Author: Christian Lopes
Date: 2011-01-25 16:01:44 -0800 (Tue, 25 Jan 2011)
New Revision: 23620
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java
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/XGMMLNetworkViewReaderFactory.java
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
Log:
Fixed data type (String) of table column used by the Discrete Mappers when
building a style from XGMML. Using Visual Lexicon's lookup to get some visual
properties.
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java
2011-01-25 23:21:02 UTC (rev 23619)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java
2011-01-26 00:01:44 UTC (rev 23620)
@@ -58,8 +58,8 @@
*/
public class VisualStyleBuilder {
- Map<VisualProperty<?>, Map<Object, Object>> valueMaps;
- Map<VisualProperty<?>, Map<Object, Integer>> counts;
+ Map<VisualProperty<?>, Map<String, Object>> valueMaps;
+ Map<VisualProperty<?>, Map<String, Integer>> counts;
String name;
private boolean nodeSizeLocked = true;
@@ -94,8 +94,8 @@
this.nodesTable = nodesTable;
this.edgesTable = edgesTable;
- this.valueMaps = new Hashtable<VisualProperty<? extends Object>,
Map<Object, Object>>();
- this.counts = new Hashtable<VisualProperty<? extends Object>,
Map<Object, Integer>>();
+ this.valueMaps = new Hashtable<VisualProperty<? extends Object>,
Map<String, Object>>();
+ this.counts = new Hashtable<VisualProperty<? extends Object>,
Map<String, Integer>>();
}
/**
@@ -106,7 +106,7 @@
* @param defStyle
* the default syle
*/
- public <V, K> VisualStyle buildStyle() {
+ public <V> VisualStyle buildStyle() {
// Create the new style
VisualStyle style =
styleFactory.getInstance(visMappingManager.getDefaultVisualStyle());
String styleName = name + " style";
@@ -120,7 +120,7 @@
for (VisualProperty<?> _vp : valueMaps.keySet()) {
final VisualProperty<V> vp = (VisualProperty<V>) _vp;
final Class<?> type = vp.getTargetDataType();
- Map<K, V> valMap = (Map<K, V>) valueMaps.get(vp);
+ Map<String, V> valMap = (Map<String, V>) valueMaps.get(vp);
if (createMapping(vp)) {
// If there is more than one value specified for a given visual
@@ -128,7 +128,7 @@
// then create a mapping and calculator.
final String attrName = getAttrName(vp);
- DiscreteMapping<K, V> dm = (DiscreteMapping<K, V>)
discreteMappingFactory
+ DiscreteMapping<String, V> dm = (DiscreteMapping<String, V>)
discreteMappingFactory
.createVisualMappingFunction(attrName, String.class,
vp);
dm.putAll(valMap);
@@ -136,7 +136,7 @@
} else {
// Otherwise, set the default appearance value for the visual
// style and then remove the attribute that was created.
- for (Object key : valMap.keySet()) {
+ for (String key : valMap.keySet()) {
V val = (V) valMap.get(key);
style.setDefaultValue(vp, val);
}
@@ -193,12 +193,12 @@
}
// store the value
- if (!valueMaps.containsKey(vp)) valueMaps.put(vp, new
Hashtable<Object, Object>());
+ if (!valueMaps.containsKey(vp)) valueMaps.put(vp, new
Hashtable<String, Object>());
valueMaps.get(vp).put(vString, value);
// store the count
- if (!counts.containsKey(vp)) counts.put(vp, new Hashtable<Object,
Integer>());
+ if (!counts.containsKey(vp)) counts.put(vp, new Hashtable<String,
Integer>());
if (!counts.get(vp).containsKey(vString)) counts.get(vp).put(vString,
0);
counts.get(vp).put(vString, counts.get(vp).get(vString) + 1);
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
2011-01-25 23:21:02 UTC (rev 23619)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
2011-01-26 00:01:44 UTC (rev 23620)
@@ -37,8 +37,11 @@
package org.cytoscape.io.internal.read.xgmml;
import java.awt.Color;
+import java.awt.Font;
import java.io.IOException;
import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Map.Entry;
@@ -56,10 +59,14 @@
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTableEntry;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
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.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
@@ -88,6 +95,7 @@
protected static final String CY_NAMESPACE =
"http://www.cytoscape.org";;
+ private final RenderingEngineManager renderingEngineManager;
private final XGMMLParser parser;
private final ReadDataManager readDataManager;
private final AttributeValueUtil attributeValueUtil;
@@ -96,14 +104,20 @@
private final VisualMappingFunctionFactory discreteMappingFactory;
private final CyProperty<Properties> properties;
+ private VisualLexicon lexicon;
+
private CyNetworkView view;
+ private final List<GraphicsConverter<?>> nodeGraphics;
+ private final List<GraphicsConverter<?>> edgeGraphics;
+
private static final Logger logger =
LoggerFactory.getLogger(XGMMLNetworkViewReader.class);
/**
* Constructor.
