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Use NetworkImageFactory service to create network images. #6

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Use NetworkImageFactory service to create network images. #6

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304d84f
Use NetworkImageFactory service to create network images.
mikekucera Dec 4, 2020
da3e6c7
Merge branch 'master' into feature/network_image_factory
chrtannus Jun 1, 2022
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4 changes: 2 additions & 2 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@
<properties>
<bundle.symbolicName>org.cytoscape.mcode</bundle.symbolicName>
<bundle.namespace>ca.utoronto.tdccbr.mcode.internal</bundle.namespace>
<cytoscape.api.version>3.8.0</cytoscape.api.version>
<cytoscape.impl.version>3.8.0</cytoscape.impl.version>
<cytoscape.api.version>3.9.0-SNAPSHOT</cytoscape.api.version>
<cytoscape.impl.version>3.9.0-SNAPSHOT</cytoscape.impl.version>
<maven.build.timestamp.format>MMMM yyyy</maven.build.timestamp.format>
<buildDate>${maven.build.timestamp}</buildDate>
</properties>
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14 changes: 2 additions & 12 deletions src/main/java/ca/utoronto/tdccbr/mcode/internal/CyActivator.java
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@@ -1,13 +1,6 @@
package ca.utoronto.tdccbr.mcode.internal;

import static org.cytoscape.work.ServiceProperties.COMMAND;
import static org.cytoscape.work.ServiceProperties.COMMAND_DESCRIPTION;
import static org.cytoscape.work.ServiceProperties.COMMAND_EXAMPLE_JSON;
import static org.cytoscape.work.ServiceProperties.COMMAND_LONG_DESCRIPTION;
import static org.cytoscape.work.ServiceProperties.COMMAND_NAMESPACE;
import static org.cytoscape.work.ServiceProperties.COMMAND_SUPPORTS_JSON;
import static org.cytoscape.work.ServiceProperties.PREFERRED_MENU;
import static org.cytoscape.work.ServiceProperties.TITLE;
import static org.cytoscape.work.ServiceProperties.*;

import java.util.Properties;

Expand All @@ -29,7 +22,6 @@
import org.cytoscape.util.swing.FileUtil;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
Expand Down Expand Up @@ -89,7 +81,6 @@ public class CyActivator extends AbstractCyActivator {
private MainPanelMediator mainPanelMediator;

@Override
@SuppressWarnings("unchecked")
public void start(BundleContext bc) {
registrar = getService(bc, CyServiceRegistrar.class);

Expand All @@ -101,7 +92,6 @@ public void start(BundleContext bc) {
var rootNetworkMgr = getService(bc, CyRootNetworkManager.class);

var swingApp = getService(bc, CySwingApplication.class);
var dingRenderingEngineFactory = getService(bc, RenderingEngineFactory.class, "(id=ding)");

var visualStyleFactory = getService(bc, VisualStyleFactory.class);
var visualMappingMgr = getService(bc, VisualMappingManager.class);
Expand All @@ -110,7 +100,7 @@ public void start(BundleContext bc) {

var fileUtil = getService(bc, FileUtil.class);

mcodeUtil = new MCODEUtil(dingRenderingEngineFactory, netViewFactory, rootNetworkMgr,
mcodeUtil = new MCODEUtil(netViewFactory, rootNetworkMgr,
appMgr, netMgr, netViewMgr, visualStyleFactory,
visualMappingMgr, swingApp, discreteMappingFactory,
continuousMappingFactory, fileUtil);
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24 changes: 2 additions & 22 deletions src/main/java/ca/utoronto/tdccbr/mcode/internal/util/MCODEUtil.java
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@@ -1,18 +1,6 @@
package ca.utoronto.tdccbr.mcode.internal.util;

import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_PAINT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_SELECTED_PAINT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_STROKE_SELECTED_PAINT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_STROKE_UNSELECTED_PAINT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_UNSELECTED_PAINT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.EDGE_WIDTH;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_BORDER_WIDTH;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_FILL_COLOR;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_HEIGHT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_PAINT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_SHAPE;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_SIZE;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_WIDTH;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.*;

import java.awt.Color;
import java.awt.Font;
Expand All @@ -36,7 +24,6 @@
import java.util.Set;

import javax.swing.JOptionPane;
import javax.swing.JPanel;

import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.NetworkViewRenderer;
Expand All @@ -56,8 +43,6 @@
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.presentation.RenderingEngine;
import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.view.presentation.property.BasicVisualLexicon;
import org.cytoscape.view.presentation.property.NodeShapeVisualProperty;
import org.cytoscape.view.presentation.property.values.NodeShape;
Expand Down Expand Up @@ -143,7 +128,7 @@ public class MCODEUtil {
private static final Color NODE_MIN_COLOR = Color.BLACK;
private static final Color NODE_MAX_COLOR = Color.RED;

private final RenderingEngineFactory<CyNetwork> renderingEngineFactory;
// private final RenderingEngineFactory<CyNetwork> renderingEngineFactory;
private final CyNetworkViewFactory networkViewFactory;
private final CyRootNetworkManager rootNetworkMgr;
private final CyApplicationManager applicationMgr;
Expand All @@ -169,7 +154,6 @@ public class MCODEUtil {
private static final Logger logger = LoggerFactory.getLogger(MCODEUtil.class);

public MCODEUtil(
RenderingEngineFactory<CyNetwork> renderingEngineFactory,
CyNetworkViewFactory networkViewFactory,
CyRootNetworkManager rootNetworkMgr,
CyApplicationManager applicationMgr,
Expand All @@ -182,7 +166,6 @@ public MCODEUtil(
VisualMappingFunctionFactory continuousMappingFactory,
FileUtil fileUtil
) {
this.renderingEngineFactory = renderingEngineFactory;
this.networkViewFactory = networkViewFactory;
this.rootNetworkMgr = rootNetworkMgr;
this.applicationMgr = applicationMgr;
Expand Down Expand Up @@ -365,9 +348,6 @@ public CyNetworkView createNetworkView(CyNetwork net, VisualStyle vs) {
return view;
}

