/*
* Copyright 2012 EMBL - European Bioinformatics Institute
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package uk.ac.ebi.fg.annotare2.magetabcheck.modelimpl.limpopo.sdrf;
import uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.AssayNode;
import uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.SDRFAttribute;
import uk.ac.ebi.fg.annotare2.magetabcheck.model.sdrf.*;
import java.util.Collection;
import java.util.List;
import static com.google.common.collect.Lists.newArrayList;
/**
* @author Olga Melnichuk
*/
class LimpopoBasedAssayNode extends LimpopoBasedSdrfNode<AssayNode> implements SdrfAssayNode {
protected LimpopoBasedAssayNode(AssayNode node, SdrfHelper helper) {
super(node, helper);
}
@Override
protected Collection<SDRFAttribute> getRawAttributes() {
List<SDRFAttribute> attributes = newArrayList();
attributes.add(node().technologyType);
attributes.addAll(node().factorValues);
attributes.addAll(node().arrayDesigns);
return attributes;
}
@Override
public SdrfTechnologyTypeAttribute getTechnologyType() {
return getAttribute(SdrfTechnologyTypeAttribute.class);
}
@Override
public Collection<SdrfFactorValueAttribute> getFactorValues() {
return getAttributes(SdrfFactorValueAttribute.class);
}
@Override
public Collection<SdrfArrayDesignAttribute> getArrayDesigns() {
return getAttributes(SdrfArrayDesignAttribute.class);
}
@Override
public Collection<SdrfComment> getComments() {
List<SdrfComment> comments = newArrayList();
for (String commentName : node().comments.keySet()) {
comments.add(new LimpopoBasedSdrfComment(commentName, node().comments.get(commentName)));
}
return comments;
}
}