Import Debian changes 0.5.0~beta2-1

elki (0.5.0~beta2-1) unstable; urgency=low

  * New upstream beta release.
  * Needs GNU Trove 3, in NEW.
  * Build with OpenJDK7, as OpenJDK6 complains.

elki (0.5.0~beta1-1) unstable; urgency=low

  * New upstream beta release.
  * Needs GNU Trove 3, not yet in Debian (private package)
  * Build with OpenJDK7, as OpenJDK6 complains.

1 files changed, 12 insertions, 14 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborPreprocessor.java b/src/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborPreprocessor.java
index 43bd7e30..46f47a33 100644
--- a/src/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborPreprocessor.java
+++ b/src/de/lmu/ifi/dbs/elki/index/preprocessed/snn/SharedNearestNeighborPreprocessor.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.index.preprocessed.snn;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
@@ -23,19 +23,16 @@ package de.lmu.ifi.dbs.elki.index.preprocessed.snn;
  along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-import java.util.List;
-
 import de.lmu.ifi.dbs.elki.data.type.TypeInformation;
 import de.lmu.ifi.dbs.elki.database.QueryUtil;
 import de.lmu.ifi.dbs.elki.database.datastore.DataStoreFactory;
 import de.lmu.ifi.dbs.elki.database.datastore.DataStoreUtil;
+import de.lmu.ifi.dbs.elki.database.ids.ArrayDBIDs;
+import de.lmu.ifi.dbs.elki.database.ids.ArrayModifiableDBIDs;
 import de.lmu.ifi.dbs.elki.database.ids.DBID;
 import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
-import de.lmu.ifi.dbs.elki.database.ids.SetDBIDs;
-import de.lmu.ifi.dbs.elki.database.ids.TreeSetDBIDs;
-import de.lmu.ifi.dbs.elki.database.ids.TreeSetModifiableDBIDs;
-import de.lmu.ifi.dbs.elki.database.query.DistanceResultPair;
 import de.lmu.ifi.dbs.elki.database.query.knn.KNNQuery;
+import de.lmu.ifi.dbs.elki.database.query.knn.KNNResult;
 import de.lmu.ifi.dbs.elki.database.relation.Relation;
 import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction;
 import de.lmu.ifi.dbs.elki.distance.distancefunction.EuclideanDistanceFunction;
@@ -75,7 +72,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
  */
 @Title("Shared nearest neighbor Preprocessor")
 @Description("Computes the k nearest neighbors of objects of a certain database.")
-public class SharedNearestNeighborPreprocessor<O, D extends Distance<D>> extends AbstractPreprocessorIndex<O, TreeSetDBIDs> implements SharedNearestNeighborIndex<O> {
+public class SharedNearestNeighborPreprocessor<O, D extends Distance<D>> extends AbstractPreprocessorIndex<O, ArrayDBIDs> implements SharedNearestNeighborIndex<O> {
   /**
    * Get a logger for this class.
    */
@@ -111,23 +108,24 @@ public class SharedNearestNeighborPreprocessor<O, D extends Distance<D>> extends
     if(getLogger().isVerbose()) {
       getLogger().verbose("Assigning nearest neighbor lists to database objects");
     }
-    storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, SetDBIDs.class);
+    storage = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_TEMP, ArrayDBIDs.class);
     KNNQuery<O, D> knnquery = QueryUtil.getKNNQuery(relation, distanceFunction, numberOfNeighbors);
 
     FiniteProgress progress = getLogger().isVerbose() ? new FiniteProgress("assigning nearest neighbor lists", relation.size(), getLogger()) : null;
     for(DBID id : relation.iterDBIDs()) {
-      TreeSetModifiableDBIDs neighbors = DBIDUtil.newTreeSet(numberOfNeighbors);
-      List<DistanceResultPair<D>> kNN = knnquery.getKNNForDBID(id, numberOfNeighbors);
+      ArrayModifiableDBIDs neighbors = DBIDUtil.newArray(numberOfNeighbors);
+      KNNResult<D> kNN = knnquery.getKNNForDBID(id, numberOfNeighbors);
       for(int i = 0; i < kNN.size(); i++) {
         final DBID nid = kNN.get(i).getDBID();
         // if(!id.equals(nid)) {
         neighbors.add(nid);
         // }
-        // Size limitation to exaclty numberOfNeighbors
+        // Size limitation to exactly numberOfNeighbors
         if(neighbors.size() >= numberOfNeighbors) {
           break;
         }
       }
+      neighbors.sort();
       storage.put(id, neighbors);
       if(progress != null) {
         progress.incrementProcessed(getLogger());
@@ -139,7 +137,7 @@ public class SharedNearestNeighborPreprocessor<O, D extends Distance<D>> extends
   }
 
   @Override
-  public TreeSetDBIDs getNearestNeighborSet(DBID objid) {
+  public ArrayDBIDs getNearestNeighborSet(DBID objid) {
     if(storage == null) {
       preprocess();
     }
@@ -269,7 +267,7 @@ public class SharedNearestNeighborPreprocessor<O, D extends Distance<D>> extends
       @Override
       protected void makeOptions(Parameterization config) {
         super.makeOptions(config);
-        final IntParameter numberOfNeighborsP = new IntParameter(NUMBER_OF_NEIGHBORS_ID, new GreaterEqualConstraint(1), 1);
+        final IntParameter numberOfNeighborsP = new IntParameter(NUMBER_OF_NEIGHBORS_ID, new GreaterEqualConstraint(1));
         if(config.grab(numberOfNeighborsP)) {
           numberOfNeighbors = numberOfNeighborsP.getValue();
         }