Author: mes
Date: 2011-11-30 10:48:05 -0800 (Wed, 30 Nov 2011)
New Revision: 27642
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkFactory.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/MapBioPaxToCytoscapeImpl.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/NewEmptyNetworkTask.java
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLParser.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/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/GOPTAlgorithm.java
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/ui/NetworkMergeFrame.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/PsiMiTabParser.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/reader/ontology/OBOReader.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
core3/impl/trunk/table-import-impl/src/test/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReaderTest.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
core3/impl/trunk/vizmap-impl/impl/src/test/java/org/cytoscape/view/vizmap/VisualStyleTest.java
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
core3/support/trunk/samples/sample05/src/main/java/org/cytoscape/sample/internal/MyNetworkTask.java
core3/support/trunk/samples/sample05a/src/main/java/org/cytoscape/sample/internal/Sample05aTask.java
Log:
Changed CyNetworkFactory method names to be more consistent.
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkFactory.java
===================================================================
---
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkFactory.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNetworkFactory.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -39,11 +39,11 @@
* Returns a new, empty {@link CyNetwork} object.
* @return A new, empty {@link CyNetwork} object.
*/
- CyNetwork getInstance();
+ CyNetwork createNetwork();
/**
* Returns a new, empty {@link CyNetwork} object where the associated
default tables are private.
* @return A new, empty {@link CyNetwork} object.
*/
- CyNetwork getInstanceWithPrivateTables();
+ CyNetwork createNetworkWithPrivateTables();
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/MapBioPaxToCytoscapeImpl.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/MapBioPaxToCytoscapeImpl.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/MapBioPaxToCytoscapeImpl.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -173,7 +173,7 @@
*/
@Override
public CyNetwork createCyNetwork(String networkName) {
- CyNetwork network = networkFactory.getInstance();
+ CyNetwork network = networkFactory.createNetwork();
// First, create nodes for all Entity class objects
createEntityNodes(network);
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -103,7 +103,7 @@
}
private CyNetwork cloneNetwork(CyNetwork origNet) {
- final CyNetwork newNet = netFactory.getInstance();
+ final CyNetwork newNet = netFactory.createNetwork();
final CyTable nodeTable = newNet.getDefaultNodeTable();
final CyTable edgeTable = newNet.getDefaultEdgeTable();
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/NewEmptyNetworkTask.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -68,7 +68,7 @@
public void run(TaskMonitor tm) {
tm.setProgress(0.0);
- final CyNetwork newNet = cnf.getInstance();
+ final CyNetwork newNet = cnf.createNetwork();
tm.setProgress(0.2);
newNet.getCyRow().set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle("Network"));
tm.setProgress(0.4);
Modified:
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLParser.java
===================================================================
---
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLParser.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLParser.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -142,7 +142,7 @@
if (networkStack.size() == 0) {
// Root network.
- currentNetwork = networkFactory.getInstance();
+ currentNetwork = networkFactory.createNetwork();
} else {
final CyNetwork parentNetwork = networkStack.peek();
currentNetwork =
rootNetworkManager.getRootNetwork(parentNetwork).addSubNetwork();
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -192,7 +192,7 @@
taskMonitor.setProgress(0.1);
readGML(keyVals, taskMonitor); // read the GML file
taskMonitor.setProgress(0.3);
- network = cyNetworkFactory.getInstance();
+ network = cyNetworkFactory.createNetwork();
createGraph(taskMonitor);
taskMonitor.setProgress(0.8);
this.cyNetworks = new CyNetwork[] { network };
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -100,7 +100,7 @@
new BufferedReader(new InputStreamReader(inputStream),
128*1024);
Map<String, CyNode> nMap = new HashMap<String, CyNode>(10000);
- CyNetwork network = cyNetworkFactory.getInstance();
+ CyNetwork network = cyNetworkFactory.createNetwork();
final CyTable nodeTable = network.getDefaultNodeTable();
final CyTable edgeTable = network.getDefaultEdgeTable();
