Author: Christian Lopes
Date: 2011-03-29 14:09:09 -0700 (Tue, 29 Mar 2011)
New Revision: 24615
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLNetworkViewWriterFactory.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Refactored the XGMML Writer, so it iterates over all the visual properties
available in the Visual Lexicon (still incomplete, because it depends on the
RichLexicon implementation)
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
2011-03-29 19:54:37 UTC (rev 24614)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
2011-03-29 21:09:09 UTC (rev 24615)
@@ -100,8 +100,8 @@
private final VisualStyleFactory styleFactory;
private final VisualMappingManager visMappingManager;
private final CyProperty<Properties> properties;
-
- private VisualLexicon lexicon;
+ private final VisualLexicon visualLexicon;
+
private CyNetworkView view;
private List<GraphicsConverter<?>> nodeConverters;
@@ -130,7 +130,7 @@
this.visMappingManager = visMappingManager;
this.parser = parser;
this.properties = properties;
- this.lexicon = renderingEngineManager.getDefaultVisualLexicon();
+ this.visualLexicon = renderingEngineManager.getDefaultVisualLexicon();
createConverters();
}
@@ -350,7 +350,7 @@
if (!buildStyle && !conv.isBypass()) continue;
String key = conv.getKey();
- VisualProperty vp = lexicon.lookup(type, key);
+ VisualProperty vp = visualLexicon.lookup(type, key);
if (vp != null) {
Object value = conv.getValue(attr, attributeValueUtil, vp);
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLNetworkViewWriterFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLNetworkViewWriterFactory.java
2011-03-29 19:54:37 UTC (rev 24614)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLNetworkViewWriterFactory.java
2011-03-29 21:09:09 UTC (rev 24615)
@@ -3,15 +3,19 @@
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.internal.write.AbstractCyNetworkViewWriterFactory;
import org.cytoscape.io.write.CyWriter;
+import org.cytoscape.view.presentation.RenderingEngineManager;
public class XGMMLNetworkViewWriterFactory extends
AbstractCyNetworkViewWriterFactory {
-
- public XGMMLNetworkViewWriterFactory(CyFileFilter filter) {
- super(filter);
- }
-
- @Override
- public CyWriter getWriterTask() {
- return new XGMMLWriter(outputStream, view, true);
- }
+
+ protected RenderingEngineManager renderingEngineManager;
+
+ public XGMMLNetworkViewWriterFactory(CyFileFilter filter,
RenderingEngineManager renderingEngineManager) {
+ super(filter);
+ this.renderingEngineManager = renderingEngineManager;
+ }
+
+ @Override
+ public CyWriter getWriterTask() {
+ return new XGMMLWriter(outputStream, renderingEngineManager, view,
true);
+ }
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-03-29 19:54:37 UTC (rev 24614)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-03-29 21:09:09 UTC (rev 24615)
@@ -39,6 +39,7 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import org.cytoscape.io.write.CyWriter;
import org.cytoscape.model.CyColumn;
@@ -47,8 +48,12 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.VisualLexicon;
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
@@ -155,6 +160,7 @@
private final OutputStream outputStream;
private final CyNetwork network;
+ private final VisualLexicon visualLexicon;
private final CyNetworkView networkView;
private boolean isMixed;
@@ -169,11 +175,15 @@
private boolean doFullEncoding;
- public XGMMLWriter(OutputStream outputStream, CyNetworkView networkView,
boolean noCytoscapeGraphics) {
+ public XGMMLWriter(final OutputStream outputStream,
+ final RenderingEngineManager renderingEngineManager,
+ final CyNetworkView networkView,
+ final boolean noCytoscapeGraphics) {
this.outputStream = outputStream;
this.networkView = networkView;
this.network = networkView.getModel();
