/**
* @param graph the graph to be ordered
* @param orderByDegree should the vertices be ordered by their degree. This speeds up the VF2
* algorithm.
* @param cacheEdges if true, the class creates a adjacency matrix and two arrays for incoming and
* outgoing edges for fast access.
*/
public GraphOrdering(Graph<V, E> graph, boolean orderByDegree, boolean cacheEdges) {
this.graph = graph;
this.cacheEdges = cacheEdges;
List<V> vertexSet = new ArrayList<>(graph.vertexSet());
if (orderByDegree) {
java.util.Collections.sort(vertexSet, new GeneralVertexDegreeComparator<>(graph));
}
vertexCount = vertexSet.size();
mapVertexToOrder = new HashMap<>();
mapOrderToVertex = new ArrayList<>(vertexCount);
if (cacheEdges) {
outgoingEdges = new int[vertexCount][];
incomingEdges = new int[vertexCount][];
adjMatrix = new Boolean[vertexCount][vertexCount];
}
Integer i = 0;
for (V vertex : vertexSet) {
mapVertexToOrder.put(vertex, i++);
mapOrderToVertex.add(vertex);
}
}
/** {@inheritDoc} */
protected void encounterVertexAgain(V vertex, E edge) {
super.encounterVertexAgain(vertex, edge);
int i;
if (root != null) {
// For rooted detection, the path must either
// double back to the root, or to a node of a cycle
// which has already been detected.
if (vertex.equals(root)) {
i = 0;
} else if ((cycleSet != null) && cycleSet.contains(vertex)) {
i = 0;
} else {
return;
}
} else {
i = path.indexOf(vertex);
}
if (i > -1) {
if (cycleSet == null) {
// we're doing yes/no cycle detection
throw new CycleDetectedException();
} else {
for (; i < path.size(); ++i) {
cycleSet.add(path.get(i));
}
}
}
}
/** Calculate the shortest paths (not done per default) */
private void lazyCalculatePaths() {
// already we have calculated it once.
if (paths != null) {
return;
}
lazyCalculateMatrix();
Map<VertexPair<V>, GraphPath<V, E>> sps = new HashMap<VertexPair<V>, GraphPath<V, E>>();
int n = vertices.size();
nShortestPaths = 0;
for (int i = 0; i < n; i++) {
V v_i = vertices.get(i);
for (int j = 0; j < n; j++) {
// don't count this.
if (i == j) {
continue;
}
V v_j = vertices.get(j);
GraphPath<V, E> path = getShortestPathImpl(v_i, v_j);
// we got a path
if (path != null) {
sps.put(new VertexPair<V>(v_i, v_j), path);
nShortestPaths++;
}
}
}
this.paths = sps;
}
/** Calculates the matrix of all shortest paths, but does not populate the paths map. */
private void lazyCalculateMatrix() {
if (d != null) {
// already done
return;
}
int n = vertices.size();
// init the backtrace matrix
backtrace = new int[n][n];
for (int i = 0; i < n; i++) {
Arrays.fill(backtrace[i], -1);
}
// initialize matrix, 0
d = new double[n][n];
for (int i = 0; i < n; i++) {
Arrays.fill(d[i], Double.POSITIVE_INFINITY);
}
// initialize matrix, 1
for (int i = 0; i < n; i++) {
d[i][i] = 0.0;
}
// initialize matrix, 2
Set<E> edges = graph.edgeSet();
for (E edge : edges) {
V v1 = graph.getEdgeSource(edge);
V v2 = graph.getEdgeTarget(edge);
int v_1 = vertices.indexOf(v1);
int v_2 = vertices.indexOf(v2);
d[v_1][v_2] = graph.getEdgeWeight(edge);
if (!(graph instanceof DirectedGraph<?, ?>)) {
d[v_2][v_1] = graph.getEdgeWeight(edge);
}
}
// run fw alg
for (int k = 0; k < n; k++) {
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
double ik_kj = d[i][k] + d[k][j];
if (ik_kj < d[i][j]) {
d[i][j] = ik_kj;
backtrace[i][j] = k;
}
}
}
}
}
private void shortestPathRecur(List<E> edges, int v_a, int v_b) {
int k = backtrace[v_a][v_b];
if (k == -1) {
E edge = graph.getEdge(vertices.get(v_a), vertices.get(v_b));
if (edge != null) {
edges.add(edge);
}
} else {
shortestPathRecur(edges, v_a, k);
shortestPathRecur(edges, k, v_b);
}
}
/** {@inheritDoc} */
protected V provideNextVertex() {
V v = super.provideNextVertex();
// backtrack
for (int i = path.size() - 1; i >= 0; --i) {
if (graph.containsEdge(path.get(i), v)) {
break;
}
path.remove(i);
}
path.add(v);
return v;
}
/**
* This method will return a list of vertices which represents the Eulerian circuit of the graph.
