Author: pwang
Date: 2010-08-17 17:18:19 -0700 (Tue, 17 Aug 2010)
New Revision: 21434
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewProducer.java
Removed:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLReader.java
Log:
Rename
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewProducer.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewProducer.java
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewProducer.java
2010-08-18 00:18:19 UTC (rev 21434)
@@ -0,0 +1,591 @@
+/*
+ File: XGMMLReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute of Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package org.cytoscape.io.internal.read.xgmml;
+
+import java.awt.geom.Point2D;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
+import org.cytoscape.io.internal.read.AbstractNetworkViewProducer;
+import org.cytoscape.io.internal.read.VisualStyleBuilder;
+import org.cytoscape.io.internal.read.xgmml.handler.AttributeValueUtil;
+import org.cytoscape.io.internal.read.xgmml.handler.ReadDataManager;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.work.TaskMonitor;
+import org.xml.sax.Attributes;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXParseException;
+import org.xml.sax.helpers.ParserAdapter;
+
+/**
+ * XGMML file reader.<br>
+ * This version is Metanode-compatible.
+ *
+ * @version 1.0
+ * @since Cytoscape 2.3
+ * @see cytoscape.data.writers.XGMMLWriter
+ * @author kono
+ *
+ */
+public class XGMMLNetworkViewProducer extends AbstractNetworkViewProducer {
+
+ protected static final String CY_NAMESPACE = "http://www.cytoscape.org";;
+
+ private XGMMLParser parser;
+ private ReadDataManager readDataManager;
+
+ private AttributeValueUtil attributeValueUtil;
+
+ private Properties prop;
+
+ private CyNetworkView view;
+
+ /**
+ * Constructor.
+ */
+ public XGMMLNetworkViewProducer() {
+ super();
+ }
+
+ public void run(TaskMonitor tm) throws IOException {
+ //?????????????
+ }
+
+ public void setReadDataManager(ReadDataManager readDataManager) {
+ this.readDataManager = readDataManager;
+ }
+
+ public void setAttributeValueUtil(AttributeValueUtil
attributeValueUtil) {
+ this.attributeValueUtil = attributeValueUtil;
+ }
+
+ /*
+ * Setters for DI
+ */
+ public void setParser(XGMMLParser parser) {
+ this.parser = parser;
+ }
+
+ public void setProperties(Properties prop) {
+ this.prop = prop;
+ }
+
+ public void setInputStream(InputStream is) {
+ readDataManager.initAllData();
+ if (is == null)
+ throw new NullPointerException("Input stream is null");
+ inputStream = is;
+
+ this.readDataManager.setNetwork(cyNetworkFactory.getInstance());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public void read() throws IOException {
+ try {
+
+ this.readXGMML();
+ //this.readObjects.put(CyNetwork.class,
readDataManager.getNetwork());
+ createView(readDataManager.getNetwork());
+ //readObjects.put(CyNetworkView.class, view);
+ } catch (SAXException e) {
+ throw new IOException("Could not parse XGMML file: ");
+ }
+
+ this.cyNetworkViews[0] = view;
+ }
+
+ /**
+ * Actual method to read XGMML documents.
+ *
+ * @throws IOException
+ * @throws IOException
+ * @throws SAXException
+ * @throws ParserConfigurationException
+ */
+ private void readXGMML() throws SAXException, IOException {
+
+ final SAXParserFactory spf = SAXParserFactory.newInstance();
+
+ try {
+ // Get our parser
+ SAXParser sp = spf.newSAXParser();
+ ParserAdapter pa = new ParserAdapter(sp.getParser());
+ pa.setContentHandler(parser);
+ pa.setErrorHandler(parser);
+ pa.parse(new InputSource(inputStream));
+
+ } catch (OutOfMemoryError oe) {
+ // It's not generally a good idea to catch
OutOfMemoryErrors, but in
+ // this case, where we know the culprit (a file that is
too large),
+ // we can at least try to degrade gracefully.
