cc = c[i];
while (cc !== node) {
if (cc.branch_length > 0) {
s += cc.branch_length;
}
cc = cc.parent;
}
}
return s / l;
};
forester.setToArray = function (set) {
let array = [];
if (set) {
set.forEach(function (e) {
array.push(e);
});
}
return array;
};
forester.setToSortedArray = function (set) {
let array = [];
if (set) {
set.forEach(function (e) {
array.push(e);
});
}
return array.sort();
};
forester.calcMinMaxInSet = function (set) {
let array = [];
let first = true;
let min = 0;
let max = 0;
if (set) {
set.forEach(function (e) {
e = parseFloat(e);
if (first) {
first = false;
min = e;
max = e;
} else {
if (e < min) {
min = e;
}
if (e > max) {
max = e;
}
}
});
}
array[0] = min;
array[1] = max;
return array;
};
forester.calcMinMeanMaxInSet = function (set) {
let array = [];
let first = true;
let min = 0;
let max = 0;
let mean = 0;
let sum = 0;
let n = 0;
if (set) {
set.forEach(function (e) {
e = parseFloat(e);
++n;
sum += e;
if (first) {
first = false;
min = e;
max = e;
} else {
if (e < min) {
min = e;
}
if (e > max) {
max = e;
}
}
});
}
if (n > 0) {
mean = sum / n;
}
array[0] = min;
array[1] = mean;
array[2] = max;
return array;
};
/**
* This collects all properties in a tree
* and returns them as dictionary of Sets mapping
* keys to values.
* It only collects properly formed properties
* (as per phyloXML standard), which means
* that 'applies_to' and 'datatype' have to be present.
*
*
* @param phy - A phyloXML-based tree object or node.
* @param appliesTo - 'phylogeny', 'clade', 'node', 'annotation', 'parent_branch', or 'other'.
* @param externalOnly - To collect from external nodes only.
* @returns {{}}
*/
forester.collectProperties = function (phy, appliesTo, externalOnly) {
let props = {};
forester.preOrderTraversalAll(phy, function (n) {
if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
if (n.properties && n.properties.length > 0) {
let propertiesLength = n.properties.length;
for (let i = 0; i < propertiesLength; ++i) {
let property = n.properties[i];
if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
let ref = property.ref;
if (!props[ref]) {
props[ref] = new Set();
}
props[ref].add(property.value);
}
}
}
}
});
return props;
};
/**
*
* Special method for IRD database.
* Returns true if at least one 'ird:Host' property with 'Avian' found
*
* @param phy
* @param targetValue
* @param fromRef
* @param toRef
* @returns {boolean}
*/
forester.splitProperty = function (phy, targetValue, fromRef, toRef) {
let found = false;
let targetValue_ = targetValue + ' ';
forester.preOrderTraversalAll(phy, function (n) {
if (n.properties && n.properties.length > 0) {
let propertiesLength = n.properties.length;
for (let i = 0; i < propertiesLength; ++i) {
let property = n.properties[i];
if (property.ref === fromRef && property.value) {
let newValue = '';
if (property.value.startsWith(targetValue_)) {
newValue = targetValue;
found = true;
} else {
newValue = property.value;
}
let newproperty = {};
newproperty.ref = toRef;
newproperty.value = newValue;
newproperty.datatype = 'xsd:string';
newproperty.applies_to = 'node';
n.properties.push(newproperty);
}
}
}
});
return found;
};
forester.collectPropertyRefs = function (phy, appliesTo, externalOnly) {
let propertyRefs = new Set();
forester.preOrderTraversalAll(phy, function (n) {
if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
if (n.properties && n.properties.length > 0) {
let propertiesLength = n.properties.length;
for (let i = 0; i < propertiesLength; ++i) {
let property = n.properties[i];
if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
propertyRefs.add(property.ref);
}
}
}
}
});
return propertyRefs;
};
forester.shortenProperties = function (phy, appliesTo, externalOnly, sourceRef, targetRef) {
forester.preOrderTraversalAll(phy, function (n) {
