graphbase-js 2.1.4

package/index.js

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+/**
+ * Copyright (c) 2014, Chris Pettitt
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ * list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ * this list of conditions and the following disclaimer in the documentation
+ * and/or other materials provided with the distribution.
+ *
+ * 3. Neither the name of the copyright holder nor the names of its contributors
+ * may be used to endorse or promote products derived from this software without
+ * specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+var lib = require("./lib");
+
+module.exports = {
+  Graph: lib.Graph,
+  json: require("./lib/json"),
+  alg: require("./lib/alg"),
+  version: lib.version
+};

package/lib/alg/components.js

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+var _ = require("../lodash");
+
+module.exports = components;
+
+function components(g) {
+  var visited = {};
+  var cmpts = [];
+  var cmpt;
+
+  function dfs(v) {
+    if (_.has(visited, v)) return;
+    visited[v] = true;
+    cmpt.push(v);
+    _.each(g.successors(v), dfs);
+    _.each(g.predecessors(v), dfs);
+  }
+
+  _.each(g.nodes(), function(v) {
+    cmpt = [];
+    dfs(v);
+    if (cmpt.length) {
+      cmpts.push(cmpt);
+    }
+  });
+
+  return cmpts;
+}

package/lib/alg/dfs.js

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+var _ = require("../lodash");
+
+module.exports = dfs;
+
+/*
+ * A helper that preforms a pre- or post-order traversal on the input graph
+ * and returns the nodes in the order they were visited. If the graph is
+ * undirected then this algorithm will navigate using neighbors. If the graph
+ * is directed then this algorithm will navigate using successors.
+ *
+ * Order must be one of "pre" or "post".
+ */
+function dfs(g, vs, order) {
+  if (!_.isArray(vs)) {
+    vs = [vs];
+  }
+
+  var navigation = (g.isDirected() ? g.successors : g.neighbors).bind(g);
+
+  var acc = [];
+  var visited = {};
+  _.each(vs, function(v) {
+    if (!g.hasNode(v)) {
+      throw new Error("Graph does not have node: " + v);
+    }
+
+    doDfs(g, v, order === "post", visited, navigation, acc);
+  });
+  return acc;
+}
+
+function doDfs(g, v, postorder, visited, navigation, acc) {
+  if (!_.has(visited, v)) {
+    visited[v] = true;
+
+    if (!postorder) { acc.push(v); }
+    _.each(navigation(v), function(w) {
+      doDfs(g, w, postorder, visited, navigation, acc);
+    });
+    if (postorder) { acc.push(v); }
+  }
+}

package/lib/alg/dijkstra-all.js

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+var dijkstra = require("./dijkstra");
+var _ = require("../lodash");
+
+module.exports = dijkstraAll;
+
+function dijkstraAll(g, weightFunc, edgeFunc) {
+  return _.transform(g.nodes(), function(acc, v) {
+    acc[v] = dijkstra(g, v, weightFunc, edgeFunc);
+  }, {});
+}

package/lib/alg/dijkstra.js

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+var _ = require("../lodash");
+var PriorityQueue = require("../data/priority-queue");
+
+module.exports = dijkstra;
+
+var DEFAULT_WEIGHT_FUNC = _.constant(1);
+
+function dijkstra(g, source, weightFn, edgeFn) {
+  return runDijkstra(g, String(source),
+    weightFn || DEFAULT_WEIGHT_FUNC,
+    edgeFn || function(v) { return g.outEdges(v); });
+}
+
+function runDijkstra(g, source, weightFn, edgeFn) {
+  var results = {};
+  var pq = new PriorityQueue();
+  var v, vEntry;
+
+  var updateNeighbors = function(edge) {
+    var w = edge.v !== v ? edge.v : edge.w;
+    var wEntry = results[w];
+    var weight = weightFn(edge);
+    var distance = vEntry.distance + weight;
+
+    if (weight < 0) {
+      throw new Error("dijkstra does not allow negative edge weights. " +
+                      "Bad edge: " + edge + " Weight: " + weight);
+    }
+
+    if (distance < wEntry.distance) {
+      wEntry.distance = distance;
+      wEntry.predecessor = v;
+      pq.decrease(w, distance);
+    }
+  };
+
+  g.nodes().forEach(function(v) {
+    var distance = v === source ? 0 : Number.POSITIVE_INFINITY;
+    results[v] = { distance: distance };
+    pq.add(v, distance);
+  });
+
+  while (pq.size() > 0) {
+    v = pq.removeMin();
+    vEntry = results[v];
+    if (vEntry.distance === Number.POSITIVE_INFINITY) {
+      break;
+    }
+
+    edgeFn(v).forEach(updateNeighbors);
+  }
+
+  return results;
+}

