Author: pwang
Date: 2012-08-03 15:09:42 -0700 (Fri, 03 Aug 2012)
New Revision: 30087
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/nnf/NNFNetworkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/nnf/NNFNetworkReaderFactory.java
Log:
Clean up for NNF format
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-08-03 22:05:58 UTC (rev 30086)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/CyActivator.java
2012-08-03 22:09:42 UTC (rev 30087)
@@ -185,7 +185,7 @@
ExpressionReaderFactory expressionReaderFactory = new
ExpressionReaderFactory(expressionFilter,cyTableFactoryServiceRef);
CyAttributesReaderFactory attrsDataReaderFactory = new
CyAttributesReaderFactory(attrsFilter,cyTableFactoryServiceRef,cyApplicationManagerServiceRef,cyNetworkManagerServiceRef,cyRootNetworkManagerServiceRef);
SIFNetworkReaderFactory sifNetworkViewReaderFactory = new
SIFNetworkReaderFactory(sifFilter,cyLayoutsServiceRef,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyEventHelperRef);
- NNFNetworkReaderFactory nnfNetworkViewReaderFactory = new
NNFNetworkReaderFactory(nnfFilter,cyLayoutsServiceRef,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,cyEventHelperRef,
cyNetworkManagerServiceRef);
+ NNFNetworkReaderFactory nnfNetworkViewReaderFactory = new
NNFNetworkReaderFactory(nnfFilter,cyLayoutsServiceRef,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,
cyNetworkManagerServiceRef);
UnrecognizedVisualPropertyManager
unrecognizedVisualPropertyManager = new
UnrecognizedVisualPropertyManager(cyTableFactoryServiceRef,cyTableManagerServiceRef);
GMLNetworkReaderFactory gmlNetworkViewReaderFactory = new
GMLNetworkReaderFactory(gmlFilter,cyNetworkViewFactoryServiceRef,cyNetworkFactoryServiceRef,renderingEngineManagerServiceRef,unrecognizedVisualPropertyManager);
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/nnf/NNFNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/nnf/NNFNetworkReader.java
2012-08-03 22:05:58 UTC (rev 30086)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/nnf/NNFNetworkReader.java
2012-08-03 22:09:42 UTC (rev 30087)
@@ -62,7 +62,6 @@
public class NNFNetworkReader extends AbstractNetworkReader {
private static final Logger logger =
LoggerFactory.getLogger(NNFNetworkReader.class);
- private final CyEventHelper eventHelper;
private final CyLayoutAlgorithmManager layouts;
// Optional comments start with this character and extend to the end of
line.
private static final char COMMENT_CHAR = '#';
@@ -71,10 +70,9 @@
public NNFNetworkReader(InputStream is, CyLayoutAlgorithmManager
layouts,
CyNetworkViewFactory cyNetworkViewFactory,
CyNetworkFactory cyNetworkFactory,
- final CyEventHelper eventHelper,CyNetworkManager
cyNetworkManagerServiceRef) {
+ CyNetworkManager cyNetworkManagerServiceRef) {
super(is, cyNetworkViewFactory, cyNetworkFactory);
this.layouts = layouts;
- this.eventHelper = eventHelper;
this.parser = new NNFParser(cyNetworkManagerServiceRef,
cyNetworkFactory);
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/nnf/NNFNetworkReaderFactory.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/nnf/NNFNetworkReaderFactory.java
2012-08-03 22:05:58 UTC (rev 30086)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/nnf/NNFNetworkReaderFactory.java
2012-08-03 22:09:42 UTC (rev 30087)
@@ -41,20 +41,18 @@
public class NNFNetworkReaderFactory extends AbstractNetworkReaderFactory {
private final CyLayoutAlgorithmManager layouts;
- private final CyEventHelper eventHelper;
private final CyNetworkManager cyNetworkManagerServiceRef;
public NNFNetworkReaderFactory(CyFileFilter filter,
CyLayoutAlgorithmManager layouts,
CyNetworkViewFactory cyNetworkViewFactory,
CyNetworkFactory cyNetworkFactory,
- final CyEventHelper eventHelper, CyNetworkManager
cyNetworkManagerServiceRef) {
+ CyNetworkManager cyNetworkManagerServiceRef) {
super(filter, cyNetworkViewFactory, cyNetworkFactory);
this.layouts = layouts;
- this.eventHelper = eventHelper;
this.cyNetworkManagerServiceRef = cyNetworkManagerServiceRef;
}
public TaskIterator createTaskIterator(InputStream inputStream, String
inputName) {
return new TaskIterator(new NNFNetworkReader(inputStream,
layouts, cyNetworkViewFactory, cyNetworkFactory,
- eventHelper,cyNetworkManagerServiceRef));
+ cyNetworkManagerServiceRef));
}
}
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