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, 42 insertions, 42 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/algorithm/outlier/AggarwalYuEvolutionary.java b/src/de/lmu/ifi/dbs/elki/algorithm/outlier/AggarwalYuEvolutionary.java
index aba5576e..5d357744 100644
--- a/src/de/lmu/ifi/dbs/elki/algorithm/outlier/AggarwalYuEvolutionary.java
+++ b/src/de/lmu/ifi/dbs/elki/algorithm/outlier/AggarwalYuEvolutionary.java
@@ -1,26 +1,27 @@
 package de.lmu.ifi.dbs.elki.algorithm.outlier;

-/*
-This file is part of ELKI:
-Environment for Developing KDD-Applications Supported by Index-Structures
-
-Copyright (C) 2011
-Ludwig-Maximilians-Universität München
-Lehr- und Forschungseinheit für Datenbanksysteme
-ELKI Development Team
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU Affero General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program 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 Affero General Public License for more details.
-
-You should have received a copy of the GNU Affero General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
+

+/*

+ This file is part of ELKI:

+ Environment for Developing KDD-Applications Supported by Index-Structures
+

+ Copyright (C) 2012

+ Ludwig-Maximilians-Universität München

+ Lehr- und Forschungseinheit für Datenbanksysteme

+ ELKI Development Team
+

+ This program is free software: you can redistribute it and/or modify

+ it under the terms of the GNU Affero General Public License as published by

+ the Free Software Foundation, either version 3 of the License, or

+ (at your option) any later version.
+

+ This program 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 Affero General Public License for more details.
+

+ You should have received a copy of the GNU Affero General Public License

+ along with this program.  If not, see <http://www.gnu.org/licenses/>.

+ */

 

 import java.util.ArrayList;

 import java.util.Arrays;

@@ -35,13 +36,13 @@ import de.lmu.ifi.dbs.elki.data.type.TypeUtil;
 import de.lmu.ifi.dbs.elki.database.Database;

 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.datastore.WritableDataStore;

+import de.lmu.ifi.dbs.elki.database.datastore.WritableDoubleDataStore;

 import de.lmu.ifi.dbs.elki.database.ids.DBID;

 import de.lmu.ifi.dbs.elki.database.ids.DBIDs;

+import de.lmu.ifi.dbs.elki.database.relation.MaterializedRelation;

 import de.lmu.ifi.dbs.elki.database.relation.Relation;

 import de.lmu.ifi.dbs.elki.logging.Logging;

 import de.lmu.ifi.dbs.elki.math.DoubleMinMax;

-import de.lmu.ifi.dbs.elki.database.relation.MaterializedRelation;

 import de.lmu.ifi.dbs.elki.result.outlier.InvertedOutlierScoreMeta;

 import de.lmu.ifi.dbs.elki.result.outlier.OutlierResult;

 import de.lmu.ifi.dbs.elki.result.outlier.OutlierScoreMeta;

@@ -65,8 +66,7 @@ import de.lmu.ifi.dbs.elki.utilities.pairs.Pair;
  * detect outliers for high dimensional data.

  * <p>

  * Reference: <br />

- * Outlier detection for high dimensional data Outlier detection for high

- * dimensional data <br />

+ * Outlier detection for high dimensional data<br />

  * C.C. Aggarwal, P. S. Yu <br />

  * Proceedings of the 2001 ACM SIGMOD international conference on Management of

  * data 2001, Santa Barbara, California, United States

@@ -147,23 +147,23 @@ public class AggarwalYuEvolutionary<V extends NumberVector<?, ?>> extends Abstra
 

     Collection<Individuum> individuums = (new EvolutionarySearch(relation, ranges, m, seed)).run();

 

-    WritableDataStore<Double> outlierScore = DataStoreUtil.makeStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC, Double.class);

+    WritableDoubleDataStore outlierScore = DataStoreUtil.makeDoubleStorage(relation.getDBIDs(), DataStoreFactory.HINT_HOT | DataStoreFactory.HINT_STATIC);

     for(Individuum ind : individuums) {

       DBIDs ids = computeSubspaceForGene(ind.getGene(), ranges);

       double sparsityC = sparsity(ids.size(), dbsize, k);

       for(DBID id : ids) {

-        Double prev = outlierScore.get(id);

-        if(prev == null || sparsityC < prev) {

-          outlierScore.put(id, sparsityC);

+        double prev = outlierScore.doubleValue(id);

+        if(Double.isNaN(prev) || sparsityC < prev) {

+          outlierScore.putDouble(id, sparsityC);

         }

       }

     }

 

     DoubleMinMax minmax = new DoubleMinMax();

     for(DBID id : relation.iterDBIDs()) {

-      Double val = outlierScore.get(id);

-      if(val == null) {

-        outlierScore.put(id, 0.0);

+      double val = outlierScore.doubleValue(id);

+      if(Double.isNaN(val)) {

+        outlierScore.putDouble(id, 0.0);

         val = 0.0;

       }

       minmax.put(val);

@@ -224,9 +224,10 @@ public class AggarwalYuEvolutionary<V extends NumberVector<?, ?>> extends Abstra
       this.m = m;

       this.dbsize = database.size();

       this.dim = DatabaseUtil.dimensionality(database);

-      if (seed != null) {

+      if(seed != null) {

         this.random = new Random(seed);

-      } else {

+      }

+      else {

         this.random = new Random();

       }

     }

@@ -274,7 +275,6 @@ public class AggarwalYuEvolutionary<V extends NumberVector<?, ?>> extends Abstra
 

     /**

      * check the termination criterion

-     * 

      */

     private boolean checkConvergence(Collection<Individuum> pop) {

       if(pop.size() == 0) {

@@ -683,15 +683,15 @@ public class AggarwalYuEvolutionary<V extends NumberVector<?, ?>> extends Abstra
   }

 

   /**

-   * Parameterization class.
-   *
-   * @author Erich Schubert
-   *
-   * @apiviz.exclude
+   * Parameterization class.

+   * 

+   * @author Erich Schubert

+   * 

+   * @apiviz.exclude

    */

   public static class Parameterizer<V extends NumberVector<?, ?>> extends AbstractAggarwalYuOutlier.Parameterizer {

     protected int m = 0;

-    

+

     protected Long seed = null;

 

     @Override