package/lib/alg/find-cycles.js

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+var _ = require("../lodash");
+var tarjan = require("./tarjan");
+
+module.exports = findCycles;
+
+function findCycles(g) {
+  return _.filter(tarjan(g), function(cmpt) {
+    return cmpt.length > 1 || (cmpt.length === 1 && g.hasEdge(cmpt[0], cmpt[0]));
+  });
+}

package/lib/alg/floyd-warshall.js

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+var _ = require("../lodash");
+
+module.exports = floydWarshall;
+
+var DEFAULT_WEIGHT_FUNC = _.constant(1);
+
+function floydWarshall(g, weightFn, edgeFn) {
+  return runFloydWarshall(g,
+    weightFn || DEFAULT_WEIGHT_FUNC,
+    edgeFn || function(v) { return g.outEdges(v); });
+}
+
+function runFloydWarshall(g, weightFn, edgeFn) {
+  var results = {};
+  var nodes = g.nodes();
+
+  nodes.forEach(function(v) {
+    results[v] = {};
+    results[v][v] = { distance: 0 };
+    nodes.forEach(function(w) {
+      if (v !== w) {
+        results[v][w] = { distance: Number.POSITIVE_INFINITY };
+      }
+    });
+    edgeFn(v).forEach(function(edge) {
+      var w = edge.v === v ? edge.w : edge.v;
+      var d = weightFn(edge);
+      results[v][w] = { distance: d, predecessor: v };
+    });
+  });
+
+  nodes.forEach(function(k) {
+    var rowK = results[k];
+    nodes.forEach(function(i) {
+      var rowI = results[i];
+      nodes.forEach(function(j) {
+        var ik = rowI[k];
+        var kj = rowK[j];
+        var ij = rowI[j];
+        var altDistance = ik.distance + kj.distance;
+        if (altDistance < ij.distance) {
+          ij.distance = altDistance;
+          ij.predecessor = kj.predecessor;
+        }
+      });
+    });
+  });
+
+  return results;
+}

package/lib/alg/index.js

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+module.exports = {
+  components: require("./components"),
+  dijkstra: require("./dijkstra"),
+  dijkstraAll: require("./dijkstra-all"),
+  findCycles: require("./find-cycles"),
+  floydWarshall: require("./floyd-warshall"),
+  isAcyclic: require("./is-acyclic"),
+  postorder: require("./postorder"),
+  preorder: require("./preorder"),
+  prim: require("./prim"),
+  tarjan: require("./tarjan"),
+  topsort: require("./topsort")
+};

package/lib/alg/is-acyclic.js

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+var topsort = require("./topsort");
+
+module.exports = isAcyclic;
+
+function isAcyclic(g) {
+  try {
+    topsort(g);
+  } catch (e) {
+    if (e instanceof topsort.CycleException) {
+      return false;
+    }
+    throw e;
+  }
+  return true;
+}

package/lib/alg/postorder.js

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+var dfs = require("./dfs");
+
+module.exports = postorder;
+
+function postorder(g, vs) {
+  return dfs(g, vs, "post");
+}

package/lib/alg/preorder.js

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+var dfs = require("./dfs");
+
+module.exports = preorder;
+
+function preorder(g, vs) {
+  return dfs(g, vs, "pre");
+}