+ System.gc();
+ throw new RuntimeException(
+ "Out of memory error caught! The
network being loaded is too large for the current memory allocation. Use the
-Xmx flag for the java virtual machine to increase the amount of memory
available, e.g. java -Xmx1G cytoscape.jar -p plugins ....");
+ } catch (ParserConfigurationException e) {
+ } catch (SAXParseException e) {
+ System.err.println("XGMMLParser: fatal parsing error on
line "
+ + e.getLineNumber() + " -- '" +
e.getMessage() + "'");
+ throw e;
+ } finally {
+ if (inputStream != null) {
+ inputStream.close();
+ inputStream = null;
+ }
+ }
+ }
+
+ /**
+ * layout the graph based on the graphic attributes
+ *
+ * @param myView
+ * the view of the network we want to layout
+ */
+ private void layout() {
+ if ((view == null) || (view.getModel().getNodeCount() == 0))
+ return;
+
+ // TODO: Inject correct property
+ // String vsbSwitch = prop.getProperty("visualStyleBuilder");
+
+ boolean buildStyle = false;
+
+ // TODO: make VS builder working with new code.
+ // if (vsbSwitch != null && vsbSwitch.equals("off"))
+ // buildStyle = false;
+ //
+ // VisualStyleBuilder graphStyle = new
+ // VisualStyleBuilder(readDataManager
+ // .getNetworkName(), false);
+
+ // Set background clolor
+ // TODO update with new view
+// if (readDataManager.getBackgroundColor() != null)
+//
view.setBackgroundPaint(readDataManager.getBackgroundColor());
+
+ // Layout nodes
+ layoutNodes(null, buildStyle);
+
+ // Layout edges
+ layoutEdges(null, buildStyle);
+ view.updateView();
+
+ // if (buildStyle)
+ // graphStyle.buildStyle();
+ }
+
+ /**
+ * Layout nodes if view is available.
+ *
+ * @param myView
+ * GINY's graph view object for the current network.
+ * @param graphStyle
+ * the visual style creator object
+ * @param buildStyle
+ * if true, build the graphical style
+ */
+ private void layoutNodes(final VisualStyleBuilder graphStyle,
+ boolean buildStyle) {
+ /*
+ String label = null;
+ int tempid = 0;
+ View<CyNode> nv = null;
+
+ final Map<CyNode, Attributes> nodeGraphicsMap = readDataManager
+ .getNodeGraphics();
+
+ for (CyNode node : nodeGraphicsMap.keySet()) {
+ nv = view.getNodeView(node);
+ label = node.attrs().get("name", String.class);
+
+ if ((label != null) && (nv != null)) {
+ nv.getLabel().setText(label);
+ } else if (view != null) {
+ nv.getLabel().setText("node(" + tempid + ")");
+ tempid++;
+ }
+
+ if ((nodeGraphicsMap != null) && (nv != null)) {
+ layoutNodeGraphics(nodeGraphicsMap.get(node),
nv, graphStyle,
+ buildStyle);
+ }
+ }
+ */
+ }
+
+ /**
+ * Extract node graphics information from JAXB object.<br>
+ *
+ * @param graphics
+ * Graphics information for a node as JAXB object.
+ * @param nodeView
+ * Actual node view for the target node.
