Author: Christian Lopes
Date: 2011-03-10 12:59:05 -0800 (Thu, 10 Mar 2011)
New Revision: 24383
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
Log:
fixed bug: Import a network, save a session, restore the session, the network
name is "null"
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
2011-03-10 20:39:22 UTC (rev 24382)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-03-10 20:59:05 UTC (rev 24383)
@@ -27,7 +27,6 @@
*/
package org.cytoscape.io.internal.write.xgmml;
-
import java.awt.Color;
import java.awt.Font;
import java.awt.Paint;
@@ -54,12 +53,28 @@
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
-
enum GraphicsType {
- ARC("arc"), BITMAP("bitmap"), IMAGE("image"), LINE("line"), OVAL("oval"),
POLYGON("polygon"), RECTANGLE("rectangle"), TEXT(
- "text"), BOX("box"), CIRCLE("circle"),
VER_ELLIPSIS("ver_ellipsis"), HOR_ELLIPSIS("hor_ellipsis"), RHOMBUS(
- "rhombus"), TRIANGLE("triangle"), PENTAGON("pentagon"),
HEXAGON("hexagon"), OCTAGON("octagon"), ELLIPSE(
- "ellipse"), DIAMOND("diamond"), PARALLELOGRAM("parallelogram"),
ROUNDED_RECTANGLE("rounded_rectangle");
+ ARC("arc"),
+ BITMAP("bitmap"),
+ IMAGE("image"),
+ LINE("line"),
+ OVAL("oval"),
+ POLYGON("polygon"),
+ RECTANGLE("rectangle"),
+ TEXT("text"),
+ BOX("box"),
+ CIRCLE("circle"),
+ VER_ELLIPSIS("ver_ellipsis"),
+ HOR_ELLIPSIS("hor_ellipsis"),
+ RHOMBUS("rhombus"),
+ TRIANGLE("triangle"),
+ PENTAGON("pentagon"),
+ HEXAGON("hexagon"),
+ OCTAGON("octagon"),
+ ELLIPSE("ellipse"),
+ DIAMOND("diamond"),
+ PARALLELOGRAM("parallelogram"),
+ ROUNDED_RECTANGLE("rounded_rectangle");
private final String value;
@@ -73,7 +88,13 @@
}
enum ObjectType {
- LIST("list"), STRING("string"), REAL("real"), INTEGER("integer"),
BOOLEAN("boolean"), MAP("map"), COMPLEX("complex");
+ LIST("list"),
+ STRING("string"),
+ REAL("real"),
+ INTEGER("integer"),
+ BOOLEAN("boolean"),
+ MAP("map"),
+ COMPLEX("complex");
private final String value;
@@ -102,52 +123,51 @@
public class XGMMLWriter extends AbstractTask implements CyWriter {
// XML preamble information
- public static final String ENCODING = "UTF-8";
- private static final String XML_STRING = "<?xml
version=\"1.0\" encoding=\"" + ENCODING
- + "\"
standalone=\"yes\"?>";
+ public static final String ENCODING = "UTF-8";
+ private static final String XML_STRING = "<?xml version=\"1.0\"
encoding=\"" + ENCODING + "\" standalone=\"yes\"?>";
- private static final String[] NAMESPACES = {
"xmlns:dc=\"http://purl.org/dc/elements/1.1/\"";,
+ private static final String[] NAMESPACES = {
"xmlns:dc=\"http://purl.org/dc/elements/1.1/\"";,
"xmlns:xlink=\"http://www.w3.org/1999/xlink\"";,
"xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"";,
"xmlns:cy=\"http://www.cytoscape.org\"";,
- "xmlns=\"http://www.cs.rpi.edu/XGMML\""; };
+ "xmlns=\"http://www.cs.rpi.edu/XGMML\""; };
// File format version. For compatibility.