package/lib/alg/prim.js

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+var _ = require("../lodash");
+var Graph = require("../graph");
+var PriorityQueue = require("../data/priority-queue");
+
+module.exports = prim;
+
+function prim(g, weightFunc) {
+  var result = new Graph();
+  var parents = {};
+  var pq = new PriorityQueue();
+  var v;
+
+  function updateNeighbors(edge) {
+    var w = edge.v === v ? edge.w : edge.v;
+    var pri = pq.priority(w);
+    if (pri !== undefined) {
+      var edgeWeight = weightFunc(edge);
+      if (edgeWeight < pri) {
+        parents[w] = v;
+        pq.decrease(w, edgeWeight);
+      }
+    }
+  }
+
+  if (g.nodeCount() === 0) {
+    return result;
+  }
+
+  _.each(g.nodes(), function(v) {
+    pq.add(v, Number.POSITIVE_INFINITY);
+    result.setNode(v);
+  });
+
+  // Start from an arbitrary node
+  pq.decrease(g.nodes()[0], 0);
+
+  var init = false;
+  while (pq.size() > 0) {
+    v = pq.removeMin();
+    if (_.has(parents, v)) {
+      result.setEdge(v, parents[v]);
+    } else if (init) {
+      throw new Error("Input graph is not connected: " + g);
+    } else {
+      init = true;
+    }
+
+    g.nodeEdges(v).forEach(updateNeighbors);
+  }
+
+  return result;
+}

package/lib/alg/tarjan.js

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+var _ = require("../lodash");
+
+module.exports = tarjan;
+
+function tarjan(g) {
+  var index = 0;
+  var stack = [];
+  var visited = {}; // node id -> { onStack, lowlink, index }
+  var results = [];
+
+  function dfs(v) {
+    var entry = visited[v] = {
+      onStack: true,
+      lowlink: index,
+      index: index++
+    };
+    stack.push(v);
+
+    g.successors(v).forEach(function(w) {
+      if (!_.has(visited, w)) {
+        dfs(w);
+        entry.lowlink = Math.min(entry.lowlink, visited[w].lowlink);
+      } else if (visited[w].onStack) {
+        entry.lowlink = Math.min(entry.lowlink, visited[w].index);
+      }
+    });
+
+    if (entry.lowlink === entry.index) {
+      var cmpt = [];
+      var w;
+      do {
+        w = stack.pop();
+        visited[w].onStack = false;
+        cmpt.push(w);
+      } while (v !== w);
+      results.push(cmpt);
+    }
+  }
+
+  g.nodes().forEach(function(v) {
+    if (!_.has(visited, v)) {
+      dfs(v);
+    }
+  });
+
+  return results;
+}

package/lib/alg/topsort.js

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+var _ = require("../lodash");
+
+module.exports = topsort;
+topsort.CycleException = CycleException;
+
+function topsort(g) {
+  var visited = {};
+  var stack = {};
+  var results = [];
+
+  function visit(node) {
+    if (_.has(stack, node)) {
+      throw new CycleException();
+    }
+
+    if (!_.has(visited, node)) {
+      stack[node] = true;
+      visited[node] = true;
+      _.each(g.predecessors(node), visit);
+      delete stack[node];
+      results.push(node);
+    }
+  }
+
+  _.each(g.sinks(), visit);
+
+  if (_.size(visited) !== g.nodeCount()) {
+    throw new CycleException();
+  }
+
+  return results;
+}
+
+function CycleException() {}
+CycleException.prototype = new Error(); // must be an instance of Error to pass testing

