/**
*
* @return Edges
*/
public function getEdges()
{
$returnEdges = array();
// Create minimum spanning tree
$minimumSpanningTreeAlgorithm = new MstKruskal($this->graph);
$minimumSpanningTree = $minimumSpanningTreeAlgorithm->createGraph();
$alg = new SearchDepthFirst($minimumSpanningTree->getVertices()->getVertexFirst());
// Depth first search in minmum spanning tree (for the eulerian path)
$startVertex = NULL;
$oldVertex = NULL;
// connect vertices in order of the depth first search
foreach ($alg->getVertices() as $vertex) {
// get vertex from the original graph (not from the depth first search)
$vertex = $this->graph->getVertex($vertex->getId());
// need to clone the edge from the original graph, therefore i need the original edge
if ($startVertex === NULL) {
$startVertex = $vertex;
} else {
// get edge(s) to clone, multiple edges are possible (returns an array if undirected edge)
$returnEdges[] = $oldVertex->getEdgesTo($vertex)->getEdgeFirst();
}
$oldVertex = $vertex;
}
// connect last vertex with start vertex
// multiple edges are possible (returns an array if undirected edge)
$returnEdges[] = $oldVertex->getEdgesTo($startVertex)->getEdgeFirst();
return new Edges($returnEdges);
}
/**
* Filters the graph so that only entities connected to the root are left
*
* Should be run after you've added some set of associations with from()
*
* @return void
*/
public function filterConnected()
{
$alg = new BreadthFirst($this->graph->getVertex($this->root));
$alg->setDirection(BreadthFirst::DIRECTION_REVERSE);
$vertices = $alg->getVertices();
$this->graph = $this->graph->createGraphCloneVertices($vertices);
}
public function createGraph()
{
$graph = new Graph();
$file = $this->getLines();
$vertexCount = $this->readInt($file[0]);
$edgeCounter = 0;
if (count($file) !== $vertexCount + 1) {
throw new UnexpectedValueException('Expects ' . ($vertexCount + 1) . ' lines, but found ' . count($file));
}
$graph->createVertices($vertexCount);
$parts = array_fill(0, $vertexCount, 'int');
for ($i = 0; $i < $vertexCount; $i++) {
// Add Vertices
$this->writeDebugMessage("Adding vertex {$i}, ");
$thisVertex = $graph->getVertex($i);
$currentEdgeList = $this->readLine($file[$i + 1], $parts);
// $currentEdgeList = explode("\t", $file[$i + 1]);
for ($k = 0; $k < $vertexCount; $k++) {
// Add edges
if ($currentEdgeList[$k] != 0) {
$this->writeDebugMessage(" and edge #{$edgeCounter}: {$i} -> {$k} ");
if ($this->directedEdges) {
$thisVertex->createEdgeTo($graph->getVertex($k));
} else {
$thisVertex->createEdge($graph->getVertex($k));
}
$edgeCounter++;
}
}
$this->writeDebugMessage("\n");
}
return $graph;
}
public function createGraph()
{
$graph = new Graph();
$file = $this->getLines();
$countOfAllVertices = $this->readInt($file[0]);
$countOfVerticesInA = $this->readInt($file[1]);
if ($countOfVerticesInA > $countOfAllVertices || $countOfVerticesInA < 0) {
throw new UnexpectedValueException('Invalid value for number of vertices in group 0');
}
$graph->createVertices($countOfAllVertices);
for ($i = 0; $i < $countOfVerticesInA; ++$i) {
$graph->getVertex($i)->setGroup(0);
}
for ($k = $countOfVerticesInA; $k < $countOfAllVertices; ++$k) {
$graph->getVertex($k)->setGroup(1);
}
unset($file[0]);
unset($file[1]);
foreach ($file as $zeile) {
$parts = $this->readLine($zeile, array('vertex', 'vertex'), $graph);
if ($this->directedEdges) {
$edge = $parts[0]->createEdgeTo($parts[1]);
} else {
$edge = $parts[0]->createEdge($parts[1]);
}
}
$alg = new AlgorithmGroups($graph);
if (!$alg->isBipartit()) {
throw new UnexpectedValueException('Graph read from file does not form a valid bipartit graph');
}
return $graph;
}
/**
* Create edges between versions graph
*
* @param Graph $graph
* @param string $className
*/
private function createEdges(Graph $graph, $className)
{
$migrationsAnnotations = $this->reader->getClassMigrationMethodInfo($className);