- private static final String FORMAT_VERSION = "documentVersion";
- private static final float VERSION = (float) 1.1;
- private static final String METADATA_NAME = "networkMetadata";
- private static final String METADATA_ATTR_NAME = "Network Metadata";
+ private static final String FORMAT_VERSION = "documentVersion";
+ private static final float VERSION = (float) 1.1;
+ private static final String METADATA_NAME = "networkMetadata";
+ private static final String METADATA_ATTR_NAME = "Network Metadata";
// Node types
- protected static final String NORMAL = "normal";
- protected static final String METANODE = "group";
- protected static final String REFERENCE = "reference";
+ protected static final String NORMAL = "normal";
+ protected static final String METANODE = "group";
+ protected static final String REFERENCE = "reference";
// Object types
- protected static final int NODE = 1;
- protected static final int EDGE = 2;
- protected static final int NETWORK = 3;
+ protected static final int NODE = 1;
+ protected static final int EDGE = 2;
+ protected static final int NETWORK = 3;
- public static final String BACKGROUND = "backgroundColor";
- public static final String GRAPH_VIEW_ZOOM = "GRAPH_VIEW_ZOOM";
- public static final String GRAPH_VIEW_CENTER_X =
"GRAPH_VIEW_CENTER_X";
- public static final String GRAPH_VIEW_CENTER_Y =
"GRAPH_VIEW_CENTER_Y";
- public static final String ENCODE_PROPERTY =
"cytoscape.encode.xgmml.attributes";
+ public static final String BACKGROUND = "backgroundColor";
+ public static final String GRAPH_VIEW_ZOOM = "GRAPH_VIEW_ZOOM";
+ public static final String GRAPH_VIEW_CENTER_X = "GRAPH_VIEW_CENTER_X";
+ public static final String GRAPH_VIEW_CENTER_Y = "GRAPH_VIEW_CENTER_Y";
+ public static final String ENCODE_PROPERTY =
"cytoscape.encode.xgmml.attributes";
- private final OutputStream outputStream;
- private final CyNetwork network;
- private final CyNetworkView networkView;
+ private final OutputStream outputStream;
+ private final CyNetwork network;
+ private final CyNetworkView networkView;
- private boolean isMixed;
- private HashMap<CyNode, CyNode> nodeMap = new HashMap<CyNode,
CyNode>();
- private HashMap<CyEdge, CyEdge> edgeMap = new HashMap<CyEdge,
CyEdge>();
- private boolean noCytoscapeGraphics = false;
+ private boolean isMixed;
+ private HashMap<CyNode, CyNode> nodeMap = new HashMap<CyNode, CyNode>();
+ private HashMap<CyEdge, CyEdge> edgeMap = new HashMap<CyEdge, CyEdge>();
+ private boolean noCytoscapeGraphics = false;
- private int depth = 0;
// XML
+ private int depth = 0; // XML
// depth
- private String indentString = "";
- private Writer writer = null;
+ private String indentString = "";
+ private Writer writer = null;
- private boolean doFullEncoding;
+ private boolean doFullEncoding;
public XGMMLWriter(OutputStream outputStream, CyNetworkView networkView,
boolean noCytoscapeGraphics) {
this.outputStream = outputStream;
@@ -201,8 +221,8 @@
private void writePreamble() throws IOException {
String directed = getDirectionality();
writeElement(XML_STRING + "\n");
- writeElement("<graph label=\"" + network.getCyRow().get("title",
String.class) + "\" directed=\"" + directed
- + "\" ");
+ writeElement("<graph label=\"" + getNetworkName(network) + "\"
directed=\"" +
+ directed + "\" ");
for (int ns = 0; ns < NAMESPACES.length; ns++)