+ * @param graphStyle
+ * the visual style creator object
+ * @param buildStyle
+ * if true, build the graphical style
+ *
+ */
+ private void layoutNodeGraphics(final Attributes graphics,
+ final View<CyNode> nodeView, final VisualStyleBuilder
graphStyle,
+ final boolean buildStyle) {
+
+ // The identifier of this node
+ CyRow nodeAttrs = nodeView.getModel().attrs();
+ /*
+
+ // Location and size of the node
+ double x;
+
+ // Location and size of the node
+ double y;
+
+ // Location and size of the node
+ double h;
+
+ // Location and size of the node
+ double w;
+
+ x = attributeValueUtil.getDoubleAttribute(graphics, "x");
+ y = attributeValueUtil.getDoubleAttribute(graphics, "y");
+ h = attributeValueUtil.getDoubleAttribute(graphics, "h");
+ w = attributeValueUtil.getDoubleAttribute(graphics, "w");
+
+ nodeView.setXPosition(x);
+ nodeView.setYPosition(y);
+
+ if (buildStyle && h != 0.0) {
+ // nodeView.setHeight(h);
+ graphStyle.addProperty(nodeAttrs,
VisualPropertyType.NODE_HEIGHT,
+ "" + h);
+ }
+ if (buildStyle && w != 0.0) {
+ // nodeView.setWidth(w);
+ graphStyle.addProperty(nodeAttrs,
VisualPropertyType.NODE_WIDTH, ""
+ + w);
+ }
+
+ // Set color
+ if (buildStyle
+ && attributeValueUtil.getAttribute(graphics,
"fill") != null) {
+ String fillColor = attributeValueUtil
+ .getAttribute(graphics, "fill");
+ graphStyle.addProperty(nodeAttrs,
+ VisualPropertyType.NODE_FILL_COLOR,
fillColor);
+ // nodeView.setUnselectedPaint(fillColor);
+ }
+
+ // Set border line color
+ if (buildStyle
+ && attributeValueUtil.getAttribute(graphics,
"outline") != null) {
+ String outlineColor =
attributeValueUtil.getAttribute(graphics,
+ "outline");
+ // nodeView.setBorderPaint(outlineColor);
+ graphStyle.addProperty(nodeAttrs,
+ VisualPropertyType.NODE_BORDER_COLOR,
outlineColor);
+ }
+
+ // Set border line width
+ if (buildStyle
+ && attributeValueUtil.getAttribute(graphics,
"width") != null) {
+ String lineWidth =
attributeValueUtil.getAttribute(graphics,
+ "width");
+ // nodeView.setBorderWidth(lineWidth);
+ graphStyle.addProperty(nodeAttrs,
+ VisualPropertyType.NODE_LINE_WIDTH,
lineWidth);
+ }
+
+ if (buildStyle
+ && 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);
+ }
+ */
+ }
+
+ /**
+ * Layout edges if view is available.
+ *
+ * @param myView
+ * GINY's graph view object for the current network.
+ * @param graphStyle
+ * the visual style creator object
+ * @param buildStyle
+ * if true, build the graphical style
+ */
+ private void layoutEdges(final VisualStyleBuilder graphStyle,
+ final boolean buildStyle) {
+ String label = null;
+ int tempid = 0;
+ View<CyEdge> ev = null;
+ Map<CyEdge, Attributes> edgeGraphicsMap = readDataManager
+ .getEdgeGraphics();
+
+ for (CyEdge edge : edgeGraphicsMap.keySet()) {
+ ev = view.getEdgeView(edge);
+
+ if ((edgeGraphicsMap != null) && (ev != null)) {
+ layoutEdgeGraphics(edgeGraphicsMap.get(edge),
ev, graphStyle,
+ buildStyle);
+ }
+ }
+ }
+
+ /**
+ * Layout an edge using the stored graphics attributes
+ *
+ * @param graphics
+ * Graphics information for an edge as SAX attributes.
+ * @param edgeView
+ * Actual edge view for the target edge.
+ *
+ */
+ private void layoutEdgeGraphics(final Attributes graphics,
+ final View<CyEdge> edgeView, final VisualStyleBuilder
graphStyle,
+ final boolean buildStyle) {
+ CyRow edgeAttrs = edgeView.getModel().attrs();
+ // TODO fix for new style view
+/*
+ if (buildStyle
+ && attributeValueUtil.getAttribute(graphics,
"width") != null) {
+ String lineWidth =
attributeValueUtil.getAttribute(graphics,
+ "width");
+ // edgeView.setStrokeWidth(lineWidth);
+ graphStyle.addProperty(edgeAttrs,
+ VisualPropertyType.EDGE_LINE_WIDTH,
lineWidth);
+ }
+
+ if (buildStyle
+ && attributeValueUtil.getAttribute(graphics,
"fill") != null) {
+ String edgeColor = attributeValueUtil
+ .getAttribute(graphics, "fill");
+ // edgeView.setUnselectedPaint(edgeColor);
+ graphStyle.addProperty(edgeAttrs,
VisualPropertyType.EDGE_COLOR,
+ edgeColor);
+ }
+
+ if (buildStyle
+ && 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 (buildStyle
+ && 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 (buildStyle
+ && 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 (buildStyle
+ && 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 < handles.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);
+ }
+ }
+ */
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param network
+ * DOCUMENT ME!
