/*
* #%L
* gitools-core
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.analysis.clustering.annotations;
import org.gitools.analysis.clustering.ClusteringData;
import org.gitools.analysis.clustering.ClusteringDataInstance;
import org.gitools.heatmap.HeatmapDimension;
import org.gitools.utils.textpattern.TextPattern;
import org.gitools.utils.textpattern.TextPattern.VariableValueResolver;
public class AnnPatClusteringData implements ClusteringData {
public final static String NA = "N/A";
private final HeatmapDimension dimension;
private final TextPattern pat;
public AnnPatClusteringData(HeatmapDimension dimension, String pattern) {
this.dimension = dimension;
this.pat = new TextPattern(pattern);
}
@Override
public int getSize() {
return dimension.size();
}
@Override
public String getLabel(int index) {
return dimension.getLabel(index);
}
@Override
public Iterable<String> getLabels() {
return dimension;
}
@Override
public ClusteringDataInstance getInstance(String label) {
return new Instance(new AnnotationResolver(dimension.getAnnotations(), label, NA));
}
public class Instance implements ClusteringDataInstance {
private final VariableValueResolver resolver;
public Instance(VariableValueResolver resolver) {
this.resolver = resolver;
}
@Override
public int getNumAttributes() {
return 1;
}
@Override
public String getAttributeName(int attribute) {
return "value";
}
@Override
public Class<?> getValueClass(int attribute) {
return String.class;
}
@Override
public Object getValue(int attribute) {
return pat.generate(resolver);
}
@Override
public <T> T getTypedValue(int attribute, Class<T> valueClass) {
if (!String.class.equals(valueClass)) {
throw new RuntimeException("Unsupported value class: " + valueClass.getName());
}
return (T) getValue(attribute);
}
}
}