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)

11 files changed, 111 insertions, 44 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/AbstractParameterization.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/AbstractParameterization.java
index 75a5be86..6b804777 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/AbstractParameterization.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/AbstractParameterization.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ChainedParameterization.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ChainedParameterization.java
index 97cdb51f..9d8c171b 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ChainedParameterization.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ChainedParameterization.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/EmptyParameterization.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/EmptyParameterization.java
index 02802593..b43fed45 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/EmptyParameterization.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/EmptyParameterization.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ListParameterization.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ListParameterization.java
index b870b57b..3cb309f5 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ListParameterization.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/ListParameterization.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/MergedParameterization.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/MergedParameterization.java
index 9f765963..8e6e10c8 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/MergedParameterization.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/MergedParameterization.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/Parameterization.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/Parameterization.java
index 01c46583..32ab5bdb 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/Parameterization.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/Parameterization.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/SerializedParameterization.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/SerializedParameterization.java
index b3e3f214..7eb3cf45 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/SerializedParameterization.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/SerializedParameterization.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackParameters.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackParameters.java
index 5a20bd9e..a9ccda98 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackParameters.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackParameters.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
@@ -32,11 +32,9 @@ import java.util.Map;
 import de.lmu.ifi.dbs.elki.logging.LoggingUtil;
 import de.lmu.ifi.dbs.elki.utilities.ClassGenericsUtil;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.InternalParameterizationErrors;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.ParameterException;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.GlobalParameterConstraint;
 import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter;
-import de.lmu.ifi.dbs.elki.utilities.pairs.Pair;
 
 /**
  * Utility wrapper to track parameters for a configuration session.
@@ -54,7 +52,7 @@ public class TrackParameters implements Parameterization {
   /**
    * Tracking storage
    */
-  List<Pair<Object, Parameter<?>>> options = new ArrayList<>();
+  List<TrackedParameter> options = new ArrayList<>();
 
   /**
    * Tree information: parent links
@@ -70,7 +68,7 @@ public class TrackParameters implements Parameterization {
   /**
    * Current parent for nested parameterization
    */
-  Object cur = null;
+  Object owner = null;
 
   /**
    * Constructor.
@@ -83,18 +81,30 @@ public class TrackParameters implements Parameterization {
   }
 
   /**
+   * Constructor.
+   * 
+   * @param inner Inner parameterization to wrap.
+   * @param owner Class/instance owning the parameter
+   */
+  public TrackParameters(Parameterization inner, Object owner) {
+    super();
+    this.inner = inner;
+    this.owner = owner;
+  }
+
+  /**
    * Internal constructor, for nested tracking.
    * 
    * @param inner Inner parameterization
-   * @param option Option
+   * @param owner Object owning the current parameters
    * @param options List of options
    * @param parents Parent map
    * @param children Child map
    */
-  private TrackParameters(Parameterization inner, Object option, List<Pair<Object, Parameter<?>>> options, Map<Object, Object> parents, Map<Object, List<Object>> children) {
+  private TrackParameters(Parameterization inner, Object owner, List<TrackedParameter> options, Map<Object, Object> parents, Map<Object, List<Object>> children) {
     super();
-    this.inner = inner.descend(option);
-    this.cur = option;
+    this.inner = inner.descend(owner);
+    this.owner = owner;
     this.options = options;
     this.parents = parents;
     this.children = children;
@@ -113,7 +123,7 @@ public class TrackParameters implements Parameterization {
   @Override
   public boolean grab(Parameter<?> opt) {
     registerChild(opt);
-    options.add(new Pair<Object, Parameter<?>>(cur, opt));
+    options.add(new TrackedParameter(owner, opt));
     return inner.grab(opt);
   }
 
@@ -130,7 +140,7 @@ public class TrackParameters implements Parameterization {
   @Override
   public boolean setValueForOption(Parameter<?> opt) throws ParameterException {
     registerChild(opt);
-    options.add(new Pair<Object, Parameter<?>>(cur, opt));
+    options.add(new TrackedParameter(owner, opt));
     return inner.setValueForOption(opt);
   }
 
@@ -139,33 +149,19 @@ public class TrackParameters implements Parameterization {
    * 
    * @return Parameters seen
    */
-  public Collection<Pair<Object, Parameter<?>>> getAllParameters() {
+  public Collection<TrackedParameter> getAllParameters() {
     return options;
   }
 
