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chrtannuschrtannus
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Using a Task to filter nodes/edges in order to prevent the UI from being frozen.
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-124
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3 files changed

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-124
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‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/ApplicationModule.java‎

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import org.baderlab.csplugins.enrichmentmap.task.CreateEMNetworkTask;
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import org.baderlab.csplugins.enrichmentmap.task.CreateEMViewTask;
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import org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory;
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import org.baderlab.csplugins.enrichmentmap.task.FilterNodesEdgesTask;
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import org.baderlab.csplugins.enrichmentmap.task.RemoveSignatureDataSetsTask;
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import org.baderlab.csplugins.enrichmentmap.view.creation.EditDataSetPanel;
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import org.baderlab.csplugins.enrichmentmap.view.creation.ErrorMessageDialog;
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installFactory(CreateEMNetworkTask.Factory.class);
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installFactory(CreateEMViewTask.Factory.class);
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installFactory(ApplyEMStyleTask.Factory.class);
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installFactory(FilterNodesEdgesTask.Factory.class);
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installFactory(ClusterRankingOption.Factory.class);
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installFactory(HeatMapParentPanel.Factory.class);
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installFactory(HeatMapMainPanel.Factory.class);

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/FilterNodesEdgesTask.java‎

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package org.baderlab.csplugins.enrichmentmap.task;
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import static org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder.FILTERED_OUT_EDGE_TRANSPARENCY;
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import static org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder.FILTERED_OUT_NODE_TRANSPARENCY;
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import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_LABEL_TRANSPARENCY;
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import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_TRANSPARENCY;
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import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_VISIBLE;
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import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_BORDER_TRANSPARENCY;
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import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_LABEL_TRANSPARENCY;
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import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_TRANSPARENCY;
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import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_VISIBLE;
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import java.util.List;
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import java.util.Set;
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import org.baderlab.csplugins.enrichmentmap.style.NullCustomGraphics;
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import org.cytoscape.model.CyEdge;
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import org.cytoscape.model.CyNetwork;
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import org.cytoscape.model.CyNode;
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import org.cytoscape.view.model.CyNetworkView;
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import org.cytoscape.view.model.View;
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import org.cytoscape.view.model.VisualLexicon;
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import org.cytoscape.view.model.VisualProperty;
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import org.cytoscape.view.presentation.RenderingEngineManager;
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import org.cytoscape.work.AbstractTask;
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import org.cytoscape.work.TaskMonitor;
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import com.google.inject.Inject;
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import com.google.inject.assistedinject.Assisted;
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public class FilterNodesEdgesTask extends AbstractTask {
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public enum FilterMode {
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HIDE("Hide filtered out nodes and edges"),
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HIGHLIGHT("Highlight filtered nodes and edges"),
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SELECT("Select filtered nodes and edges");
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private final String label;
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private FilterMode(String label) {
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this.label = label;
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}
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@Override
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public String toString() {
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return label;
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}
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}
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@Inject private RenderingEngineManager renderingEngineManager;
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private final CyNetworkView networkView;
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private final Set<CyNode> nodes;
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private final Set<CyEdge> edges;
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private final FilterMode filterMode;
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public interface Factory {
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FilterNodesEdgesTask create(CyNetworkView networkView, Set<CyNode> nodes, Set<CyEdge> filteredEdges,
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FilterMode filterMode);
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}
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@Inject
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public FilterNodesEdgesTask(@Assisted CyNetworkView networkView, @Assisted Set<CyNode> nodes,
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@Assisted Set<CyEdge> edges, @Assisted FilterMode filterMode) {
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this.networkView = networkView;
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this.nodes = nodes;
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this.edges = edges;
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this.filterMode = filterMode;
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}
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@Override
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public void run(TaskMonitor taskMonitor) {
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taskMonitor.setTitle("Filtering Nodes and Edges");
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taskMonitor.setStatusMessage("Filtering nodes...");
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taskMonitor.setProgress(0.0);
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filterNodes(nodes, taskMonitor);
