/**
* Resolves unwanted text node adjacency which can result from structural changes in the database.
* Adjacent text nodes are two text nodes A and B, where PRE(B)=PRE(A)+1 and PARENT(A)=PARENT(B).
*/
private void resolveTextAdjacency() {
// Text node merges are also gathered on a separate list to leverage optimizations.
final AtomicUpdateList allMerges = new AtomicUpdateList(data);
// keep track of the visited locations to avoid superfluous checks
final IntSet s = new IntSet();
// Text nodes have to be merged from the highest to the lowest pre value
for (int i = 0; i < updStructural.size(); i++) {
final BasicUpdate u = updStructural.get(i);
final Data insseq = u.getInsertionData();
// calculate the new location of the update, here we have to check for adjacency
final int newLocation = u.location + u.accumulatedShifts - u.shifts;
final int beforeNewLocation = newLocation - 1;
// check surroundings of this location for adjacent text nodes depending on the
// kind of update, first the one with higher PRE values (due to shifts!)
// ... for insert/replace ...
if (insseq != null) {
// calculate the current following node
final int followingNode = newLocation + insseq.meta.size;
final int beforeFollowingNode = followingNode - 1;
// check the nodes at the end of/after the insertion sequence
if (!s.contains(beforeFollowingNode)) {
final AtomicUpdateList merges = necessaryMerges(beforeFollowingNode, allMerges.data);
mergeNodes(merges);
allMerges.merge(merges);
s.add(beforeFollowingNode);
}
}
// check nodes for delete and for insert before the updated location
if (!s.contains(beforeNewLocation)) {
final AtomicUpdateList merges = necessaryMerges(beforeNewLocation, allMerges.data);
mergeNodes(merges);
allMerges.merge(merges);
s.add(beforeNewLocation);
}
}
allMerges.updateDistances();
allMerges.clear();
}
/**
* Updates distances to restore parent-child relationships that have been invalidated by
* structural updates.
*
* <p>Each structural update (insert/delete) leads to a shift of higher PRE values. This
* invalidates parent-child relationships. Distances are only updated after all structural updates
* have been carried out to make sure each node (that has to be updated) is only touched once.
*/
public void updateDistances() {
accumulatePreValueShifts();
final IntSet alreadyUpdatedNodes = new IntSet();
for (final BasicUpdate update : updStructural) {
int newPreOfAffectedNode = update.preOfAffectedNode + update.accumulatedShifts;
/* Update distance for the affected node and all following siblings of nodes
* on the ancestor-or-self axis. */
while (newPreOfAffectedNode < data.meta.size) {
if (alreadyUpdatedNodes.contains(newPreOfAffectedNode)) break;
data.dist(
newPreOfAffectedNode,
data.kind(newPreOfAffectedNode),
calculateNewDistance(newPreOfAffectedNode));
alreadyUpdatedNodes.add(newPreOfAffectedNode);
newPreOfAffectedNode += data.size(newPreOfAffectedNode, data.kind(newPreOfAffectedNode));
}
}
}
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;
}
