Author: clopes
Date: 2012-11-21 10:39:40 -0800 (Wed, 21 Nov 2012)
New Revision: 30828
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SessionXGMMLNetworkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SessionXGMMLNetworkViewReader.java
Log:
Minor changes to improve performance.
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReader.java
2012-11-21 15:34:36 UTC (rev 30827)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/GenericXGMMLReader.java
2012-11-21 18:39:40 UTC (rev 30828)
@@ -107,7 +107,7 @@
}
@Override
- public void run(TaskMonitor tm) throws Exception {
+ public void run(final TaskMonitor tm) throws Exception {
tm.setProgress(0.0);
init(tm);
@@ -146,14 +146,14 @@
return netView;
}
- protected void init(TaskMonitor tm) {
+ protected void init(final TaskMonitor tm) {
readDataMgr.init();
readDataMgr.setViewFormat(false); // TODO: refactor readDataMgr
and delete this line
// Now user has the option to import network into different
collection
-
this.initNodeMap(name2RootMap.get(rootNetworkList.getSelectedValue()),
this.targetColumnList.getSelectedValue());
- this.readDataMgr.setNodeMap(this.nMap);
-
this.readDataMgr.setParentNetwork(name2RootMap.get(rootNetworkList.getSelectedValue()));
+
initNodeMap(name2RootMap.get(rootNetworkList.getSelectedValue()),
this.targetColumnList.getSelectedValue());
+ readDataMgr.setNodeMap(this.nMap);
+
readDataMgr.setParentNetwork(name2RootMap.get(rootNetworkList.getSelectedValue()));
}
protected void complete(TaskMonitor tm) {
@@ -168,7 +168,7 @@
* @throws SAXException
* @throws ParserConfigurationException
*/
- protected void readXGMML(TaskMonitor tm) throws SAXException,
IOException {
+ protected void readXGMML(final TaskMonitor tm) throws SAXException,
IOException {
final SAXParserFactory spf = SAXParserFactory.newInstance();
try {
@@ -198,45 +198,54 @@
}
}
- protected void setNetworkViewProperties(CyNetworkView netView) {
+ protected void setNetworkViewProperties(final CyNetworkView netView) {
final CyNetwork network = netView.getModel();
+ final String name = network.getRow(network).get(CyNetwork.NAME,
String.class);
- String name = network.getRow(network).get(CyNetwork.NAME,
String.class);
-
if (name != null)
netView.setVisualProperty(BasicVisualLexicon.NETWORK_TITLE, name);
- Map<String, String> atts =
readDataMgr.getGraphicsAttributes(network);
+ final Map<String, String> atts =
readDataMgr.getGraphicsAttributes(network);
setVisualProperties(netView, netView, atts);
}
- protected void setNodeViewProperties(CyNetworkView netView,
View<CyNode> nodeView) {
+ protected void setNodeViewProperties(final CyNetworkView netView, final
View<CyNode> nodeView) {
final CyNode node = nodeView.getModel();
final Map<String, String> atts =
readDataMgr.getGraphicsAttributes(node);
setVisualProperties(netView, nodeView, atts);
}
- protected void setEdgeViewProperties(CyNetworkView netView,
View<CyEdge> edgeView) {
+ protected void setEdgeViewProperties(final CyNetworkView netView, final
View<CyEdge> edgeView) {
final CyEdge edge = edgeView.getModel();
final Map<String, String> atts =
readDataMgr.getGraphicsAttributes(edge);
setVisualProperties(netView, edgeView, atts);
+
+ // For 2.x compatibility
+ final Bend bend =
edgeView.getVisualProperty(BasicVisualLexicon.EDGE_BEND);
+
+ if (bend != null && bend !=
EdgeBendVisualProperty.DEFAULT_EDGE_BEND) {
+ final List<Handle> handles = bend.getAllHandles();
+
+ for (final Handle handle : handles)
+ handle.defineHandle(netView, edgeView,
Double.NaN, Double.NaN);
+ }
}
@SuppressWarnings({ "rawtypes", "unchecked" })
protected void setVisualProperties(final CyNetworkView netView, final
View<? extends CyIdentifiable> view,
- Map<String, String> atts) {
+ final Map<String, String> atts) {
if (view != null && atts != null) {
- CyIdentifiable model = view.getModel();
