Author: mes
Date: 2011-11-30 10:54:59 -0800 (Wed, 30 Nov 2011)
New Revision: 27644
Modified:
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewFactory.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxNetworkViewReaderTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingViewModelFactory.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/NetworkViewTestSupport.java
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderTask.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
core3/impl/trunk/vizmap-impl/impl/src/test/java/org/cytoscape/view/vizmap/VisualStyleTest.java
core3/support/trunk/samples/sample06/src/main/java/org/cytoscape/sample/internal/MyNetworkViewTask.java
Log:
Renamed factory methods to be more consistent.
Modified:
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewFactory.java
===================================================================
---
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewFactory.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/CyNetworkViewFactory.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -53,7 +53,7 @@
* @param network for which the CyNetworkView is to be created
* @return the view model for the network data model
*/
- public CyNetworkView getNetworkView(final CyNetwork network);
+ public CyNetworkView createNetworkView(final CyNetwork network);
/**
* Creates view with or without using viewThreshold property.
@@ -63,5 +63,5 @@
*
* @return View model for the given data model.
*/
- public CyNetworkView getNetworkView(final CyNetwork network, final
Boolean useThreshold);
+ public CyNetworkView createNetworkView(final CyNetwork network, final
Boolean useThreshold);
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxNetworkViewReaderTask.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxNetworkViewReaderTask.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxNetworkViewReaderTask.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -145,7 +145,7 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
- CyNetworkView view = viewFactory.getNetworkView(network);
+ CyNetworkView view = viewFactory.createNetworkView(network);
networkListener.registerNetwork(view);
// Set-up the BioPax Visual Style
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/AbstractNetworkFromSelectionTask.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -137,7 +137,7 @@
tm.setProgress(0.7);
// create new view
- final CyNetworkView newView =
viewFactory.getNetworkView(newNet);
+ final CyNetworkView newView =
viewFactory.createNetworkView(newNet);
networkViewManager.addNetworkView(newView);
tm.setProgress(0.8);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -165,7 +165,7 @@
*
*/
private void copyView(final CyNetwork newNet, final CyNetworkView
origView) {
- final CyNetworkView newView =
netViewFactory.getNetworkView(newNet);
+ final CyNetworkView newView =
netViewFactory.createNetworkView(newNet);
// Copy node locations since this is controlled outside of
visual style.
for (final View<CyNode> origNodeView : origView.getNodeViews())
{
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -51,7 +51,7 @@
;
final CyNetworkView view =
- viewFactory.getNetworkView(network, /* useThreshold =
*/ false);
+ viewFactory.createNetworkView(network, /* useThreshold
= */ false);
networkViewManager.addNetworkView(view);
for (final View<CyNode> nodeView : view.getNodeViews())
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewTask.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -80,7 +80,7 @@
// By calling this task, actual view will be created
even if it's a
// large network.
taskMonitor.setProgress(0.4);
- final CyNetworkView view =
viewFactory.getNetworkView(network, false);
+ final CyNetworkView view =
viewFactory.createNetworkView(network, false);
taskMonitor.setProgress(0.8);
networkViewManager.addNetworkView(view);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -72,7 +72,7 @@
tm.setProgress(0.2);
newNet.getCyRow().set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle("Network"));
tm.setProgress(0.4);
- view = cnvf.getNetworkView(newNet);
+ view = cnvf.createNetworkView(newNet);
tm.setProgress(0.6);
networkManager.addNetwork(newNet);
tm.setProgress(0.8);
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingViewModelFactory.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingViewModelFactory.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DingViewModelFactory.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -60,12 +60,12 @@
}
@Override
- public CyNetworkView getNetworkView(final CyNetwork network) {
- return getNetworkView(network, false);
+ public CyNetworkView createNetworkView(final CyNetwork network) {
+ return createNetworkView(network, false);
}
@Override
- public CyNetworkView getNetworkView(final CyNetwork network, final
Boolean useThreshold) {
+ public CyNetworkView createNetworkView(final CyNetwork network, final
Boolean useThreshold) {
if (network == null)
throw new IllegalArgumentException("Cannot create view
without model.");
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/NetworkViewTestSupport.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/NetworkViewTestSupport.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/test/java/org/cytoscape/ding/NetworkViewTestSupport.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -46,7 +46,7 @@
}
public CyNetworkView getNetworkView() {
- return viewFactory.getNetworkView( getNetwork() );
+ return viewFactory.createNetworkView( getNetwork() );