writer.write(NAMESPACES[ns] + " ");
writer.write(">\n");
@@ -285,7 +305,7 @@
java.text.DateFormat df = new java.text.SimpleDateFormat("yyyy-MM-dd
HH:mm:ss");
writeElement("<dc:date>" + df.format(now) + "</dc:date>\n");
// TODO fix the use of hardcoded "name" here
- writeElement("<dc:title>" + encode(network.getCyRow().get("name",
String.class)) + "</dc:title>\n");
+ writeElement("<dc:title>" + getNetworkName(network) + "</dc:title>\n");
writeElement("<dc:source>http://www.cytoscape.org/</dc:source>\n");
writeElement("<dc:format>Cytoscape-XGMML</dc:format>\n");
depth--;
@@ -302,105 +322,105 @@
* @throws IOException
*/
private void writeNetworkAttributes() throws IOException {
- if (networkView != null) {
- // Get our background color
- Paint paint =
networkView.getVisualProperty(TwoDVisualLexicon.NETWORK_BACKGROUND_PAINT);
- String bgColor = paint2string(paint, Color.WHITE);
+ if (networkView != null) {
+ // Get our background color
+ Paint paint =
networkView.getVisualProperty(TwoDVisualLexicon.NETWORK_BACKGROUND_PAINT);
+ String bgColor = paint2string(paint, Color.WHITE);
- writeElement("<att type=\"string\" name=\"" + BACKGROUND +
"\" value=\"" + bgColor + "\"/>\n");
+ writeElement("<att type=\"string\" name=\"" + BACKGROUND + "\"
value=\"" + bgColor + "\"/>\n");
- // Write the graph zoom
- final Double zoom =
networkView.getVisualProperty(TwoDVisualLexicon.NETWORK_SCALE_FACTOR);
- writeAttributeXML(GRAPH_VIEW_ZOOM, ObjectType.REAL, zoom,
true);
+ // Write the graph zoom
+ final Double zoom =
networkView.getVisualProperty(TwoDVisualLexicon.NETWORK_SCALE_FACTOR);
+ writeAttributeXML(GRAPH_VIEW_ZOOM, ObjectType.REAL, zoom, true);
- // Write the graph center
- final Double cx =
networkView.getVisualProperty(TwoDVisualLexicon.NETWORK_CENTER_X_LOCATION);
- writeAttributeXML(GRAPH_VIEW_CENTER_X, ObjectType.REAL, cx,
true);
+ // Write the graph center
+ final Double cx =
networkView.getVisualProperty(TwoDVisualLexicon.NETWORK_CENTER_X_LOCATION);
+ writeAttributeXML(GRAPH_VIEW_CENTER_X, ObjectType.REAL, cx, true);
- final Double cy =
networkView.getVisualProperty(TwoDVisualLexicon.NETWORK_CENTER_Y_LOCATION);
- writeAttributeXML(GRAPH_VIEW_CENTER_Y, ObjectType.REAL, cy,
true);
+ final Double cy =
networkView.getVisualProperty(TwoDVisualLexicon.NETWORK_CENTER_Y_LOCATION);
+ writeAttributeXML(GRAPH_VIEW_CENTER_Y, ObjectType.REAL, cy, true);
- // TODO: Figure out if our node height and width is locked
- // VisualStyle networkStyle =
Cytoscape.getCurrentNetworkView().getVisualStyle();
- // VisualPropertyDependency vpd =
networkStyle.getDependency();
- // if
(vpd.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED))
- // writeAttributeXML(NODE_SIZE_LOCKED,
ObjectType.BOOLEAN, Boolean.TRUE ,true);
- }
+ // TODO: Figure out if our node height and width is locked
+ // VisualStyle networkStyle =
Cytoscape.getCurrentNetworkView().getVisualStyle();
+ // VisualPropertyDependency vpd =
networkStyle.getDependency();
+ // if
(vpd.check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED))
+ // writeAttributeXML(NODE_SIZE_LOCKED,
ObjectType.BOOLEAN, Boolean.TRUE ,true);
+ }
- // Now handle all of the other network attributes
- CyRow row = network.getCyRow();
- CyTable table = row.getTable();
+ // Now handle all of the other network attributes
+ CyRow row = network.getCyRow();
+ CyTable table = row.getTable();
