Author: mes
Date: 2011-03-08 15:26:51 -0800 (Tue, 08 Mar 2011)
New Revision: 24341
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNode.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CySubNetwork.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/DummyCyNode.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCyRootNetworkTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCySubNetworkTest.java
Log:
added better support for groups/metanodes based on mini retreat discussion
Modified: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNode.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNode.java
2011-03-08 23:16:32 UTC (rev 24340)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNode.java
2011-03-08 23:26:51 UTC (rev 24341)
@@ -38,13 +38,6 @@
*/
public interface CyNode extends CyTableEntry {
- /** The column name for the nested network associated with a
<code>CyNode</code> in the user table. */
- final static String NESTED_NETWORK_ATTR = "NestedNetwork";
-
- /** The column name for the attribute that allows testing of whether a
<code>CyNode</code>
- has an associated nested network or not. (Found in the user
table.) */
- final static String HAS_NESTED_NETWORK_ATTR = "hasNestedNetwork";
-
/**
* An index of this node within this network. The index is guaranteed
to
* be between 0 and (the number of nodes in the network) - 1. This index
@@ -55,28 +48,27 @@
int getIndex();
/**
- * Returns the nested network associated with this node. If no nested
+ * Returns the network referenced by this node. If no
* network has been specified this method will return null.
*
- * @return A reference to the nested CyNetwork if one exists,
+ * @return A reference to a CyNetwork if one exists,
* returns null otherwise.
*/
- CyNetwork getNestedNetwork();
+ CyNetwork getNetwork();
/**
- * Allows the nested network for this network to be set. Only one
- * nested network may be set for a given node. Any CyNetwork may
- * be used (the network does not need to be a subnetwork of the
- * network that contains this node). To unset a nested network, use
+ * Allows a network reference for this node to be set. Only one
+ * network may be set for a given node. Any CyNetwork may
+ * be used (the network may be a subnetwork of the network that
+ * contains this node, but it is not mandatory). To unset a network, use
* null as an argument.
*
- * @param nestedNetwork The network that is to be referenced by this
node. If
+ * @param network The network that is to be referenced by this node. If
* this value is null, any existing reference will be removed.
*
- * Note that this if a previous nested network is being replaced or
nulled out, an
- * {@link UnsetNestedNetworkEvent} will be fired and if a new nested
network will be set a
- * {@link SetNestedNetworkEvent} will be fired. Furthermore the (@link
NESTED_NETWORK_ATTR}
- * and {@link HAS_NESTED_NETWORK_ATTR} columns in the user table will
be updated.
+ * Note that this if a previous referenced network is being replaced or
nulled out, an
+ * {@link UnsetNestedNetworkEvent} will be fired and if a new network
will be set a
+ * {@link SetNestedNetworkEvent} will be fired.
*/
- void setNestedNetwork(CyNetwork nestedNetwork);
+ void setNetwork(CyNetwork network);
}
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
2011-03-08 23:16:32 UTC (rev 24340)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
2011-03-08 23:26:51 UTC (rev 24341)
@@ -72,6 +72,17 @@
CySubNetwork addSubNetwork();
/**
+ * Create a {@link CySubNetwork} containing the specified {@link
CyNode}s and
+ * {@link CyEdge}s. The nodes and edges must already exist in this root
network.
+ * Nodes defining the source and target of edges that have not yet been
added
+ * to the subnetwork will be added.
+ * @param nodes The nodes to be added to the network. May be null or
empty.
+ * @param edges The edges to be added to the network. May be null or
empty.
+ * @return The created {@link CySubNetwork}.
+ */
+ CySubNetwork addSubNetwork(Iterable<CyNode> nodes, Iterable<CyEdge>
edges);
+
+ /**
* Removes the subnetwork from the root network, but not the nodes and
edges contained
* in the subnetwork.
* @param sub the {@link CySubNetwork} to remove.
@@ -89,4 +100,11 @@
* began with something, and this network is that something.
*/
CySubNetwork getBaseNetwork();
+
+ /**
+ * Returns true if the network to be checked is a subnetwork of this
root network and
+ * returns false otherwise. Will return false if the network is null.
