Import Debian changes 0.6.0-1

elki (0.6.0-1) unstable; urgency=low

  * New upstream final.
  * 3DPC extension is not included, but may be uploaded as a separate
    package when there is actual need (it is a demo software, not meant
    for use outside of research, so just get the source code!)
  * Upgrade to policy 3.9.5.0 (no changes)

1 files changed, 289 insertions, 0 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/database/ids/generic/DoubleDistanceDBIDPairKNNListHeap.java b/src/de/lmu/ifi/dbs/elki/database/ids/generic/DoubleDistanceDBIDPairKNNListHeap.java
new file mode 100644
index 00000000..ca00129b
--- /dev/null
+++ b/src/de/lmu/ifi/dbs/elki/database/ids/generic/DoubleDistanceDBIDPairKNNListHeap.java
@@ -0,0 +1,289 @@
+package de.lmu.ifi.dbs.elki.database.ids.generic;
+
+/*
+ This file is part of ELKI:
+ Environment for Developing KDD-Applications Supported by Index-Structures
+
+ Copyright (C) 2013
+ 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.Arrays;
+
+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.distance.DoubleDistanceDBIDListIter;
+import de.lmu.ifi.dbs.elki.database.ids.distance.DoubleDistanceDBIDPair;
+import de.lmu.ifi.dbs.elki.database.ids.distance.DoubleDistanceKNNHeap;
+import de.lmu.ifi.dbs.elki.database.ids.distance.DoubleDistanceKNNList;
+import de.lmu.ifi.dbs.elki.distance.distancevalue.DoubleDistance;
+
+/**
+ * Finalized KNN List.
+ * 
+ * @author Erich Schubert
+ * 
+ * @apiviz.composedOf DoubleDistanceDBIDPair
+ * @apiviz.has DoubleDistanceDBIDListIter
+ */
+public class DoubleDistanceDBIDPairKNNListHeap implements DoubleDistanceKNNList, DoubleDistanceKNNHeap {
+  /**
+   * The value of k this was materialized for.
+   */
+  private final int k;
+
+  /**
+   * The actual data array.
+   */
+  private DoubleDistanceDBIDPair[] data;
+
+  /**
+   * Current size
+   */
+  private int size;
+
+  /**
+   * Constructor.
+   * 
+   * @param k K parameter
+   */
+  public DoubleDistanceDBIDPairKNNListHeap(int k) {
+    super();
+    this.data = new DoubleDistanceDBIDPair[k + 11];
+    this.k = k;
+  }
+
+  @Override
+  public void clear() {
+    size = 0;
+    Arrays.fill(data, null);
+  }
+
+  @Override
+  public double insert(double distance, DBIDRef id) {
+    if (size < k || distance <= data[k - 1].doubleDistance()) {
+      insert(DBIDUtil.newDistancePair(distance, id));
+    }
+    return (size < k) ? Double.POSITIVE_INFINITY :  get(k - 1).doubleDistance();
+  }
+
+  @Override
+  @Deprecated
+  public void insert(Double distance, DBIDRef id) {
+    insert(DBIDUtil.newDistancePair(distance.doubleValue(), id));
+  }
+
+  @Override
+  @Deprecated
+  public void insert(DoubleDistance dist, DBIDRef id) {
+    insert(DBIDUtil.newDistancePair(dist.doubleValue(), id));
+  }
+
+  @Override
+  public void insert(DoubleDistanceDBIDPair e) {
+    if (size >= k) {
+      if (e.doubleDistance() > data[size - 1].doubleDistance()) {
+        return;
+      }
+      // Ensure we have enough space.
+      final int len = data.length;
+      if (size > len) {
+        final int newlength = len + (len >>> 1);
+        assert (newlength > size);
+        data = Arrays.copyOf(data, newlength);
+      }
+    }
+    insertionSort(e);
+    // Truncate if necessary:
+    if (size > k && data[k].doubleDistance() > data[k - 1].doubleDistance()) {