- for (final CyColumn column : table.getColumns())
- writeAttribute(row, column.getName());
+ for (final CyColumn column : table.getColumns())
+ writeAttribute(row, column.getName());
}
- /**
- * Output Cytoscape nodes as XGMML
- *
- * @throws IOException
- */
- private void writeNodes() throws IOException {
- for (CyNode node : network.getNodeList()) {
- // TODO
- // if (!CyGroupManager.isaGroup(curNode))
- writeNode(node, null);
- }
- }
+ /**
+ * Output Cytoscape nodes as XGMML
+ *
+ * @throws IOException
+ */
+ private void writeNodes() throws IOException {
+ for (CyNode node : network.getNodeList()) {
+ // TODO
+ // if (!CyGroupManager.isaGroup(curNode))
+ writeNode(node, null);
+ }
+ }
- /**
- * Output a single CyNode as XGMML
- *
- * @param node the node to output
- * @throws IOException
- */
- private void writeNode(CyNode node, List<CyNode> groupList) throws
IOException {
- // Remember that we've seen this node
- nodeMap.put(node, node);
+ /**
+ * Output a single CyNode as XGMML
+ *
+ * @param node the node to output
+ * @throws IOException
+ */
+ private void writeNode(CyNode node, List<CyNode> groupList) throws
IOException {
+ // Remember that we've seen this node
+ nodeMap.put(node, node);
- // Output the node
- writeElement("<node label=" + quote(node.getCyRow().get("name",
String.class)));
- writer.write(" id=" + quote(Integer.toString(node.getIndex()))
+ ">\n");
- depth++;
+ // Output the node
+ writeElement("<node label=" + quote(node.getCyRow().get("name",
String.class)));
+ writer.write(" id=" + quote(Integer.toString(node.getIndex())) +
">\n");
+ depth++;
- // Output the node attributes
- // TODO This isn't handling namespaces
- for (final CyColumn column :
node.getCyRow().getTable().getColumns())
- writeAttribute(node.getCyRow(), column.getName());
+ // Output the node attributes
+ // TODO This isn't handling namespaces
+ for (final CyColumn column : node.getCyRow().getTable().getColumns())
+ writeAttribute(node.getCyRow(), column.getName());
- // TODO deal with groups
- // if (groupList != null && groupList.size() > 0) {
- // // If we're a group, output the graph attribute
now
- // writeElement("<att>\n");
- // depth++;
- // writeElement("<graph>\n");
- // depth++;
- // for (CyNode childNode : groupList) {
- // if (CyGroupManager.isaGroup(childNode)) {
- // // We have an embeddedgroup -- recurse
- // CyGroup childGroup =
CyGroupManager.getCyGroup(childNode);
- // writeNode(childGroup.getGroupNode(),
childGroup.getNodes());
- // } else {
- // if (nodeMap.containsKey(childNode))
- // writeElement("<node xlink:href=\"#" +
childNode.getIndex() + "\"/>\n");
- // else
- // writeNode(childNode, null);
- // }
- // }
- // depth--;
- // writeElement("</graph>\n");
- // depth--;
- // writeElement("</att>\n");
- // }
+ // TODO deal with groups
+ // if (groupList != null && groupList.size() > 0) {
+ // // If we're a group, output the graph attribute now
+ // writeElement("<att>\n");
+ // depth++;
+ // writeElement("<graph>\n");
+ // depth++;
+ // for (CyNode childNode : groupList) {
+ // if (CyGroupManager.isaGroup(childNode)) {
+ // // We have an embeddedgroup -- recurse
+ // CyGroup childGroup =
CyGroupManager.getCyGroup(childNode);
+ // writeNode(childGroup.getGroupNode(),
childGroup.getNodes());
+ // } else {
+ // if (nodeMap.containsKey(childNode))
+ // writeElement("<node xlink:href=\"#" +