*/
public XGMMLNetworkViewReader(InputStream inputStream,
+ RenderingEngineManager
renderingEngineManager,
CyNetworkViewFactory cyNetworkViewFactory,
CyNetworkFactory cyNetworkFactory,
ReadDataManager readDataManager,
@@ -114,6 +128,7 @@
XGMMLParser parser,
CyProperty<Properties> properties) {
super(inputStream, cyNetworkViewFactory, cyNetworkFactory);
+ this.renderingEngineManager = renderingEngineManager;
this.readDataManager = readDataManager;
this.attributeValueUtil = attributeValueUtil;
this.styleFactory = styleFactory;
@@ -121,6 +136,30 @@
this.discreteMappingFactory = discreteMappingFactory;
this.parser = parser;
this.properties = properties;
+ this.lexicon = renderingEngineManager.getDefaultVisualLexicon();
+
+ nodeGraphics = new ArrayList<GraphicsConverter<?>>();
+ edgeGraphics = new ArrayList<GraphicsConverter<?>>();
+
+ // TODO: should add x/y to style?
+ // nodeProps.put("x", Double.class);
+ // nodeProps.put("y", Double.class);
+ // TODO: NODE_SIZE: locking h/w
+ nodeGraphics.add(new GraphicsConverter<Double>("h", Double.class));
+ nodeGraphics.add(new GraphicsConverter<Double>("w", Double.class));
+ nodeGraphics.add(new GraphicsConverter<Color>("fill", Color.class));
+ nodeGraphics.add(new GraphicsConverter<Color>("outline", Color.class));
+ nodeGraphics.add(new GraphicsConverter<Double>("width", Double.class));
+ // nodeProps.add(new ValueMapping<Object>("borderLineType",
Object.class));
+ nodeGraphics.add(new GraphicsConverter<Font>("nodeLabelFont",
Font.class, CY_NAMESPACE));
+ nodeGraphics.add(new GraphicsConverter<Integer>("nodeTransparency",
Integer.class, CY_NAMESPACE));
+ // nodeProps.add(new ValueMapping<Object>("type",
Object.class));
+
+ // TODO: add more
+ edgeGraphics.add(new GraphicsConverter<Double>("width", Double.class));
+ edgeGraphics.add(new GraphicsConverter<Color>("fill", Color.class));
+ edgeGraphics.add(new GraphicsConverter<Font>("edgeLabelFont",
Font.class, CY_NAMESPACE));
+ edgeGraphics.add(new GraphicsConverter<Integer>("edgeTransparency",
Integer.class, CY_NAMESPACE));
}
@Override
@@ -223,7 +262,7 @@
String netName = readDataManager.getNetworkName();
netRow.set(NODE_NAME_ATTR_LABEL, netName);
-
+
if (styleBuilder != null) {
// Network name
styleBuilder.addProperty(netRow, TwoDVisualLexicon.NETWORK_TITLE,
netName);
@@ -310,107 +349,32 @@
nodeView.setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION, x);
nodeView.setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION, y);
- // The attributes of this node
- CyRow row = nodeView.getModel().getCyRow();
+ layoutGraphics(graphics, nodeView, styleBuilder, nodeGraphics);
- if (styleBuilder != null) {
- // Size
- double h = attributeValueUtil.getDoubleAttribute(graphics, "h");
- double w = attributeValueUtil.getDoubleAttribute(graphics, "w");
-
- // TODO: NODE_SIZE: locking h/w
- if (h != 0.0) {
- styleBuilder.addProperty(row, TwoDVisualLexicon.NODE_Y_SIZE,
h);
- }
- if (w != 0.0) {
- styleBuilder.addProperty(row, TwoDVisualLexicon.NODE_X_SIZE,
w);
- }
-
- if (w != 0.0) {
- styleBuilder.addProperty(row, TwoDVisualLexicon.NODE_SIZE, w);
- }
-
- // Color
- Color fillColor = attributeValueUtil.getColorAttribute(graphics,
"fill");
-
