Author: clopes
Date: 2011-12-05 12:38:30 -0800 (Mon, 05 Dec 2011)
New Revision: 27692
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
Log:
Fixed bug when reading XGMML with XLinks (edges could be parsed before creating
source/target nodes).
Fixed saving/restoring network view width/height.
When saving view-format XGMML files into the cys file, the XGMML writer only
writes edge tags that have locked visual properties, to prevent empty edge tags.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
2011-12-03 00:36:19 UTC (rev 27691)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/Cy2SessionReaderImpl.java
2011-12-05 20:38:30 UTC (rev 27692)
@@ -44,6 +44,7 @@
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
+import java.math.BigInteger;
import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.Arrays;
@@ -74,10 +75,13 @@
import org.cytoscape.property.bookmark.Bookmarks;
import org.cytoscape.property.session.Child;
import org.cytoscape.property.session.Cysession;
+import org.cytoscape.property.session.Desktop;
import org.cytoscape.property.session.Edge;
import org.cytoscape.property.session.Network;
+import org.cytoscape.property.session.NetworkFrame;
import org.cytoscape.property.session.Node;
import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
/**
* Session reader implementation that handles the Cytoscape 2.x session format.
@@ -203,7 +207,7 @@
is = findEntry(entryName);
if (is != null) {
- rootNetwork = extractNetworks(is,
entryName, parent, childNet.isViewAvailable());
+ rootNetwork =
extractNetworksAndViews(is, entryName, parent, childNet.isViewAvailable());
} else {
logger.error("Cannot find network file
\"" + entryName + "\": ");
}
@@ -236,8 +240,8 @@
* @return The root-network of the extracted networks
* @throws Exception
*/
- private CyRootNetwork extractNetworks(InputStream is, String entryName,
CyRootNetwork parent, boolean createView)
- throws Exception {
+ private CyRootNetwork extractNetworksAndViews(InputStream is, String
entryName, CyRootNetwork parent,
+ boolean createView) throws Exception {
this.tm.setStatusMessage("Extracting network: " + entryName);
CyRootNetwork rootNetwork = null;
@@ -264,19 +268,23 @@
views = new CyNetworkView[netArray.length];
int i = 0;
+ String netName = null;
for (CyNetwork net : netArray) {
- networkLookup.put(entryName, net);
+ netName = net.getCyRow().get(CyNetwork.NAME,
String.class);
+
+ networkLookup.put(netName, net);
networks.add(net);
if (createView) {
- views[i] =
reader.buildCyNetworkView(net);
+ CyNetworkView netView =
reader.buildCyNetworkView(net);
+ views[i] = netView;
i++;
}
}
if (views != null) {
- networkViewLookup.put(entryName, views);
+ networkViewLookup.put(netName, views);
networkViews.addAll(Arrays.asList(views));
}
}
@@ -354,66 +362,93 @@
}
private void processNetworks() throws Exception {
- if (cysession.getNetworkTree() == null)
- return;
-
- for (final Network net :
cysession.getNetworkTree().getNetwork()) {
- // We no longer have the concept of one top-level
network root,
- // so let's ignore a network with that name.
- if (net.getId().equals(NETWORK_ROOT))
- continue;
-
- final String fileName = net.getFilename();
- final CyNetworkView view = getNetworkView(fileName);
-
- if (view != null) {
- String vsName = net.getVisualStyle();
-
- if (vsName != null)
- visualStyleMap.put(view, vsName);
+ if (cysession == null) return;
+
+ // Network attributes and visual styles
+ if (cysession.getNetworkTree() != null) {
+ for (final Network net :
cysession.getNetworkTree().getNetwork()) {
+ // We no longer have the concept of one
top-level network root,
+ // so let's ignore a network with that name.
+ if (net.getId().equals(NETWORK_ROOT))
+ continue;
+
+ final String netName = net.getId();
+ final CyNetworkView[] views =
getNetworkViews(netName);
+
+ if (views != null) {
+ for (CyNetworkView nv : views) {
+ String vsName =
net.getVisualStyle();
+
+ if (vsName != null)
+ visualStyleMap.put(nv,
vsName);
+ }
+ }
+
+ final CyNetwork cyNet = getNetwork(netName);
+
+ if (cyNet != null) {
+ // TODO: check if should delete from
network
+// if (net.getHiddenNodes() != null)
+// setBooleanNodeAttr(cyNet,
net.getHiddenNodes().getNode().iterator(), "hidden");
+// if (net.getHiddenEdges() != null)
+// setBooleanEdgeAttr(cyNet,
net.getHiddenEdges().getEdge().iterator(), "hidden");
+
+ // From Cytoscape 3.0, the selection
info is stored inside CyTables,
+ // but 2.x stores that info in the
cysession.xml file.
