diff options
Diffstat (limited to 'src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering')
3 files changed, 12 insertions, 16 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/AbstractBiclustering.java b/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/AbstractBiclustering.java index 8b875340..f57a66e3 100644 --- a/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/AbstractBiclustering.java +++ b/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/AbstractBiclustering.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.algorithm.clustering.biclustering; 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 @@ -58,7 +58,7 @@ import de.lmu.ifi.dbs.elki.utilities.exceptions.ExceptionMessages; * columns relate to the attribute values of these objects * @param <M> Cluster model type */ -public abstract class AbstractBiclustering<V extends NumberVector<?>, M extends BiclusterModel> extends AbstractAlgorithm<Clustering<M>> implements ClusteringAlgorithm<Clustering<M>> { +public abstract class AbstractBiclustering<V extends NumberVector, M extends BiclusterModel> extends AbstractAlgorithm<Clustering<M>> implements ClusteringAlgorithm<Clustering<M>> { /** * Keeps the currently set database. */ @@ -218,7 +218,7 @@ public abstract class AbstractBiclustering<V extends NumberVector<?>, M extends * @return integer column ids */ protected int[] colsBitsetToIDs(long[] cols) { - int[] colIDs = new int[(int) BitsUtil.cardinality(cols)]; + int[] colIDs = new int[BitsUtil.cardinality(cols)]; int colsIndex = 0; for (int cpos = 0, clpos = 0; clpos < cols.length; ++clpos) { long clong = cols[clpos]; @@ -243,7 +243,7 @@ public abstract class AbstractBiclustering<V extends NumberVector<?>, M extends * @return integer row ids */ protected ArrayDBIDs rowsBitsetToIDs(long[] rows) { - ArrayModifiableDBIDs rowIDs = DBIDUtil.newArray((int) BitsUtil.cardinality(rows)); + ArrayModifiableDBIDs rowIDs = DBIDUtil.newArray(BitsUtil.cardinality(rows)); DBIDArrayIter iter = this.rowIDs.iter(); outer: for (int rlpos = 0; rlpos < rows.length; ++rlpos) { long rlong = rows[rlpos]; @@ -265,7 +265,7 @@ public abstract class AbstractBiclustering<V extends NumberVector<?>, M extends } /** - * Provides the number of rows of the data matrix. + * The number of rows of the data matrix. * * @return the number of rows of the data matrix */ @@ -274,7 +274,7 @@ public abstract class AbstractBiclustering<V extends NumberVector<?>, M extends } /** - * Provides the number of columns of the data matrix. + * The number of columns of the data matrix. * * @return the number of columns of the data matrix */ diff --git a/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/ChengAndChurch.java b/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/ChengAndChurch.java index e110faff..57511b3e 100644 --- a/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/ChengAndChurch.java +++ b/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/ChengAndChurch.java @@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.algorithm.clustering.biclustering; 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 @@ -64,7 +64,7 @@ import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter; * @param <V> Vector type. */ @Reference(authors = "Y. Cheng, G. M. Church", title = "Biclustering of expression data", booktitle = "Proc. 8th International Conference on Intelligent Systems for Molecular Biology (ISMB)") -public class ChengAndChurch<V extends NumberVector<?>> extends AbstractBiclustering<V, BiclusterWithInversionsModel> { +public class ChengAndChurch<V extends NumberVector> extends AbstractBiclustering<V, BiclusterWithInversionsModel> { /** * The logger for this class. */ @@ -555,9 +555,7 @@ public class ChengAndChurch<V extends NumberVector<?>> extends AbstractBicluster // LOG.verbose("Total number of masked values: " + maskedVals.size() + // "\n"); } - if(prog != null) { - prog.incrementProcessed(LOG); - } + LOG.incrementProcessed(prog); } // Add a noise cluster, full-dimensional. if(!noise.isEmpty()) { @@ -565,9 +563,7 @@ public class ChengAndChurch<V extends NumberVector<?>> extends AbstractBicluster BiclusterWithInversionsModel model = new BiclusterWithInversionsModel(colsBitsetToIDs(allcols), DBIDUtil.EMPTYDBIDS); result.addToplevelCluster(new Cluster<>(noise, true, model)); } - if(prog != null) { - prog.ensureCompleted(LOG); - } + LOG.ensureCompleted(prog); return result; } @@ -805,7 +801,7 @@ public class ChengAndChurch<V extends NumberVector<?>> extends AbstractBicluster * * @param <V> Vector type */ - public static class Parameterizer<V extends NumberVector<?>> extends AbstractParameterizer { + public static class Parameterizer<V extends NumberVector> extends AbstractParameterizer { /** * Parameter to specify the distribution of replacement values when masking * a cluster. diff --git a/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/package-info.java b/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/package-info.java index 21363bfc..ed3c8c64 100644 --- a/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/package-info.java +++ b/src/de/lmu/ifi/dbs/elki/algorithm/clustering/biclustering/package-info.java @@ -7,7 +7,7 @@ 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 |