Import Debian changes 0.6.5~20141030-1

elki (0.6.5~20141030-1) unstable; urgency=medium

  * New upstream beta release
  * Urgency medium: 0.6.0 suffers from a performance issue with duplicates.
  * Repackaged tarball from .jar to .tar.bz2
  * Add dependency on libsvm3-java
  * Enable line numbers for debugging (ant debuglevel)

2 files changed, 162 insertions, 0 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/Unique.java b/src/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/Unique.java
new file mode 100644
index 00000000..ab149c39
--- /dev/null
+++ b/src/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/Unique.java
@@ -0,0 +1,132 @@
+package de.lmu.ifi.dbs.elki.utilities.datastructures.hash;
+
+/*
+ This file is part of ELKI:
+ Environment for Developing KDD-Applications Supported by Index-Structures
+
+ Copyright (C) 2014
+ 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 gnu.trove.impl.hash.TObjectHash;
+
+import java.util.Arrays;
+
+/**
+ * This hash set is designed to keep only a unique copy of each object (hence
+ * its name). For this, the method {@link #addOrGet} is the key API, which
+ * allows retrieving existing values.
+ * 
+ * @author Erich Schubert
+ *
+ * @param <E>
+ */
+public class Unique<E> extends TObjectHash<E> {
+  /**
+   * Serial version number.
+   */
+  static final long serialVersionUID = 1L;
+
+  /**
+   * Constructor with default size and load factors.
+   */
+  public Unique() {
+    super();
+  }
+
+  /**
+   * Constructor with desired initial size.
+   *
+   * @param initialCapacity desired initial size.
+   */
+  public Unique(int initialCapacity) {
+    super(initialCapacity);
+  }
+
+  /**
+   * Constructor with desired initial size, and with the specified load factor.
+   *
+   * @param initialCapacity desired initial size
+   * @param loadFactor load factor
+   */
+  public Unique(int initialCapacity, float loadFactor) {
+    super(initialCapacity, loadFactor);
+  }
+
+  /**
+   * Inserts a value into the set, unless it is already present.
+   * 
+   * This function returns the existing value, if present.
+   *
+   * @param obj Object to insert or retrieve
+   * @return Existing object if already present, or the new object.
+   */
+  @SuppressWarnings("unchecked")
+  public E addOrGet(E obj) {
+    int index = insertKey(obj);
+
+    if(index < 0) {
+      obj = (E) _set[-index - 1];
+    }
+
+    postInsertHook(consumeFreeSlot);
+    return obj;
+  }
+
+  /**
+   * Removes an existing object from the set.
+   *
+   * @param obj Object to remove
+   * @return true if the object was found and removed.
+   */
+  public boolean remove(Object obj) {
+    int index = index(obj);
+    if(index >= 0) {
+      removeAt(index);
+      return true;
+    }
+    return false;
+  }
+
+  @Override
+  public void clear() {
+    super.clear();
+
+    Arrays.fill(_set, 0, _set.length, FREE);
+  }
+
+  @SuppressWarnings("unchecked")
+  @Override
+  protected void rehash(int newCapacity) {
+    final int oldCapacity = _set.length, oldSize = size();
+    // Replace data storage:
+    Object oldSet[] = _set;
+    _set = new Object[newCapacity];
+    Arrays.fill(_set, FREE);
+
+    // Reinsert all objects:
+    for(int i = oldCapacity; i-- > 0;) {
+      E o = (E) oldSet[i];
+      if(o != FREE && o != REMOVED) {
+        insertKey(o);
+      }
+    }
+    // Last check: size before and after should be the same
+    reportPotentialConcurrentMod(size(), oldSize);
+  }
+}
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/package-info.java b/src/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/package-info.java
new file mode 100644
index 00000000..03746389
--- /dev/null
+++ b/src/de/lmu/ifi/dbs/elki/utilities/datastructures/hash/package-info.java
@@ -0,0 +1,30 @@
+/**
+ * Hashing based data structures.
+ * 
+ * Note: much of the desired functionality is provided by the very good GNU Trove library.
+ * 
+ * This package will only contain slight extensions or variations, not provided by Trove already.
+ */
+/*
+ This file is part of ELKI:
+ Environment for Developing KDD-Applications Supported by Index-Structures
+
+ Copyright (C) 2014
+ 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/>.
+ */
+package de.lmu.ifi.dbs.elki.utilities.datastructures.hash;
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