Author: jm
Date: 2013-01-10 12:47:07 -0800 (Thu, 10 Jan 2013)
New Revision: 31036
Removed:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/SUIDToEdgeMapper.java
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/SUIDToNodeMapper.java
Modified:
core3/gui-distribution/trunk/features/src/main/resources/features.xml
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/CyActivator.java
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/FunctionRegistrar.java
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/Degree.java
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/InDegree.java
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/OutDegree.java
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/SourceID.java
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/TargetID.java
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/DegreeTest.java
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/InDegreeTest.java
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/OutDegreeTest.java
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/SourceIDTest.java
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/TargetIDTest.java
Log:
Fixes #1680: functions-equations-impl now works
Modified: core3/gui-distribution/trunk/features/src/main/resources/features.xml
===================================================================
--- core3/gui-distribution/trunk/features/src/main/resources/features.xml
2013-01-10 20:12:03 UTC (rev 31035)
+++ core3/gui-distribution/trunk/features/src/main/resources/features.xml
2013-01-10 20:47:07 UTC (rev 31036)
@@ -123,6 +123,7 @@
<bundle
start-level="160">mvn:org.cytoscape/group-view-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="165">mvn:org.cytoscape/biopax-impl/${cytoscape.impl.version}</bundle>
+ <bundle
start-level="165">mvn:org.cytoscape/equations-functions-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="170">mvn:org.cytoscape/search-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="170">mvn:org.cytoscape/table-browser-impl/${cytoscape.impl.version}</bundle>
Modified:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/CyActivator.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/CyActivator.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -1,26 +1,10 @@
-
-
-
-
package org.cytoscape.equations.internal;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.equations.EquationCompiler;
-
-import org.cytoscape.equations.internal.SUIDToEdgeMapper;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
-import org.cytoscape.equations.internal.FunctionRegistrar;
-
-
-
+import org.cytoscape.service.util.AbstractCyActivator;
import org.osgi.framework.BundleContext;
-import org.cytoscape.service.util.AbstractCyActivator;
-
-import java.util.Properties;
-
-
-
public class CyActivator extends AbstractCyActivator {
public CyActivator() {
super();
@@ -32,13 +16,8 @@
EquationCompiler compilerServiceRef =
getService(bc,EquationCompiler.class);
CyApplicationManager applicationManagerServiceRef =
getService(bc,CyApplicationManager.class);
- SUIDToEdgeMapper suidToEdgeMapper = new SUIDToEdgeMapper();
- SUIDToNodeMapper suidToNodeMapper = new SUIDToNodeMapper();
- FunctionRegistrar functionRegistrar = new
FunctionRegistrar(compilerServiceRef,applicationManagerServiceRef,suidToNodeMapper,suidToEdgeMapper);
-
- registerAllServices(bc,suidToEdgeMapper, new Properties());
- registerAllServices(bc,suidToNodeMapper, new Properties());
-
+ FunctionRegistrar functionRegistrar = new
FunctionRegistrar(compilerServiceRef,applicationManagerServiceRef);
+ functionRegistrar.registerAllFunctions();
}
}
Modified:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/FunctionRegistrar.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/FunctionRegistrar.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/FunctionRegistrar.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -10,27 +10,19 @@
public class FunctionRegistrar {
private final EquationCompiler compiler;
private final CyApplicationManager applicationManager;
- private final SUIDToNodeMapper suidToNodeMapper;
- private final SUIDToEdgeMapper suidToEdgeMapper;
- public FunctionRegistrar(final EquationCompiler compiler, final
CyApplicationManager applicationManager,
- final SUIDToNodeMapper suidToNodeMapper,
- final SUIDToEdgeMapper suidToEdgeMapper)
+ public FunctionRegistrar(final EquationCompiler compiler, final