*
* @param g The graph to find an Eulerian circuit
* @return null if no Eulerian circuit exists, or a list of vertices representing the Eulerian
* circuit if one does exist
*/
public static <V, E> List<V> getEulerianCircuitVertices(UndirectedGraph<V, E> g) {
// If the graph is not Eulerian then just return a null since no
// Eulerian circuit exists
if (!isEulerian(g)) {
return null;
}
// The circuit will be represented by a linked list
List<V> path = new LinkedList<V>();
UndirectedGraph<V, E> sg = new UndirectedSubgraph<V, E>(g, null, null);
path.add(sg.vertexSet().iterator().next());
// Algorithm for finding an Eulerian circuit Basically this will find an
// arbitrary circuit, then it will find another arbitrary circuit until
// every edge has been traversed
while (sg.edgeSet().size() > 0) {
V v = null;
// Find a vertex which has an edge that hasn't been traversed yet,
// and keep its index position in the circuit list
int index = 0;
for (Iterator<V> iter = path.iterator(); iter.hasNext(); index++) {
v = iter.next();
if (sg.degreeOf(v) > 0) {
break;
}
}
// Finds an arbitrary circuit of the current vertex and
// appends this into the circuit list
while (sg.degreeOf(v) > 0) {
for (Iterator<V> iter = sg.vertexSet().iterator(); iter.hasNext(); ) {
V temp = iter.next();
if (sg.containsEdge(v, temp)) {
path.add(index, temp);
sg.removeEdge(v, temp);
v = temp;
break;
}
}
}
}
return path;
}
/**
* Compute the unique decomposition of the input graph G (atoms of G). Implementation of algorithm
* Atoms as described in Berry et al. (2010), DOI:10.3390/a3020197, <a
* href="http://www.mdpi.com/1999-4893/3/2/197">http://www.mdpi.com/1999-4893/3/2/197</a>
*/
private void computeAtoms() {
if (chordalGraph == null) {
computeMinimalTriangulation();
}
separators = new HashSet<>();
// initialize g' as subgraph of graph (same vertices and edges)
UndirectedGraph<V, E> gprime = copyAsSimpleGraph(graph);
// initialize h' as subgraph of chordalGraph (same vertices and edges)
UndirectedGraph<V, E> hprime = copyAsSimpleGraph(chordalGraph);
atoms = new HashSet<>();
Iterator<V> iterator = meo.descendingIterator();
while (iterator.hasNext()) {
V v = iterator.next();
if (generators.contains(v)) {
Set<V> separator = new HashSet<>(Graphs.neighborListOf(hprime, v));
if (isClique(graph, separator)) {
if (separator.size() > 0) {
if (separators.contains(separator)) {
fullComponentCount.put(separator, fullComponentCount.get(separator) + 1);
} else {
fullComponentCount.put(separator, 2);
separators.add(separator);
}
}
UndirectedGraph<V, E> tmpGraph = copyAsSimpleGraph(gprime);
tmpGraph.removeAllVertices(separator);
ConnectivityInspector<V, E> con = new ConnectivityInspector<>(tmpGraph);
if (con.isGraphConnected()) {
throw new RuntimeException("separator did not separate the graph");
}
for (Set<V> component : con.connectedSets()) {
if (component.contains(v)) {
gprime.removeAllVertices(component);
component.addAll(separator);
atoms.add(new HashSet<>(component));
assert (component.size() > 0);
break;
}
}
}
}
hprime.removeVertex(v);
}
if (gprime.vertexSet().size() > 0) {
atoms.add(new HashSet<>(gprime.vertexSet()));
}
}
private GraphPath<V, E> getShortestPathImpl(V a, V b) {
int v_a = vertices.indexOf(a);
int v_b = vertices.indexOf(b);
List<E> edges = new ArrayList<E>();
shortestPathRecur(edges, v_a, v_b);
// no path, return null
if (edges.size() < 1) {
return null;
}
double weight = 0.;
for (E e : edges) {
weight += graph.getEdgeWeight(e);
}
GraphPathImpl<V, E> path = new GraphPathImpl<V, E>(graph, a, b, edges, weight);
return path;
}
public Set<JavaClass> findClasses(Collection<File> changedFiles) {
// First update class index
List<String> changedClassesNames = new ArrayList<String>();
for (File changedFile : changedFiles) {
String changedClassname = builder.classFileChanged(changedFile);
if (changedClassname != null) {
changedClassesNames.add(changedClassname);
}
}
// Then find dependencies
Set<JavaClass> changedClasses = newHashSet();
for (String changedClassesName : changedClassesNames) {
JavaClass javaClass = builder.getClass(changedClassesName);
if (javaClass != null) {
addToIndex(javaClass);
changedClasses.add(javaClass);
}
}
builder.clear();
return changedClasses;
}
/**
* @return the diameter (longest of all the shortest paths) computed for the graph. If the graph
* is vertexless, return 0.0.