if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
if (n.properties && n.properties.length > 0) {
let propertiesLength = n.properties.length;
for (let i = 0; i < propertiesLength; ++i) {
let property = n.properties[i];
if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
if (property.ref === sourceRef) {
let s = property.value.trim().split(/\s+/);
if (s && s.length > 1) {
let newProp = {};
newProp.ref = targetRef;
if (s.length === 2) {
newProp.value = s[0];
} else {
newProp.value = s[0] + ' ' + s[1];
}
newProp.datatype = property.datatype;
newProp.applies_to = property.applies_to;
n.properties.push(newProp);
}
}
}
}
}
}
});
};
forester.collectBasicTreeProperties = function (tree) {
let properties = {};
properties.internalNodeData = false;
properties.nodeNames = false;
properties.longestNodeName = 0;
properties.branchLengths = false;
properties.confidences = false;
properties.nodeEvents = false;
properties.sequences = false;
properties.taxonomies = false;
properties.alignedMolSeqs = true;
properties.maxMolSeqLength = 0;
properties.externalNodesCount = 0;
properties.molSeqResiduesPerPosition = null;
properties.averageBranchLength = 0;
let bl_counter = 0;
let bl_sum = 0;
let molSeqs = [];
forester.preOrderTraversalAll(tree, function (n) {
if (n.name && n.name.length > 0) {
properties.nodeNames = true;
if (n.name.length > properties.longestNodeName) {
properties.longestNodeName = n.name.length;
}
if ((n.children || n._children) && (n.parent)) {
properties.internalNodeData = true;
}
}
if (!(n.children || n._children)) {
properties.externalNodesCount += 1;
}
if (n.branch_length && n.branch_length > 0) {
properties.branchLengths = true;
bl_sum += n.branch_length;
bl_counter += 1;
}
if (n.events) {
properties.nodeEvents = true;
}
if (n.sequences && n.sequences.length > 0) {
properties.sequences = true;
if (n.children || n._children) {
properties.internalNodeData = true;
} else {
let s = n.sequences[0];
if (s.mol_seq && s.mol_seq.value) {
if (s.mol_seq.value.length > properties.maxMolSeqLength) {
properties.maxMolSeqLength = s.mol_seq.value.length;
}
if (!s.mol_seq.is_aligned) {
properties.alignedMolSeqs = false;
} else {
molSeqs.push(s.mol_seq.value);
}
}
}
}
if (n.taxonomies && n.taxonomies.length > 0) {
properties.taxonomies = true;
if (n.children || n._children) {
properties.internalNodeData = true;
}
}
if (n.confidences && n.confidences.length > 0) {
properties.confidences = true;
}
if (n.properties && n.properties.length > 0) {
let l = n.properties.length;
for (let p = 0; p < l; ++p) {
if (n.properties[p].ref === BRANCH_EVENT_REF && n.properties[p].datatype === BRANCH_EVENT_DATATYPE && n.properties[p].applies_to === BRANCH_EVENT_APPLIES_TO) {
properties.branchEvents = true;
}
}
}
});
if (properties.alignedMolSeqs) {
properties.molSeqResiduesPerPosition = [];
for (let p = 0, maxLen = properties.maxMolSeqLength; p < maxLen; ++p) {
let mySet = new Set();
for (let i = 0, seqsLen = molSeqs.length; i < seqsLen; ++i) {
let molSeq = molSeqs[i];
let c = molSeq[p];
if (c) {
c = c.toUpperCase();
mySet.add(c);
if (!MSA_RESIDUE_SORT_MAP.has(c)) {
throw ("Unknown MSA residue '" + c + "'");
}
}
}
let myArray = forester.setToArray(mySet);
myArray.sort(function (a, b) {
return MSA_RESIDUE_SORT_MAP.get(a) - MSA_RESIDUE_SORT_MAP.get(b);
});
properties.molSeqResiduesPerPosition.push(myArray);
}
}
if (bl_counter > 0) {
properties.averageBranchLength = bl_sum / bl_counter;
}
return properties;
};
forester.searchData = function (query, phy, caseSensitive, partial, regex, searchProperties) {
let nodes = new Set();
if (!phy || !query || query.length < 1) {
return nodes;
}
let my_query = query.trim();
if (my_query.length < 1) {
return nodes;
}
my_query = my_query.replace(/\s\s+/g, ' ');
if (!regex) {
my_query = my_query.replace(/\+\++/g, '+');
}
let queries = [];