+ */
+ private void createView(CyNetwork network) {
+
+ // Get the view. Note that for large networks this might be the
null
+ // view
+ view = cyNetworkViewFactory.getNetworkView(network);
+
+ layout();
+
+ // Now that we have a network, handle the groups
+ // This is done here rather than in layout because layout is
+ // only called when we create a view. For large networks,
+ // we don't create views by default, but groups should still
+ // exist even when we don't create the view
+ /*
+ * // TODO Map<CyNode,List<CyNode>>groupMap =
parser.getGroupMap(); if
+ * (groupMap != null) {
+ *
+ * for (CyNode groupNode: groupMap.keySet()) { CyGroup newGroup
= null;
+ * List<CyNode> childList = groupMap.get(groupNode); // TODO
USER
+ * namespace here? String viewer =
+ * groupNode.attrs().get(CyGroup.GROUP_VIEWER_ATTR,
String.class);
+ *
+ * // Note that we need to leave the group node in the network
so that
+ * the saved // location information (if there is any) can be
utilized
+ * by the group viewer. // This means that it will be the
responsibility
+ * of the group viewer to remove // the node if they don't want
it to be
+ * visible
+ *
+ * // Do we already have a view? if (view == null ) { // No,
just create
+ * the group, but don't assign a viewer newGroup =
+ * CyGroupManager.createGroup(groupNode, childList, null); }
else { //
+ * Yes, see if the group already exists newGroup =
+ * CyGroupManager.getCyGroup(groupNode); if (newGroup == null)
{ // No,
+ * OK so create it and pass down the viewer
+ * CyGroupManager.createGroup(groupNode, childList, viewer); }
else { //
+ * Either the group doesn't have a viewer or it has a different
viewer
+ * -- change it CyGroupManager.setGroupViewer(newGroup, viewer,
view,
+ * true); } } } }
+ */
+
+ }
+
+}
Deleted:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLReader.java
2010-08-18 00:17:32 UTC (rev 21433)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLReader.java
2010-08-18 00:18:19 UTC (rev 21434)
@@ -1,586 +0,0 @@
-/*
- File: XGMMLReader.java
-
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute of Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-package org.cytoscape.io.internal.read.xgmml;
-
-import java.awt.geom.Point2D;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Map;
-import java.util.Properties;
-
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
-
-import org.cytoscape.io.internal.read.AbstractNetworkReader;
-import org.cytoscape.io.internal.read.VisualStyleBuilder;
-import org.cytoscape.io.internal.read.xgmml.handler.AttributeValueUtil;
-import org.cytoscape.io.internal.read.xgmml.handler.ReadDataManager;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.view.model.View;
-import org.cytoscape.view.model.CyNetworkView;
-import org.xml.sax.Attributes;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-import org.xml.sax.SAXParseException;
-import org.xml.sax.helpers.ParserAdapter;
-
-/**
- * XGMML file reader.<br>
- * This version is Metanode-compatible.
- *
- * @version 1.0
- * @since Cytoscape 2.3
- * @see cytoscape.data.writers.XGMMLWriter
- * @author kono
- *
- */
-public class XGMMLReader extends AbstractNetworkReader {
-
- protected static final String CY_NAMESPACE = "http://www.cytoscape.org";;
-
- private XGMMLParser parser;
- private ReadDataManager readDataManager;
-
- private AttributeValueUtil attributeValueUtil;
-
- private Properties prop;
-
- private CyNetworkView view;
-
- /**
- * Constructor.
