Import Upstream version 0.5.0~beta2

20 files changed, 75 insertions, 80 deletions

diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/MultipleFilesOutput.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/MultipleFilesOutput.java
index 51eb5f8e..d891f1ee 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/MultipleFilesOutput.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/MultipleFilesOutput.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/SingleStreamOutput.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/SingleStreamOutput.java
index 1e4e5773..46472f52 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/SingleStreamOutput.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/SingleStreamOutput.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/StreamFactory.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/StreamFactory.java
index 1656d76d..0f27b354 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/StreamFactory.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/StreamFactory.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriteable.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriteable.java
index ffc522eb..a8de4c46 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriteable.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriteable.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriter.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriter.java
index bbe3212b..d947547f 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriter.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriter.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
@@ -29,8 +29,8 @@ import java.io.PrintStream;
 import java.util.BitSet;
 import java.util.Collection;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.Iterator;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 
@@ -51,7 +51,6 @@ import de.lmu.ifi.dbs.elki.datasource.bundle.SingleObjectBundle;
 import de.lmu.ifi.dbs.elki.distance.distancevalue.Distance;
 import de.lmu.ifi.dbs.elki.math.linearalgebra.Vector;
 import de.lmu.ifi.dbs.elki.result.CollectionResult;
-import de.lmu.ifi.dbs.elki.result.HierarchicalResult;
 import de.lmu.ifi.dbs.elki.result.IterableResult;
 import de.lmu.ifi.dbs.elki.result.OrderingResult;
 import de.lmu.ifi.dbs.elki.result.Result;
@@ -225,63 +224,57 @@ public class TextWriter {
    * @throws IOException on IO error
    */
   public void output(Database db, Result r, StreamFactory streamOpener) throws UnableToComplyException, IOException {
-    List<Relation<?>> ra = null;
-    List<OrderingResult> ro = null;
-    List<Clustering<? extends Model>> rc = null;
-    List<IterableResult<?>> ri = null;
-    List<SettingsResult> rs = null;
-    HashSet<Result> otherres = null;
+    List<Relation<?>> ra = new LinkedList<Relation<?>>();
+    List<OrderingResult> ro = new LinkedList<OrderingResult>();
+    List<Clustering<?>> rc = new LinkedList<Clustering<?>>();
+    List<IterableResult<?>> ri = new LinkedList<IterableResult<?>>();
+    List<SettingsResult> rs = new LinkedList<SettingsResult>();
+    List<Result> otherres = new LinkedList<Result>();
 
-    ra = ResultUtil.getRelations(r);
-    ro = ResultUtil.getOrderingResults(r);
-    rc = ResultUtil.getClusteringResults(r);
-    ri = ResultUtil.getIterableResults(r);
-    rs = ResultUtil.getSettingsResults(r);
     // collect other results
-    if(r instanceof HierarchicalResult) {
-      final List<Result> resultList = ResultUtil.filterResults((HierarchicalResult) r, Result.class);
-      otherres = new HashSet<Result>(resultList);
-      otherres.removeAll(ra);
-      otherres.removeAll(ro);
-      otherres.removeAll(rc);
-      otherres.removeAll(ri);
-      otherres.removeAll(rs);
-      otherres.remove(db);
-      Iterator<Result> it = otherres.iterator();
-      while(it.hasNext()) {
-        if(it.next() instanceof HierarchicalResult) {
-          it.remove();
+    {
+      for(Result res : ResultUtil.filteredResults(r, Result.class)) {
+        if(res instanceof Database) {
+          continue;
+        }
+        if(res instanceof Relation) {
+          ra.add((Relation<?>) res);
+          continue;
+        }
+        if(res instanceof OrderingResult) {
+          ro.add((OrderingResult) res);
+          continue;
+        }
+        if(res instanceof Clustering) {
+          rc.add((Clustering<?>) res);
+          continue;
+        }
+        if(res instanceof IterableResult) {
+          ri.add((IterableResult<?>) res);
+          continue;
+        }
+        if(res instanceof SettingsResult) {
+          rs.add((SettingsResult) res);
+          continue;
         }
+        otherres.add(res);
       }
     }
 
-    if(ra == null && ro == null && rc == null && ri == null) {
-      throw new UnableToComplyException("No printable result found.");
+    for(IterableResult<?> rii : ri) {
+      writeIterableResult(streamOpener, rii, rs);
     }
-
-    if(ri != null && ri.size() > 0) {
-      // TODO: associations are not passed to ri results.
-      for(IterableResult<?> rii : ri) {
-        writeIterableResult(streamOpener, rii, rs);
-      }
-    }
-    if(rc != null && rc.size() > 0) {
-      for(Clustering<?> c : rc) {
-        NamingScheme naming = new SimpleEnumeratingScheme(c);
-        for(Cluster<?> clus : c.getAllClusters()) {
-          writeClusterResult(db, streamOpener, clus, ra, naming, rs);
-        }
+    for(Clustering<?> c : rc) {
+      NamingScheme naming = new SimpleEnumeratingScheme(c);
+      for(Cluster<?> clus : c.getAllClusters()) {
+        writeClusterResult(db, streamOpener, clus, ra, naming, rs);
       }
     }
-    if(ro != null && ro.size() > 0) {
-      for(OrderingResult ror : ro) {
-        writeOrderingResult(db, streamOpener, ror, ra, rs);
-      }
+    for(OrderingResult ror : ro) {
+      writeOrderingResult(db, streamOpener, ror, ra, rs);
     }
-    if(otherres != null && otherres.size() > 0) {
-      for(Result otherr : otherres) {
-        writeOtherResult(streamOpener, otherr, rs);
-      }
+    for(Result otherr : otherres) {
+      writeOtherResult(streamOpener, otherr, rs);
     }
   }
 