+ final CyIdentifiable model = view.getModel();
Class<?> type = CyNetwork.class;
if (model instanceof CyNode) type = CyNode.class;
else if (model instanceof CyEdge) type = CyEdge.class;
- Set<String> attSet = atts.keySet();
+ final Set<String> attSet = atts.keySet();
- for (String attName : attSet) {
+ for (final String attName : attSet) {
String attValue = atts.get(attName);
- VisualProperty vp = visualLexicon.lookup(type,
attName);
+ final VisualProperty vp =
visualLexicon.lookup(type, attName);
if (vp != null) {
if (isXGMMLTransparency(attName))
@@ -254,43 +263,45 @@
unrecognizedVisualPropertyMgr.addUnrecognizedVisualProperty(netView, view,
attName, attValue);
}
}
-
- // For 2.x compatibility
- final Bend bend =
view.getVisualProperty(BasicVisualLexicon.EDGE_BEND);
- if (bend != null && bend !=
EdgeBendVisualProperty.DEFAULT_EDGE_BEND) {
- final List<Handle> handles =
bend.getAllHandles();
- for (Handle handle : handles) {
- handle.defineHandle(netView,
(View<CyEdge>) view, Double.NaN, Double.NaN);
- }
- }
}
}
+ private static final Pattern DIRECT_NODE_PROPS_PATTERN =
Pattern.compile("x|y|z");
+ private static final Pattern DIRECT_NET_PROPS_PATTERN = Pattern.compile(
+
"GRAPH_VIEW_(ZOOM|CENTER_(X|Y))|NETWORK_(WIDTH|HEIGHT|SCALE_FACTOR|CENTER_(X|Y|Z)_LOCATION)");
+
/**
* It tells which graphics attributes should be set as locked
properties.
* @param element
* @param attName
* @return
*/
- protected boolean isLockedVisualProperty(final CyIdentifiable element,
String attName) {
- // These are NOT locked properties
- boolean b = !((element instanceof CyNode) &&
attName.matches("x|y|z"));
- b = b &&
- !((element instanceof CyNetwork) &&
-
attName.matches("GRAPH_VIEW_(ZOOM|CENTER_(X|Y))|" +
-
"NETWORK_(WIDTH|HEIGHT|SCALE_FACTOR|CENTER_(X|Y|Z)_LOCATION)"));
+ protected boolean isLockedVisualProperty(final CyIdentifiable element,
final String attName) {
+ boolean locked = true;
+
+ // These must NOT be set as locked properties
+ if (element instanceof CyNetwork) {
+ final Matcher netMatcher =
DIRECT_NET_PROPS_PATTERN.matcher(attName);
+ locked = !netMatcher.matches();
+ } else if (element instanceof CyNode) {
+ final Matcher nodeMatcher =
DIRECT_NODE_PROPS_PATTERN.matcher(attName);
+ locked = !nodeMatcher.matches();
+ } else if (element instanceof CyEdge) {
+ // Nothing to do here; all edge properties are locked
by default.
+ }
- return b;
+ return locked;
}
-
private static final Pattern TRANSPARENCY_PATTERN =
Pattern.compile("(cy:)?(node|edge)Transparency");
+
static boolean isXGMMLTransparency(final String attName) {
final Matcher matcher = TRANSPARENCY_PATTERN.matcher(attName);
return matcher.matches();
}
private static final Pattern OLD_FONT_PATTERN =
Pattern.compile("(cy:)?(node|edge)LabelFont");
+
static boolean isOldFont(final String attName) {
final Matcher matcher = OLD_FONT_PATTERN.matcher(attName);
return matcher.matches();
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SessionXGMMLNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SessionXGMMLNetworkReader.java
2012-11-21 15:34:36 UTC (rev 30827)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SessionXGMMLNetworkReader.java
2012-11-21 18:39:40 UTC (rev 30828)
@@ -27,7 +27,6 @@
private final CyRootNetworkManager cyRootNetworkManager;
private CyRootNetwork parent;
- //private CyApplicationManager cyApplicationManager;
public SessionXGMMLNetworkReader(final InputStream inputStream,
final
CyNetworkViewFactory cyNetworkViewFactory,
@@ -43,35 +42,34 @@
unrecognizedVisualPropertyMgr,
cyNetworkManager, cyRootNetworkManager, cyApplicationManager);
this.cyRootNetworkManager = cyRootNetworkManager;
- //this.cyApplicationManager = cyApplicationManager;
}
- public void setParent(CyNetwork n) {
+ public void setParent(final CyNetwork n) {
this.parent = n != null ?