- */
- public XGMMLReader() {
- super();
- }
-
- public void setReadDataManager(ReadDataManager readDataManager) {
- this.readDataManager = readDataManager;
- }
-
- public void setAttributeValueUtil(AttributeValueUtil
attributeValueUtil) {
- this.attributeValueUtil = attributeValueUtil;
- }
-
- /*
- * Setters for DI
- */
- public void setParser(XGMMLParser parser) {
- this.parser = parser;
- }
-
- public void setProperties(Properties prop) {
- this.prop = prop;
- }
-
- public void setInputStream(InputStream is) {
- readDataManager.initAllData();
- if (is == null)
- throw new NullPointerException("Input stream is null");
- inputStream = is;
-
- this.readDataManager.setNetwork(cyNetworkFactory.getInstance());
- }
-
- /**
- * DOCUMENT ME!
- *
- * @throws IOException
- * DOCUMENT ME!
- */
- public Map<Class<?>, Object> read() throws IOException {
- try {
-
- this.readXGMML();
- this.readObjects.put(CyNetwork.class,
readDataManager.getNetwork());
- createView(readDataManager.getNetwork());
- readObjects.put(CyNetworkView.class, view);
- } catch (SAXException e) {
- throw new IOException("Could not parse XGMML file: ");
- }
-
- return readObjects;
- }
-
- /**
- * Actual method to read XGMML documents.
- *
- * @throws IOException
- * @throws IOException
- * @throws SAXException
- * @throws ParserConfigurationException
- */
- private void readXGMML() throws SAXException, IOException {
-
- final SAXParserFactory spf = SAXParserFactory.newInstance();
-
- try {
- // Get our parser
- SAXParser sp = spf.newSAXParser();
- ParserAdapter pa = new ParserAdapter(sp.getParser());
- pa.setContentHandler(parser);
- pa.setErrorHandler(parser);
- pa.parse(new InputSource(inputStream));
-
- } catch (OutOfMemoryError oe) {
- // It's not generally a good idea to catch
OutOfMemoryErrors, but in
- // this case, where we know the culprit (a file that is
too large),
- // we can at least try to degrade gracefully.
- System.gc();
- throw new RuntimeException(
- "Out of memory error caught! The
network being loaded is too large for the current memory allocation. Use the
-Xmx flag for the java virtual machine to increase the amount of memory
available, e.g. java -Xmx1G cytoscape.jar -p plugins ....");
- } catch (ParserConfigurationException e) {
- } catch (SAXParseException e) {
- System.err.println("XGMMLParser: fatal parsing error on
line "
- + e.getLineNumber() + " -- '" +
e.getMessage() + "'");
- throw e;
- } finally {
- if (inputStream != null) {
- inputStream.close();
- inputStream = null;
- }
- }
- }
-
- /**
- * layout the graph based on the graphic attributes
- *
- * @param myView
- * the view of the network we want to layout
- */
- private void layout() {
- if ((view == null) || (view.getModel().getNodeCount() == 0))
- return;
-
- // TODO: Inject correct property
- // String vsbSwitch = prop.getProperty("visualStyleBuilder");
-
- boolean buildStyle = false;
-
- // TODO: make VS builder working with new code.
- // if (vsbSwitch != null && vsbSwitch.equals("off"))
- // buildStyle = false;
- //
- // VisualStyleBuilder graphStyle = new
- // VisualStyleBuilder(readDataManager
- // .getNetworkName(), false);
-
- // Set background clolor
- // TODO update with new view
-// if (readDataManager.getBackgroundColor() != null)
-//
view.setBackgroundPaint(readDataManager.getBackgroundColor());
-
- // Layout nodes
- layoutNodes(null, buildStyle);
-
- // Layout edges
- layoutEdges(null, buildStyle);
- view.updateView();
-
- // if (buildStyle)
- // graphStyle.buildStyle();
- }
-
- /**
- * Layout nodes if view is available.
- *
- * @param myView
- * GINY's graph view object for the current network.