public RenderingEngine<CyNetwork> createRenderingEngine(JPanel panel, CyNetworkView view) {
return renderingEngineFactory.createRenderingEngine(panel, view);
}

public void displayNetworkView(CyNetworkView view) {
networkMgr.addNetwork(view.getModel());
Expand Down
38 changes: 10 additions & 28 deletions src/main/java/ca/utoronto/tdccbr/mcode/internal/view/MainPanelMediator.java
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Expand Up @@ -6,16 +6,13 @@
import static org.cytoscape.util.swing.LookAndFeelUtil.isMac;
import static org.cytoscape.util.swing.LookAndFeelUtil.makeSmall;
import static org.cytoscape.util.swing.LookAndFeelUtil.setDefaultOkCancelKeyStrokes;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NETWORK_BACKGROUND_PAINT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NETWORK_HEIGHT;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NETWORK_WIDTH;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_X_LOCATION;
import static org.cytoscape.view.presentation.property.BasicVisualLexicon.NODE_Y_LOCATION;

import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dialog.ModalityType;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
Expand All @@ -38,7 +35,6 @@
import javax.swing.JFrame;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JSlider;
import javax.swing.SwingUtilities;
Expand All @@ -62,6 +58,7 @@
import org.cytoscape.util.swing.IconManager;
import org.cytoscape.util.swing.TextIcon;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.presentation.NetworkImageFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
Expand Down Expand Up @@ -664,30 +661,15 @@ private void createClusterImage(MCODECluster cluster, MCODEResult res, VisualSty
layouter.doLayout();
}

invokeOnEDT(() -> {
try {
var panel = new JPanel();
var size = new Dimension(width, height);
panel.setPreferredSize(size);
panel.setSize(size);
panel.setMinimumSize(size);
panel.setMaximumSize(size);
panel.setBackground((Color) style.getDefaultValue(NETWORK_BACKGROUND_PAINT));

var re = mcodeUtil.createRenderingEngine(panel, clusterView);
style.apply(clusterView);
clusterView.updateView();
clusterView.fitContent();

if (!clusterView.getNodeViews().isEmpty())
cluster.setView(clusterView);

var image = re.createImage(width, height);
cluster.setImage(image);
} catch (Exception ex) {
logger.error("Cannot update cluster image.", ex);
}
});

style.apply(clusterView);

var networkImageFactory = registrar.getService(NetworkImageFactory.class);
var image = networkImageFactory.createImage(clusterView, width, height);

cluster.setView(clusterView);
cluster.setImage(image);

} catch (Exception ex) {
logger.error("Cannot create cluster image.", ex);
}
Expand Down
4 changes: 1 addition & 3 deletions src/test/java/org/cytoscape/mcode/internal/model/MCODEAlgorithmTest.java
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Expand Up @@ -17,7 +17,6 @@
import org.cytoscape.util.swing.FileUtil;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
Expand Down Expand Up @@ -74,7 +73,6 @@ public class MCODEAlgorithmTest extends AbstractMCODETest {

CyNetwork networkSmall;

@Mock RenderingEngineFactory<CyNetwork> rendererFactory;
@Mock CyRootNetworkManager rootNetMgr;
@Mock CyApplicationManager appMgr;
@Mock CyNetworkManager netMgr;
Expand All @@ -96,7 +94,7 @@ public void setUp() throws Exception {
rootNetMgr = netViewTestSupport.getRootNetworkFactory();
netViewFactory = netViewTestSupport.getNetworkViewFactory();

mcodeUtil = new MCODEUtil(rendererFactory, netViewFactory, rootNetMgr, appMgr, netMgr, netViewMgr,
mcodeUtil = new MCODEUtil(netViewFactory, rootNetMgr, appMgr, netMgr, netViewMgr,
styleFactory, vmMgr, swingApp, vmfFactory, vmfFactory, fileUtil);
resultsMgr = new MCODEResultsManager(mcodeUtil);
// networkSmall = Cytoscape.createNetworkFromFile("testData" + File.separator + "smallTest.sif");
Expand Down
4 changes: 1 addition & 3 deletions src/test/java/org/cytoscape/mcode/internal/util/MCODEUtilTest.java
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Expand Up @@ -15,7 +15,6 @@
import org.cytoscape.util.swing.FileUtil;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
Expand Down Expand Up @@ -72,7 +71,6 @@
public class MCODEUtilTest extends AbstractMCODETest {

CyNetwork networkSmall;
@Mock RenderingEngineFactory<CyNetwork> rendererFactory;
@Mock CyRootNetworkManager rootNetMgr;
@Mock CyApplicationManager appMgr;
@Mock CyNetworkManager netMgr;
Expand All @@ -91,7 +89,7 @@ public void setUp() throws Exception {
rootNetMgr = netViewTestSupport.getRootNetworkFactory();
netViewFactory = netViewTestSupport.getNetworkViewFactory();

mcodeUtil = new MCODEUtil(rendererFactory, netViewFactory, rootNetMgr, appMgr, netMgr, netViewMgr,
mcodeUtil = new MCODEUtil(netViewFactory, rootNetMgr, appMgr, netMgr, netViewMgr,
styleFactory, vmMgr, swingApp, vmfFactory, vmfFactory, fileUtil);
resultsMgr = new MCODEResultsManager(mcodeUtil);
}
Expand Down