- if (fillColor != null) {
- styleBuilder.addProperty(row, TwoDVisualLexicon.NODE_PAINT,
fillColor);
- }
-
- // Border color
- Color borderColor = attributeValueUtil.getColorAttribute(graphics,
"outline");
- // TODO:
- // if (borderColor != null) {
- // styleBuilder.addProperty(row,
- // TwoDVisualLexicon.NODE_BORDER_COLOR, borderColor);
- // }
-
- // Border width
- double borderWidth =
attributeValueUtil.getDoubleAttribute(graphics, "width");
- // TODO:
- // if (borderWidth >= 0) {
- // styleBuilder.addProperty(row,
- // TwoDVisualLexicon.NODE_BORDER_WIDTH, borderWidth);
- // }
-
- // if (attributeValueUtil.getAttributeNS(graphics,
- // "nodeTransparency", CY_NAMESPACE) != null) {
- // String opString = attributeValueUtil.getAttributeNS(graphics,
- // "nodeTransparency", CY_NAMESPACE);
- // float opacity = (float) Double.parseDouble(opString) * 255;
- // // Opacity is saved as a float from 0-1, but internally we use
- // 0-255
- // // nodeView.setTransparency(opacity);
- // graphStyle.addProperty(nodeAttrs,
- // VisualPropertyType.NODE_OPACITY,
- // "" + opacity);
- // }
- //
- // if (buildStyle
- // && attributeValueUtil.getAttributeNS(graphics, "opacity",
- // CY_NAMESPACE) != null) {
- // String opString = attributeValueUtil.getAttributeNS(graphics,
- // "opacity", CY_NAMESPACE);
- // float opacity = (float) Double.parseDouble(opString);
- // // nodeView.setTransparency(opacity);
- // graphStyle.addProperty(nodeAttrs,
- // VisualPropertyType.NODE_OPACITY,
- // opString);
- // }
- //
- // // These are saved in the exported XGMML, but it's not clear how
- // they
- // // get set
- // if (buildStyle
- // && attributeValueUtil.getAttributeNS(graphics, "nodeLabelFont",
- // CY_NAMESPACE) != null) {
- // String nodeLabelFont =
- // attributeValueUtil.getAttributeNS(graphics,
- // "nodeLabelFont", CY_NAMESPACE);
- // graphStyle.addProperty(nodeAttrs,
- // VisualPropertyType.NODE_FONT_FACE, nodeLabelFont);
- // }
- //
- // if (buildStyle
- // && attributeValueUtil.getAttributeNS(graphics,
- // "borderLineType", CY_NAMESPACE) != null) {
- // String borderLineType =
- // attributeValueUtil.getAttributeNS(graphics,
- // "borderLineType", CY_NAMESPACE);
- // graphStyle.addProperty(nodeAttrs,
- // VisualPropertyType.NODE_LINE_STYLE, borderLineType);
- // }
- //
- // String type = attributeValueUtil.getAttribute(graphics, "type");
- // if (buildStyle && type != null) {
- // if (type.equals("rhombus"))
- // graphStyle.addProperty(nodeAttrs,
- // VisualPropertyType.NODE_SHAPE, "parallelogram");
- // else
- // graphStyle.addProperty(nodeAttrs,
- // VisualPropertyType.NODE_SHAPE, type);
- // }
- }
+ // // These are saved in the exported XGMML, but it's not clear how
they get set
+ // if (zattributeValueUtil.getAttributeNS(graphics, "nodeLabelFont",
CY_NAMESPACE) != null) {
+ // String nodeLabelFont = attributeValueUtil.getAttributeNS(graphics,
"nodeLabelFont", CY_NAMESPACE);
+ // graphStyle.addProperty(nodeAttrs,
VisualPropertyType.NODE_FONT_FACE, nodeLabelFont);
+ // }
+ //
+ // if (attributeValueUtil.getAttributeNS(graphics,
+ // "borderLineType", CY_NAMESPACE) != null) {
+ // String borderLineType =
+ // attributeValueUtil.getAttributeNS(graphics,