- * @param graphStyle
- * the visual style creator object
- * @param buildStyle
- * if true, build the graphical style
- */
- private void layoutNodes(final VisualStyleBuilder graphStyle,
- boolean buildStyle) {
- /*
- String label = null;
- int tempid = 0;
- View<CyNode> nv = null;
-
- final Map<CyNode, Attributes> nodeGraphicsMap = readDataManager
- .getNodeGraphics();
-
- for (CyNode node : nodeGraphicsMap.keySet()) {
- nv = view.getNodeView(node);
- label = node.attrs().get("name", String.class);
-
- if ((label != null) && (nv != null)) {
- nv.getLabel().setText(label);
- } else if (view != null) {
- nv.getLabel().setText("node(" + tempid + ")");
- tempid++;
- }
-
- if ((nodeGraphicsMap != null) && (nv != null)) {
- layoutNodeGraphics(nodeGraphicsMap.get(node),
nv, graphStyle,
- buildStyle);
- }
- }
- */
- }
-
- /**
- * Extract node graphics information from JAXB object.<br>
- *
- * @param graphics
- * Graphics information for a node as JAXB object.
- * @param nodeView
- * Actual node view for the target node.
- * @param graphStyle
- * the visual style creator object
- * @param buildStyle
- * if true, build the graphical style
- *
- */
- private void layoutNodeGraphics(final Attributes graphics,
- final View<CyNode> nodeView, final VisualStyleBuilder
graphStyle,
- final boolean buildStyle) {
-
- // The identifier of this node
- CyRow nodeAttrs = nodeView.getModel().attrs();
- /*
-
- // Location and size of the node
- double x;
-
- // Location and size of the node
- double y;
-
- // Location and size of the node
- double h;
-
- // Location and size of the node
- double w;
-
- x = attributeValueUtil.getDoubleAttribute(graphics, "x");
- y = attributeValueUtil.getDoubleAttribute(graphics, "y");
- h = attributeValueUtil.getDoubleAttribute(graphics, "h");
- w = attributeValueUtil.getDoubleAttribute(graphics, "w");
-
- nodeView.setXPosition(x);
- nodeView.setYPosition(y);
-
- if (buildStyle && h != 0.0) {
- // nodeView.setHeight(h);
- graphStyle.addProperty(nodeAttrs,
VisualPropertyType.NODE_HEIGHT,
- "" + h);
- }
- if (buildStyle && w != 0.0) {
- // nodeView.setWidth(w);
- graphStyle.addProperty(nodeAttrs,
VisualPropertyType.NODE_WIDTH, ""
- + w);
- }
-
- // Set color
- if (buildStyle
- && attributeValueUtil.getAttribute(graphics,
"fill") != null) {
- String fillColor = attributeValueUtil
- .getAttribute(graphics, "fill");
- graphStyle.addProperty(nodeAttrs,
- VisualPropertyType.NODE_FILL_COLOR,
fillColor);
- // nodeView.setUnselectedPaint(fillColor);
- }
-
- // Set border line color
- if (buildStyle
- && attributeValueUtil.getAttribute(graphics,
"outline") != null) {
- String outlineColor =
attributeValueUtil.getAttribute(graphics,
- "outline");
- // nodeView.setBorderPaint(outlineColor);
- graphStyle.addProperty(nodeAttrs,
- VisualPropertyType.NODE_BORDER_COLOR,
outlineColor);
- }
-
- // Set border line width
- if (buildStyle
- && attributeValueUtil.getAttribute(graphics,
"width") != null) {
- String lineWidth =
attributeValueUtil.getAttribute(graphics,
- "width");
- // nodeView.setBorderWidth(lineWidth);
- graphStyle.addProperty(nodeAttrs,
- VisualPropertyType.NODE_LINE_WIDTH,
lineWidth);
- }
-
- if (buildStyle
- && 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);
- }
- */
- }
-
- /**
- * Layout edges if view is available.
- *
- * @param myView
- * GINY's graph view object for the current network.