childNode.getIndex() + "\"/>\n");
+ // else
+ // writeNode(childNode, null);
+ // }
+ // }
+ // depth--;
+ // writeElement("</graph>\n");
+ // depth--;
+ // writeElement("</att>\n");
+ // }
- // Output the node graphics if we have a view
- if (networkView != null) {
- writeNodeGraphics(node, networkView.getNodeView(node));
- }
+ // Output the node graphics if we have a view
+ if (networkView != null) {
+ writeNodeGraphics(node, networkView.getNodeView(node));
+ }
- depth--;
- writeElement("</node>\n");
- }
+ depth--;
+ writeElement("</node>\n");
+ }
/**
* Output the node graphics
@@ -537,110 +557,109 @@
*
* @throws IOException
*/
- private void writeEdges() throws IOException {
- for (CyEdge edge : network.getEdgeList()) {
- edgeMap.put(edge, edge);
- writeEdge(edge);
- }
- }
+ private void writeEdges() throws IOException {
+ for (CyEdge edge : network.getEdgeList()) {
+ edgeMap.put(edge, edge);
+ writeEdge(edge);
+ }
+ }
- /**
- * Output a Cytoscape edge as XGMML
- *
- * @param curEdge the edge to output
- *
- * @throws IOException
- */
- private void writeEdge(CyEdge curEdge) throws IOException {
- // Write the edge
- String target =
quote(Integer.toString(curEdge.getTarget().getIndex()));
- String source =
quote(Integer.toString(curEdge.getSource().getIndex()));
+ /**
+ * Output a Cytoscape edge as XGMML
+ *
+ * @param curEdge the edge to output
+ *
+ * @throws IOException
+ */
+ private void writeEdge(CyEdge curEdge) throws IOException {
+ // Write the edge
+ String target =
quote(Integer.toString(curEdge.getTarget().getIndex()));
+ String source =
quote(Integer.toString(curEdge.getSource().getIndex()));
- // Make sure these nodes exist
- if (!nodeMap.containsKey(curEdge.getTarget()) ||
!nodeMap.containsKey(curEdge.getSource())) return;
+ // Make sure these nodes exist
+ if (!nodeMap.containsKey(curEdge.getTarget()) ||
!nodeMap.containsKey(curEdge.getSource())) return;
- String directed = quote(curEdge.isDirected() ? "1" : "0");
+ String directed = quote(curEdge.isDirected() ? "1" : "0");
- writeElement("<edge label=" +
quote(curEdge.getCyRow().get("name", String.class)) + " source=" + source
- + " target=" + target + " cy:directed=" + directed
+ ">\n");
+ writeElement("<edge label=" + quote(curEdge.getCyRow().get("name",
String.class)) + " source=" + source +
+ " target=" + target + " cy:directed=" + directed + ">\n");
- depth++;
+ depth++;
- // Write the edge attributes
- // TODO This isn't handling namespaces
- for (final CyColumn column :
curEdge.getCyRow().getTable().getColumns())
- writeAttribute(curEdge.getCyRow(), column.getName());
+ // Write the edge attributes
+ // TODO This isn't handling namespaces
+ for (final CyColumn column :
curEdge.getCyRow().getTable().getColumns())
+ writeAttribute(curEdge.getCyRow(), column.getName());
- // Write the edge graphics
- if (networkView != null)
- writeEdgeGraphics(curEdge,
networkView.getEdgeView(curEdge));
+ // Write the edge graphics
+ if (networkView != null) writeEdgeGraphics(curEdge,
networkView.getEdgeView(curEdge));
- depth--;
- writeElement("</edge>\n");
- }
+ 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;
+ /**
+ * 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;
- writeElement("<graphics");
+ writeElement("<graphics");
- // Width
- Double width =
edgeView.getVisualProperty(TwoDVisualLexicon.EDGE_WIDTH);
