Import Debian changes 0.6.0~beta2-1

elki (0.6.0~beta2-1) unstable; urgency=low

  * New upstream beta release.
  * 3DPC extension is not yet included.

1 files changed, 35 insertions, 76 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeIndex.java b/src/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeIndex.java
index 9776de63..2a630bf0 100644
--- a/src/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeIndex.java
+++ b/src/de/lmu/ifi/dbs/elki/index/tree/metrical/mtreevariants/mktrees/mkapp/MkAppTreeIndex.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.mktrees.mkapp;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2012
+ Copyright (C) 2013
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
@@ -28,9 +28,7 @@ import java.util.List;
 
 import de.lmu.ifi.dbs.elki.database.ids.DBID;
 import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDRef;
 import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
-import de.lmu.ifi.dbs.elki.database.ids.DBIDs;
 import de.lmu.ifi.dbs.elki.database.query.DatabaseQuery;
 import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery;
 import de.lmu.ifi.dbs.elki.database.query.knn.KNNQuery;
@@ -43,12 +41,9 @@ import de.lmu.ifi.dbs.elki.distance.distancevalue.NumberDistance;
 import de.lmu.ifi.dbs.elki.index.KNNIndex;
 import de.lmu.ifi.dbs.elki.index.RKNNIndex;
 import de.lmu.ifi.dbs.elki.index.RangeIndex;
-import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.AbstractMTree;
-import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.mktrees.AbstractMkTree;
 import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.query.MTreeQueryUtil;
 import de.lmu.ifi.dbs.elki.index.tree.metrical.mtreevariants.query.MkTreeRKNNQuery;
 import de.lmu.ifi.dbs.elki.persistent.PageFile;
-import de.lmu.ifi.dbs.elki.utilities.exceptions.ExceptionMessages;
 
 /**
  * MkAppTree used as database index.
@@ -69,16 +64,11 @@ public class MkAppTreeIndex<O, D extends NumberDistance<D, ?>> extends MkAppTree
    * 
    * @param relation Relation to index
    * @param pageFile Page file
-   * @param distanceQuery Distance query
-   * @param distanceFunction Distance function
-   * @param k_max Maximum value of k supported
-   * @param p Parameter p
-   * @param log Logspace flag
+   * @param settings Tree settings
    */
-  public MkAppTreeIndex(Relation<O> relation, PageFile<MkAppTreeNode<O, D>> pageFile, DistanceQuery<O, D> distanceQuery, DistanceFunction<O, D> distanceFunction, int k_max, int p, boolean log) {
-    super(pageFile, distanceQuery, distanceFunction, k_max, p, log);
+  public MkAppTreeIndex(Relation<O> relation, PageFile<MkAppTreeNode<O, D>> pageFile, MkAppTreeSettings<O, D> settings) {
+    super(relation, pageFile, settings);
     this.relation = relation;
-    this.initialize();
   }
 
   /**
@@ -89,119 +79,88 @@ public class MkAppTreeIndex<O, D extends NumberDistance<D, ?>> extends MkAppTree
    * @param parentDistance the distance from the object to the routing object of
    *        the parent node
    */
-  protected MkAppEntry<D> createNewLeafEntry(DBID id, O object, D parentDistance) {
-    return new MkAppLeafEntry<D>(id, parentDistance, null);
+  protected MkAppEntry createNewLeafEntry(DBID id, O object, double parentDistance) {
+    return new MkAppLeafEntry(id, parentDistance, null);
   }
 
   @Override
-  public void insert(DBIDRef id) {
-    throw new UnsupportedOperationException("Insertion of single objects is not supported!");
-  }
-
-  @Override
-  public void insertAll(DBIDs ids) {
-    List<MkAppEntry<D>> objs = new ArrayList<MkAppEntry<D>>(ids.size());
-    for (DBIDIter iter = ids.iter(); iter.valid(); iter.advance()) {
+  public void initialize() {
+    super.initialize();
+    List<MkAppEntry> objs = new ArrayList<>(relation.size());
+    for (DBIDIter iter = relation.iterDBIDs(); iter.valid(); iter.advance()) {
       DBID id = DBIDUtil.deref(iter);
       final O object = relation.get(id);
-      objs.add(createNewLeafEntry(id, object, getDistanceFactory().undefinedDistance()));
+      objs.add(createNewLeafEntry(id, object, Double.NaN));
     }
     insertAll(objs);
   }
 