- * @param graphStyle
- * the visual style creator object
- * @param buildStyle
- * if true, build the graphical style
- */
- private void layoutEdges(final VisualStyleBuilder graphStyle,
- final boolean buildStyle) {
- String label = null;
- int tempid = 0;
- View<CyEdge> ev = null;
- Map<CyEdge, Attributes> edgeGraphicsMap = readDataManager
- .getEdgeGraphics();
-
- for (CyEdge edge : edgeGraphicsMap.keySet()) {
- ev = view.getEdgeView(edge);
-
- if ((edgeGraphicsMap != null) && (ev != null)) {
- layoutEdgeGraphics(edgeGraphicsMap.get(edge),
ev, graphStyle,
- buildStyle);
- }
- }
- }
-
- /**
- * Layout an edge using the stored graphics attributes
- *
- * @param graphics
- * Graphics information for an edge as SAX attributes.
- * @param edgeView
- * Actual edge view for the target edge.
- *
- */
- private void layoutEdgeGraphics(final Attributes graphics,
- final View<CyEdge> edgeView, final VisualStyleBuilder
graphStyle,
- final boolean buildStyle) {
- CyRow edgeAttrs = edgeView.getModel().attrs();
- // TODO fix for new style view
-/*
- if (buildStyle
- && attributeValueUtil.getAttribute(graphics,
"width") != null) {
- String lineWidth =
attributeValueUtil.getAttribute(graphics,
- "width");
- // edgeView.setStrokeWidth(lineWidth);
- graphStyle.addProperty(edgeAttrs,
- VisualPropertyType.EDGE_LINE_WIDTH,
lineWidth);
- }
-
- if (buildStyle
- && attributeValueUtil.getAttribute(graphics,
"fill") != null) {
- String edgeColor = attributeValueUtil
- .getAttribute(graphics, "fill");
- // edgeView.setUnselectedPaint(edgeColor);
- graphStyle.addProperty(edgeAttrs,
VisualPropertyType.EDGE_COLOR,
- edgeColor);
- }
-
- if (buildStyle
- && 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 (buildStyle
- && 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 (buildStyle
- && 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 (buildStyle
- && 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 < handles.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);
- }
- }
- */
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param network
- * DOCUMENT ME!
- */
- private void createView(CyNetwork network) {
-
- // Get the view. Note that for large networks this might be the
null
- // view
- view = cyNetworkViewFactory.getNetworkView(network);
-
- layout();
-
- // Now that we have a network, handle the groups
- // This is done here rather than in layout because layout is
- // only called when we create a view. For large networks,
- // we don't create views by default, but groups should still
- // exist even when we don't create the view
- /*
- * // TODO Map<CyNode,List<CyNode>>groupMap =
parser.getGroupMap(); if
- * (groupMap != null) {
- *
- * for (CyNode groupNode: groupMap.keySet()) { CyGroup newGroup
= null;
- * List<CyNode> childList = groupMap.get(groupNode); // TODO
USER
- * namespace here? String viewer =
- * groupNode.attrs().get(CyGroup.GROUP_VIEWER_ATTR,
String.class);
- *
- * // Note that we need to leave the group node in the network
so that
- * the saved // location information (if there is any) can be
utilized
- * by the group viewer. // This means that it will be the
responsibility
- * of the group viewer to remove // the node if they don't want
it to be
- * visible
- *
- * // Do we already have a view? if (view == null ) { // No,
just create
- * the group, but don't assign a viewer newGroup =
- * CyGroupManager.createGroup(groupNode, childList, null); }
else { //
- * Yes, see if the group already exists newGroup =
- * CyGroupManager.getCyGroup(groupNode); if (newGroup == null)
{ // No,
- * OK so create it and pass down the viewer
- * CyGroupManager.createGroup(groupNode, childList, viewer); }
else { //
- * Either the group doesn't have a viewer or it has a different
viewer
- * -- change it CyGroupManager.setGroupViewer(newGroup, viewer,
view,
- * true); } } } }
- */
-
- }
-
-}
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