- if (width == null) width = new Double(0);
+ // Width
+ Double width =
edgeView.getVisualProperty(TwoDVisualLexicon.EDGE_WIDTH);
+ if (width == null) width = new Double(0);
- writeAttributePair("width", Integer.toString(width.intValue()));
+ writeAttributePair("width", Integer.toString(width.intValue()));
- // Color
- Paint paint =
edgeView.getVisualProperty(TwoDVisualLexicon.EDGE_PAINT);
- writeAttributePair("fill", paint2string(paint,
Color.DARK_GRAY));
+ // Color
+ Paint paint = edgeView.getVisualProperty(TwoDVisualLexicon.EDGE_PAINT);
+ writeAttributePair("fill", paint2string(paint, Color.DARK_GRAY));
- // 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()));
- //
- // 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");
- // }
- }
+ // 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()));
+ //
+ // 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");
+ // }
+ }
- // TODO: Handle bends
- // final Bend bendData = edgeView.getBend();
- final List<Point2D> handles = new ArrayList<Point2D>(); //final
List<Point2D> handles = bendData.getHandles();
+ // TODO: Handle bends
+ // final Bend bendData = edgeView.getBend();
+ final List<Point2D> handles = new ArrayList<Point2D>(); //final
List<Point2D> handles = bendData.getHandles();
- 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");
- }
- }
+ 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");
+ }
+ }
/**
* Creates an attribute to write into XGMML file.
@@ -656,103 +675,105 @@
* @throws IOException
*/
private void writeAttribute(final CyRow row, final String attName) throws
IOException {
- // create an attribute and its type:
- final CyColumn column = row.getTable().getColumn(attName);
- if (column == null)
- return;
- final Class<?> attType = column.getType();
+ // create an attribute and its type:
+ final CyColumn column = row.getTable().getColumn(attName);
+ if (column == null) return;
+ final Class<?> attType = column.getType();
- String value = null;
- String type = null;
+ String value = null;
+ String type = null;
- // TODO: Equations
- // final Equation equation = row.getEquation(id,
attributeName);
+ // TODO: Equations
+ // final Equation equation = row.getEquation(id, attributeName);
- if (attType == Double.class) {
- // if (equation != null) {
- // writeEquationAttributeXML(attName,
ObjectType.REAL, equation.toString(),
- // true, hidden,
editable);
- // } else {
- Double dAttr = row.get(attName, Double.class);
- writeAttributeXML(attName, ObjectType.REAL, dAttr, true);
- // }
- } else {
- if (attType == Integer.class) {
- // if (equation != null) {
- //
writeEquationAttributeXML(attName, ObjectType.INTEGER, equation.toString(),
true, hidden, editable);
- // } else {
- Integer iAttr = row.get(attName, Integer.class);
- writeAttributeXML(attName, ObjectType.INTEGER,
iAttr, true);
- // }
- } else if (attType == String.class) {
- // if (equation != null) {
- //
writeEquationAttributeXML(attName, ObjectType.STRING, equation.toString(),
- //
true, hidden, editable);
- // } else {
- String sAttr = row.get(attName, String.class);
- // Protect tabs and returns
- if (sAttr != null) {
- sAttr = sAttr.replace("\n", "\\n");
- sAttr = sAttr.replace("\t", "\\t");
- }
- // TODO: nested networks
- // if
(attName.equals(CyNode.NESTED_NETWORK_ID_ATTR)) {
- // // This is a special
attribute for nested network.
