Author: Christian Lopes
Date: 2011-03-08 15:01:38 -0800 (Tue, 08 Mar 2011)
New Revision: 24337
Modified:
core3/io-impl/trunk/pom.xml
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/handler/HandleEdgeGraphics.java
Log:
XGMMLNetworkViewReader: parsing more visual properties, including node and
arrow shapes.
Modified: core3/io-impl/trunk/pom.xml
===================================================================
--- core3/io-impl/trunk/pom.xml 2011-03-08 22:48:55 UTC (rev 24336)
+++ core3/io-impl/trunk/pom.xml 2011-03-08 23:01:38 UTC (rev 24337)
@@ -119,7 +119,7 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>default-mappings</artifactId>
- <version>3.0.0-alpha1</version>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>com.lowagie.text</groupId>
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
2011-03-08 22:48:55 UTC (rev 24336)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewReader.java
2011-03-08 23:01:38 UTC (rev 24337)
@@ -233,7 +233,6 @@
layoutEdges(styleBuilder);
}
- // TODO: find a better place to do this:
CyRow netRow = view.getModel().getCyRow();
String netName = readDataManager.getNetworkName();
@@ -315,15 +314,6 @@
nodeView.setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION, y);
layoutGraphics(attr, nodeView, styleBuilder);
-
- // TODO: Depends on Ding! Wait for Visual Lexicon redesign
- // String type = attributeValueUtil.getAttribute(attr, "type");
- // if (type != null) {
- // if (type.equals("rhombus"))
- // graphStyle.addProperty(attr, VisualPropertyType.NODE_SHAPE,
"parallelogram");
- // else
- // graphStyle.addProperty(attr, VisualPropertyType.NODE_SHAPE,
type);
- // }
}
/**
@@ -364,31 +354,7 @@
layoutGraphics(attr, edgeView, styleBuilder);
- // TODO missing styles: depends on Ding implementation!
- // if (attributeValueUtil.getAttributeNS(attr, "sourceArrow",
CY_NAMESPACE) != null) {
- // Integer arrowType =
attributeValueUtil.getIntegerAttributeNS(attr, "sourceArrow", CY_NAMESPACE);
- // ArrowShape shape = ArrowShape.getArrowShape(arrowType);
- // String arrowName = shape.getName();
- // styleBuilder.addProperty(edgeAttrs,
VisualPropertyType.EDGE_SRCARROW_SHAPE, arrowName);
- // }
- // if (attributeValueUtil.getAttributeNS(attr, "targetArrow",
CY_NAMESPACE) != null) {
- // Integer arrowType =
attributeValueUtil.getIntegerAttributeNS(attr, "targetArrow", CY_NAMESPACE);
- // ArrowShape shape = ArrowShape.getArrowShape(arrowType);
- // String arrowName = shape.getName();
- // styleBuilder.addProperty(edgeAttrs,
VisualPropertyType.EDGE_TGTARROW_SHAPE, arrowName);
- // }
- // if (attributeValueUtil.getAttributeNS(attr,
"sourceArrowColor", CY_NAMESPACE) != null) {
- // String arrowColor =
attributeValueUtil.getAttributeNS(attr, "sourceArrowColor", CY_NAMESPACE);
- // styleBuilder.addProperty(edgeAttrs,
VisualPropertyType.EDGE_SRCARROW_COLOR, arrowColor);
- // }
- // if (attributeValueUtil.getAttributeNS(attr,
"targetArrowColor", CY_NAMESPACE) != null) {
- // String arrowColor =
attributeValueUtil.getAttributeNS(attr, "targetArrowColor", CY_NAMESPACE);
- // styleBuilder.addProperty(edgeAttrs,
VisualPropertyType.EDGE_TGTARROW_COLOR, arrowColor);
- // }
- // if (attributeValueUtil.getAttributeNS(attr, "edgeLineType",
CY_NAMESPACE) != null) {
- // String value = attributeValueUtil.getAttributeNS(attr,
"edgeLineType", CY_NAMESPACE);
- // styleBuilder.addProperty(edgeAttrs,
VisualPropertyType.EDGE_LINE_STYLE, value);
- // }
+ // TODO missing styles:
// if (attributeValueUtil.getAttributeNS(attr, "curved",
CY_NAMESPACE) != null) {
// String value = attributeValueUtil.getAttributeNS(attr,
"curved", CY_NAMESPACE);
// if (value.equals("STRAIGHT_LINES")) {
@@ -425,7 +391,7 @@
VisualProperty vp = lexicon.lookup(type, key);
if (vp != null) {
- Object value = conv.getValue(attr, attributeValueUtil);
+ Object value = conv.getValue(attr, attributeValueUtil, vp);
if (value != null) {
if (conv.isBypass()) {
@@ -462,20 +428,23 @@
nodeConverters.add(new GraphicsConverter<Color>("fill", Color.class));
nodeConverters.add(new GraphicsConverter<Color>("outline",
Color.class));
nodeConverters.add(new GraphicsConverter<Double>("width",
Double.class));
- // nodeConverters.add(new
ValueMapping<Object>("borderLineType", Object.class));
+ nodeConverters.add(new GraphicsConverter<Object>("borderLineType",
