/*
* This file is part of ADDIS (Aggregate Data Drug Information System).
* ADDIS is distributed from http://drugis.org/.
* Copyright © 2009 Gert van Valkenhoef, Tommi Tervonen.
* Copyright © 2010 Gert van Valkenhoef, Tommi Tervonen, Tijs Zwinkels,
* Maarten Jacobs, Hanno Koeslag, Florin Schimbinschi, Ahmad Kamal, Daniel
* Reid.
* Copyright © 2011 Gert van Valkenhoef, Ahmad Kamal, Daniel Reid, Florin
* Schimbinschi.
* Copyright © 2012 Gert van Valkenhoef, Daniel Reid, Joël Kuiper, Wouter
* Reckman.
* Copyright © 2013 Gert van Valkenhoef, Joël Kuiper.
*
* 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/>.
*/
package org.drugis.addis.presentation.wizard;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.util.List;
import org.apache.commons.collections15.Predicate;
import org.drugis.addis.entities.Arm;
import org.drugis.addis.entities.BasicMeasurement;
import org.drugis.addis.entities.BasicRateMeasurement;
import org.drugis.addis.entities.Indication;
import org.drugis.addis.entities.OutcomeMeasure;
import org.drugis.addis.entities.RateVariableType;
import org.drugis.addis.entities.Study;
import org.drugis.addis.entities.analysis.BenefitRiskAnalysis.AnalysisType;
import org.drugis.addis.entities.analysis.DecisionContext;
import org.drugis.addis.entities.analysis.StudyBenefitRiskAnalysis;
import org.drugis.addis.presentation.ModifiableHolder;
import org.drugis.addis.presentation.ValueHolder;
import org.drugis.common.beans.FilteredObservableList;
import com.jgoodies.binding.list.ArrayListModel;
import com.jgoodies.binding.list.ObservableList;
import com.jgoodies.binding.value.ValueModel;
public class StudyCriteriaAndAlternativesPresentation extends CriteriaAndAlternativesPresentation<Arm> {
public class IndicationFilter implements Predicate<Study> {
private final Indication d_indication;
public IndicationFilter(Indication i) {
d_indication = i;
}
public boolean evaluate(Study s) {
return s.getIndication().equals(d_indication);
}
}
private final ModifiableHolder<Study> d_studyModel;
private final ArrayListModel<OutcomeMeasure> d_availableCriteria;
private final FilteredObservableList<Study> d_studiesWithIndicationHolder;
public StudyCriteriaAndAlternativesPresentation(ValueHolder<Indication> indication, ModifiableHolder<AnalysisType> analysisType, ObservableList<Study> studies) {
super(indication, analysisType);
d_studyModel = new ModifiableHolder<Study>();
d_availableCriteria = new ArrayListModel<OutcomeMeasure>();
d_studyModel.addValueChangeListener(new PropertyChangeListener() {
@Override
public void propertyChange(PropertyChangeEvent evt) {
studyChanged();
}
});
d_studiesWithIndicationHolder = new FilteredObservableList<Study>(studies, new IndicationFilter(d_indicationModel.getValue()));
d_indicationModel.addValueChangeListener(new PropertyChangeListener() {
@Override
public void propertyChange(PropertyChangeEvent evt) {
d_studiesWithIndicationHolder.setFilter(new IndicationFilter(d_indicationModel.getValue()));
}
});
}
@Override
public ValueModel getCompleteModel() {
return d_completeModel;
}
public ModifiableHolder<Study> getStudyModel() {
return d_studyModel;
}
@Override
public ObservableList<OutcomeMeasure> getCriteriaListModel() {
return d_availableCriteria;
}
@Override
protected void reset() {
d_studyModel.setValue(null);
}
private void studyChanged() {
d_selectedCriteria.clear();
d_selectedAlternatives.clear();
d_availableCriteria.clear();
d_availableAlternatives.clear();
d_baselineModel.setValue(null);
if (d_indicationModel.getValue() != null && d_studyModel.getValue() != null) {
initializeValues();
}
}
private void initializeValues() {
d_availableCriteria.addAll(d_studyModel.getValue().getOutcomeMeasures());
initCriteria();
initAlternatives(d_studyModel.getValue().getArms());
}
@Override
public StudyBenefitRiskAnalysis createAnalysis(String name, DecisionContext context) {
List<Arm> alternatives = getSelectedAlternatives();
List<OutcomeMeasure> studyAnalyses = getSelectedCriteria();
StudyBenefitRiskAnalysis sbr = new StudyBenefitRiskAnalysis(name, d_indicationModel.getValue(), d_studyModel.getValue(),
studyAnalyses, (Arm) d_baselineModel.getValue(), alternatives, d_analysisTypeHolder.getValue(), context);
return sbr;
}
@Override
protected boolean getAlternativeShouldBeEnabled(Arm alt) {
if (!super.getAlternativeShouldBeEnabled(alt) || d_studyModel.getValue() == null) {
return false;
}
for (OutcomeMeasure crit : getSelectedCriteria()) {
BasicMeasurement measurement = d_studyModel.getValue().getMeasurement(crit, alt);
if (measurement == null || !measurement.isComplete()) {
return false;
}
}
return true;
}
@Override
protected boolean getCriterionShouldBeEnabled(OutcomeMeasure crit) {
if (d_studyModel.getValue() == null) {
return false;
}
Study study = d_studyModel.getValue();
// Check that there are at least 2 non-missing measurements
List<Arm> goodArms = new ArrayListModel<Arm>();
for (Arm arm : study.getArms()) {
if (study.getMeasurement(crit, arm) != null && study.getMeasurement(crit, arm).isComplete()) {
goodArms.add(arm);
}
}
if (goodArms.size() < 2) {
return false;
}
// Check that at least one arm has non-zero measurement
if (crit.getVariableType() instanceof RateVariableType) {
boolean haveNonZero = false;
boolean haveNonSat = false;
for (Arm arm : goodArms) {
BasicRateMeasurement m = (BasicRateMeasurement) study.getMeasurement(crit, arm);
if (!m.getRate().equals(0)) {
haveNonZero = true;
}
if (!m.getRate().equals(m.getSampleSize())) {
haveNonSat = true;
}
}
if (!haveNonZero || !haveNonSat) {
return false;
}
}
return super.getCriterionShouldBeEnabled(crit);
}
public ObservableList<Study> getStudiesWithIndication() {
return d_studiesWithIndicationHolder;
}
}