$parentVertex = $graph->hasVertex($className) ? $graph->getVertex($className) : $graph->createVertex($className);
foreach ($migrationsAnnotations as $migrationsAnnotation) {
if ($migrationsAnnotation->annotation->from) {
$fromClass = $migrationsAnnotation->annotation->from;
$fromVertex = $graph->hasVertex($fromClass) ? $graph->getVertex($fromClass) : $graph->createVertex($fromClass);
if (!$parentVertex->hasEdgeTo($fromVertex)) {
$edge = $fromVertex->createEdgeTo($parentVertex);
$this->annotations[$this->getEdgeId($edge)] = $migrationsAnnotation;
$this->createEdges($graph, $fromClass);
}
}
if ($migrationsAnnotation->annotation->to) {
$toClass = $migrationsAnnotation->annotation->to;
$fromVertex = $graph->hasVertex($toClass) ? $graph->getVertex($toClass) : $graph->createVertex($toClass);
if (!$parentVertex->hasEdgeTo($fromVertex)) {
$edge = $parentVertex->createEdgeTo($fromVertex);
$this->annotations[$this->getEdgeId($edge)] = $migrationsAnnotation;
$this->createEdges($graph, $toClass);
}
}
}
}
public function createGraph()
{
$start = microtime(true);
$graph = new Graph();
$n = $this->numberOfVertices;
$this->writeDebugMessage("start creating vertices\n");
$graph->createVertices($n);
$this->writeDebugMessage("start creating edges\n");
for ($i = 0; $i < $n; ++$i) {
$vertex = $graph->getVertex($i);
if ($this->directedEdges) {
for ($j = 0; $j < $n; ++$j) {
if ($j !== $i) {
$vertex->createEdgeTo($graph->getVertex($j));
}
}
} else {
for ($j = $i + 1; $j < $n; ++$j) {
$vertex->createEdge($graph->getVertex($j));
}
}
}
$end = microtime(true);
$this->writeDebugMessage($end - $start . " done ...\n");
return $graph;
}
public function setUp()
{
$graph = new Graph();
$graph->createVertex(1);
$graph->createVertex(2);
// 1 -> 2
$this->edge = $graph->getVertex(1)->createEdge($graph->getVertex(2));
}
protected function createGraphParallelEdge()
{
// v1 -> v2, v1 -> v2
$graph = new Graph();
$graph->createVertex('v1')->createEdgeTo($graph->createVertex('v2'));
$graph->getVertex('v1')->createEdgeTo($graph->getVertex('v2'));
return $graph;
}
/**
* @expectedException UnexpectedValueException
*/
public function testFailCycle()
{
$graph = new Graph();
$graph->createVertex(1)->createEdgeTo($graph->createVertex(2));
$graph->getVertex(2)->createEdgeTo($graph->getVertex(1));
$alg = new TopologicalSort($graph);
$alg->getVertices();
}
public function testGraphAntiparallelIsSymmetricr()
{
// 1 -> 2 -> 1
$graph = new Graph();
$graph->createVertex(1)->createEdgeTo($graph->createVertex(2));
$graph->getVertex(2)->createEdgeTo($graph->getVertex(1));
$alg = new AlgorithmSymmetric($graph);
$this->assertTrue($alg->isSymmetric());
}
/**
* test an edge with capacity remaining
*/
public function testEdgePartial()
{
$graph = new Graph();
$graph->createVertex(0)->createEdgeTo($graph->createVertex(1))->setFlow(1)->setCapacity(2)->setWeight(3);
$alg = new ResidualGraph($graph);
$residual = $alg->createGraph();
$expected = new Graph();
$expected->createVertex(0);
$expected->createVertex(1);
// remaining edge
$expected->getVertex(0)->createEdgeTo($expected->getVertex(1))->setFlow(0)->setCapacity(1)->setWeight(3);
// back edge
$expected->getVertex(1)->createEdgeTo($expected->getVertex(0))->setFlow(0)->setCapacity(1)->setWeight(-3);
$this->assertGraphEquals($expected, $residual);
}
public function testGraphEdgeDirections()
{
// 1 -- 2 -> 3 <- 4
$graph = new Graph();
$graph->createVertex(1)->createEdge($graph->createVertex(2));
$graph->getVertex(2)->createEdgeTo($graph->createVertex(3));
$graph->createVertex(4)->createEdgeTo($graph->getVertex(3));
$alg = new AlgorithmConnected($graph);
$this->assertEquals(1, $alg->getNumberOfComponents());
$this->assertTrue($alg->isSingle());
$graphs = $alg->createGraphsComponents();
$this->assertCount(1, $graphs);
$this->assertGraphEquals($graph, reset($graphs));
$this->assertGraphEquals($graph, $alg->createGraphComponentVertex($graph->getVertex(1)));
}
/**
* Build out-tree graph from defined Processes and their relations.