this.noCytoscapeGraphics = noCytoscapeGraphics;
+ this.visualLexicon = renderingEngineManager.getDefaultVisualLexicon();
// Create our indent string (480 blanks);
for (int i = 0; i < 20; i++)
@@ -221,8 +231,7 @@
private void writePreamble() throws IOException {
String directed = getDirectionality();
writeElement(XML_STRING + "\n");
- writeElement("<graph label=\"" + getNetworkName(network) + "\"
directed=\"" +
- directed + "\" ");
+ writeElement("<graph label=\"" + getNetworkName(network) + "\"
directed=\"" + directed + "\" ");
for (int ns = 0; ns < NAMESPACES.length; ns++)
writer.write(NAMESPACES[ns] + " ");
writer.write(">\n");
@@ -414,113 +423,12 @@
// }
// Output the node graphics if we have a view
- if (networkView != null) {
- writeNodeGraphics(node, networkView.getNodeView(node));
- }
+ if (networkView != null) writeGraphics(networkView.getNodeView(node));
depth--;
writeElement("</node>\n");
}
- /**
- * Output the node graphics
- * <graphics y="17276.9" x="15552.7" width="5" outline="#000000"
fill="#44f687" type="diamond" w="35.0" h="35.0">
- * <att name="cytoscapeNodeGraphicsAttributes">
- * <att value="1.0" name="nodeTransparency"/>
- * <att value="Arial Bold-0-6" name="nodeLabelFont"/>
- * <att value="solid" name="borderLineType"/>
- * </att>
- * </graphics>
- *
- * @param node the node whose graphics we're outputting
- * @param nodeView the view for this node
- *
- * @throws IOException
- */
- private void writeNodeGraphics(CyNode node, View<CyNode> nodeView) throws
IOException {
- if (nodeView == null) return;
-
- writeElement("<graphics");
-
- // Node size and position
- Double size = nodeView.getVisualProperty(TwoDVisualLexicon.NODE_SIZE);
- Double h = size != null ? size :
nodeView.getVisualProperty(TwoDVisualLexicon.NODE_Y_SIZE);
- Double w = size != null ? size :
nodeView.getVisualProperty(TwoDVisualLexicon.NODE_X_SIZE);
-
- writeAttributePair("h", Double.toString(h));
- writeAttributePair("w", Double.toString(w));
- writeAttributePair("x",
Double.toString(nodeView.getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION)));
- writeAttributePair("y",
Double.toString(nodeView.getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION)));
-
- // Node color
- Paint paint = nodeView.getVisualProperty(TwoDVisualLexicon.NODE_COLOR);
- writeAttributePair("fill", paint2string(paint, Color.LIGHT_GRAY));
-
- // TODO fix for new style view
- // // In case node is hidden, we temporarily show the node view
- // // and then hide it later on.
- // boolean rehideNode = false;
- // if (nodeView.getWidth() == -1) {
- // networkView.showGraphObject(nodeView);
- // rehideNode = true;
- // }
- //
- // // Node shape
- // GraphicsType shape = number2shape(nodeView.getShape());
- // if (shape == GraphicsType.PARALLELOGRAM)
- // writeAttributePair("type",GraphicsType.RHOMBUS);
- // else
- // writeAttributePair("type",shape);
- //
- // // Node color
- // writeAttributePair("fill",
toHexColorString(nodeView.getUnselectedPaint()));
- //
- // // Node border basic info.
- // final BasicStroke borderType = (BasicStroke)
nodeView.getBorder();
- // writeAttributePair("width",
Integer.toString(((int)borderType.getLineWidth())));
- // writeAttributePair("outline",
toHexColorString(nodeView.getBorderPaint()));
- //
- // // Write out the Cytoscape-specific attributes
- // if (!noCytoscapeGraphics) {
- // // Get the opacity
- // Integer tp = ((Color)
nodeView.getUnselectedPaint()).getAlpha();
- // double transparency = 1.0;
- // if (tp != null && tp.intValue() != 255)
- // transparency = tp.doubleValue()/255.0;
- //
- // writeAttributePair("cy:nodeTransparency",
Double.toString(transparency));
- // writeAttributePair("cy:nodeLabelFont",
encodeFont(nodeView.getLabel().getFont()));
- //
- // // Where should we store line-type info???
