Java tutorial
/* * 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, Jol Kuiper, Wouter * Reckman. * Copyright 2013 Gert van Valkenhoef, Jol 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; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; import java.util.HashSet; import java.util.Map; import java.util.Set; import javax.swing.event.ListDataEvent; import javax.swing.event.ListDataListener; import org.apache.commons.collections15.CollectionUtils; import org.drugis.addis.entities.Arm; import org.drugis.addis.entities.OutcomeMeasure; import org.drugis.addis.entities.Study; import org.drugis.addis.entities.treatment.TreatmentDefinition; import org.jgrapht.graph.ListenableUndirectedGraph; import com.jgoodies.binding.list.ObservableList; public class TreatmentDefinitionsGraphModel extends ListenableUndirectedGraph<TreatmentDefinitionsGraphModel.Vertex, TreatmentDefinitionsGraphModel.Edge> { private static final long serialVersionUID = -7829573824453914937L; public static class Vertex { private TreatmentDefinition d_definition; private int d_sampleSize; public Vertex(TreatmentDefinition def, int size) { d_definition = def; d_sampleSize = size; } public TreatmentDefinition getTreatmentDefinition() { return d_definition; } public int getSampleSize() { return d_sampleSize; } @Override public String toString() { return d_definition.getLabel(); } } public static class Edge { private int d_studies; public Edge(int studies) { d_studies = studies; } public int getStudyCount() { return d_studies; } public void setStudyCount(int studies) { d_studies = studies; } @Override public String toString() { return Integer.toString(d_studies); } } protected ObservableList<TreatmentDefinition> d_definitions; private ObservableList<Study> d_studies; protected boolean d_rebuildNeeded; private final ValueHolder<OutcomeMeasure> d_om; private Map<TreatmentDefinition, Set<Study>> d_studiesMeasuringDefinition; public TreatmentDefinitionsGraphModel(ObservableList<Study> studies, ObservableList<TreatmentDefinition> definitions, ValueHolder<OutcomeMeasure> om) { super(Edge.class); d_definitions = definitions; d_studies = studies; d_om = om; ListDataListener rebuildNeededListener = new ListDataListener() { public void intervalRemoved(ListDataEvent e) { d_rebuildNeeded = true; } public void intervalAdded(ListDataEvent e) { d_rebuildNeeded = true; } public void contentsChanged(ListDataEvent e) { d_rebuildNeeded = true; } }; d_rebuildNeeded = true; d_studies.addListDataListener(rebuildNeededListener); d_definitions.addListDataListener(rebuildNeededListener); rebuildGraph(); } public void rebuildGraph() { if (!d_rebuildNeeded) { return; } initStudiesMeasuringDefinition(); // Add vertices ArrayList<Vertex> verts = new ArrayList<Vertex>(vertexSet()); removeAllVertices(verts); for (TreatmentDefinition d : d_definitions) { addVertex(new Vertex(d, calculateSampleSize(d))); } // Add edges ArrayList<Edge> edges = new ArrayList<Edge>(edgeSet()); removeAllEdges(edges); for (int i = 0; i < (d_definitions.size() - 1); ++i) { for (int j = i + 1; j < d_definitions.size(); ++j) { Collection<Study> studies = getStudies(d_definitions.get(i), d_definitions.get(j)); if (studies.size() > 0) { addEdge(findVertex(d_definitions.get(i)), findVertex(d_definitions.get(j)), new Edge(studies.size())); } } } d_rebuildNeeded = false; } private void initStudiesMeasuringDefinition() { d_studiesMeasuringDefinition = new HashMap<TreatmentDefinition, Set<Study>>(); for (TreatmentDefinition d : d_definitions) { d_studiesMeasuringDefinition.put(d, new HashSet<Study>()); for (Study s : d_studies) { for (Arm arm : s.getArms()) { if (d.match(s, arm) && s.getOutcomeMeasures().contains(d_om.getValue())) { d_studiesMeasuringDefinition.get(d).add(s); } } } } } public Vertex findVertex(TreatmentDefinition definition) { for (Vertex v : vertexSet()) { if (v.getTreatmentDefinition().equals(definition)) { return v; } } return null; } private int calculateSampleSize(TreatmentDefinition d) { int n = 0; for (Study s : getStudies(d)) { n += s.getSampleSize(); } return n; } /** * Return the list of drugs that are included in at least one of the studies having the correct indication * and outcome. */ public ObservableList<TreatmentDefinition> getDefinitions() { return d_definitions; } /** * Return the studies with the correct indication and outcome that compare the given drugs. */ public Collection<Study> getStudies(TreatmentDefinition a, TreatmentDefinition b) { return CollectionUtils.intersection(getStudies(a), getStudies(b)); } /** * Return the studies with the correct indication and outcome that include the given drug. */ public Collection<Study> getStudies(TreatmentDefinition d) { return d_studiesMeasuringDefinition.get(d); } }