*
* @return OutTree
*/
public function buildTree()
{
if (!$this->tree) {
$root = $this->graph->createVertex(0);
// Create edges directed from the root node
foreach ($this->processes as $processClassName => $processObject) {
$vertex = $this->graph->getVertex($processClassName);
if (!$processObject->delayMinutes) {
// process doesn't depend on anything => link it to the root node
$root->createEdgeTo($vertex)->setWeight(0);
} else {
// link process to its dependency
// Throw error if dependency is to not existing vertex
if (!$this->graph->hasVertex($processObject->delayAfter)) {
throw new \InvalidArgumentException(sprintf('Testcase "%s" has @delayAfter dependency on "%s", but this testcase was not defined.', $processClassName, $processObject->delayAfter));
}
$this->graph->getVertex($processObject->delayAfter)->createEdgeTo($vertex)->setWeight($processObject->delayMinutes);
}
}
}
$this->tree = new OutTree($this->graph);
if (!$this->tree->isTree()) {
throw new \InvalidArgumentException(sprintf('Cannot build tree graph from tests dependencies. Probably some cyclic dependency is present.'));
}
return $this->tree;
}
/**
*
* @param string $dir
* @return \Fhaculty\Graph\Graph
*/
public function createGraph()
{
$graph = new Graph();
foreach ($this->dependencyGraph->getPackages() as $package) {
$name = $package->getName();
$start = $graph->createVertex($name, true);
$label = $name;
if ($package->getVersion() !== null) {
$label .= ': ' . $package->getVersion();
}
$this->setLayout($start, array('label' => $label) + $this->layoutVertex);
foreach ($package->getOutEdges() as $requires) {
$targetName = $requires->getDestPackage()->getName();
$target = $graph->createVertex($targetName, true);
$label = $requires->getVersionConstraint();
$edge = $start->createEdgeTo($target);
$this->setLayout($edge, array('label' => $label) + $this->layoutEdge);
if ($requires->isDevDependency()) {
$this->setLayout($edge, $this->layoutEdgeDev);
}
}
}
$root = $graph->getVertex($this->dependencyGraph->getRootPackage()->getName());
$this->setLayout($root, $this->layoutVertexRoot);
return $graph;
}
/**
* @expectedException UnexpectedValueException
*/
public function testVertexWithUndirectedEdgeHasInvalidFlow()
{
// 1 -- 2
$graph = new Graph();
$graph->createVertex(1)->createEdge($graph->createVertex(2))->setFlow(10);
$alg = new AlgorithmFlow($graph);
$alg->getFlowVertex($graph->getVertex(1));
}
public function testGraphDirectedLoop()
{
// 1 -> 1
$graph = new Graph();
$graph->createVertex(1)->createEdgeTo($v1 = $graph->getVertex(1));
$alg = new AlgorithmLoop($graph);
$this->assertTrue($alg->hasLoop());
$this->assertTrue($alg->hasLoopVertex($v1));
}
/**
* create subgraph for all classes connected to given class (i.e. return it's connected component)
*
* @param string $class
* @return Graph
* @throws Exception
*/
public function createGraphComponent($class)
{
try {
$vertex = $this->graph->getVertex($class);
} catch (Exception $e) {
throw new Exception('Given class is unknown');
}
$alg = new AlgorithmConnectedComponents($this->graph);
return $alg->createGraphComponentVertex($vertex);
}
public function testGraphMixed()
{
// 1 -- 2 -> 3
$graph = new Graph();
$graph->createVertex(1)->createEdge($graph->createVertex(2));
$graph->getVertex(2)->createEdgeTo($graph->createVertex(3));
$alg = new AlgorithmDirected($graph);
$this->assertTrue($alg->hasDirected());
$this->assertTrue($alg->hasUndirected());
