protected void finalize() throws Throwable {
super.finalize();
nodes.clear();
nodes.getRecordManager().commit();
nodes.getRecordManager().close();
nodesReverse.clear();
nodesReverse.getRecordManager().commit();
nodesReverse.getRecordManager().close();
}
public Graph(WeightedBVGraph graph, String[] names) {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
if (names.length != graph.numNodes())
throw new Error("Problem with the list of names for the nodes in the graph.");
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
this.graph = graph;
WeightedArcSet list = new WeightedArcSet();
ArcLabelledNodeIterator it = graph.nodeIterator();
while (it.hasNext()) {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
Integer aux1 = it.nextInt();
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
list.add(arc);
this.nodes.put(aux1, names[aux1]);
this.nodes.put(aux2, names[aux2]);
this.nodesReverse.put(names[aux1], aux1);
this.nodesReverse.put(names[aux2], aux2);
} catch (Exception ex) {
throw new Error(ex);
}
}
reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
public void commit() {
try {
nodes.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
try {
nodesReverse.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
};
public void writeIdToVertexMap(String filePath) {
try {
BufferedWriter bw = new BufferedWriter(new FileWriter(new File(filePath)));
for (Entry<Integer, String> entry : nodes.entrySet()) {
bw.write(entry.getKey() + " " + entry.getValue() + "\n");
}
bw.close();
} catch (Exception ex) {
ex.printStackTrace();
System.exit(-1);
}
}
public Graph neighbourhoodGraph(int nnodes[], int hops) {
PrimaryHashMap<Integer, String> nodes;
PrimaryHashMap<String, Integer> nodesReverse;
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
WeightedArcSet list1 = new WeightedArcSet();
Int2IntAVLTreeMap map = new Int2IntAVLTreeMap();
IntSet set = new IntLinkedOpenHashSet();
int numIterators = 100;
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
for (int n : nnodes) map.put(n, 0);
NodeIterator its[] = new NodeIterator[numIterators];
int itNum[] = new int[numIterators];
for (int n = 0; n < its.length; n++) {
its[n] = nodeIterator();
itNum[n] = 0;
}
while (map.size() != 0) {
Integer node = 0;
for (int n = 0; n < its.length; n++) if (itNum[n] <= node) node = itNum[n];
node = map.tailMap(node).firstKey();
if (node == null) map.firstKey();
NodeIterator it = null;
Integer aux1 = 0;
int iit = 0;
for (int n = 0; n < its.length; n++) {
if (!its[n].hasNext()) {
its[n] = nodeIterator();
itNum[n] = 0;
}
if (itNum[n] == node) {
it = its[n];
aux1 = itNum[n];
iit = 0;
break;
}
if (itNum[n] < node && itNum[n] >= aux1) {
it = its[n];
aux1 = itNum[n];
iit = n;
}
}
if (it == null) {
its[0] = nodeIterator();
itNum[0] = 0;
it = its[0];
}
while (it != null && (aux1 = it.nextInt()) != null && aux1 >= 0 && aux1 < node) {}
itNum[iit] = aux1 + 1;
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
try {
nodes.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
try {
nodesReverse.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
}
if (!nodesReverse.containsKey(this.nodes.get(aux1))) {
nodes.put(nodes.size(), this.nodes.get(aux1));
nodesReverse.put(this.nodes.get(aux1), nodesReverse.size());
}
if (!nodesReverse.containsKey(this.nodes.get(aux2))) {
nodes.put(nodes.size(), this.nodes.get(aux2));
nodesReverse.put(this.nodes.get(aux2), nodesReverse.size());
}
int aaux1 = nodesReverse.get(this.nodes.get(aux1));
int aaux2 = nodesReverse.get(this.nodes.get(aux2));
WeightedArc arc1 =
(WeightedArc) cons[0].newInstance(aaux1, aaux2, suc.label().getFloat());
list1.add(arc1);
if (map.get(node) < hops) {
if (!set.contains(aux1) && (map.get(aux1) == null || map.get(aux1) > map.get(node) + 1))
map.put(aux1.intValue(), map.get(node) + 1);
if (!set.contains(aux2) && (map.get(aux2) == null || map.get(aux2) > map.get(node) + 1))
map.put(aux2.intValue(), map.get(node) + 1);
}
} catch (Exception ex) {
ex.printStackTrace();
throw new Error(ex);
}
ArcLabelledNodeIterator.LabelledArcIterator anc = it.ancestors();
while ((aux2 = anc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
try {
nodes.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
try {
nodesReverse.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
}