+ if (net.getSelectedNodes() != null)
+ setBooleanNodeAttr(cyNet,
net.getSelectedNodes().getNode().iterator(), CyNetwork.SELECTED);
+ if (net.getSelectedEdges() != null)
+ setBooleanEdgeAttr(cyNet,
net.getSelectedEdges().getEdge().iterator(), CyNetwork.SELECTED);
+ }
}
+ }
+
+ // Network view sizes
+ if (cysession.getSessionState() != null) {
+ Desktop desktop =
cysession.getSessionState().getDesktop();
+
+ if (desktop != null && desktop.getNetworkFrames() !=
null) {
+ List<NetworkFrame> frames =
desktop.getNetworkFrames().getNetworkFrame();
- final CyNetwork cyNet = getNetwork(fileName);
-
- if (cyNet != null) {
- // TODO: check if should delete from network
-// if (net.getHiddenNodes() != null)
-// setBooleanNodeAttr(cyNet,
net.getHiddenNodes().getNode().iterator(), "hidden");
-// if (net.getHiddenEdges() != null)
-// setBooleanEdgeAttr(cyNet,
net.getHiddenEdges().getEdge().iterator(), "hidden");
-
- // From Cytoscape 3.0, the selection info is
stored inside CyTables,
- // but 2.x stores that info in the
cysession.xml file.
- if (net.getSelectedNodes() != null)
- setBooleanNodeAttr(cyNet,
net.getSelectedNodes().getNode().iterator(), CyNetwork.SELECTED);
- if (net.getSelectedEdges() != null)
- setBooleanEdgeAttr(cyNet,
net.getSelectedEdges().getEdge().iterator(), CyNetwork.SELECTED);
+ for (NetworkFrame nf : frames) {
+ // Set sizes
+ CyNetworkView[] views =
getNetworkViews(nf.getFrameID());
+
+ if (views != null) {
+ for (CyNetworkView nv : views) {
+ BigInteger w =
nf.getWidth();
+ BigInteger h =
nf.getHeight();
+
+ if (w != null)
+
nv.setVisualProperty(MinimalVisualLexicon.NETWORK_WIDTH, w.doubleValue());
+ if (h != null)
+
nv.setVisualProperty(MinimalVisualLexicon.NETWORK_HEIGHT, h.doubleValue());
+ }
+ }
+ }
}
}
}
- private CyNetworkView getNetworkView(final String name) {
+ private CyNetworkView[] getNetworkViews(final String name) {
+ CyNetworkView[] views = null;
+
for (String s : networkViewLookup.keySet()) {
String decode = s;
try {
decode = URLDecoder.decode(s, "UTF-8");
+
+ if (decode.endsWith(name)) {
+ // this is OK since XGMML only ever
reads one network
+ views = networkViewLookup.get(s);
+ }
} catch (UnsupportedEncodingException e) {
e.printStackTrace();
- return null;
}
-
- if (decode.endsWith("/" + name)) {
- // this is OK since XGMML only ever reads one
network
- CyNetworkView[] views =
networkViewLookup.get(s);
-
- if (views != null && views.length > 0) {
- return views[0];
- }
- }
}
- return null;
+ return views;
}
private CyNetwork getNetwork(final String name) {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2011-12-03 00:36:19 UTC (rev 27691)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2011-12-05 20:38:30 UTC (rev 27692)
@@ -1,6 +1,8 @@
package org.cytoscape.io.internal.read.xgmml.handler;
import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import org.cytoscape.io.internal.read.xgmml.MetadataEntries;
import org.cytoscape.io.internal.read.xgmml.MetadataParser;
@@ -23,6 +25,8 @@
static final String ATTR_LABEL = "label";
static final String ATTR_VALUE = "value";
static final String LOCKED_VISUAL_PROPS = "lockedVisualProperties";
+
+ static final Pattern XLINK_PATTERN = Pattern.compile(".*#(\\d+)");
private Locator locator;
@@ -218,4 +222,9 @@
return version;
}
+
+ public static String getIdFromXLink(String href) {
+ Matcher matcher = XLINK_PATTERN.matcher(href);
+ return matcher.matches() ? matcher.group(1) : null;
+ }
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java
2011-12-03 00:36:19 UTC (rev 27691)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNode.java
2011-12-05 20:38:30 UTC (rev 27692)
@@ -1,7 +1,9 @@
package org.cytoscape.io.internal.read.xgmml.handler;
import org.cytoscape.io.internal.read.xgmml.ParseState;
+import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.subnetwork.CySubNetwork;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
@@ -26,9 +28,22 @@
node.getCyRow().set(CyNode.NAME, label);
}
} else {
- // The node might not have been created yet!