- // final float[] dash = borderType.getDashArray();
- //
- // if (dash == null) {
- // // CyLogger.getLogger().info("##Border is NORMAL
LINE");
- // writeAttributePair("cy:borderLineType", "solid");
- // } else {
- // // CyLogger.getLogger().info("##Border is DASHED
LINE");
- // String dashArray = null;
- // final StringBuilder dashBuf = new StringBuilder();
- //
- // for (int i = 0; i < dash.length; i++) {
- // dashBuf.append(Double.toString(dash[i]));
- //
- // if (i < (dash.length - 1)) {
- // dashBuf.append(",");
- // }
- // }
- //
- // dashArray = dashBuf.toString();
- // writeAttributePair("cy:borderLineType", dashArray);
- // }
- // }
- //
- // if ( rehideNode )
- // networkView.hideGraphObject(nodeView);
-
- writer.write("/>\n");
- }
-
/*
* // TODO fix! private void writeGroups() throws IOException { // Two pass
* approach. First, walk through the list // and see if any of the children
@@ -592,73 +500,85 @@
writeAttribute(curEdge.getCyRow(), column.getName());
// Write the edge graphics
- if (networkView != null) writeEdgeGraphics(curEdge,
networkView.getEdgeView(curEdge));
+ if (networkView != null)
writeGraphics(networkView.getEdgeView(curEdge));
depth--;
writeElement("</edge>\n");
}
- /**
- * Output the edge graphics
- *
- * @param edge the edge whose graphics we're outputting
- * @param edgeView the view for this edge
- *
- * @throws IOException
- */
- private void writeEdgeGraphics(CyEdge edge, View<CyEdge> edgeView) throws
IOException {
- if (edgeView == null) return;
+ private void writeGraphics(View<? extends CyTableEntry> view) throws
IOException {
+ if (view == null) return;
+ CyTableEntry element = view.getModel();
writeElement("<graphics");
- // Width
- Double width =
edgeView.getVisualProperty(TwoDVisualLexicon.EDGE_WIDTH);
- if (width == null) width = new Double(0);
+ Set<VisualProperty<?>> visualProperties =
visualLexicon.getAllVisualProperties();
- writeAttributePair("width", Integer.toString(width.intValue()));
+ for (VisualProperty vp : visualProperties) {
+ if (!vp.getTargetDataType().isAssignableFrom(element.getClass()))
continue;
+
+ String key = getGraphicsKey(vp);
+ Object value = view.getVisualProperty(vp);
- // Color
- Paint paint = edgeView.getVisualProperty(TwoDVisualLexicon.EDGE_PAINT);
- writeAttributePair("fill", paint2string(paint, Color.DARK_GRAY));
+ if (key != null && value != null) {
+ writeAttributePair(key, vp.toSerializableString(value));
+ }
+ }
- // TODO: Store Cytoscape-local graphical attributes
- if (!noCytoscapeGraphics) {
- // writeAttributePair("cy:sourceArrow",
Integer.toString(edgeView.getSourceEdgeEnd()));
- // writeAttributePair("cy:targetArrow",
Integer.toString(edgeView.getTargetEdgeEnd()));
- // writeAttributePair("cy:sourceArrowColor",
toHexColorString(edgeView.getSourceEdgeEndPaint()));
- // writeAttributePair("cy:targetArrowColor",
toHexColorString(edgeView.getTargetEdgeEndPaint()));
+ // TODO: Handle bends
+ if (element instanceof CyEdge) {
+ // final Bend bendData = edgeView.getBend();
+ // final List<Point2D> handles = new ArrayList<Point2D>();
//final List<Point2D> handles = bendData.getHandles();
//
- // writeAttributePair("cy:edgeLabelFont",
encodeFont(edgeView.getLabel().getFont()));
- // writeAttributePair("cy:edgeLineType",
LineStyle.extractLineStyle(edgeView.getStroke()).toString());
- // // Set curved or not
- // if (edgeView.getLineType() == EdgeView.CURVED_LINES)