+ * @param n The network to be checked.
+ */
+ boolean containsNetwork(CyNetwork n);
}
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CySubNetwork.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CySubNetwork.java
2011-03-08 23:16:32 UTC (rev 24340)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CySubNetwork.java
2011-03-08 23:26:51 UTC (rev 24341)
@@ -54,7 +54,7 @@
/**
* Adds a node to this {@link CySubNetwork}. Note that the added node
- * is not a new node, and must already exist in the {@link
CyRootNetwork}.
+ * is not a new node and must already exist in the {@link
CyRootNetwork}.
* @param node CyNode to add to this subnetwork
* @return true if the node was successfully added to the subnetwork,
* false otherwise.
@@ -63,7 +63,10 @@
/**
* Adds an edge to this {@link CySubNetwork}. Note that the added edge
- * is not a new edge, and must already exist in the {@link
CyRootNetwork}.
+ * is not a new edge and must already exist in the {@link
CyRootNetwork}.
+ * If the nodes that define the source and target of the edge are not
yet
+ * contained in the subnetwork, they will be added. The nodes must also
+ * already exist in the {@link CyRootNetwork}.
* @param edge CyEdge to add to this subnetwork
* @return true if the edge was successfully added to the subnetwork,
* false otherwise.
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2011-03-08 23:16:32 UTC (rev 24340)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2011-03-08 23:26:51 UTC (rev 24341)
@@ -71,23 +71,23 @@
// by default a node should have a null nested network
public void testInitGetNestedNetwork() {
CyNode n1 = net.addNode();
- assertNull(n1.getNestedNetwork());
+ assertNull(n1.getNetwork());
}
public void testSetNestedNetwork() {
CyNode n1 = net.addNode();
CyNetwork net2 = mock(CyNetwork.class);
- n1.setNestedNetwork( net2 );
- assertNotNull(n1.getNestedNetwork());
- assertEquals(net2, n1.getNestedNetwork());
+ n1.setNetwork( net2 );
+ assertNotNull(n1.getNetwork());
+ assertEquals(net2, n1.getNetwork());
}
// self nested networks are allowed
public void testSetSelfNestedNetwork() {
CyNode n1 = net.addNode();
- n1.setNestedNetwork( net );
- assertNotNull(n1.getNestedNetwork());
- assertEquals(net, n1.getNestedNetwork());
+ n1.setNetwork( net );
+ assertNotNull(n1.getNetwork());
+ assertEquals(net, n1.getNetwork());
}
// null nested networks are allowed
@@ -96,13 +96,13 @@
// put a real network here first
CyNetwork net2 = mock(CyNetwork.class);
- n1.setNestedNetwork( net2 );
- assertNotNull(n1.getNestedNetwork());
- assertEquals(net2, n1.getNestedNetwork());
+ n1.setNetwork( net2 );
+ assertNotNull(n1.getNetwork());
+ assertEquals(net2, n1.getNetwork());
// now put a null network to verify that we've "unset" things
- n1.setNestedNetwork( null );
- assertNull(n1.getNestedNetwork());
+ n1.setNetwork( null );
+ assertNull(n1.getNetwork());
}
public void testRemoveNodeIndexStaysConstant() {
@@ -131,20 +131,4 @@
assertNull(net.getNode(0));
assertEquals(n1,net.getNode(1));
}
-
- public void testNestedNetworkUserTableUpdates() {
- CyNode n1 = net.addNode();
- CyNetwork net2 = mock(CyNetwork.class);
- when(net2.getSUID()).thenReturn(223L);
- final CyRow row = n1.getCyRow();
- assertFalse(row.isSet(CyNode.NESTED_NETWORK_ATTR));
- assertFalse(row.get(CyNode.HAS_NESTED_NETWORK_ATTR,
