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HermiT is reasoner for ontologies written using the Web
Ontology Language (OWL). Given an OWL file, HermiT can determine whether or
not the ontology is consistent, identify subsumption relationships between
classes, and much more.
This is the maven build of HermiT and is designed for people who wish to use
HermiT from within the OWL API. It is now versioned in the main HermiT
version repository, although not officially supported by the HermiT
developers.
The version number of this package is a composite of the HermiT version and
an value representing releases of this packaged version. So, 1.3.7.1 is the
first release of the mavenized version of HermiT based on the 1.3.7 release
of HermiT.
This package includes the Jautomata library
(http://jautomata.sourceforge.net/), and builds with it directly. This
library appears to be no longer under active development, and so a "fork"
seems appropriate. No development is intended or anticipated on this code
base.
/* Copyright 2008, 2009, 2010 by the Oxford University Computing Laboratory
This file is part of HermiT.
HermiT is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
HermiT is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with HermiT. If not, see =node.getNodeID())
m_firstChangedNode=null;
if (m_lastValidatedUnchangedNode!=null && node.getNodeID() {
public final String m_violatedConstraint;
public final Integer m_numberOfViolations;
public ViolationStatistic(String violatedConstraint,Integer numberOfViolations) {
m_violatedConstraint=violatedConstraint;
m_numberOfViolations=numberOfViolations;
}
public int compareTo(ViolationStatistic that) {
if (this==that)
return 0;
if (that==null)
throw new NullPointerException("Comparing to a null object is illegal. ");
if (this.m_numberOfViolations==that.m_numberOfViolations)
return m_violatedConstraint.compareTo(that.m_violatedConstraint);
else
return that.m_numberOfViolations-this.m_numberOfViolations;
}
public String toString() {
return m_numberOfViolations+": "+m_violatedConstraint.replaceAll("http://www.co-ode.org/ontologies/galen#","");
}
}
public boolean isExact() {
return false;
}
public void dlClauseBodyCompiled(List workers,DLClause dlClause,List variables,Object[] valuesBuffer,boolean[] coreVariables) {
if (m_useSimpleCore) {
for (int i=0;i1) {
for (int i=0;i1) {
workers.add(new ComputeCoreVariables(dlClause,variables,valuesBuffer,coreVariables));
}
}
}
}
protected static final class ComputeCoreVariables implements DLClauseEvaluator.Worker,Serializable {
private static final long serialVersionUID=899293772370136783L;
protected final DLClause m_dlClause;
protected final List m_variables;
protected final Object[] m_valuesBuffer;
protected final boolean[] m_coreVariables;
public ComputeCoreVariables(DLClause dlClause,List variables,Object[] valuesBuffer,boolean[] coreVariables) {
m_dlClause=dlClause;
m_variables=variables;
m_valuesBuffer=valuesBuffer;
m_coreVariables=coreVariables;
}
public void clear() {
}
public int execute(int programCounter) {
Node potentialNonCore=null;
// find the root of the subtree induced by the mapped nodes that node cannot be core
for (int variableIndex=m_coreVariables.length-1;variableIndex>=0;--variableIndex) {
Node node=(Node)m_valuesBuffer[variableIndex];
if (node.getNodeType()==NodeType.TREE_NODE && (potentialNonCore==null || node.getTreeDepth()=0;--variableIndex) {
Node node=(Node)m_valuesBuffer[variableIndex];
if (!node.isRootNode() && potentialNonCore!=node && potentialNonCore.getTreeDepth()();
entry.m_hashCode=0;
m_emptyEntries=entry;
m_numberOfElements--;
}
else {
if (entry.m_nodes.contains(node)) {
for (int i=entry.m_nodes.size()-1;i>=entry.m_nodes.indexOf(node);i--) {
entry.m_nodes.get(i).setBlockingCargo(null);
}
entry.m_nodes.subList(entry.m_nodes.indexOf(node),entry.m_nodes.size()).clear();
}
else {
throw new IllegalStateException("Internal error: entry not in cache!");
}
}
return true;
}
lastEntry=entry;
entry=entry.m_nextEntry;
}
throw new IllegalStateException("Internal error: entry not in cache!");
}
return false;
}
public void addNode(Node node) {
int hashCode=m_directBlockingChecker.blockingHashCode(node);
int bucketIndex=getIndexFor(hashCode,m_buckets.length);
CacheEntry entry=m_buckets[bucketIndex];
while (entry!=null) {
if (hashCode==entry.m_hashCode && m_directBlockingChecker.isBlockedBy(entry.m_nodes.get(0),node)) {
if (!entry.m_nodes.contains(node)) {
entry.add(node);
node.setBlockingCargo(entry);
return;
}
else {
throw new IllegalStateException("Internal error: node already in the cache!");
}
}
entry=entry.m_nextEntry;
}
if (m_emptyEntries==null)
entry=new CacheEntry();
else {
entry=m_emptyEntries;
m_emptyEntries=m_emptyEntries.m_nextEntry;
}
entry.initialize(node,hashCode,m_buckets[bucketIndex]);
m_buckets[bucketIndex]=entry;
// When a node is added to the cache, we record with the node the entry.
// This is used to remove nodes from the cache. Note that changes to a node
// can affect its label. Therefore, we CANNOT remove a node by taking its present
// blocking hash-code, as this can be different from the hash-code used at the
// time the node has been added to the cache.
node.setBlockingCargo(entry);
m_numberOfElements++;
if (m_numberOfElements>=m_threshold)
resize(m_buckets.length*2);
}
protected void resize(int newCapacity) {
CacheEntry[] newBuckets=new CacheEntry[newCapacity];
for (int i=0;i getPossibleBlockers(Node node) {
if (m_directBlockingChecker.canBeBlocked(node)) {
int hashCode=m_directBlockingChecker.blockingHashCode(node);
int bucketIndex=getIndexFor(hashCode,m_buckets.length);
CacheEntry entry=m_buckets[bucketIndex];
while (entry!=null) {
if (hashCode==entry.m_hashCode && m_directBlockingChecker.isBlockedBy(entry.m_nodes.get(0),node)) {
assert !entry.m_nodes.contains(node); // we try to block a node that is in the cache
return entry.m_nodes;
}
entry=entry.m_nextEntry;
}
}
return new ArrayList();
}
protected static int getIndexFor(int hashCode,int tableLength) {
hashCode+=~(hashCode<<9);
hashCode^=(hashCode>>>14);
hashCode+=(hashCode<<4);
hashCode^=(hashCode>>>10);
return hashCode&(tableLength-1);
}
public String toString() {
String buckets="";
for (int i=0;i m_nodes;
protected int m_hashCode;
protected CacheEntry m_nextEntry;
public void initialize(Node node,int hashCode,CacheEntry nextEntry) {
m_nodes=new ArrayList();
add(node);
m_hashCode=hashCode;
m_nextEntry=nextEntry;
}
public boolean add(Node node) {
for (Node n : m_nodes) {
assert n.getNodeID()<=node.getNodeID();
}
return m_nodes.add(node);
}
public String toString() {
String nodes="HashCode: "+m_hashCode+" Nodes: ";
for (Node n : m_nodes) {
nodes+=n.getNodeID()+" ";
}
return nodes;
}
}
}
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