CyApplicationManager applicationManager)
{
this.compiler = compiler;
this.applicationManager = applicationManager;
- this.suidToNodeMapper = suidToNodeMapper;
- this.suidToEdgeMapper = suidToEdgeMapper;
-
- registerAllFunctions();
}
- private void registerAllFunctions() {
+ void registerAllFunctions() {
final EquationParser parser = compiler.getParser();
- parser.registerFunction(new Degree(applicationManager,
suidToNodeMapper));
- parser.registerFunction(new InDegree(applicationManager,
suidToNodeMapper));
- parser.registerFunction(new OutDegree(applicationManager,
suidToNodeMapper));
- parser.registerFunction(new SourceID(suidToEdgeMapper));
- parser.registerFunction(new TargetID(suidToEdgeMapper));
+ parser.registerFunction(new Degree(applicationManager));
+ parser.registerFunction(new InDegree(applicationManager));
+ parser.registerFunction(new OutDegree(applicationManager));
+ parser.registerFunction(new SourceID(applicationManager));
+ parser.registerFunction(new TargetID(applicationManager));
}
}
Deleted:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/SUIDToEdgeMapper.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/SUIDToEdgeMapper.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/SUIDToEdgeMapper.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -1,32 +0,0 @@
-package org.cytoscape.equations.internal;
-
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.events.AboutToRemoveEdgesEvent;
-import org.cytoscape.model.events.AboutToRemoveEdgesListener;
-import org.cytoscape.model.events.AddedEdgesEvent;
-import org.cytoscape.model.events.AddedEdgesListener;
-
-
-public class SUIDToEdgeMapper implements AddedEdgesListener,
AboutToRemoveEdgesListener {
- private final Map<Long, CyEdge> suidToEdgeMap = new HashMap<Long,
CyEdge>();
-
- public void handleEvent(final AddedEdgesEvent event) {
- for (CyEdge edge : event.getPayloadCollection()) {
- suidToEdgeMap.put(edge.getSUID(), edge);
- }
- }
-
- public void handleEvent(final AboutToRemoveEdgesEvent event) {
- for (CyEdge edge : event.getEdges()) {
- suidToEdgeMap.remove(edge.getSUID());
- }
- }
-
- public CyEdge getEdge(final Long id) {
- return suidToEdgeMap.get(id);
- }
-}
\ No newline at end of file
Deleted:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/SUIDToNodeMapper.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/SUIDToNodeMapper.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/SUIDToNodeMapper.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -1,32 +0,0 @@
-package org.cytoscape.equations.internal;
-
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.events.AboutToRemoveNodesEvent;
-import org.cytoscape.model.events.AboutToRemoveNodesListener;
-import org.cytoscape.model.events.AddedNodesEvent;
-import org.cytoscape.model.events.AddedNodesListener;
-
-
-public class SUIDToNodeMapper implements AddedNodesListener,
AboutToRemoveNodesListener {
- private final Map<Long, CyNode> suidToNodeMap = new HashMap<Long,
CyNode>();
-
- public void handleEvent(final AddedNodesEvent event) {
- for (CyNode node : event.getPayloadCollection()) {
- suidToNodeMap.put(node.getSUID(), node);
- }
- }
-
- public void handleEvent(final AboutToRemoveNodesEvent event) {
- for (CyNode node : event.getNodes()) {
- suidToNodeMap.remove(node.getSUID());
- }
- }
-
- public CyNode getNode(final Long id) {
- return suidToNodeMap.get(id);
- }
-}
\ No newline at end of file
Modified:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/Degree.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/Degree.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/Degree.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -30,28 +30,22 @@
package org.cytoscape.equations.internal.functions;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.equations.AbstractFunction;
import org.cytoscape.equations.ArgDescriptor;
import org.cytoscape.equations.ArgType;
import org.cytoscape.equations.FunctionUtil;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
public class Degree extends AbstractFunction {
private final CyApplicationManager applicationManager;
- private final SUIDToNodeMapper suidToNodeMapper;
- public Degree(final CyApplicationManager applicationManager, final
SUIDToNodeMapper suidToNodeMapper) {
+ public Degree(final CyApplicationManager applicationManager) {
super(new ArgDescriptor[] { new ArgDescriptor(ArgType.INT,