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkReader.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -113,7 +113,7 @@
readDataMgr.initAllData();
readDataMgr.setSessionFormat(sessionFormat);
- readDataMgr.setNetwork(cyNetworkFactory.getInstance());
+ readDataMgr.setNetwork(cyNetworkFactory.createNetwork());
tm.setProgress(0.1);
try {
readXGMML();
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNetworkFactoryImpl.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -80,7 +80,7 @@
* {@inheritDoc}
*/
@Override
- public CyNetwork getInstance() {
+ public CyNetwork createNetwork() {
ArrayGraph net = new ArrayGraph(help, mgr, networkTableMgr,
tableFactory, serviceRegistrar, true);
logger.info("CyNetwork w/ public tables created: ID = " +
net.getSUID());
logger.info("CyNetwork w/ public tables created: Base Graph ID
= " + net.getBaseNetwork().getSUID());
@@ -91,7 +91,7 @@
* {@inheritDoc}
*/
@Override
- public CyNetwork getInstanceWithPrivateTables() {
+ public CyNetwork createNetworkWithPrivateTables() {
ArrayGraph net = new ArrayGraph(help, mgr, networkTableMgr,
tableFactory, serviceRegistrar, false);
logger.info("CyNetwork w/ private tables created: ID = " +
net.getSUID());
logger.info("CyNetwork w/ private tables created: Base Graph ID
= " + net.getBaseNetwork().getSUID());
Modified:
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/model-impl/impl/src/test/java/org/cytoscape/model/NetworkTestSupport.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -37,7 +37,7 @@
}
public CyNetwork getNetwork() {
- return networkFactory.getInstance();
+ return networkFactory.createNetwork();
}
public CyNetworkFactory getNetworkFactory() {
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/GOPTAlgorithm.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/GOPTAlgorithm.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/GOPTAlgorithm.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -162,7 +162,7 @@
// TODO This should be refactored out into a Task
private CyNetwork createNetwork(String name) {
- CyNetwork n = netFactory.getInstance();
+ CyNetwork n = netFactory.createNetwork();
n.getCyRow().set("name",name);
netMgr.addNetwork(n);
return n;
Modified:
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/ui/NetworkMergeFrame.java
===================================================================
---
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/ui/NetworkMergeFrame.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/ui/NetworkMergeFrame.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -810,7 +810,7 @@
// frame.setAlwaysOnTop(isFrameAlwaysOnTop);
}
- CyNetwork net = cnf.getInstance();
+ CyNetwork net = cnf.createNetwork();
String netName =
cnn.getSuggestedNetworkTitle(mergeNodeAttributeTable.getMergedNetworkName());
//TODO: set network name
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -64,7 +64,7 @@
taskMonitor.setProgress(0.25);
// Now map to Cytoscape network objects.
- network = networkFactory.getInstance();
+ network = networkFactory.createNetwork();
MapToCytoscape mapper2 = new MapToCytoscape(network,
interactions, MapToCytoscape.SPOKE_VIEW);
mapper2.doMapping();
Modified:
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/psi-mi-impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabParser.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -84,7 +84,7 @@
String[] edgeScore;
- final CyNetwork network = cyNetworkFactory.getInstance();
+ final CyNetwork network = cyNetworkFactory.createNetwork();
final CyTable nodeTable = network.getDefaultNodeTable();
if(nodeTable.getColumn(INTERACTOR_TYPE) == 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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/sbml-impl/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -79,7 +79,7 @@
String xml = readString(stream);
SBMLDocument document = JSBML.readSBMLFromString(xml);
- network = networkFactory.getInstance();
+ network = networkFactory.createNetwork();
//view = viewFactory.getNetworkView(network);
Model model = document.getModel();
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/reader/ontology/OBOReader.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -94,7 +94,7 @@
String line;
// Create new DAG
- this.ontologyDAG = cyNetworkFactory.getInstance();
+ this.ontologyDAG = cyNetworkFactory.createNetwork();
try {
// Phase 1: read header information
header = new HashMap<String, String>();
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportNetworkTask.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -69,7 +69,7 @@
protected VisualStyle[] visualstyles;
private final GraphReader reader;
- final CyNetwork network =
CytoscapeServices.cyNetworkFactory.getInstance();
+ final CyNetwork network =
CytoscapeServices.cyNetworkFactory.createNetwork();
/**
* Creates a new ImportNetworkTask object.
