Author: chenpei
Date: Tue Nov 4 17:41:43 2014
New Revision: 1636663
URL: http://svn.apache.org/r1636663
Log:
CTAKES-321 - Remove trove as a dependency.
Modified:
ctakes/trunk/ctakes-ytex/pom.xml
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDao.java
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java
Modified: ctakes/trunk/ctakes-ytex/pom.xml
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/pom.xml?rev=1636663&r1=1636662&r2=1636663&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/pom.xml (original)
+++ ctakes/trunk/ctakes-ytex/pom.xml Tue Nov 4 17:41:43 2014
@@ -178,12 +178,6 @@
<artifactId>ehcache-core</artifactId>
<version>2.4.6</version>
</dependency>
-
- <dependency>
- <groupId>net.sf.trove4j</groupId>
- <artifactId>trove4j</artifactId>
- <version>3.0.3</version>
- </dependency>
<dependency>
<groupId>com.rubiconproject.oss</groupId>
<artifactId>jchronic</artifactId>
Modified:
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java?rev=1636663&r1=1636662&r2=1636663&view=diff
==============================================================================
---
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java
(original)
+++
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java
Tue Nov 4 17:41:43 2014
@@ -18,10 +18,6 @@
*/
package org.apache.ctakes.ytex.kernel;
-import gnu.trove.iterator.TIntIterator;
-import gnu.trove.set.TIntSet;
-import gnu.trove.set.hash.TIntHashSet;
-
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
@@ -30,6 +26,7 @@ import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Properties;
@@ -146,18 +143,18 @@ public class IntrinsicInfoContentEvaluat
* @return
* @throws IOException
*/
- private TIntSet getLeaves(ConcRel concept,
- SoftReference<TIntSet>[] leafCache,
+ private HashSet<Integer> getLeaves(ConcRel concept,
+ SoftReference<HashSet<Integer>>[] leafCache,
Map<String, IntrinsicICInfo> icInfoMap, ConceptGraph cg,
- BufferedWriter w, TIntSet visitedNodes) throws
IOException {
+ BufferedWriter w, HashSet<Integer> visitedNodes) throws
IOException {
// look in cache
- SoftReference<TIntSet> refLeaves =
leafCache[concept.getNodeIndex()];
+ SoftReference<HashSet<Integer>> refLeaves =
leafCache[concept.getNodeIndex()];
if (refLeaves != null && refLeaves.get() != null) {
return refLeaves.get();
}
// not in cache - compute recursively
- TIntSet leaves = new TIntHashSet();
- leafCache[concept.getNodeIndex()] = new
SoftReference<TIntSet>(leaves);
+ HashSet<Integer> leaves = new HashSet<Integer>();
+ leafCache[concept.getNodeIndex()] = new
SoftReference<HashSet<Integer>>(leaves);
if (concept.isLeaf()) {
// for leaves, just add the concept id
leaves.add(concept.getNodeIndex());
@@ -168,7 +165,7 @@ public class IntrinsicInfoContentEvaluat
// if no, then compute it now and revisit previously
visited nodes
// if we have to
boolean needLeaves = (icInfo != null &&
icInfo.getLeafCount() == 0);
- TIntSet visitedNodesLocal = visitedNodes;
+ HashSet<Integer> visitedNodesLocal = visitedNodes;
if (needLeaves || visitedNodesLocal == null) {
// allocate a set to keep track of nodes we've
already visited
// so that we don't revisit them. if we have
already computed
@@ -177,7 +174,7 @@ public class IntrinsicInfoContentEvaluat
// if we haven't already computed this node's
leaf count,
// allocate a new set to avoid duplications in
the traversal for
// this node
- visitedNodesLocal = new TIntHashSet();
+ visitedNodesLocal = new HashSet<Integer>();
}
// for inner nodes, recurse
for (ConcRel child : concept.getChildren()) {
@@ -204,7 +201,7 @@ public class IntrinsicInfoContentEvaluat
w.write("\t");
w.write(Integer.toString(leaves.size()));
w.write("\t");