Boolean.class));
- n1.setNestedNetwork(net2);
- assertTrue(row.isSet(CyNode.NESTED_NETWORK_ATTR));
- assertTrue(row.get(CyNode.HAS_NESTED_NETWORK_ATTR,
Boolean.class));
- assertEquals("223", row.get(CyNode.NESTED_NETWORK_ATTR,
String.class));
- n1.setNestedNetwork(null);
- assertFalse(row.isSet(CyNode.NESTED_NETWORK_ATTR));
- assertFalse(row.get(CyNode.HAS_NESTED_NETWORK_ATTR,
Boolean.class));
- }
}
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/DummyCyNode.java
===================================================================
--- core3/model-api/trunk/src/test/java/org/cytoscape/model/DummyCyNode.java
2011-03-08 23:16:32 UTC (rev 24340)
+++ core3/model-api/trunk/src/test/java/org/cytoscape/model/DummyCyNode.java
2011-03-08 23:26:51 UTC (rev 24341)
@@ -65,11 +65,11 @@
return new ArrayList<CyEdge>();
}
- public CyNetwork getNestedNetwork() {
+ public CyNetwork getNetwork() {
return nested;
}
- public void setNestedNetwork(CyNetwork n) {
+ public void setNetwork(CyNetwork n) {
nested = n;
}
}
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCyRootNetworkTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCyRootNetworkTest.java
2011-03-08 23:16:32 UTC (rev 24340)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCyRootNetworkTest.java
2011-03-08 23:26:51 UTC (rev 24341)
@@ -48,6 +48,8 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.DummyCyNode;
+import org.cytoscape.model.DummyCyEdge;
import java.lang.RuntimeException;
@@ -55,6 +57,7 @@
import java.util.List;
import java.util.ArrayList;
import java.util.Map;
+import java.util.Arrays;
/**
@@ -530,4 +533,130 @@
fail("shouldn't throw exception for trying to remove
null network");
}
}
+
+ public void testContainsNetwork() {
+ CySubNetwork s1 = root.addSubNetwork();
+ assertTrue(root.containsNetwork(s1));
+ }
+
+ public void testNotContainsNetwork() {
+ CySubNetwork s2 = root2.addSubNetwork();
+ assertFalse(root.containsNetwork(s2));
+ }
+
+ public void testNullContainsNetwork() {
+ assertFalse(root.containsNetwork(null));
+ }
+
+ public void testAddSubNetworkWithGoodNodesAndGoodEdges() {
+ CyNode n1 = root.addNode();
+ CyNode n2 = root.addNode();
+ CyNode n3 = root.addNode();
+ CyEdge e1 = root.addEdge(n1,n2,false);
+
+ List<CyNode> nodes = Arrays.asList(n1, n2, n3 );
+ List<CyEdge> edges = Arrays.asList( e1 );
+
+ CySubNetwork n = root.addSubNetwork(nodes, edges);
+
+ assertTrue( n.containsNode(n1) );
+ assertTrue( n.containsNode(n2) );
+ assertTrue( n.containsNode(n3) );
+ assertTrue( n.containsEdge(e1) );
+ }
+
+ public void testAddSubNetworkWithNullNodesAndGoodEdges() {
+ CyNode n1 = root.addNode();
+ CyNode n2 = root.addNode();
+ CyEdge e1 = root.addEdge(n1,n2,false);
+
+ List<CyEdge> edges = Arrays.asList( e1 );
+
+ CySubNetwork n = root.addSubNetwork(null, edges);
+
+ assertTrue(n.containsNode(n1) );
+ assertTrue(n.containsNode(n2) );
+ assertTrue(n.containsEdge(e1) );
+ }
+
+ public void testAddSubNetworkWithGoodNodesAndNullEdges() {
+ CyNode n1 = root.addNode();
+ CyNode n2 = root.addNode();
+ CyNode n3 = root.addNode();
+
+ List<CyNode> nodes = Arrays.asList( n1, n2, n3 );
+
+ CySubNetwork n = root.addSubNetwork(nodes, null);
+
+ assertTrue( n.containsNode(n1) );
+ assertTrue( n.containsNode(n2) );
+ assertTrue( n.containsNode(n3) );