package/lib/data/priority-queue.js

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+var _ = require("../lodash");
+
+module.exports = PriorityQueue;
+
+/**
+ * A min-priority queue data structure. This algorithm is derived from Cormen,
+ * et al., "Introduction to Algorithms". The basic idea of a min-priority
+ * queue is that you can efficiently (in O(1) time) get the smallest key in
+ * the queue. Adding and removing elements takes O(log n) time. A key can
+ * have its priority decreased in O(log n) time.
+ */
+function PriorityQueue() {
+  this._arr = [];
+  this._keyIndices = {};
+}
+
+/**
+ * Returns the number of elements in the queue. Takes `O(1)` time.
+ */
+PriorityQueue.prototype.size = function() {
+  return this._arr.length;
+};
+
+/**
+ * Returns the keys that are in the queue. Takes `O(n)` time.
+ */
+PriorityQueue.prototype.keys = function() {
+  return this._arr.map(function(x) { return x.key; });
+};
+
+/**
+ * Returns `true` if **key** is in the queue and `false` if not.
+ */
+PriorityQueue.prototype.has = function(key) {
+  return _.has(this._keyIndices, key);
+};
+
+/**
+ * Returns the priority for **key**. If **key** is not present in the queue
+ * then this function returns `undefined`. Takes `O(1)` time.
+ *
+ * @param {Object} key
+ */
+PriorityQueue.prototype.priority = function(key) {
+  var index = this._keyIndices[key];
+  if (index !== undefined) {
+    return this._arr[index].priority;
+  }
+};
+
+/**
+ * Returns the key for the minimum element in this queue. If the queue is
+ * empty this function throws an Error. Takes `O(1)` time.
+ */
+PriorityQueue.prototype.min = function() {
+  if (this.size() === 0) {
+    throw new Error("Queue underflow");
+  }
+  return this._arr[0].key;
+};
+
+/**
+ * Inserts a new key into the priority queue. If the key already exists in
+ * the queue this function returns `false`; otherwise it will return `true`.
+ * Takes `O(n)` time.
+ *
+ * @param {Object} key the key to add
+ * @param {Number} priority the initial priority for the key
+ */
+PriorityQueue.prototype.add = function(key, priority) {
+  var keyIndices = this._keyIndices;
+  key = String(key);
+  if (!_.has(keyIndices, key)) {
+    var arr = this._arr;
+    var index = arr.length;
+    keyIndices[key] = index;
+    arr.push({key: key, priority: priority});
+    this._decrease(index);
+    return true;
+  }
+  return false;
+};
+
+/**
+ * Removes and returns the smallest key in the queue. Takes `O(log n)` time.
+ */
+PriorityQueue.prototype.removeMin = function() {
+  this._swap(0, this._arr.length - 1);
+  var min = this._arr.pop();
+  delete this._keyIndices[min.key];
+  this._heapify(0);
+  return min.key;
+};
+
+/**
+ * Decreases the priority for **key** to **priority**. If the new priority is
+ * greater than the previous priority, this function will throw an Error.
+ *
+ * @param {Object} key the key for which to raise priority
+ * @param {Number} priority the new priority for the key
+ */
+PriorityQueue.prototype.decrease = function(key, priority) {
+  var index = this._keyIndices[key];
+  if (priority > this._arr[index].priority) {
+    throw new Error("New priority is greater than current priority. " +
+        "Key: " + key + " Old: " + this._arr[index].priority + " New: " + priority);
+  }
+  this._arr[index].priority = priority;
+  this._decrease(index);
+};
+
+PriorityQueue.prototype._heapify = function(i) {
+  var arr = this._arr;
+  var l = 2 * i;
+  var r = l + 1;
+  var largest = i;
+  if (l < arr.length) {
+    largest = arr[l].priority < arr[largest].priority ? l : largest;
+    if (r < arr.length) {
+      largest = arr[r].priority < arr[largest].priority ? r : largest;
+    }
+    if (largest !== i) {
+      this._swap(i, largest);
+      this._heapify(largest);
+    }
+  }
+};
+
+PriorityQueue.prototype._decrease = function(index) {
+  var arr = this._arr;
+  var priority = arr[index].priority;
+  var parent;
+  while (index !== 0) {
+    parent = index >> 1;
+    if (arr[parent].priority < priority) {
+      break;
+    }
+    this._swap(index, parent);
+    index = parent;
+  }
+};
+
+PriorityQueue.prototype._swap = function(i, j) {
+  var arr = this._arr;
+  var keyIndices = this._keyIndices;
+  var origArrI = arr[i];
+  var origArrJ = arr[j];
+  arr[i] = origArrJ;
+  arr[j] = origArrI;
+  keyIndices[origArrJ.key] = i;
+  keyIndices[origArrI.key] = j;
+};