*/
public double getDiameter() {
lazyCalculateMatrix();
if (Double.isNaN(diameter)) {
diameter = 0.0;
int n = vertices.size();
for (int i = 0; i < n; i++) {
for (int j = 0; j < n; j++) {
if (!Double.isInfinite(d[i][j]) && d[i][j] > diameter) {
diameter = d[i][j];
}
}
}
}
return diameter;
}
public void testNonSimplePath() {
List<Integer> vertexList = Arrays.asList(0, 1, 2, 3, 2, 3, 4);
List<DefaultEdge> edgeList = new ArrayList<>();
for (int i = 0; i < vertexList.size() - 1; i++)
edgeList.add(completeGraph.getEdge(vertexList.get(i), vertexList.get(i + 1)));
GraphPath<Integer, DefaultEdge> p1 = new GraphWalk<>(completeGraph, 0, 4, edgeList, 10);
assertEquals(0, p1.getStartVertex().intValue());
assertEquals(4, p1.getEndVertex().intValue());
assertEquals(vertexList, p1.getVertexList());
assertEquals(edgeList.size(), p1.getLength());
assertEquals(10.0, p1.getWeight());
GraphPath<Integer, DefaultEdge> p2 = new GraphWalk<>(completeGraph, vertexList, 10);
assertEquals(0, p2.getStartVertex().intValue());
assertEquals(4, p2.getEndVertex().intValue());
assertEquals(edgeList, p2.getEdgeList());
assertEquals(edgeList.size(), p2.getLength());
assertEquals(10.0, p2.getWeight());
}
/**
* Get the length of a shortest path.
*
* @param a first vertex
* @param b second vertex
* @return shortest distance between a and b
*/
public double shortestDistance(V a, V b) {
lazyCalculateMatrix();
return d[vertices.indexOf(a)][vertices.indexOf(b)];
}
/**
* Compute the minimal triangulation of the graph. Implementation of Algorithm MCS-M+ as described
* in Berry et al. (2010), DOI:10.3390/a3020197 <a href="http://www.mdpi.com/1999-4893/3/2/197">
* http://www.mdpi.com/1999-4893/3/2/197</a>
*/
private void computeMinimalTriangulation() {
// initialize chordGraph with same vertices as graph
chordalGraph = new SimpleGraph<>(graph.getEdgeFactory());
for (V v : graph.vertexSet()) {
chordalGraph.addVertex(v);
}
// initialize g' as subgraph of graph (same vertices and edges)
final UndirectedGraph<V, E> gprime = copyAsSimpleGraph(graph);
int s = -1;
generators = new ArrayList<>();
meo = new LinkedList<>();
final Map<V, Integer> vertexLabels = new HashMap<>();
for (V v : gprime.vertexSet()) {
vertexLabels.put(v, 0);
}
for (int i = 1, n = graph.vertexSet().size(); i <= n; i++) {
V v = getMaxLabelVertex(vertexLabels);
LinkedList<V> Y = new LinkedList<>(Graphs.neighborListOf(gprime, v));
if (vertexLabels.get(v) <= s) {
generators.add(v);
}
s = vertexLabels.get(v);
// Mark x reached and all other vertices of gprime unreached
HashSet<V> reached = new HashSet<>();
reached.add(v);
// mark neighborhood of x reached and add to reach(label(y))
HashMap<Integer, HashSet<V>> reach = new HashMap<>();
// mark y reached and add y to reach
for (V y : Y) {
reached.add(y);
addToReach(vertexLabels.get(y), y, reach);
}
for (int j = 0; j < graph.vertexSet().size(); j++) {
if (!reach.containsKey(j)) {
continue;
}
while (reach.get(j).size() > 0) {
// remove a vertex y from reach(j)
V y = reach.get(j).iterator().next();
reach.get(j).remove(y);
for (V z : Graphs.neighborListOf(gprime, y)) {
if (!reached.contains(z)) {
reached.add(z);
if (vertexLabels.get(z) > j) {
Y.add(z);
E fillEdge = graph.getEdgeFactory().createEdge(v, z);
fillEdges.add(fillEdge);
addToReach(vertexLabels.get(z), z, reach);
} else {
addToReach(j, z, reach);
}
}
}
}
}
for (V y : Y) {
chordalGraph.addEdge(v, y);
vertexLabels.put(y, vertexLabels.get(y) + 1);
}
meo.addLast(v);
gprime.removeVertex(v);
vertexLabels.remove(v);
}
}
/**
* Reads the geometry and connectivity.