}
public CyNetworkViewFactory getNetworkViewFactory() {
Modified:
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReader.java
===================================================================
---
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReader.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReader.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -96,7 +96,7 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
- final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
+ final CyNetworkView view =
cyNetworkViewFactory.createNetworkView(network);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
layout.setNetworkView(view);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -201,7 +201,7 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
- view = cyNetworkViewFactory.getNetworkView(network);
+ view = cyNetworkViewFactory.createNetworkView(network);
releaseStructures();
layout(view);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -184,7 +184,7 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
- final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
+ final CyNetworkView view =
cyNetworkViewFactory.createNetworkView(network);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
layout.setNetworkView(view);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -134,7 +134,7 @@
public CyNetworkView buildCyNetworkView(CyNetwork network) {
// any existing equations should be parsed first
readDataMgr.parseAllEquations();
- netView = cyNetworkViewFactory.getNetworkView(network);
+ netView = cyNetworkViewFactory.createNetworkView(network);
if (netView != null) {
// Network Title
Modified:
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -97,7 +97,7 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
- final CyNetworkView networkView =
networkViewFactory.getNetworkView(network);
+ final CyNetworkView networkView =
networkViewFactory.createNetworkView(network);
CyLayoutAlgorithm taskFactory = layouts.getDefaultLayout();
taskFactory.setNetworkView(networkView);
Modified:
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -77,7 +77,7 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
- final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
+ final CyNetworkView view =
cyNetworkViewFactory.createNetworkView(network);
String pref = CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME;
if(prop != null)
Modified:
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
===================================================================
---
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -207,6 +207,6 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
- return viewFactory.getNetworkView(network);
+ return viewFactory.createNetworkView(network);
}
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderTask.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ImportNetworkTableReaderTask.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -71,7 +71,7 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork arg0) {
- final CyNetworkView view =
CytoscapeServices.cyNetworkViewFactory.getNetworkView(arg0);
+ final CyNetworkView view =
CytoscapeServices.cyNetworkViewFactory.createNetworkView(arg0);
return view;
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -326,7 +326,7 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork arg0) {
- final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(ontologyDAG);
+ final CyNetworkView view =
cyNetworkViewFactory.createNetworkView(ontologyDAG);
return view;
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -99,7 +99,7 @@
return;
}
- final CyNetworkView view =
CytoscapeServices.cyNetworkViewFactory.getNetworkView(network);
+ final CyNetworkView view =
CytoscapeServices.cyNetworkViewFactory.createNetworkView(network);
CytoscapeServices.cyNetworkManager.addNetwork(network);
CytoscapeServices.cyNetworkViewManager.addNetworkView(view);
Modified:
core3/impl/trunk/vizmap-impl/impl/src/test/java/org/cytoscape/view/vizmap/VisualStyleTest.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/test/java/org/cytoscape/view/vizmap/VisualStyleTest.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/impl/trunk/vizmap-impl/impl/src/test/java/org/cytoscape/view/vizmap/VisualStyleTest.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -39,7 +39,7 @@
nodeTable.getRow(node2.getSUID()).set(attrName, "green");
nodeTable.getRow(node3.getSUID()).set(attrName, "foo");
- networkView = nvts.getNetworkViewFactory().getNetworkView(network);
+ networkView = nvts.getNetworkViewFactory().createNetworkView(network);
// Create root node.
final VisualLexiconManager lexManager =
mock(VisualLexiconManager.class);
Modified:
core3/support/trunk/samples/sample06/src/main/java/org/cytoscape/sample/internal/MyNetworkViewTask.java
===================================================================
---
core3/support/trunk/samples/sample06/src/main/java/org/cytoscape/sample/internal/MyNetworkViewTask.java
2011-11-30 18:51:35 UTC (rev 27643)
+++
core3/support/trunk/samples/sample06/src/main/java/org/cytoscape/sample/internal/MyNetworkViewTask.java
2011-11-30 18:54:59 UTC (rev 27644)
@@ -32,7 +32,7 @@
if(networkViewManager.getNetworkView(currNet.getSUID())
== null){
// create a new view for current network
- CyNetworkView myView =
cnvf.getNetworkView(currNet);
+ CyNetworkView myView =
cnvf.createNetworkView(currNet);
networkViewManager.addNetworkView(myView);
}
else {
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