+ // "borderLineType", CY_NAMESPACE);
+ // graphStyle.addProperty(nodeAttrs,
+ // VisualPropertyType.NODE_LINE_STYLE, borderLineType);
+ // }
+ //
+ // String type = attributeValueUtil.getAttribute(graphics, "type");
+ // if (type != null) {
+ // if (type.equals("rhombus"))
+ // graphStyle.addProperty(nodeAttrs,
+ // VisualPropertyType.NODE_SHAPE, "parallelogram");
+ // else
+ // graphStyle.addProperty(nodeAttrs,
+ // VisualPropertyType.NODE_SHAPE, type);
+ // }
}
/**
@@ -448,83 +412,88 @@
private void layoutEdgeGraphics(final Attributes graphics,
final View<CyEdge> edgeView,
final VisualStyleBuilder styleBuilder) {
- // The attributes of this node
- CyRow row = edgeView.getModel().getCyRow();
- if (styleBuilder != null) {
- // Color
- Color edgeColor = attributeValueUtil.getColorAttribute(graphics,
"fill");
+ layoutGraphics(graphics, edgeView, styleBuilder, edgeGraphics);
- if (edgeColor != null) {
- styleBuilder.addProperty(row, TwoDVisualLexicon.EDGE_PAINT,
edgeColor);
- }
+ // TODO fix for new style view
+ // if (attributeValueUtil.getAttributeNS(graphics, "sourceArrow",
+ // CY_NAMESPACE) != null) { Integer arrowType =
+ // attributeValueUtil.getIntegerAttributeNS( graphics,
+ // "sourceArrow", CY_NAMESPACE); ArrowShape shape =
+ // ArrowShape.getArrowShape(arrowType); String arrowName =
+ // shape.getName(); // edgeView.setSourceEdgeEnd(arrowType);
+ // graphStyle.addProperty(edgeAttrs,
+ // VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName); }
+ //
+ // if (attributeValueUtil.getAttributeNS(graphics, "targetArrow",
+ // CY_NAMESPACE) != null) { Integer arrowType =
+ // attributeValueUtil.getIntegerAttributeNS( graphics,
+ // "targetArrow", CY_NAMESPACE); ArrowShape shape =
+ // ArrowShape.getArrowShape(arrowType); String arrowName =
+ // shape.getName(); // edgeView.setTargetEdgeEnd(arrowType);
+ // graphStyle.addProperty(edgeAttrs,
+ // VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName); }
+ //
+ // if (attributeValueUtil.getAttributeNS(graphics,
+ // "sourceArrowColor", CY_NAMESPACE) != null) { String arrowColor
+ //
+ // attributeValueUtil.getAttributeNS(graphics, "sourceArrowColor",
+ // CY_NAMESPACE); // edgeView.setSourceEdgeEndPaint(arrowColor);
+ // graphStyle.addProperty(edgeAttrs,
+ // VisualPropertyType.EDGE_SRCARROW_COLOR, arrowColor); }
+ //
+ // if (attributeValueUtil.getAttributeNS(graphics,
+ // "targetArrowColor", CY_NAMESPACE) != null) { String arrowColor
+ //
+ // attributeValueUtil.getAttributeNS(graphics, "targetArrowColor",
+ // CY_NAMESPACE); // edgeView.setTargetEdgeEndPaint(arrowColor);
+ // graphStyle.addProperty(edgeAttrs,
+ // VisualPropertyType.EDGE_TGTARROW_COLOR, arrowColor); }
+ //
+ // if (attributeValueUtil.getAttributeNS(graphics, "edgeLineType",
+ // CY_NAMESPACE) != null) { String value =
+ // attributeValueUtil.getAttributeNS(graphics, "edgeLineType",
+ // CY_NAMESPACE); graphStyle.addProperty(edgeAttrs,
+ // VisualPropertyType.EDGE_LINE_STYLE, value); }
+ //
+ // if (attributeValueUtil.getAttributeNS(graphics, "curved",
+ // CY_NAMESPACE) != null) { String value =
+ // attributeValueUtil.getAttributeNS(graphics, "curved",