- // So just save the reference so it can be added to the
network after the whole graph is parsed.
- manager.addElementLink(href, CyNode.class);
+ // Try to get the node from the internal cache
+ String id = AttributeValueUtil.getIdFromXLink(href);
+ CyNode node = manager.getNode(id);
+
+ if (node != null) {
+ CyNetwork net = manager.getCurrentNetwork();
+
+ if (net instanceof CySubNetwork)
+ ((CySubNetwork) net).addNode(node);
+ else
+ logger.error("Cannot add existing node
\"" + id + "\" to a network which is not a CySubNetwork");
+ } else {
+ // The node might not have been created yet!
+ // So just save the reference so it can be
added to the network after the whole graph is parsed.
+ manager.addElementLink(href, CyNode.class);
+ }
}
return current;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2011-12-03 00:36:19 UTC (rev 27691)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2011-12-05 20:38:30 UTC (rev 27692)
@@ -40,7 +40,7 @@
public class ReadDataManager {
protected final static String XLINK = "http://www.w3.org/1999/xlink";;
-
+
/* RDF Data */
protected String RDFDate;
protected String RDFTitle;
@@ -471,7 +471,7 @@
protected void addElementLink(String href, Class<? extends
CyTableEntry> clazz) {
Map<CyNetwork, Set<String>> map = null;
- String id = href.replace("#", "").trim();
+ String id = AttributeValueUtil.getIdFromXLink(href);
if (clazz == CyNode.class) map = nodeLinkMap;
else if (clazz == CyEdge.class) map = edgeLinkMap;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-12-03 00:36:19 UTC (rev 27691)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-12-05 20:38:30 UTC (rev 27692)
@@ -554,21 +554,34 @@
* @throws IOException
*/
private void writeEdgeView(View<CyEdge> view) throws IOException {
- writeElement("<edge");
- writeAttributePair("id", view.getSUID());
- writeAttributePair("label", getLabel(view.getModel()));
- writeAttributePair("cy:edgeId", view.getModel().getSUID());
- write(">\n");
- depth++;
-
- // Write the edge graphics
- writeGraphics(view);
-
- depth--;
- writeElement("</edge>\n");
+ // It is not necessary to write edges that have no locked
visual properties
+ boolean hasLockedVisualProps = false;
+ Collection<VisualProperty<?>> visualProperties =
visualLexicon.getAllDescendants(MinimalVisualLexicon.EDGE);
+
+ for (VisualProperty<?> vp : visualProperties) {
+ if (view.isValueLocked(vp)) {
+ hasLockedVisualProps = true;
+ break;
+ }
+ }
+
+ if (hasLockedVisualProps) {
+ writeElement("<edge");
+ writeAttributePair("id", view.getSUID());
+ writeAttributePair("label", getLabel(view.getModel()));
+ writeAttributePair("cy:edgeId",
view.getModel().getSUID());
+ write(">\n");
+ depth++;
+
+ // Write the edge graphics
+ writeGraphics(view);
+
+ depth--;
+ writeElement("</edge>\n");
+ }
}
- @SuppressWarnings("unchecked")
+ @SuppressWarnings({"unchecked", "rawtypes"})
private void writeGraphics(View<? extends CyTableEntry> view) throws
IOException {
if (view == null) return;
writeElement("<graphics");
@@ -595,8 +608,10 @@
Object value = view.getVisualProperty(vp);
- if (value != null && view.isValueLocked(vp))
+ if (value != null && view.isValueLocked(vp)) {
lockedProperties.add(vp);
+ continue;
+ }
// Use XGMML graphics attribute names for some visual properties
String key = getGraphicsKey(vp);
@@ -723,15 +738,18 @@
}
/**
+ * Do not use this method with locked visual properties.
* @param element
* @param attName
* @return
*/
private boolean ignoreGraphicsAttribute(final CyTableEntry element, String
attName) {
+ // If a session format, only those visual properties that belong to the
view
+ // (not a visual style) should be saved in the XGMML file.
boolean b = (sessionFormat && (element instanceof CyNode) &&
!attName.matches("x|y|z"));
b = b || (sessionFormat && (element instanceof CyEdge));
b = b || (sessionFormat && (element instanceof CyNetwork) &&
-
!attName.matches(MinimalVisualLexicon.NETWORK_BACKGROUND_PAINT.getIdString()));
+
attName.matches(MinimalVisualLexicon.NETWORK_BACKGROUND_PAINT.getIdString()));
return b;
}
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