if (!nodesReverse.containsKey(this.nodes.get(aux1))) {
nodes.put(nodes.size(), this.nodes.get(aux1));
nodesReverse.put(this.nodes.get(aux1), nodesReverse.size());
}
if (!nodesReverse.containsKey(this.nodes.get(aux2))) {
nodes.put(nodes.size(), this.nodes.get(aux2));
nodesReverse.put(this.nodes.get(aux2), nodesReverse.size());
}
int aaux1 = nodesReverse.get(this.nodes.get(aux1));
int aaux2 = nodesReverse.get(this.nodes.get(aux2));
WeightedArc arc1 =
(WeightedArc) cons[0].newInstance(aaux2, aaux1, anc.label().getFloat());
list1.add(arc1);
if (map.get(node) < hops) {
if (!set.contains(aux1) && (map.get(aux1) == null || map.get(aux1) > map.get(node) + 1))
map.put(aux1.intValue(), map.get(node) + 1);
if (!set.contains(aux2) && (map.get(aux2) == null || map.get(aux2) > map.get(node) + 1))
map.put(aux2.intValue(), map.get(node) + 1);
}
} catch (Exception ex) {
ex.printStackTrace();
throw new Error(ex);
}
map.remove(node);
set.add(node);
}
Graph newGraph = new Graph(list1.toArray(new WeightedArc[0]));
newGraph.nodes.clear();
newGraph.nodesReverse.clear();
newGraph.nodes = nodes;
newGraph.nodesReverse = nodesReverse;
return newGraph;
}
public Graph neighbourhoodGraph(String nodes[], int hops) {
int nnodes[] = new int[nodes.length];
for (int i = 0; i < nodes.length; i++) nnodes[i] = nodesReverse.get(nodes[i]);
return neighbourhoodGraph(nnodes, hops);
}
public void setNode(int nodeNum, String node) {
nodes.put(nodeNum, node);
}
public int node(String node) {
return nodesReverse.get(node);
}
public String node(int nodeNum) {
return nodes.get(nodeNum);
}
public Graph(String file) throws IOException {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
String aux = null;
Float weight = (float) 1.0;
WeightedArcSet list = new WeightedArcSet();
BufferedReader br;
try {
br =
new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(file))));
} catch (Exception ex) {
br = new BufferedReader(new FileReader(file));
}
while ((aux = br.readLine()) != null)
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
String parts[] = aux.split("\t");
String l1 = new String(parts[0]);
String l2 = new String(parts[1]);
if (!nodesReverse.containsKey(l1)) {
nodesReverse.put(l1, nodesReverse.size());
nodes.put(nodes.size(), l1);
}
if (!nodesReverse.containsKey(l2)) {
nodesReverse.put(l2, nodesReverse.size());
nodes.put(nodes.size(), l2);
}
if (parts.length == 3) weight = new Float(parts[2]);
list.add(
(WeightedArc) cons[0].newInstance(nodesReverse.get(l1), nodesReverse.get(l2), weight));
} catch (Exception ex) {
throw new Error(ex);
}
this.graph = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
br.close();
list = new WeightedArcSet();
br = new BufferedReader(new FileReader(file));
while ((aux = br.readLine()) != null)
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
String parts[] = aux.split("\t");
String l1 = new String(parts[0]);
String l2 = new String(parts[1]);
if (parts.length == 3) weight = new Float(parts[2]);
list.add(
(WeightedArc) cons[0].newInstance(nodesReverse.get(l2), nodesReverse.get(l1), weight));
} catch (Exception ex) {
throw new Error(ex);
}
br.close();
this.reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
public Graph(BVGraph graph) {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
Integer aux1 = null;
WeightedArcSet list = new WeightedArcSet();
it.unimi.dsi.webgraph.NodeIterator it = graph.nodeIterator();
while ((aux1 = it.nextInt()) != null) {
LazyIntIterator suc = it.successors();
Integer aux2 = null;
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
list.commit();
}
list.add((WeightedArc) cons[0].newInstance(aux1, aux2, (float) 1.0));
} catch (Exception ex) {
throw new Error(ex);
}
}
this.graph = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
list = new WeightedArcSet();
it = graph.nodeIterator();
while ((aux1 = it.nextInt()) != null) {
LazyIntIterator suc = it.successors();
Integer aux2 = null;
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
list.add((WeightedArc) cons[0].newInstance(aux2, aux1, (float) 1.0));
this.nodes.put(aux1, "" + aux1);
this.nodes.put(aux2, "" + aux2);
this.nodesReverse.put("" + aux1, aux1);
this.nodesReverse.put("" + aux2, aux2);
} catch (Exception ex) {
throw new Error(ex);
}
}
this.reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}