+ // CY_NAMESPACE); if (value.equals("STRAIGHT_LINES")) {
+ // edgeView.setLineType(EdgeView.STRAIGHT_LINES); } else if
+ // (value.equals("CURVED_LINES")) {
+ // edgeView.setLineType(EdgeView.CURVED_LINES); } }
+ //
+ // if (attributeValueUtil.getAttribute(graphics, "edgeHandleList")
+ // != null) { // System.out.println("See edgeHandleList"); String
+ // handles[] = attributeValueUtil.getAttribute(graphics,
+ // "edgeHandleList").split(";"); for (int i = 0; i <
+ // andles.length;
+ // i++) { String points[] = handles[i].split(","); double x = (new
+ // Double(points[0])).doubleValue(); double y = (new
+ // Double(points[1])).doubleValue(); Point2D.Double point = new
+ // Point2D.Double(); point.setLocation(x, y);
+ // edgeView.getBend().addHandle(point); } }
+ }
- // Width
- double lineWidth = attributeValueUtil.getDoubleAttribute(graphics,
"width");
+ private void layoutGraphics(final Attributes graphics,
+ final View<? extends CyTableEntry> view,
+ final VisualStyleBuilder styleBuilder,
+ final List<GraphicsConverter<?>> converters) {
- if (lineWidth >= 0) {
- styleBuilder.addProperty(row, TwoDVisualLexicon.EDGE_WIDTH,
lineWidth);
+ // The attributes of this view
+ CyRow row = view.getModel().getCyRow();
+
+ if (styleBuilder != null) {
+ for (GraphicsConverter<?> conv : converters) {
+ String key = conv.getKey();
+ VisualProperty vp = lexicon.lookup(CyNode.class, key);
+
+ if (vp != null) {
+ Object value = conv.getValue(graphics, attributeValueUtil);
+ if (value != null) styleBuilder.addProperty(row, vp,
value);
+ }
}
-
- // TODO fix for new style view
- // if (attributeValueUtil.getAttributeNS(graphics, "sourceArrow",
- // CY_NAMESPACE) != null) { Integer arrowType =
- // attributeValueUtil.getIntegerAttributeNS( graphics,
- // "sourceArrow", CY_NAMESPACE); ArrowShape shape =
- // ArrowShape.getArrowShape(arrowType); String arrowName =
- // shape.getName(); // edgeView.setSourceEdgeEnd(arrowType);
- // graphStyle.addProperty(edgeAttrs,
- // VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName); }
- //
- // if (attributeValueUtil.getAttributeNS(graphics, "targetArrow",
- // CY_NAMESPACE) != null) { Integer arrowType =
- // attributeValueUtil.getIntegerAttributeNS( graphics,
- // "targetArrow", CY_NAMESPACE); ArrowShape shape =
- // ArrowShape.getArrowShape(arrowType); String arrowName =
- // shape.getName(); // edgeView.setTargetEdgeEnd(arrowType);
- // graphStyle.addProperty(edgeAttrs,
- // VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName); }
- //
- // if (attributeValueUtil.getAttributeNS(graphics,
- // "sourceArrowColor", CY_NAMESPACE) != null) { String arrowColor
- //
- // attributeValueUtil.getAttributeNS(graphics, "sourceArrowColor",
- // CY_NAMESPACE); // edgeView.setSourceEdgeEndPaint(arrowColor);
- // graphStyle.addProperty(edgeAttrs,
- // VisualPropertyType.EDGE_SRCARROW_COLOR, arrowColor); }
- //
- // if (buildStyle && attributeValueUtil.getAttributeNS(graphics,
- // "targetArrowColor", CY_NAMESPACE) != null) { String arrowColor
- //
- // attributeValueUtil.getAttributeNS(graphics, "targetArrowColor",
- // CY_NAMESPACE); // edgeView.setTargetEdgeEndPaint(arrowColor);
- // graphStyle.addProperty(edgeAttrs,