cyRootNetworkManager.getRootNetwork(n) : null;
}
@Override
- protected void init(TaskMonitor tm) {
+ protected void init(final TaskMonitor tm) {
super.init(tm);
readDataMgr.setViewFormat(false);
readDataMgr.setParentNetwork(parent);
}
@Override
- protected void setNetworkViewProperties(CyNetworkView netView) {
+ protected void setNetworkViewProperties(final CyNetworkView netView) {
// Only for Cytocape 2.x files. In Cy3 the visual properties
are saved in the view xgmml file.
if (readDataMgr.getDocumentVersion() < 3.0)
super.setNetworkViewProperties(netView);
}
@Override
- protected void setNodeViewProperties(CyNetworkView netView,
View<CyNode> nodeView) {
+ protected void setNodeViewProperties(final CyNetworkView netView, final
View<CyNode> nodeView) {
if (readDataMgr.getDocumentVersion() < 3.0)
super.setNodeViewProperties(netView, nodeView);
}
@Override
- protected void setEdgeViewProperties(CyNetworkView netView,
View<CyEdge> edgeView) {
+ protected void setEdgeViewProperties(final CyNetworkView netView, final
View<CyEdge> edgeView) {
if (readDataMgr.getDocumentVersion() < 3.0)
super.setEdgeViewProperties(netView, edgeView);
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SessionXGMMLNetworkViewReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SessionXGMMLNetworkViewReader.java
2012-11-21 15:34:36 UTC (rev 30827)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/SessionXGMMLNetworkViewReader.java
2012-11-21 18:39:40 UTC (rev 30828)
@@ -71,13 +71,13 @@
}
@Override
- protected void init(TaskMonitor tm) {
+ protected void init(final TaskMonitor tm) {
super.init(tm);
readDataMgr.setViewFormat(true);
}
@Override
- protected void setNetworkViewProperties(CyNetworkView netView) {
+ protected void setNetworkViewProperties(final CyNetworkView netView) {
// Direct visual properties
Map<String, String> atts =
readDataMgr.getViewGraphicsAttributes(readDataMgr.getNetworkId(), false);
this.settingLockedVisualProperties = false;
@@ -93,12 +93,12 @@
}
@Override
- protected void setNodeViewProperties(CyNetworkView netView,
View<CyNode> nodeView) {
+ protected void setNodeViewProperties(final CyNetworkView netView, final
View<CyNode> nodeView) {
final CyNode node = nodeView.getModel();
// When parsing view-format XGMML, the manager does not have
the network model
// to create a map by CyNode objects, so the graphics mapping
is indexed by the old element id.
- Object oldId = readDataMgr.getCache().getOldId(node.getSUID());
+ final Object oldId =
readDataMgr.getCache().getOldId(node.getSUID());
// Direct visual properties
Map<String, String> atts =
readDataMgr.getViewGraphicsAttributes(oldId, false);
@@ -112,12 +112,12 @@
}
@Override
- protected void setEdgeViewProperties(CyNetworkView netView,
View<CyEdge> edgeView) {
+ protected void setEdgeViewProperties(final CyNetworkView netView, final
View<CyEdge> edgeView) {
final CyEdge edge = edgeView.getModel();
// When parsing view-format XGMML, the manager does not have
the network model
// to create a map by CyEdge objects, so the graphics mapping
is indexed by the old element id.
- Object oldId = readDataMgr.getCache().getOldId(edge.getSUID());
+ final Object oldId =
readDataMgr.getCache().getOldId(edge.getSUID());
// Direct visual properties
Map<String, String> atts =
readDataMgr.getViewGraphicsAttributes(oldId, false);
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