*
* @param filename the location of the gjf file
*/
public GJFfile(String filename) {
super(filename);
// read geometry
String name = "";
List<Atom> contents = new ArrayList<>();
SimpleWeightedGraph<Atom, DefaultWeightedEdge> connectivity =
new SimpleWeightedGraph<>(DefaultWeightedEdge.class);
int blanks = 0;
boolean lastBlank = false;
boolean inGeometryBlock = false;
for (List<String> line : fileContents) {
// keep track of how many blanks we have seen
if (line.size() == 1 && line.get(0).length() == 0) {
if (lastBlank == false) {
blanks++;
lastBlank = true;
}
continue;
} else lastBlank = false;
// read the metadata
if (blanks == 1) {
for (String s : line) {
String[] fields = s.split("@");
if (fields.length != 3) continue;
String identifier = fields[1].toLowerCase();
String value = fields[2];
// System.out.println(s);
// System.out.println(identifier + " : " + value);
if (identifier.equals("o1")) O1Number = Integer.parseInt(value);
else if (identifier.equals("o2")) O2Number = Integer.parseInt(value);
else if (identifier.equals("n3")) N3Number = Integer.parseInt(value);
else if (identifier.equals("cl1")) Cl1Number = Integer.parseInt(value);
else if (identifier.equals("su2")) Su2Number = Integer.parseInt(value);
else if (identifier.equals("ol3")) Ol3Number = Integer.parseInt(value);
else if (identifier.equals("mem")) mem = Integer.parseInt(value);
else if (identifier.equals("nprocshared")) nprocshared = Integer.parseInt(value);
else if (identifier.equals("method")) method = value;
else if (identifier.equals("basis")) basis = value;
else System.out.println("unrecognized entry: " + s);
}
continue;
} else if (blanks != 2) continue;
// deal with the charge and multiplicity card (by ignoring it)
if (line.size() == 2 && inGeometryBlock == false) {
inGeometryBlock = true;
continue;
}
if (line.size() != 4 && inGeometryBlock == false)
throw new IllegalArgumentException(
"unexpected text in geometry block in " + filename + ":\n" + line.toString());
// create atom
// tinker atom types will be nonsense, of course
Atom newAtom =
new Atom(
line.get(0),
new Vector3D(
Double.parseDouble(line.get(1)),
Double.parseDouble(line.get(2)),
Double.parseDouble(line.get(3))),
1);
contents.add(newAtom);
connectivity.addVertex(newAtom);
}
// read connectivity
blanks = 0;
lastBlank = false;
for (List<String> line : fileContents) {
// read the fourth block of text
if (line.size() == 1 && line.get(0).length() == 0) {
if (lastBlank == false) {
blanks++;
lastBlank = true;
}
continue;
} else lastBlank = false;
// only read connectivity lines
if (blanks != 3) continue;
Atom fromAtom = contents.get(Integer.parseInt(line.get(0)) - 1);
for (int i = 1; i < line.size(); i += 2) {
int toAtomIndex = Integer.parseInt(line.get(i)) - 1;
Atom toAtom = contents.get(toAtomIndex);
double bondOrder = Double.parseDouble(line.get(i + 1));
DefaultWeightedEdge thisEdge = connectivity.addEdge(fromAtom, toAtom);
connectivity.setEdgeWeight(thisEdge, bondOrder);
}
}
// create the molecule
molecule = new Molecule(name, contents, connectivity, 0.0);
}