- // sAttr =
Cytoscape.getNetwork(sAttr).getTitle();
- // }
- writeAttributeXML(attName, ObjectType.STRING,
sAttr, true);
- // }
- } else if (attType == Boolean.class) {
- // if (equation != null) {
- //
writeEquationAttributeXML(attName, ObjectType.BOOLEAN, equation.toString(),
true, hidden, editable);
- // } else {
- Boolean bAttr = row.get(attName, Boolean.class);
- writeAttributeXML(attName, ObjectType.BOOLEAN,
bAttr, true);
- // }
- } else if (attType == List.class) {
- final List<?> listAttr = row.get(attName,
List.class);
- writeAttributeXML(attName, ObjectType.LIST, null,
false);
+ if (attType == Double.class) {
+ // if (equation != null) {
+ // writeEquationAttributeXML(attName,
ObjectType.REAL, equation.toString(),
+ // true, hidden,
editable);
+ // } else {
+ Double dAttr = row.get(attName, Double.class);
+ writeAttributeXML(attName, ObjectType.REAL, dAttr, true);
+ // }
+ } else {
+ if (attType == Integer.class) {
+ // if (equation != null) {
+ // writeEquationAttributeXML(attName,
ObjectType.INTEGER, equation.toString(), true, hidden, editable);
+ // } else {
+ Integer iAttr = row.get(attName, Integer.class);
+ writeAttributeXML(attName, ObjectType.INTEGER, iAttr, true);
+ // }
+ } else if (attType == String.class) {
+ // if (equation != null) {
+ // writeEquationAttributeXML(attName,
ObjectType.STRING, equation.toString(),
+ // true, hidden,
editable);
+ // } else {
+ String sAttr = row.get(attName, String.class);
+ // Protect tabs and returns
+ if (sAttr != null) {
+ sAttr = sAttr.replace("\n", "\\n");
+ sAttr = sAttr.replace("\t", "\\t");
+ }
+ // TODO: nested networks
+ // if
(attName.equals(CyNode.NESTED_NETWORK_ID_ATTR)) {
+ // // This is a special attribute for
nested network.
+ // sAttr =
Cytoscape.getNetwork(sAttr).getTitle();
+ // }
+ writeAttributeXML(attName, ObjectType.STRING, sAttr, true);
+ // }
+ } else if (attType == Boolean.class) {
+ // if (equation != null) {
+ // writeEquationAttributeXML(attName,
ObjectType.BOOLEAN, equation.toString(), true, hidden, editable);
+ // } else {
+ Boolean bAttr = row.get(attName, Boolean.class);
+ writeAttributeXML(attName, ObjectType.BOOLEAN, bAttr, true);
+ // }
+ } else if (attType == List.class) {
+ final List<?> listAttr = row.getList(attName,
column.getListElementType());
+ writeAttributeXML(attName, ObjectType.LIST, null, false);
- depth++;
- // interate through the list
- for (Object obj : listAttr) {
- // Protect tabs and returns (if necessary)
- String sAttr = obj.toString();
- if (sAttr != null) {
- sAttr = sAttr.replace("\n", "\\n");
- sAttr = sAttr.replace("\t", "\\t");
- }
- // set child attribute value & label
- writeAttributeXML(attName, checkType(obj),
sAttr, true);
- }
- depth--;
- writeAttributeXML(null, null, null, true);
- } else if (attType == Map.class) {
- // process SIMPLE MAP
- // get the attribute map
- final Map mapAttr = row.get(attName, Map.class);
- writeAttributeXML(attName, ObjectType.MAP, null,
false);
+ if (listAttr != null) {
+ depth++;
+ // interate through the list
+ for (Object obj : listAttr) {
+ // Protect tabs and returns (if necessary)
+ String sAttr = obj.toString();
+ if (sAttr != null) {
+ sAttr = sAttr.replace("\n", "\\n");
+ sAttr = sAttr.replace("\t", "\\t");
+ }
+ // set child attribute value & label
+ writeAttributeXML(attName, checkType(obj), sAttr,
true);
+ }
+ depth--;
+ }
+ writeAttributeXML(null, null, null, true);