"node_ID", "An ID identifying a node.") });
this.applicationManager = applicationManager;
- this.suidToNodeMapper = suidToNodeMapper;
}
/**
@@ -66,7 +60,7 @@
*/
public String getFunctionSummary() { return "Returns degree of a
node."; }
- public Class getReturnType() { return Long.class; }
+ public Class<?> getReturnType() { return Long.class; }
/**
* @param args the function arguments which must be either one object
of type Double or Long
@@ -79,7 +73,7 @@
if (currentNetwork == null)
return (Long)(-1L);
- final CyNode node = suidToNodeMapper.getNode(nodeID);
+ final CyNode node = currentNetwork.getNode(nodeID);
if (node == null)
throw new IllegalArgumentException("\"" + nodeID + "\"
is not a valid node identifier.");
Modified:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/InDegree.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/InDegree.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/InDegree.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -30,29 +30,24 @@
package org.cytoscape.equations.internal.functions;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.equations.AbstractFunction;
import org.cytoscape.equations.ArgDescriptor;
import org.cytoscape.equations.ArgType;
import org.cytoscape.equations.FunctionUtil;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
public class InDegree extends AbstractFunction {
private final CyApplicationManager applicationManager;
- private final SUIDToNodeMapper suidToNodeMapper;
- public InDegree(final CyApplicationManager applicationManager,
- final SUIDToNodeMapper suidToNodeMapper)
+ public InDegree(final CyApplicationManager applicationManager)
{
super(new ArgDescriptor[] { new ArgDescriptor(ArgType.INT,
"node_ID", "An ID identifying a node.") });
this.applicationManager = applicationManager;
- this.suidToNodeMapper = suidToNodeMapper;
}
/**
@@ -67,7 +62,7 @@
*/
public String getFunctionSummary() { return "Returns indegree of a
node."; }
- public Class getReturnType() { return Long.class; }
+ public Class<?> getReturnType() { return Long.class; }
/**
* @param args the function arguments which must be either one object
of type Double or Long
@@ -80,7 +75,7 @@
if (currentNetwork == null)
return (Long)(-1L);
- final CyNode node = suidToNodeMapper.getNode(nodeID);
+ final CyNode node = currentNetwork.getNode(nodeID);
if (node == null)
throw new IllegalArgumentException("\"" + nodeID + "\"
is not a valid node identifier.");
Modified:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/OutDegree.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/OutDegree.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/OutDegree.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -30,29 +30,24 @@
package org.cytoscape.equations.internal.functions;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.equations.AbstractFunction;
import org.cytoscape.equations.ArgDescriptor;
import org.cytoscape.equations.ArgType;
import org.cytoscape.equations.FunctionUtil;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
public class OutDegree extends AbstractFunction {
private final CyApplicationManager applicationManager;
- private final SUIDToNodeMapper suidToNodeMapper;
- public OutDegree(final CyApplicationManager applicationManager,
- final SUIDToNodeMapper suidToNodeMapper)
+ public OutDegree(final CyApplicationManager applicationManager)
{
super(new ArgDescriptor[] { new ArgDescriptor(ArgType.INT,
"node_ID", "An ID identifying a node.") });
this.applicationManager = applicationManager;
- this.suidToNodeMapper = suidToNodeMapper;
}
/**
@@ -67,7 +62,7 @@
*/
public String getFunctionSummary() { return "Returns indegree of a
node."; }
- public Class getReturnType() { return Long.class; }
+ public Class<?> getReturnType() { return Long.class; }
/**
* @param args the function arguments which must be either one object
of type Double or Long
@@ -80,7 +75,7 @@
if (currentNetwork == null)
return (Long)(-1L);
- final CyNode node = suidToNodeMapper.getNode(nodeID);
+ final CyNode node = currentNetwork.getNode(nodeID);
if (node == null)
throw new IllegalArgumentException("\"" + nodeID + "\"
is not a valid node identifier.");
Modified:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/SourceID.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/SourceID.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/SourceID.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -35,19 +35,19 @@