-  /**
-   * Throws an UnsupportedOperationException since deletion of objects is not
-   * yet supported by an M-Tree.
-   * 
-   * @throws UnsupportedOperationException thrown, since deletions aren't
-   *         implemented yet.
-   */
-  @Override
-  public final boolean delete(DBIDRef id) {
-    throw new UnsupportedOperationException(ExceptionMessages.UNSUPPORTED_NOT_YET);
-  }
-
-  /**
-   * Throws an UnsupportedOperationException since deletion of objects is not
-   * yet supported by an M-Tree.
-   * 
-   * @throws UnsupportedOperationException thrown, since deletions aren't
-   *         implemented yet.
-   */
-  @Override
-  public void deleteAll(DBIDs ids) {
-    throw new UnsupportedOperationException(ExceptionMessages.UNSUPPORTED_NOT_YET);
-  }
-
   @SuppressWarnings("unchecked")
   @Override
   public <S extends Distance<S>> KNNQuery<O, S> getKNNQuery(DistanceQuery<O, S> distanceQuery, Object... hints) {
     // Query on the relation we index
-    if(distanceQuery.getRelation() != relation) {
+    if (distanceQuery.getRelation() != relation) {
       return null;
     }
-    DistanceFunction<? super O, S> distanceFunction = distanceQuery.getDistanceFunction();
-    if(!this.distanceFunction.equals(distanceFunction)) {
-      if(getLogger().isDebugging()) {
+    DistanceFunction<? super O, D> distanceFunction = (DistanceFunction<? super O, D>) distanceQuery.getDistanceFunction();
+    if (!this.getDistanceFunction().equals(distanceFunction)) {
+      if (getLogger().isDebugging()) {
         getLogger().debug("Distance function not supported by index - or 'equals' not implemented right!");
       }
       return null;
     }
     // Bulk is not yet supported
-    for(Object hint : hints) {
-      if(hint == DatabaseQuery.HINT_BULK) {
+    for (Object hint : hints) {
+      if (hint == DatabaseQuery.HINT_BULK) {
         return null;
       }
     }
-    AbstractMTree<O, S, ?, ?> idx = (AbstractMTree<O, S, ?, ?>) this;
-    DistanceQuery<O, S> dq = distanceFunction.instantiate(relation);
-    return MTreeQueryUtil.getKNNQuery(idx, dq, hints);
+    DistanceQuery<O, D> dq = distanceFunction.instantiate(relation);
+    return (KNNQuery<O, S>) MTreeQueryUtil.getKNNQuery(this, dq, hints);
   }
 
   @SuppressWarnings("unchecked")
   @Override
   public <S extends Distance<S>> RangeQuery<O, S> getRangeQuery(DistanceQuery<O, S> distanceQuery, Object... hints) {
     // Query on the relation we index
-    if(distanceQuery.getRelation() != relation) {
+    if (distanceQuery.getRelation() != relation) {
       return null;
     }
-    DistanceFunction<? super O, S> distanceFunction = distanceQuery.getDistanceFunction();
-    if(!this.distanceFunction.equals(distanceFunction)) {
-      if(getLogger().isDebugging()) {
+    DistanceFunction<? super O, D> distanceFunction = (DistanceFunction<? super O, D>) distanceQuery.getDistanceFunction();
+    if (!this.getDistanceFunction().equals(distanceFunction)) {
+      if (getLogger().isDebugging()) {
         getLogger().debug("Distance function not supported by index - or 'equals' not implemented right!");
       }
       return null;
     }
     // Bulk is not yet supported
-    for(Object hint : hints) {
-      if(hint == DatabaseQuery.HINT_BULK) {
+    for (Object hint : hints) {
+      if (hint == DatabaseQuery.HINT_BULK) {
         return null;
       }
     }
-    AbstractMTree<O, S, ?, ?> idx = (AbstractMTree<O, S, ?, ?>) this;
-    DistanceQuery<O, S> dq = distanceFunction.instantiate(relation);
-    return MTreeQueryUtil.getRangeQuery(idx, dq, hints);
+    DistanceQuery<O, D> dq = distanceFunction.instantiate(relation);
+    return (RangeQuery<O, S>) MTreeQueryUtil.getRangeQuery(this, dq, hints);
   }
 
   @SuppressWarnings("unchecked")
   @Override
   public <S extends Distance<S>> RKNNQuery<O, S> getRKNNQuery(DistanceQuery<O, S> distanceQuery, Object... hints) {
-    DistanceFunction<? super O, S> distanceFunction = distanceQuery.getDistanceFunction();
-    if(!this.getDistanceFunction().equals(distanceFunction)) {
-      if(getLogger().isDebugging()) {
+    DistanceFunction<? super O, D> distanceFunction = (DistanceFunction<? super O, D>) distanceQuery.getDistanceFunction();
+    if (!this.getDistanceFunction().equals(distanceFunction)) {
+      if (getLogger().isDebugging()) {
         getLogger().debug("Distance function not supported by index - or 'equals' not implemented right!");
       }
       return null;
     }
     // Bulk is not yet supported
-    for(Object hint : hints) {
-      if(hint == DatabaseQuery.HINT_BULK) {
+    for (Object hint : hints) {
+      if (hint == DatabaseQuery.HINT_BULK) {
         return null;
       }
     }
-    AbstractMkTree<O, S, ?, ?> idx = (AbstractMkTree<O, S, ?, ?>) this;
-    DistanceQuery<O, S> dq = distanceFunction.instantiate(relation);
-    return new MkTreeRKNNQuery<O, S>(idx, dq);
+    DistanceQuery<O, D> dq = distanceFunction.instantiate(relation);
+    return (RKNNQuery<O, S>) new MkTreeRKNNQuery<>(this, dq);
   }
 
   @Override
@@ -213,4 +172,4 @@ public class MkAppTreeIndex<O, D extends NumberDistance<D, ?>> extends MkAppTree
   public String getShortName() {
     return "mkapptree";
   }
-}
\ No newline at end of file
+}