+ } else if (attType == Map.class) {
+ // process SIMPLE MAP
+ // get the attribute map
+ final Map mapAttr = row.get(attName, Map.class);
+ writeAttributeXML(attName, ObjectType.MAP, null, false);
- depth++;
- // interate through the map
- for (Object obj : mapAttr.keySet()) {
- // get the attribute from the map
- String key = (String) obj;
- Object val = mapAttr.get(key);
- String sAttr = val.toString();
- if (sAttr != null) {
- sAttr = sAttr.replace("\n", "\\n");
- sAttr = sAttr.replace("\t", "\\t");
- }
+ if (mapAttr != null) {
+ depth++;
+ // interate through the map
+ for (Object obj : mapAttr.keySet()) {
+ // get the attribute from the map
+ String key = (String) obj;
+ Object val = mapAttr.get(key);
+ String sAttr = val.toString();
+ if (sAttr != null) {
+ sAttr = sAttr.replace("\n", "\\n");
+ sAttr = sAttr.replace("\t", "\\t");
+ }
- writeAttributeXML(key, checkType(val),
sAttr, true);
- }
- depth--;
- writeAttributeXML(null, null, null, true);
- }
- }
+ writeAttributeXML(key, checkType(val), sAttr, true);
+ }
+ depth--;
+ }
+ writeAttributeXML(null, null, null, true);
+ }
+ }
-
// TODO: process COMPLEX MAP
// else if (attType == CyAttributes.TYPE_COMPLEX) {
// MultiHashMap mmap = attributes.getMultiHashMap();
@@ -982,8 +1003,9 @@
c = defColor == null ? Color.WHITE : defColor;
return ("#" // +Integer.toHexString(c.getRGB());
- + Integer.toHexString(256 + c.getRed()).substring(1)
- + Integer.toHexString(256 + c.getGreen()).substring(1) +
Integer.toHexString(256 + c.getBlue())
+ +
+ Integer.toHexString(256 + c.getRed()).substring(1) +
+ Integer.toHexString(256 + c.getGreen()).substring(1) +
Integer.toHexString(256 + c.getBlue())
.substring(1));
}
@@ -1045,6 +1067,13 @@
}
*/
+ private String getNetworkName(CyNetwork network) {
+ String name = encode(network.getCyRow().get("name", String.class));
+ if (name == null) name = "UNDEFINED";
+
+ return name;
+ }
+
/**
* encode returns a quoted string appropriate for use as an XML attribute
*
@@ -1054,35 +1083,41 @@
private String encode(String str) {
// Find and replace any "magic", control, non-printable etc. characters
// For maximum safety, everything other than printable ASCII (0x20
thru 0x7E) is converted into a character entity
- StringBuilder sb = new StringBuilder(str.length());
+ String s = null;
- for (int i = 0; i < str.length(); i++) {
- char c = str.charAt(i);
+ if (str != null) {
+ StringBuilder sb = new StringBuilder(str.length());
- if ((c < ' ') || (c > '~')) {
- if (doFullEncoding) {
- sb.append("&#x");
- sb.append(Integer.toHexString((int) c));
- sb.append(";");
+ for (int i = 0; i < str.length(); i++) {
+ char c = str.charAt(i);
+
+ if ((c < ' ') || (c > '~')) {
+ if (doFullEncoding) {
+ sb.append("&#x");
+ sb.append(Integer.toHexString((int) c));
+ sb.append(";");
+ } else {
+ sb.append(c);
+ }
+ } else if (c == '"') {
+ sb.append(""");
+ } else if (c == '\'') {
+ sb.append("'");
+ } else if (c == '&') {
+ sb.append("&");
+ } else if (c == '<') {
+ sb.append("<");
+ } else if (c == '>') {
+ sb.append(">");
} else {
sb.append(c);
}
- } else if (c == '"') {
- sb.append(""");
- } else if (c == '\'') {
- sb.append("'");
- } else if (c == '&') {
- sb.append("&");
- } else if (c == '<') {
- sb.append("<");
- } else if (c == '>') {
- sb.append(">");
- } else {
- sb.append(c);
}
+
+ s = sb.toString();
}
- return sb.toString();
+ return s;
}
/**
--
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