Object.class));
nodeConverters.add(new GraphicsConverter<Font>("nodeLabelFont",
Font.class, CY_NAMESPACE));
nodeConverters.add(new GraphicsConverter<Integer>("nodeTransparency",
Integer.class, CY_NAMESPACE));
- // nodeConverters.add(new ValueMapping<Object>("type",
Object.class));
+ nodeConverters.add(new GraphicsConverter<Object>("type",
Object.class));
// TODO: add more
edgeConverters.add(new GraphicsConverter<Double>("width",
Double.class));
edgeConverters.add(new GraphicsConverter<Color>("fill", Color.class));
+ edgeConverters.add(new GraphicsConverter<Object>("sourceArrow",
Object.class, CY_NAMESPACE));
+ edgeConverters.add(new GraphicsConverter<Object>("targetArrow",
Object.class, CY_NAMESPACE));
edgeConverters.add(new GraphicsConverter<Font>("edgeLabelFont",
Font.class, CY_NAMESPACE));
edgeConverters.add(new GraphicsConverter<Integer>("edgeTransparency",
Integer.class, CY_NAMESPACE));
// attr (bypass):
// ----------------------------------
// TODO: add more
+ nodeConverters.add(new GraphicsConverter<Object>("nodeshape",
Object.class, true));
nodeConverters.add(new GraphicsConverter<Double>("nodeheight",
Double.class, true));
nodeConverters.add(new GraphicsConverter<Double>("nodewidth",
Double.class, true));
nodeConverters.add(new GraphicsConverter<Color>("nodefillcolor",
Color.class, true));
@@ -488,8 +457,7 @@
nodeConverters.add(new GraphicsConverter<Color>("nodelabelcolor",
Color.class, true));
nodeConverters.add(new GraphicsConverter<Integer>("nodelabelopacity",
Integer.class, true));
nodeConverters.add(new GraphicsConverter<Double>("nodelabelwidth",
Double.class, true));
-
-
+
edgeConverters.add(new GraphicsConverter<Double>("edgelinewidth",
Double.class, true));
edgeConverters.add(new GraphicsConverter<Color>("edgecolor",
Color.class, true));
edgeConverters.add(new GraphicsConverter<Integer>("edgeopacity",
Integer.class, true));
@@ -499,8 +467,10 @@
edgeConverters.add(new GraphicsConverter<Color>("edgelabelcolor",
Color.class, true));
edgeConverters.add(new GraphicsConverter<Integer>("edgelabelopacity",
Integer.class, true));
edgeConverters.add(new GraphicsConverter<Double>("edgelabelwidth",
Double.class, true));
+ edgeConverters.add(new GraphicsConverter<Object>("edgesourcearrow",
Object.class, true));
edgeConverters.add(new
GraphicsConverter<Color>("edgesourcearrowcolor", Color.class, true));
edgeConverters.add(new
GraphicsConverter<Integer>("edgesourcearrowopacity", Integer.class, true));
+ edgeConverters.add(new GraphicsConverter<Object>("edgetargetarrow",
Object.class, true));
edgeConverters.add(new
GraphicsConverter<Color>("edgetargetarrowcolor", Color.class, true));
edgeConverters.add(new
GraphicsConverter<Integer>("edgetargetarrowopacity", Integer.class, true));
edgeConverters.add(new GraphicsConverter<String>("edgetooltip",
String.class, true));
@@ -531,7 +501,7 @@
this.namespace = namespace;
}
- public T getValue(final Attributes attr, final AttributeValueUtil
attributeValueUtil) {
+ public T getValue(final Attributes attr, final AttributeValueUtil
attributeValueUtil, final VisualProperty<T> vp) {
Object value = null;
if (attr != null) {
@@ -575,15 +545,17 @@
value = new Font(name, style, size);
}
} else {
- // String or Number...
+ // String, Number or Object...
String s = null;
if (namespace == null)
- value = s = attributeValueUtil.getAttribute(attr, key);
+ s = attributeValueUtil.getAttribute(attr, key);
else
- value = s = attributeValueUtil.getAttributeNS(attr, key,
namespace);
+ s = attributeValueUtil.getAttributeNS(attr, key,
namespace);
- if (s != null && Number.class.isAssignableFrom(type)) {
+ if (type == String.class) {
+ value = s;
+ } else if (s != null && Number.class.isAssignableFrom(type)) {
Double d = null;
try {
@@ -604,6 +576,8 @@
value = new Float(d.floatValue());
}
}
+ } else if (s != null) {
+ value = vp.parseSerializableString(s);
}
}
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics.java
2011-03-08 22:48:55 UTC (rev 24336)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleEdgeGraphics.java
2011-03-08 23:01:38 UTC (rev 24337)
@@ -5,7 +5,6 @@
import org.cytoscape.io.internal.read.xgmml.ParseState;
import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNode;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.AttributesImpl;
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