Modified:
core3/impl/trunk/table-import-impl/src/test/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReaderTest.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/test/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReaderTest.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/table-import-impl/src/test/java/org/cytoscape/tableimport/internal/reader/ontology/GeneAssociationReaderTest.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -46,7 +46,7 @@
CyNetworkViewFactory cyNetworkViewFactory =
viewSupport.getNetworkViewFactory();
CyNetworkFactory cyNetworkFactory =
netSupport.getNetworkFactory();
tableFactory = tableSupport.getTableFactory();
- dag = cyNetworkFactory.getInstance();
+ dag = cyNetworkFactory.createNetwork();
CyEventHelper eventHelper = mock(CyEventHelper.class);
tm = mock(TaskMonitor.class);
}
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -117,7 +117,7 @@
this.selectedManager = selectedManager;
// Create dummy view.
- final CyNetwork dummyNet =
cyNetworkFactory.getInstanceWithPrivateTables();
+ final CyNetwork dummyNet =
cyNetworkFactory.createNetworkWithPrivateTables();
final CyNode source = dummyNet.addNode();
final CyNode target = dummyNet.addNode();
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 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/vizmap-impl/impl/src/test/java/org/cytoscape/view/vizmap/VisualStyleTest.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -26,7 +26,7 @@
final Class<String> type = String.class;
CyProperty<Properties> cyProperties = mock(CyProperty.class);
NetworkViewTestSupport nvts = new NetworkViewTestSupport();
- network = nvts.getNetworkFactory().getInstance();
+ network = nvts.getNetworkFactory().createNetwork();
node1 = network.addNode();
node2 = network.addNode();
Modified:
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
===================================================================
---
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/impl/trunk/webservice-ncbi-client-impl/src/main/java/org/cytoscape/webservice/ncbi/rest/EntrezRestClient.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -91,7 +91,7 @@
final CompletionService<Double> completionService = new
ExecutorCompletionService<Double>(executer);
logger.debug("Executor initialized.");
- final CyNetwork newNetwork = networkFactory.getInstance();
+ final CyNetwork newNetwork = networkFactory.createNetwork();
final ConcurrentMap<String, CyNode> nodeName2CyNodeMap = new
ConcurrentHashMap<String, CyNode>();
Modified:
core3/support/trunk/samples/sample05/src/main/java/org/cytoscape/sample/internal/MyNetworkTask.java
===================================================================
---
core3/support/trunk/samples/sample05/src/main/java/org/cytoscape/sample/internal/MyNetworkTask.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/support/trunk/samples/sample05/src/main/java/org/cytoscape/sample/internal/MyNetworkTask.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -27,7 +27,7 @@
public void run(TaskMonitor monitor) {
// Create an empty network
- CyNetwork myNet = cnf.getInstance();
+ CyNetwork myNet = cnf.createNetwork();
myNet.getCyRow().set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle("My
Network"));
Modified:
core3/support/trunk/samples/sample05a/src/main/java/org/cytoscape/sample/internal/Sample05aTask.java
===================================================================
---
core3/support/trunk/samples/sample05a/src/main/java/org/cytoscape/sample/internal/Sample05aTask.java
2011-11-30 00:06:42 UTC (rev 27641)
+++
core3/support/trunk/samples/sample05a/src/main/java/org/cytoscape/sample/internal/Sample05aTask.java
2011-11-30 18:48:05 UTC (rev 27642)
@@ -17,7 +17,7 @@
public void run(TaskMonitor monitor) {
// Create an empty network
- CyNetwork myNet = adapter.getCyNetworkFactory().getInstance();
+ CyNetwork myNet = adapter.getCyNetworkFactory().createNetwork();
myNet.getCyRow().set(CyTableEntry.NAME, "My network");
//
adapter.namingUtil.getSuggestedNetworkTitle("My Network"));
--
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