import org.cytoscape.equations.ArgDescriptor;
import org.cytoscape.equations.ArgType;
import org.cytoscape.equations.FunctionUtil;
-import org.cytoscape.equations.internal.SUIDToEdgeMapper;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
public class SourceID extends AbstractFunction {
- private final SUIDToEdgeMapper suidToEdgeMapper;
- public SourceID(final SUIDToEdgeMapper suidToEdgeMapper) {
+ private CyApplicationManager applicationManager;
+
+ public SourceID(CyApplicationManager applicationManager) {
super(new ArgDescriptor[] { new ArgDescriptor(ArgType.INT,
"edge_ID", "An ID identifying an edge.") });
- this.suidToEdgeMapper = suidToEdgeMapper;
+ this.applicationManager = applicationManager;
}
/**
@@ -62,7 +62,7 @@
*/
public String getFunctionSummary() { return "Returns source ID of an
edge."; }
- public Class getReturnType() { return Long.class; }
+ public Class<?> getReturnType() { return Long.class; }
/**
* @param args the function arguments which must be either one object
of type Double or Long
@@ -71,7 +71,11 @@
public Object evaluateFunction(final Object[] args) {
final Long edgeID = FunctionUtil.getArgAsLong(args[0]);
- final CyEdge edge = suidToEdgeMapper.getEdge(edgeID);
+ final CyNetwork currentNetwork =
applicationManager.getCurrentNetwork();
+ if (currentNetwork == null)
+ return (Long)(-1L);
+
+ final CyEdge edge = currentNetwork.getEdge(edgeID);
if (edge == null)
throw new IllegalArgumentException("\"" + edgeID + "\"
is not a valid edge identifier.");
Modified:
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/TargetID.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/TargetID.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/main/java/org/cytoscape/equations/internal/functions/TargetID.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -30,22 +30,21 @@
package org.cytoscape.equations.internal.functions;
+import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.equations.AbstractFunction;
import org.cytoscape.equations.ArgDescriptor;
import org.cytoscape.equations.ArgType;
import org.cytoscape.equations.FunctionUtil;
-import org.cytoscape.equations.internal.SUIDToEdgeMapper;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
-
import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
public class TargetID extends AbstractFunction {
- private final SUIDToEdgeMapper suidToEdgeMapper;
+ private CyApplicationManager applicationManager;
- public TargetID(final SUIDToEdgeMapper suidToEdgeMapper) {
+ public TargetID(CyApplicationManager applicationManager) {
super(new ArgDescriptor[] { new ArgDescriptor(ArgType.INT,
"edge_ID", "An ID identifying an edge.") });
- this.suidToEdgeMapper = suidToEdgeMapper;
+ this.applicationManager = applicationManager;
}
/**
@@ -60,7 +59,7 @@
*/
public String getFunctionSummary() { return "Returns target ID of an
edge."; }
- public Class getReturnType() { return Long.class; }
+ public Class<?> getReturnType() { return Long.class; }
/**
* @param args the function arguments which must be either one object
of type Double or Long
@@ -69,7 +68,11 @@
public Object evaluateFunction(final Object[] args) {
final Long edgeID = FunctionUtil.getArgAsLong(args[0]);
- final CyEdge edge = suidToEdgeMapper.getEdge(edgeID);
+ final CyNetwork currentNetwork =
applicationManager.getCurrentNetwork();
+ if (currentNetwork == null)
+ return (Long)(-1L);
+
+ final CyEdge edge = currentNetwork.getEdge(edgeID);
if (edge == null)
throw new IllegalArgumentException("\"" + edgeID + "\"
is not a valid edge identifier.");
Modified:
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/DegreeTest.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/DegreeTest.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/DegreeTest.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -42,24 +42,21 @@
import java.util.Map;
import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.equations.IdentDescriptor;
import org.cytoscape.equations.Interpreter;
import org.cytoscape.equations.internal.EquationCompilerImpl;
import org.cytoscape.equations.internal.EquationParserImpl;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.events.AddedNodesEvent;
import org.junit.Before;
import org.junit.Test;
public class DegreeTest {
- private SUIDToNodeMapper suidToNodeMapper;
private CyApplicationManager applicationManager;
@Before