$this->assertTrue($alg->isMixed());
}
public function testAdditionalEdgesToNotAffectCompleteness()
{
// 1 -> 2
// 1 -- 2
// 2 -> 1
// 1 -> 1
$graph = new Graph();
$graph->createVertex(1)->createEdgeTo($graph->createVertex(2));
$graph->getVertex(1)->createEdge($graph->getVertex(2));
$graph->getVertex(2)->createEdgeTo($graph->getVertex(1));
$graph->getVertex(1)->createEdgeTo($graph->getVertex(1));
$alg = new AlgorithmComplete($graph);
$this->assertTrue($alg->isComplete());
}
/**
* read given line string into given array of parts (int, float, vertex)
*
* @param string $line
* @param array $parts
* @param Graph $graph
* @return mixed[]
* @throws InvalidArgumentException
*/
protected function readLine($line, $parts, Graph $graph = NULL)
{
$ret = array();
$explode = explode("\t", $line);
$i = 0;
foreach ($parts as $key => $part) {
if (!isset($explode[$i])) {
throw new InvalidArgumentException('Line does not split into enough parts');
}
$value = $explode[$i++];
if ($part === 'int') {
$value = $this->readInt($value);
} elseif ($part === 'float') {
$value = $this->readFloat($value);
} elseif ($part === 'vertex') {
$value = $graph->getVertex($value);
} else {
throw new InvalidArgumentException('Invalid type "' . $part . '"');
}
$ret[$key] = $value;
}
return $ret;
}
public function testGraphWithMixedEdgesIsNotTree()
{
// v1 -> v2 -- v3 -> v4
$graph = new Graph();
$graph->createVertex('v1')->createEdgeTo($graph->createVertex('v2'));
$graph->getVertex('v2')->createEdge($graph->createVertex('v3'));
$graph->getVertex('v3')->createEdgeTo($graph->createVertex('v4'));
$tree = $this->createTreeAlg($graph);
$this->assertFalse($tree->isTree());
}
/**
* @param Graph $graph
* @expectedException InvalidArgumentException
* @depends testRemoveEdge
*/
public function testRemoveEdgeInvalid(Graph $graph)
{
$edge = $graph->getVertex(1)->createEdge($graph->getVertex(2));
$edge->destroy();
$edge->destroy();
}
public function testGraphUndirectedWithIsolatedVerticesFirst()
{
// a -- b -- c d
$graph = new Graph();
$graph->createVertices(array('a', 'b', 'c', 'd'));
$graph->getVertex('a')->createEdge($graph->getVertex('b'));
$graph->getVertex('b')->createEdge($graph->getVertex('c'));
$expected = <<<VIZ
graph G {
"d"
"a" -- "b"
"b" -- "c"
}
VIZ;
$this->assertEquals($expected, $this->graphViz->createScript($graph));
}
public function testGraphMixedIsNotTree()
{
// v1 -- v2 -> v3
$graph = new Graph();
$graph->createVertex('v1')->createEdge($graph->createVertex('v2'));
$graph->getVertex('v2')->createEdgeTo($graph->createVertex('v3'));
$tree = $this->createTree($graph);
$this->assertFalse($tree->isTree());
}
}
$parents = str_replace($id, '', $parents);
$parents = explode(',', $parents);
$parents = array_filter($parents);
if ($sequence->hasGraph()) {
$graph = $sequence->getUnSerializeGraph();
} else {
$graph = new Graph();
}
switch ($type) {
case 'session':
$type = SequenceResource::SESSION_TYPE;
$sessionInfo = api_get_session_info($id);
$name = $sessionInfo['name'];
if ($graph->hasVertex($id)) {
$main = $graph->getVertex($id);
} else {
$main = $graph->createVertex($id);
}
foreach ($parents as $parentId) {
if ($graph->hasVertex($parentId)) {
$parent = $graph->getVertex($parentId);
if (!$parent->hasEdgeTo($main)) {
$parent->createEdgeTo($main);
}
} else {
$parent = $graph->createVertex($parentId);
$parent->createEdgeTo($main);
}
}
foreach ($parents as $parentId) {