+      size = k;
+    }
+  }
+
+  /**
+   * Perform insertion sort.
+   * 
+   * @param obj Object to insert
+   */
+  private void insertionSort(DoubleDistanceDBIDPair obj) {
+    // Insertion sort:
+    int pos = size;
+    while (pos > 0) {
+      DoubleDistanceDBIDPair pobj = data[pos - 1];
+      if (pobj.doubleDistance() <= obj.doubleDistance()) {
+        break;
+      }
+      data[pos] = pobj;
+      --pos;
+    }
+    data[pos] = obj;
+    ++size;
+  }
+
+  @Override
+  public DoubleDistanceDBIDPair poll() {
+    assert (size > 0);
+    return data[size--];
+  }
+
+  @Override
+  public DoubleDistanceDBIDPair peek() {
+    assert (size > 0);
+    return data[size - 1];
+  }
+
+  @Override
+  public DoubleDistanceKNNList toKNNList() {
+    return this;
+  }
+
+  @Override
+  public int getK() {
+    return k;
+  }
+
+  @Override
+  @Deprecated
+  public DoubleDistance getKNNDistance() {
+    if (size < k) {
+      return DoubleDistance.INFINITE_DISTANCE;
+    }
+    return get(k - 1).getDistance();
+  }
+
+  @Override
+  public double doubleKNNDistance() {
+    return (size < k) ? Double.POSITIVE_INFINITY :  get(k - 1).doubleDistance();
+  }
+
+  @Override
+  public String toString() {
+    StringBuilder buf = new StringBuilder();
+    buf.append("kNNList[");
+    for (DoubleDistanceDBIDListIter iter = this.iter(); iter.valid();) {
+      buf.append(iter.doubleDistance()).append(':').append(DBIDUtil.toString(iter));
+      iter.advance();
+      if (iter.valid()) {
+        buf.append(',');
+      }
+    }
+    buf.append(']');
+    return buf.toString();
+  }
+
+  @Override
+  public DoubleDistanceDBIDPair get(int index) {
+    return data[index];
+  }
+
+  @Override
+  public DoubleDistanceDBIDListIter iter() {
+    return new Itr();
+  }
+
+  @Override
+  public int size() {
+    return data.length;
+  }
+
+  @Override
+  public boolean contains(DBIDRef o) {
+    for (DBIDIter iter = iter(); iter.valid(); iter.advance()) {
+      if (DBIDUtil.equal(iter, o)) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  @Override
+  public boolean isEmpty() {
+    return size() == 0;
+  }
+
+  /**
+   * Iterator.
+   * 
+   * @author Erich Schubert
+   * 
+   * @apiviz.exclude
+   */
+  private class Itr implements DoubleDistanceDBIDListIter {
+    /**
+     * Cursor position.
+     */
+    private int pos = 0;
+
+    @Override
+    public int internalGetIndex() {
+      return get(pos).internalGetIndex();
+    }
+
+    @Override
+    public boolean valid() {
+      return pos < data.length;
+    }
+
+    @Override
+    public void advance() {
+      pos++;
+    }
+
+    /**
+     * {@inheritDoc}
+     * 
+     * @deprecated use {@link #doubleDistance}!
+     */
+    @Override
+    @Deprecated
+    public DoubleDistance getDistance() {
+      return get(pos).getDistance();
+    }
+
+    @Override
+    public double doubleDistance() {
+      return get(pos).doubleDistance();
+    }
+
+    @Override
+    public DoubleDistanceDBIDPair getDistancePair() {
+      return get(pos);
+    }
+
+    @Override
+    public int getOffset() {
+      return pos;
+    }
+
+    @Override
+    public void advance(int count) {
+      pos += count;
+    }
+
+    @Override
+    public void retract() {
+      --pos;
+    }
+
+    @Override
+    public void seek(int off) {
+      pos = off;
+    }
+  }
+}