/*
* #%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.matrix.model.matrix;
import com.google.common.base.Strings;
import org.gitools.api.matrix.IAnnotations;
import org.gitools.api.matrix.IMatrixDimension;
import org.gitools.api.matrix.IMatrixLayer;
import org.gitools.matrix.model.MatrixLayer;
import org.gitools.matrix.model.MatrixLayers;
import org.gitools.matrix.model.hashmatrix.HashMatrix;
import java.util.AbstractList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import static org.gitools.api.matrix.MatrixDimensionKey.ROWS;
public class AnnotationMatrix extends HashMatrix implements IAnnotations {
public static String METADATA_DESCRIPTION = "description";
private Map<String, Map<String, String>> layersMetadata;
private Collection<String> labels;
public AnnotationMatrix() {
super(new MatrixLayers(), ROWS);
this.layersMetadata = new HashMap<>();
this.labels = new LabelsAdapter();
}
public void addAnnotations(IAnnotations annotations) {
// Copy all the annotations
for (String identifier : annotations.getIdentifiers()) {
for (String label : annotations.getLabels()) {
setAnnotation(identifier, label, annotations.getAnnotation(identifier, label));
}
}
// Copy annotations metadata
for (String label : annotations.getLabels()) {
for (String key : annotations.getMetadataKeys()) {
String metadata = annotations.getAnnotationMetadata(key, label);
if (!Strings.isNullOrEmpty(metadata)) {
setAnnotationMetadata(key, label, metadata);
}
}
}
}
@Override
public IMatrixDimension getIdentifiers() {
return getDimension(ROWS);
}
@Override
public Collection<String> getMetadataKeys() {
return layersMetadata.keySet();
}
@Override
public Collection<String> getLabels() {
return labels;
}
@Override
public void removeAnnotations(String label) {
// Remove metadata
for (String key : layersMetadata.keySet()) {
layersMetadata.get(key).remove(label);
}
// Remove layer values
removeLayer(getLayers().get(label));
}
@Override
public String getAnnotation(String identifier, String label) {
return get(getLayer(label), identifier);
}
private IMatrixLayer<String> getLayer(String label) {
return getLayers().get(label);
}
public void setAnnotation(String identifier, String layerId, String annotationValue) {
if (getLayer(layerId) == null) {
addLayer(new MatrixLayer<>(layerId, String.class));
}
set(getLayer(layerId), annotationValue, identifier);
}
@Override
public String getAnnotationMetadata(String key, String label) {
if (!layersMetadata.containsKey(key)) {
return null;
}
return layersMetadata.get(key).get(label);
}
public void setAnnotationMetadata(String key, String annotationLabel, String value) {
if (value == null || value.isEmpty()) {
return;
}
Map<String, String> ketMetadata = layersMetadata.get(key);
if (ketMetadata == null) {
ketMetadata = new HashMap<>();
layersMetadata.put(key, ketMetadata);
}
ketMetadata.put(annotationLabel, value);
}
private class LabelsAdapter extends AbstractList<String> {
@Override
public String get(int index) {
IMatrixLayer layer = getLayers().get(index);
return (layer == null ? null : layer.getId());
}
@Override
public int size() {
return getLayers().size();
}
}
}