@@ -72,13 +69,11 @@
final CyNetwork network = mock(CyNetwork.class);
when(network.getAdjacentEdgeList(node,
CyEdge.Type.ANY)).thenReturn(edgeList);
+ when(network.getNode(101L)).thenReturn(node);
Collection<CyNode> nodes = new ArrayList<CyNode>(1);
nodes.add(node);
- suidToNodeMapper = new SUIDToNodeMapper();
- suidToNodeMapper.handleEvent(new AddedNodesEvent(network,
nodes));
-
applicationManager = mock(CyApplicationManager.class);
when(applicationManager.getCurrentNetwork()).thenReturn(network);
}
@@ -86,7 +81,7 @@
@Test
public void test() {
final EquationCompiler compiler = new EquationCompilerImpl(new
EquationParserImpl());
- compiler.getParser().registerFunction(new
Degree(applicationManager, suidToNodeMapper));
+ compiler.getParser().registerFunction(new
Degree(applicationManager));
final Map<String, Class<?>> variableNameToTypeMap = new
HashMap<String, Class<?>>();
if (!compiler.compile("=DEGREE(101)", variableNameToTypeMap))
fail(compiler.getLastErrorMsg());
Modified:
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/InDegreeTest.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/InDegreeTest.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/InDegreeTest.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -42,24 +42,21 @@
import java.util.Map;
import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.equations.IdentDescriptor;
import org.cytoscape.equations.Interpreter;
import org.cytoscape.equations.internal.EquationCompilerImpl;
import org.cytoscape.equations.internal.EquationParserImpl;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.events.AddedNodesEvent;
import org.junit.Before;
import org.junit.Test;
public class InDegreeTest {
- private SUIDToNodeMapper suidToNodeMapper;
private CyApplicationManager applicationManager;
@Before
@@ -72,13 +69,11 @@
final CyNetwork network = mock(CyNetwork.class);
when(network.getAdjacentEdgeList(node,
CyEdge.Type.INCOMING)).thenReturn(edgeList);
+ when(network.getNode(101L)).thenReturn(node);
Collection<CyNode> nodes = new ArrayList<CyNode>(1);
nodes.add(node);
- suidToNodeMapper = new SUIDToNodeMapper();
- suidToNodeMapper.handleEvent(new AddedNodesEvent(network,
nodes));
-
applicationManager = mock(CyApplicationManager.class);
when(applicationManager.getCurrentNetwork()).thenReturn(network);
}
@@ -86,7 +81,7 @@
@Test
public void test() {
final EquationCompiler compiler = new EquationCompilerImpl(new
EquationParserImpl());
- compiler.getParser().registerFunction(new
InDegree(applicationManager, suidToNodeMapper));
+ compiler.getParser().registerFunction(new
InDegree(applicationManager));
final Map<String, Class<?>> variableNameToTypeMap = new
HashMap<String, Class<?>>();
if (!compiler.compile("=INDEGREE(101)", variableNameToTypeMap))
fail(compiler.getLastErrorMsg());
Modified:
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/OutDegreeTest.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/OutDegreeTest.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/OutDegreeTest.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -42,24 +42,21 @@
import java.util.Map;
import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.equations.Equation;
+import org.cytoscape.equations.EquationCompiler;
import org.cytoscape.equations.IdentDescriptor;
import org.cytoscape.equations.Interpreter;
import org.cytoscape.equations.internal.EquationCompilerImpl;
import org.cytoscape.equations.internal.EquationParserImpl;
-import org.cytoscape.equations.internal.SUIDToNodeMapper;
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.events.AddedNodesEvent;
import org.junit.Before;
import org.junit.Test;
public class OutDegreeTest {
- private SUIDToNodeMapper suidToNodeMapper;
private CyApplicationManager applicationManager;
@Before
@@ -72,13 +69,11 @@
final CyNetwork network = mock(CyNetwork.class);
when(network.getAdjacentEdgeList(node,
CyEdge.Type.OUTGOING)).thenReturn(edgeList);
+ when(network.getNode(101L)).thenReturn(node);
Collection<CyNode> nodes = new ArrayList<CyNode>(1);
nodes.add(node);
- suidToNodeMapper = new SUIDToNodeMapper();
- suidToNodeMapper.handleEvent(new AddedNodesEvent(network,
nodes));
-
applicationManager = mock(CyApplicationManager.class);
when(applicationManager.getCurrentNetwork()).thenReturn(network);
}
@@ -86,7 +81,7 @@
@Test
public void test() {
final EquationCompiler compiler = new EquationCompilerImpl(new