- // VisualPropertyType.EDGE_TGTARROW_COLOR, arrowColor); }
- //
- // if (attributeValueUtil.getAttributeNS(graphics, "edgeLineType",
- // CY_NAMESPACE) != null) { String value =
- // attributeValueUtil.getAttributeNS(graphics, "edgeLineType",
- // CY_NAMESPACE); graphStyle.addProperty(edgeAttrs,
- // VisualPropertyType.EDGE_LINE_STYLE, value); }
- //
- // if (attributeValueUtil.getAttributeNS(graphics, "curved",
- // CY_NAMESPACE) != null) { String value =
- // attributeValueUtil.getAttributeNS(graphics, "curved",
- // CY_NAMESPACE); if (value.equals("STRAIGHT_LINES")) {
- // edgeView.setLineType(EdgeView.STRAIGHT_LINES); } else if
- // (value.equals("CURVED_LINES")) {
- // edgeView.setLineType(EdgeView.CURVED_LINES); } }
- //
- // if (attributeValueUtil.getAttribute(graphics, "edgeHandleList")
- // != null) { // System.out.println("See edgeHandleList"); String
- // handles[] = attributeValueUtil.getAttribute(graphics,
- // "edgeHandleList").split(";"); for (int i = 0; i <
- // andles.length;
- // i++) { String points[] = handles[i].split(","); double x = (new
- // Double(points[0])).doubleValue(); double y = (new
- // Double(points[1])).doubleValue(); Point2D.Double point = new
- // Point2D.Double(); point.setLocation(x, y);
- // edgeView.getBend().addHandle(point); } }
}
}
@@ -541,3 +510,63 @@
}
}
+
+class GraphicsConverter<T> {
+
+ public String key;
+ public Class<T> type;
+ public String namespace;
+
+ public GraphicsConverter(String key, Class<T> type) {
+ this.key = key;
+ this.type = type;
+ }
+
+ public GraphicsConverter(String key, Class<T> type, String namespace) {
+ this(key, type);
+ this.namespace = namespace;
+ }
+
+ public T getValue(final Attributes graphics, final AttributeValueUtil
attributeValueUtil) {
+ Object value = null;
+
+ if (graphics != null) {
+ if (type == Integer.class) {
+ if (isTransparency()) {
+ // Opacity is saved as a float from 0.0-1.0, but
internally we use 0-255
+ Double d = attributeValueUtil.getDoubleAttribute(graphics,
key);
+ value = new Integer((int) d.doubleValue() * 255);
+ } else {
+ value = attributeValueUtil.getIntegerAttribute(graphics,
key);
+ }
+ } else if (type == Double.class) {
+ value = attributeValueUtil.getDoubleAttribute(graphics, key);
+ } else if (type == Color.class) {
+ value = attributeValueUtil.getColorAttribute(graphics, key);
+ } else if (type == Font.class) {
+ value = attributeValueUtil.getAttribute(graphics, key);
+ } else {
+ value = attributeValueUtil.getAttribute(graphics, key);
+ }
+ }
+
+ return (T) value;
+ }
+
+ public boolean isTransparency() {
+ return key.toLowerCase().contains("transparency");
+ }
+
+ public String getKey() {
+ return key;
+ }
+
+ public Class<T> getType() {
+ return type;
+ }
+
+ public String getNamespace() {
+ return namespace;
+ }
+
+}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory.java
2011-01-25 23:21:02 UTC (rev 23619)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderFactory.java
2011-01-26 00:01:44 UTC (rev 23620)
@@ -36,6 +36,7 @@
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
@@ -52,6 +53,7 @@
*/
public class XGMMLNetworkViewReaderFactory extends
AbstractNetworkViewReaderFactory {