@@ -290,16 +283,18 @@ public class TextWriter {
     // Write database element itself.
     for(int i = 0; i < bundle.metaLength(); i++) {
       Object obj = bundle.data(i);
-      TextWriterWriterInterface<?> owriter = out.getWriterFor(obj);
-      if(owriter == null) {
-        throw new UnableToComplyException("No handler for database object itself: " + obj.getClass().getSimpleName());
-      }
-      String lbl = null;
-      // TODO: ugly compatibility hack...
-      if(TypeUtil.DBID.isAssignableFromType(bundle.meta(i))) {
-        lbl = "ID";
+      if(obj != null) {
+        TextWriterWriterInterface<?> owriter = out.getWriterFor(obj);
+        if(owriter == null) {
+          throw new UnableToComplyException("No handler for database object itself: " + obj.getClass().getSimpleName());
+        }
+        String lbl = null;
+        // TODO: ugly compatibility hack...
+        if(TypeUtil.DBID.isAssignableFromType(bundle.meta(i))) {
+          lbl = "ID";
+        }
+        owriter.writeObject(out, lbl, obj);
       }
-      owriter.writeObject(out, lbl, obj);
     }
 
     Collection<Relation<?>> dbrels = db.getRelations();
@@ -307,7 +302,7 @@ public class TextWriter {
     if(ra != null) {
       for(Relation<?> a : ra) {
         // Avoid duplicated output.
-        if (dbrels.contains(a)) {
+        if(dbrels.contains(a)) {
           continue;
         }
         String label = a.getShortName();
@@ -357,7 +352,7 @@ public class TextWriter {
     // Write cluster information
     out.commentPrintLn("Cluster: " + naming.getNameFor(clus));
     Model model = clus.getModel();
-    if (model != ClusterModel.CLUSTER) {
+    if(model != ClusterModel.CLUSTER && model != null) {
       TextWriterWriterInterface<?> mwri = writers.getHandler(model);
       mwri.writeObject(out, null, model);
     }
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterStream.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterStream.java
index b59a09e9..ce60c856 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterStream.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterStream.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java
index ab572896..cfaa3373 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/TextWriterWriterInterface.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/NamingScheme.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/NamingScheme.java
index c5d9cf72..4b2c099f 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/NamingScheme.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/NamingScheme.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.naming;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/SimpleEnumeratingScheme.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/SimpleEnumeratingScheme.java
index 2341f258..baff04e2 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/SimpleEnumeratingScheme.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/SimpleEnumeratingScheme.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.naming;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/package-info.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/package-info.java
index 8d10da45..600e731e 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/package-info.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/naming/package-info.java
@@ -5,7 +5,7 @@
 This file is part of ELKI:
 Environment for Developing KDD-Applications Supported by Index-Structures
 
-Copyright (C) 2011
+Copyright (C) 2012
 Ludwig-Maximilians-Universität München
 Lehr- und Forschungseinheit für Datenbanksysteme
 ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/package-info.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/package-info.java
index b2abeb5b..872df780 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/package-info.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/package-info.java
@@ -6,7 +6,7 @@
 This file is part of ELKI:
 Environment for Developing KDD-Applications Supported by Index-Structures
 
-Copyright (C) 2011
+Copyright (C) 2012
 Ludwig-Maximilians-Universität München
 Lehr- und Forschungseinheit für Datenbanksysteme
 ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleDoublePair.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleDoublePair.java
index b8f25b6a..4af9d8a4 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleDoublePair.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterDoubleDoublePair.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.writers;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectArray.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectArray.java
index bec183d8..3a73d52a 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectArray.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectArray.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.writers;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java
index ddb753ac..d4da18f5 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectComment.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.writers;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectInline.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectInline.java
index 12717da7..a621ab4b 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectInline.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterObjectInline.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.writers;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterPair.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterPair.java
index c8bd83b2..3c1440bc 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterPair.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterPair.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.writers;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java
index 491f803d..87a3661b 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTextWriteable.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.writers;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTriple.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTriple.java
index ce3c3d70..55dd7106 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTriple.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterTriple.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.writers;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterVector.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterVector.java
index 0ebf4ae4..1452c432 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterVector.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/TextWriterVector.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.result.textwriter.writers;
  This file is part of ELKI:
  Environment for Developing KDD-Applications Supported by Index-Structures
 
- Copyright (C) 2011
+ Copyright (C) 2012
  Ludwig-Maximilians-Universität München
  Lehr- und Forschungseinheit für Datenbanksysteme
  ELKI Development Team
diff --git a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/package-info.java b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/package-info.java
index 66c5f706..c83dd767 100644
--- a/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/package-info.java
+++ b/src/de/lmu/ifi/dbs/elki/result/textwriter/writers/package-info.java
@@ -6,7 +6,7 @@
 This file is part of ELKI:
 Environment for Developing KDD-Applications Supported by Index-Structures
 
-Copyright (C) 2011
+Copyright (C) 2012
 Ludwig-Maximilians-Universität München
 Lehr- und Forschungseinheit für Datenbanksysteme
 ELKI Development Team