-  /**
-   * Get the tracked parameters that were actually set.
-   * 
-   * @return Parameters given
-   */
-  public Collection<Pair<OptionID, Object>> getGivenParameters() {
-    ArrayList<Pair<OptionID, Object>> ret = new ArrayList<>();
-    for(Pair<Object, Parameter<?>> pair : options) {
-      if(pair.second.isDefined() && pair.second.getGivenValue() != null) {
-        ret.add(new Pair<>(pair.second.getOptionID(), pair.second.getGivenValue()));
-      }
-    }
-    return ret;
-  }
-
   @Override
   public boolean checkConstraint(GlobalParameterConstraint constraint) {
     return inner.checkConstraint(constraint);
   }
 
   /**
-   * {@inheritDoc} Track parameters using a shared options list with parent
-   * tracker.
+   * {@inheritDoc}
+   * 
+   * Track parameters using a shared options list with parent tracker.
    */
   @Override
   public Parameterization descend(Object option) {
@@ -174,14 +170,14 @@ public class TrackParameters implements Parameterization {
   }
 
   private void registerChild(Object opt) {
-    if(opt == cur) {
+    if(opt == owner) {
       LoggingUtil.exception("Options shouldn't have themselves as parents!", new Throwable());
     }
-    parents.put(opt, cur);
-    List<Object> c = children.get(cur);
+    parents.put(opt, owner);
+    List<Object> c = children.get(owner);
     if(c == null) {
       c = new ArrayList<>();
-      children.put(cur, c);
+      children.put(owner, c);
     }
     if(!c.contains(opt)) {
       c.add(opt);
@@ -204,7 +200,7 @@ public class TrackParameters implements Parameterization {
       return ClassGenericsUtil.tryInstantiate(r, c, this);
     }
     catch(Exception e) {
-      reportError(new InternalParameterizationErrors("Error instantiating internal class: "+c.getName(), e));
+      reportError(new InternalParameterizationErrors("Error instantiating internal class: " + c.getName(), e));
       return null;
     }
   }
@@ -215,7 +211,7 @@ public class TrackParameters implements Parameterization {
       return ClassGenericsUtil.tryInstantiate(c, c, this);
     }
     catch(Exception e) {
-      reportError(new InternalParameterizationErrors("Error instantiating internal class: "+c.getName(), e));
+      reportError(new InternalParameterizationErrors("Error instantiating internal class: " + c.getName(), e));
       return null;
     }
   }
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackedParameter.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackedParameter.java
new file mode 100644
index 00000000..01969302
--- /dev/null
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/TrackedParameter.java
@@ -0,0 +1,71 @@
+package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
+
+/*
+ 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 de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.Parameter;
+
+/**
+ * Class containing an object, and the associated value.
+ * 
+ * @author Erich Schubert
+ */
+public class TrackedParameter {
+  /**
+   * Option ID
+   */
+  private Object owner;
+
+  /**
+   * Parameter value
+   */
+  private Parameter<?> parameter;
+
+  /**
+   * Constructor.
+   *
+   * @param owner Object owning the parameter value
+   * @param parameter Parameter
+   */
+  public TrackedParameter(Object owner, Parameter<?> parameter) {
+    this.owner = owner;
+    this.parameter = parameter;
+  }
+
+  /**
+   * Get the owner object.
+   * 
+   * @return Parameter owner
+   */
+  public Object getOwner() {
+    return owner;
+  }
+
+  /**
+   * Get the parameter observed.
+   * 
+   * @return Parameter
+   */
+  public Parameter<?> getParameter() {
+    return parameter;
+  }
+}
\ No newline at end of file
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/UnParameterization.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/UnParameterization.java
index 2a05a766..dfdbe7ac 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/UnParameterization.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/UnParameterization.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2013
+ Copyright (C) 2014
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/package-info.java b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/package-info.java
index ce9c89b4..d330d343 100644
--- a/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/package-info.java
+++ b/src/de/lmu/ifi/dbs/elki/utilities/optionhandling/parameterization/package-info.java
@@ -8,7 +8,7 @@
 This file is part of ELKI:
 Environment for Developing KDD-Applications Supported by Index-Structures
 
-Copyright (C) 2013
+Copyright (C) 2014
 Ludwig-Maximilians-Universität München
 Lehr- und Forschungseinheit für Datenbanksysteme
 ELKI Development Team