+ private final RenderingEngineManager renderingEngineManager;
private VisualStyleFactory styleFactory;
private VisualMappingManager visMappingManager;
private final VisualMappingFunctionFactory discreteMappingFactory;
@@ -61,6 +63,7 @@
private CyProperty<Properties> properties;
public XGMMLNetworkViewReaderFactory(CyFileFilter filter,
+ RenderingEngineManager
renderingEngineManager,
CyNetworkViewFactory
cyNetworkViewFactory,
CyNetworkFactory cyNetworkFactory,
ReadDataManager readDataManager,
@@ -71,6 +74,7 @@
XGMMLParser parser,
CyProperty<Properties> properties) {
super(filter, cyNetworkViewFactory, cyNetworkFactory);
+ this.renderingEngineManager = renderingEngineManager;
this.readDataManager = readDataManager;
this.attributeValueUtil = attributeValueUtil;
this.styleFactory = styleFactory;
@@ -81,9 +85,9 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new XGMMLNetworkViewReader(inputStream,
cyNetworkViewFactory, cyNetworkFactory,
- readDataManager,
attributeValueUtil, styleFactory,
- visMappingManager,
discreteMappingFactory, parser,
- properties));
+ return new TaskIterator(new XGMMLNetworkViewReader(inputStream,
renderingEngineManager, cyNetworkViewFactory,
+ cyNetworkFactory,
readDataManager, attributeValueUtil,
+ styleFactory,
visMappingManager, discreteMappingFactory,
+ parser,
properties));
}
}
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
2011-01-25 23:21:02 UTC (rev 23619)
+++ core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-26 00:01:44 UTC (rev 23620)
@@ -324,6 +324,7 @@
<bean id="xgmmlNetworkViewReaderFactory"
class="org.cytoscape.io.internal.read.xgmml.XGMMLNetworkViewReaderFactory">
<constructor-arg ref="xgmmlFilter" />
+ <constructor-arg ref="renderingEngineManagerServiceRef" />
<constructor-arg ref="cyNetworkViewFactoryServiceRef" />
<constructor-arg ref="cyNetworkFactoryServiceRef" />
<constructor-arg ref="readDataManager" />
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
2011-01-25 23:21:02 UTC (rev 23619)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReaderTest.java
2011-01-26 00:01:44 UTC (rev 23620)
@@ -22,6 +22,7 @@
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.view.vizmap.mappings.DiscreteMappingFactory;
@@ -35,6 +36,7 @@
public class XGMMLNetworkViewReaderTest extends
AbstractNetworkViewReaderTester {
+ RenderingEngineManager renderingEngineManager;
ReadDataManager readDataManager;
AttributeValueUtil attributeValueUtil;
VisualStyleFactory styleFactory;
@@ -79,10 +81,10 @@
private CyNetworkView[] getViews(String file) throws Exception {
File f = new File("./src/test/resources/testData/xgmml/" + file);
- XGMMLNetworkViewReader snvp = new XGMMLNetworkViewReader(new
FileInputStream(f), viewFactory, netFactory,
-
readDataManager, attributeValueUtil, styleFactory,
-
visMappingManager, discreteMappingFactory, parser,
- properties);
+ XGMMLNetworkViewReader snvp = new XGMMLNetworkViewReader(new
FileInputStream(f), renderingEngineManager,
+ viewFactory,
netFactory, readDataManager,
+
attributeValueUtil, styleFactory, visMappingManager,
+
discreteMappingFactory, parser, properties);
snvp.run(taskMonitor);
return snvp.getNetworkViews();
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