EquationParserImpl());
- compiler.getParser().registerFunction(new
OutDegree(applicationManager, suidToNodeMapper));
+ compiler.getParser().registerFunction(new
OutDegree(applicationManager));
final Map<String, Class<?>> variableNameToTypeMap = new
HashMap<String, Class<?>>();
if (!compiler.compile("=OUTDEGREE(101)", variableNameToTypeMap))
fail(compiler.getLastErrorMsg());
Modified:
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/SourceIDTest.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/SourceIDTest.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/SourceIDTest.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -41,24 +41,23 @@
import java.util.List;
import java.util.Map;
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.equations.Equation;
import org.cytoscape.equations.EquationCompiler;
-import org.cytoscape.equations.Equation;
import org.cytoscape.equations.IdentDescriptor;
import org.cytoscape.equations.Interpreter;
import org.cytoscape.equations.internal.EquationCompilerImpl;
import org.cytoscape.equations.internal.EquationParserImpl;
-import org.cytoscape.equations.internal.SUIDToEdgeMapper;
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.events.AddedEdgesEvent;
import org.junit.Before;
import org.junit.Test;
public class SourceIDTest {
- private SUIDToEdgeMapper suidToEdgeMapper;
+ private CyApplicationManager applicationManager;
@Before
public void init() {
@@ -77,14 +76,16 @@
Collection<CyEdge> edges = new ArrayList<CyEdge>(1);
edges.add(edge);
- suidToEdgeMapper = new SUIDToEdgeMapper();
- suidToEdgeMapper.handleEvent(new AddedEdgesEvent(network,
edges));
+ when(network.getEdge(11L)).thenReturn(edge);
+
+ applicationManager = mock(CyApplicationManager.class);
+
when(applicationManager.getCurrentNetwork()).thenReturn(network);
}
@Test
public void test() {
final EquationCompiler compiler = new EquationCompilerImpl(new
EquationParserImpl());
- compiler.getParser().registerFunction(new
SourceID(suidToEdgeMapper));
+ compiler.getParser().registerFunction(new
SourceID(applicationManager));
final Map<String, Class<?>> variableNameToTypeMap = new
HashMap<String, Class<?>>();
if (!compiler.compile("=SOURCEID(11)", variableNameToTypeMap))
fail(compiler.getLastErrorMsg());
Modified:
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/TargetIDTest.java
===================================================================
---
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/TargetIDTest.java
2013-01-10 20:12:03 UTC (rev 31035)
+++
core3/impl/trunk/equations-functions-impl/src/test/java/org/cytoscape/equations/internal/functions/TargetIDTest.java
2013-01-10 20:47:07 UTC (rev 31036)
@@ -41,24 +41,23 @@
import java.util.List;
import java.util.Map;
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.equations.Equation;
import org.cytoscape.equations.EquationCompiler;
-import org.cytoscape.equations.Equation;
import org.cytoscape.equations.IdentDescriptor;
import org.cytoscape.equations.Interpreter;
import org.cytoscape.equations.internal.EquationCompilerImpl;
import org.cytoscape.equations.internal.EquationParserImpl;
-import org.cytoscape.equations.internal.SUIDToEdgeMapper;
import org.cytoscape.equations.internal.interpreter.InterpreterImpl;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.events.AddedEdgesEvent;
import org.junit.Before;
import org.junit.Test;
public class TargetIDTest {
- private SUIDToEdgeMapper suidToEdgeMapper;
+ private CyApplicationManager applicationManager;
@Before
public void init() {
@@ -77,14 +76,16 @@
Collection<CyEdge> edges = new ArrayList<CyEdge>(1);
edges.add(edge);
- suidToEdgeMapper = new SUIDToEdgeMapper();
- suidToEdgeMapper.handleEvent(new AddedEdgesEvent(network,
edges));
+ when(network.getEdge(11L)).thenReturn(edge);
+
+ applicationManager = mock(CyApplicationManager.class);
+
when(applicationManager.getCurrentNetwork()).thenReturn(network);
}
@Test
public void test() {
final EquationCompiler compiler = new EquationCompilerImpl(new
EquationParserImpl());
- compiler.getParser().registerFunction(new
TargetID(suidToEdgeMapper));
+ compiler.getParser().registerFunction(new
TargetID(applicationManager));
final Map<String, Class<?>> variableNameToTypeMap = new
HashMap<String, Class<?>>();
if (!compiler.compile("=TARGETID(11)", variableNameToTypeMap))
fail(compiler.getLastErrorMsg());
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