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if (cancelled)
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return;
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taskMonitor.setStatusMessage("Filtering edges...");
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taskMonitor.setProgress(0.2);
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filterEdges(nodes, edges, taskMonitor, 0.2);
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taskMonitor.setProgress(1.0);
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}
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private void filterNodes(Set<CyNode> nodes, TaskMonitor taskMonitor) {
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CyNetwork net = networkView.getModel();
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for (CyNode n : net.getNodeList()) {
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if (cancelled)
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return;
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final View<CyNode> nv = networkView.getNodeView(n);
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if (nv == null)
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continue; // Should never happen!
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boolean filteredIn = nodes.contains(n);
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VisualLexicon lexicon = renderingEngineManager.getDefaultVisualLexicon();
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VisualProperty<?> customGraphics1 = lexicon.lookup(CyNode.class, "NODE_CUSTOMGRAPHICS_1");
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// Don't forget to remove all previous locked values first!
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nv.clearValueLock(NODE_VISIBLE);
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nv.clearValueLock(NODE_TRANSPARENCY);
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nv.clearValueLock(NODE_BORDER_TRANSPARENCY);
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nv.clearValueLock(NODE_LABEL_TRANSPARENCY);
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if (customGraphics1 != null)
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nv.clearValueLock(customGraphics1);
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if (filteredIn) {
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if (filterMode == FilterMode.SELECT)
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net.getRow(n).set(CyNetwork.SELECTED, true);
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} else {
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switch (filterMode) {
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case HIDE:
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net.getRow(n).set(CyNetwork.SELECTED, false);
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nv.setLockedValue(NODE_VISIBLE, false);
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break;
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case HIGHLIGHT:
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nv.setLockedValue(NODE_TRANSPARENCY, FILTERED_OUT_NODE_TRANSPARENCY);
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nv.setLockedValue(NODE_BORDER_TRANSPARENCY, FILTERED_OUT_NODE_TRANSPARENCY);
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nv.setLockedValue(NODE_LABEL_TRANSPARENCY, 0);
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if (customGraphics1 != null)
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nv.setLockedValue(customGraphics1, NullCustomGraphics.getNullObject());
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break;
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case SELECT:
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net.getRow(n).set(CyNetwork.SELECTED, false);
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break;
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}
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}
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}
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}
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private void filterEdges(Set<CyNode> nodes, Set<CyEdge> edges, TaskMonitor taskMonitor, double initialProgress) {
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CyNetwork net = networkView.getModel();
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List<CyEdge> edgeList = net.getEdgeList();
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int total = edgeList.size();
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int count = 0;
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float progress = (float) initialProgress;
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for (CyEdge e : edgeList) {
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if (cancelled)
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return;
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final View<CyEdge> ev = networkView.getEdgeView(e);
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if (ev == null)
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continue; // Should never happen!
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boolean filteredIn = edges.contains(e) && nodes.contains(e.getSource()) && nodes.contains(e.getTarget());
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// Don't forget to remove all locked values first!
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ev.clearValueLock(EDGE_VISIBLE);
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ev.clearValueLock(EDGE_TRANSPARENCY);
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ev.clearValueLock(EDGE_LABEL_TRANSPARENCY);
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if (filteredIn) {
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if (filterMode == FilterMode.SELECT)
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net.getRow(e).set(CyNetwork.SELECTED, true);
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} else {
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switch (filterMode) {
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case HIDE:
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net.getRow(e).set(CyNetwork.SELECTED, false);
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ev.setLockedValue(EDGE_VISIBLE, false);
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break;
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case HIGHLIGHT:
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ev.setLockedValue(EDGE_TRANSPARENCY, FILTERED_OUT_EDGE_TRANSPARENCY);
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ev.setLockedValue(EDGE_LABEL_TRANSPARENCY, FILTERED_OUT_EDGE_TRANSPARENCY);
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break;
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case SELECT:
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net.getRow(e).set(CyNetwork.SELECTED, false);
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break;
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}
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}
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// Use only 2 decimals to avoid too many UI updates when setting very small numbers
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float newProgress = Math.round((initialProgress + count * (1 - initialProgress) / total) * 100) / 100.0f;
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if (newProgress != progress) {
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taskMonitor.setProgress(newProgress);
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progress = newProgress;
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}
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count++;
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}
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}
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}

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