+ }
+
+ public void testAddSubNetworkWithEmptyNodesAndGoodEdges() {
+ CyNode n1 = root.addNode();
+ CyNode n2 = root.addNode();
+ CyEdge e1 = root.addEdge(n1,n2,false);
+
+ List<CyNode> nodes = new ArrayList<CyNode>();
+ List<CyEdge> edges = Arrays.asList( e1 );
+
+ CySubNetwork n = root.addSubNetwork(nodes, edges);
+
+ assertTrue( n.containsNode(n1) );
+ assertTrue( n.containsNode(n2) );
+ assertTrue( n.containsEdge(e1) );
+ }
+
+ public void testAddSubNetworkWithGoodNodesAndEmptyEdges() {
+ CyNode n1 = root.addNode();
+ CyNode n2 = root.addNode();
+ CyNode n3 = root.addNode();
+
+ List<CyNode> nodes = Arrays.asList( n1, n2, n3 );
+ List<CyEdge> edges = new ArrayList<CyEdge>();
+
+ CySubNetwork n = root.addSubNetwork(nodes, edges);
+
+ assertTrue( n.containsNode(n1) );
+ assertTrue( n.containsNode(n2) );
+ assertTrue( n.containsNode(n3) );
+ }
+
+ public void testAddSubNetworkWithInvalidNodesAndGoodEdges() {
+ CyNode n1 = root.addNode();
+ CyNode n2 = root.addNode();
+ CyEdge e1 = root.addEdge(n1,n2,false);
+
+ CyNode b1 = new DummyCyNode(74);
+ CyNode b2 = new DummyCyNode(75);
+ List<CyNode> nodes = Arrays.asList( b1, b2 );
+ List<CyEdge> edges = Arrays.asList( e1 );
+
+ try {
+ CySubNetwork n = root.addSubNetwork(nodes, edges);
+ } catch (IllegalArgumentException iae) {
+ return;
+ }
+
+ fail("shouldn't allow nodes not in root network to be used");
+ }
+
+ public void testAddSubNetworkWithGoodNodesAndInvalidEdges() {
+ CyNode n1 = root.addNode();
+ CyNode n2 = root.addNode();
+ CyNode n3 = root.addNode();
+
+ CyEdge ex = new DummyCyEdge(null,null,false,50);
+ List<CyNode> nodes = Arrays.asList( n1, n2, n3 );
+ List<CyEdge> edges = Arrays.asList( ex );
+
+ try {
+ CySubNetwork n = root.addSubNetwork(nodes, edges);
+ } catch (IllegalArgumentException iae) {
+ return;
+ }
+
+ fail("shouldn't allow edges not in root network to be used");
+ }
}
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCySubNetworkTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCySubNetworkTest.java
2011-03-08 23:16:32 UTC (rev 24340)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCySubNetworkTest.java
2011-03-08 23:26:51 UTC (rev 24341)
@@ -50,6 +50,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
+import org.cytoscape.model.DummyCyEdge;
import java.lang.RuntimeException;
@@ -301,32 +302,26 @@
assertEquals("edge list
size",r2.getEdgeList().size(),root.getEdgeList().size());
}
- public void testAddEdgeBadSource() {
+ public void testAddEdgeNotYetAddedSource() {
defaultSetup();
-
- try {
- sub.addEdge(e3);
- } catch (Exception e) {
- noChangeChecks();
- return;
- }
-
- // if we don't get an exception
- fail();
+ assertTrue(sub.addEdge(e3));
}
- public void testAddEdgeBadTarget() {
+ public void testAddEdgeNotYetAddedTarget() {
defaultSetup();
+ CyEdge e4 = root.addEdge(n4,n1,true);
+ assertTrue(sub.addEdge(e4));
+ }
+ public void testAddEdgeBadEdge() {
+ defaultSetup();
+ CyEdge ex = new DummyCyEdge(null,null,true,100);
try {
- CyEdge e4 = root.addEdge(n4,n1,true);
- sub.addEdge(e4);
- } catch (Exception e) {
+ sub.addEdge(ex);
+ } catch (IllegalArgumentException e) {
+ noChangeChecks();
return;
}
-
- // if we don't get an exception
- fail();
}
public void testAddNodeInSubNetwork() {
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