- TIntIterator iter = leaves.iterator();
+ Iterator<Integer> iter =
leaves.iterator();
while (iter.hasNext()) {
w.write(cg.getConceptList().get(iter.next())
.getConceptID());
@@ -359,8 +356,8 @@ public class IntrinsicInfoContentEvaluat
}
log.info("computing leaf counts");
@SuppressWarnings("unchecked")
- SoftReference<TIntSet>[] leafCache = (SoftReference<TIntSet>[])
Array
- .newInstance((new SoftReference<TIntSet>(new
TIntHashSet()))
+ SoftReference<HashSet<Integer>>[] leafCache =
(SoftReference<HashSet<Integer>>[]) Array
+ .newInstance((new
SoftReference<HashSet<Integer>>(new HashSet<Integer>()))
.getClass(),
cg.getConceptList().size());
// compute leaf count of all concepts in this graph
try {
Modified:
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java?rev=1636663&r1=1636662&r2=1636663&view=diff
==============================================================================
---
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java
(original)
+++
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java
Tue Nov 4 17:41:43 2014
@@ -18,9 +18,6 @@
*/
package org.apache.ctakes.ytex.kernel.dao;
-import gnu.trove.set.TIntSet;
-import gnu.trove.set.hash.TIntHashSet;
-
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
@@ -425,7 +422,7 @@ public class ConceptDaoImpl implements C
}
private boolean checkCycle(ConcRel crPar, ConcRel crChild) {
- TIntSet visitedNodes = new TIntHashSet();
+ HashSet<Integer> visitedNodes = new HashSet<Integer>();
return hasAncestor(crPar, crChild, visitedNodes);
}
@@ -442,7 +439,7 @@ public class ConceptDaoImpl implements C
* @return true if crChild is an ancestor of crPar
*/
private boolean hasAncestor(ConcRel crPar, ConcRel crChild,
- TIntSet visitedNodes) {
+ HashSet<Integer> visitedNodes) {
// see if we've already visited this node - if yes then no need
to redo
// this
if (visitedNodes.contains(crPar.getNodeIndex()))
Modified:
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDao.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDao.java?rev=1636663&r1=1636662&r2=1636663&view=diff
==============================================================================
---
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDao.java
(original)
+++
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDao.java
Tue Nov 4 17:41:43 2014
@@ -18,9 +18,7 @@
*/
package org.apache.ctakes.ytex.umls.dao;
-import gnu.trove.set.TIntSet;
-import gnu.trove.set.TShortSet;
-
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.regex.Pattern;
@@ -65,7 +63,7 @@ public interface UMLSDao {
*
* @return
*/
- public abstract TIntSet getRXNORMCuis();
+ public abstract HashSet<Integer> getRXNORMCuis();
public abstract boolean isRXNORMCui(String cui);
Modified:
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java?rev=1636663&r1=1636662&r2=1636663&view=diff
==============================================================================
---
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java
(original)
+++
ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/umls/dao/UMLSDaoImpl.java
Tue Nov 4 17:41:43 2014
@@ -18,10 +18,8 @@
*/
package org.apache.ctakes.ytex.umls.dao;
-import gnu.trove.set.TIntSet;
-import gnu.trove.set.hash.TIntHashSet;
-
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
@@ -149,8 +147,8 @@ public class UMLSDaoImpl implements UMLS
@Override
@SuppressWarnings("unchecked")
- public TIntSet getRXNORMCuis() {
- TIntSet cuis = new TIntHashSet();
+ public HashSet<Integer> getRXNORMCuis() {
+ HashSet<Integer> cuis = new HashSet();
for (String cui : (List<String>)
sessionFactory.getCurrentSession()
.getNamedQuery("getRXNORMCuis").list()) {
Matcher m = UMLSDao.cuiPattern.matcher(cui);