{
- // writeAttributePair("cy:curved", "CURVED_LINES");
- // } else if (edgeView.getLineType() ==
EdgeView.STRAIGHT_LINES) {
- // writeAttributePair("cy:curved",
"STRAIGHT_LINES");
- // }
+ // if (handles.size() == 0) {
+ // writer.write("/>\n");
+ // } else {
+ // writer.write(">\n");
+ // depth++;
+ // writeElement("<att name=\"edgeBend\">\n");
+ // depth++;
+ // for (Point2D handle: handles) {
+ // String x = Double.toString(handle.getX());
+ // String y = Double.toString(handle.getY());
+ // writeElement("<att name=\"handle\" x=\""+x+"\"
y=\""+y+"\" />\n");
+ // }
+ // depth--;
+ // writeElement("</att>\n");
+ // depth--;
+ // writeElement("</graphics>\n");
+ // }
}
- // TODO: Handle bends
- // final Bend bendData = edgeView.getBend();
- final List<Point2D> handles = new ArrayList<Point2D>(); //final
List<Point2D> handles = bendData.getHandles();
+ writer.write("/>\n");
+ }
- if (handles.size() == 0) {
- writer.write("/>\n");
- } else {
- writer.write(">\n");
- // depth++;
- // writeElement("<att name=\"edgeBend\">\n");
- // depth++;
- // for (Point2D handle: handles) {
- // String x = Double.toString(handle.getX());
- // String y = Double.toString(handle.getY());
- // writeElement("<att name=\"handle\" x=\""+x+"\"
y=\""+y+"\" />\n");
- // }
- // depth--;
- // writeElement("</att>\n");
- // depth--;
- // writeElement("</graphics>\n");
- }
+ private String getGraphicsKey(VisualProperty<?> vp) {
+ //Nodes
+ if (vp.equals(TwoDVisualLexicon.NODE_X_LOCATION)) return "x";
+ if (vp.equals(TwoDVisualLexicon.NODE_Y_LOCATION)) return "y";
+ if (vp.equals(TwoDVisualLexicon.NODE_X_SIZE)) return "w";
+ if (vp.equals(TwoDVisualLexicon.NODE_Y_SIZE)) return "h";
+ if (vp.equals(TwoDVisualLexicon.NODE_COLOR)) return "fill";
+ // TODO: Visual Lexicon has to expose these properties
+ // if (vp.equals(TwoDVisualLexicon.NODE_SHAPE)) return "type";
+ // if (vp.equals(TwoDVisualLexicon.NODE_)) return "wth";
+ // if (vp.equals(TwoDVisualLexicon.NODE_)) return "outline";
+ // if (vp.equals(TwoDVisualLexicon.NODE_)) return
"cy:nodeTransparency";
+ // if (vp.equals(TwoDVisualLexicon.NODE_)) return
"cy:borderLineType";
+ // if (vp.equals(TwoDVisualLexicon.NODE_)) return
"cy:nodeLabelFont";
+
+ // Edges
+ if (vp.equals(TwoDVisualLexicon.EDGE_WIDTH)) return "width";
+ if (vp.equals(TwoDVisualLexicon.EDGE_PAINT)) return "fill";
+ // TODO:
+ // "cy:sourceArrow"
+ // "cy:targetArrow"
+ // "cy:sourceArrowColor"
+ // "cy:targetArrowColor"
+ // "cy:edgeLabelFont"
+ // "cy:edgeLineType"
+
+ return null;
}
/**
@@ -1070,7 +990,7 @@
private String getNetworkName(CyNetwork network) {
String name = encode(network.getCyRow().get("name", String.class));
if (name == null) name = "UNDEFINED";
-
+
return name;
}
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
--- core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-03-29 19:54:37 UTC (rev 24614)
+++ core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-03-29 21:09:09 UTC (rev 24615)
@@ -282,6 +282,7 @@
<bean id="xgmmlNetworkViewWriterFactory"
class="org.cytoscape.io.internal.write.xgmml.XGMMLNetworkViewWriterFactory">
<constructor-arg ref="xgmmlFilter"/>
+ <constructor-arg ref="renderingEngineManagerServiceRef"/>
</bean>
<bean id="cysessionWriterFactory"
class="org.cytoscape.io.internal.write.cysession.CysessionWriterFactoryImpl">
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