Author: mes
Date: 2010-10-25 09:58:58 -0700 (Mon, 25 Oct 2010)
New Revision: 22350
Added:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/package-info.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/package-info.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/package-info.java
Removed:
core3/model-api/trunk/src/main/javadoc/
core3/model-api/trunk/src/test/java/org/cytoscape/model/StubTableManager.java
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyEdge.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetwork.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNode.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableEntry.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableManager.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableManagerTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCySubNetworkTest.java
Log:
updated to javadoc and other cleanup
Modified: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyEdge.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyEdge.java
2010-10-22 23:44:46 UTC (rev 22349)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyEdge.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -41,29 +41,51 @@
* and edges.
*/
public interface CyEdge extends CyTableEntry {
+
/**
+ * A String column created by default for every CyEdge that
+ * holds the interaction description of the edge.
+ */
+ String INTERACTION = "interaction";
+
+ /**
* The Type enum is used by methods in {...@link CyNetwork} to restrict
- * the edges that match a query as follows:
- * <ul>
- * <li>UNDIRECTED: matches only undirected edges</li>
- * <li>INCOMING: matches either undirected edges or directed edges that
end with this node</li>
- * <li>OUTGOING: matches either undirected edges or directed edges that
start with this node</li>
- * <li>DIRECTED: matches directed edges regardless of whether this node
is the source or the target</li>
- * <li>ANY: matches any edge</li>
- * </ul>
+ * the edges that match a query.
*/
enum Type {
+
+ /**
+ * matches only undirected edges
+ */
UNDIRECTED,
+
+ /**
+ * matches either undirected edges or directed edges that end
with this node</li>
+ */
INCOMING,
+
+ /**
+ * matches either undirected edges or directed edges that start
with this node</li>
+ */
OUTGOING,
+
+ /**
+ * matches directed edges regardless of whether this node is
the source or the target
+ */
DIRECTED,
+
+ /**
+ * matches any edge
+ */
ANY;
}
/**
* An index of this edge within this network. The index is guaranteed
to
- * be between 0 and the number of edges in the network.
+ * be between 0 and (the number of edges in the network) - 1 and
+ * serves as an index into the {...@link List} returned from
+ * {...@link CyNetwork#getEdgeList}.
* @return An index for this edge within this network.
*/
int getIndex();
Modified: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetwork.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetwork.java
2010-10-22 23:44:46 UTC (rev 22349)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetwork.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -39,31 +39,28 @@
import java.util.List;
/**
- * CyNetwork is the primary interface for representing a network (graph) data
structure.
- * All algorithms should take a
- * CyNetwork as input, and do their best to only use the API of CyNetwork.
CyNetwork
- * provides a straightforward interface to a simple graph. For an interface
to a
- * more complicated subgraph, see {...@link
org.cytoscape.model.subnetwork.CyRootNetwork}
- * and {...@link org.cytoscape.model.subnetwork.CySubNetwork}, both
- * of which inherit from CyNetwork.
- *
- * The CyNetwork interface provides most of the methods a plugin would need to
create
- * a graph, traverse it, get and set attributes, and inquire about the
existence of
- * nodes and edges.
+ * CyNetwork is the primary interface for representing a network (graph)
+ * data structure in Cytoscape. Specifically, CyNetwork represents a
+ * multi-graph as multiple edges may exist between nodes. Edges may
+ * be directed, undirected, or both.
*/
public interface CyNetwork extends Identifiable, CyTableEntry {
+
/**
- * The "USER" CyTable is created by default for CyNetworks, CyNodes, and
- * CyEdges. Other CyDataTables may also be associated -- see {...@link
CyTable}
- * for more information. The table should be referenced using this
constant:
+ * The name of the defaul <b>public</b>
+ * CyTable that is created by default for CyNetworks,
+ * CyNodes, and CyEdges. Other CyTables may also be associated with
networks
+ * -- see {...@link CyTableManager} for more information.
+ * The table should be referenced using this constant:
* <code>CyNetwork.DEFAULT_ATTRS</code>.
*/
String DEFAULT_ATTRS = "USER";
/**
- * The "HIDDEN" CyTable is created by default for CyNetworks, CyNodes,
and
- * CyEdges. Other CyDataTables may also be associated -- see {...@link
CyTable}
- * for more information.
+ * The name of the default <b>hidden</b> CyTable that is created
+ * by default for CyNetworks, CyNodes, and
+ * CyEdges. Other CyTables may also be associated with networks --
+ * see {...@link CyTableManager} for more information.
*/
String HIDDEN_ATTRS = "HIDDEN";
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
2010-10-22 23:44:46 UTC (rev 22349)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNode.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -47,40 +47,14 @@
/**
* An index of this node within this network. The index is guaranteed
to
- * be between 0 and the number of nodes in the network.
+ * be between 0 and (the number of nodes in the network) - 1 and.
+ * serves as an index into the {...@link List} returned from
+ * {...@link CyNetwork#getNodeList}.
* @return An index for this node within this network.
*/
int getIndex();
- /**
- * @param edgeType The type of edge used to determine neighbor nodes
- * (incoming, outgoing, any, etc.).
- * @return A list of neighbor CyNodes that are connected to this node
- * via the specified edge type. Will return an empty list if no
neighboring
- * nodes are found.
- */
- List<CyNode> getNeighborList(CyEdge.Type edgeType);
-
/**
- * @param edgeType The type of adjacent edge desired (incoming,
outgoing, any, etc.).
- * @return A list of CyEdges of the specified type that are members of
- * this network and that are adjacent to this node. Will return an
empty list
- * if no adjacent edges are found.
- */
- List<CyEdge> getAdjacentEdgeList(CyEdge.Type edgeType);
-
- /**
- * @param target The target node used to determine whether any
connecting
- * edges exist between this and the target node.
- * @param edgeType The type of edge used to determine whether this node
and
- * the target node are connected. The edgeType is relative to this node.
- * @return A list of CyEdges of the specified type that connect this
and the
- * specified target node. Will return an empty list if no connecting
edges
- * are found.
- */
- List<CyEdge> getConnectingEdgeList(CyNode target, CyEdge.Type edgeType);
-
- /**
* Returns the nested network associated with this node. If no nested
* network has been specified this method will return null.
*
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableEntry.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableEntry.java
2010-10-22 23:44:46 UTC (rev 22349)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableEntry.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -43,6 +43,18 @@
*/
public interface CyTableEntry extends Identifiable {
+ /**
+ * A String column created by default for every CyTableEntry that
+ * holds the name of the entry.
+ */
+ String NAME = "name";
+
+ /**
+ * A boolean column created by default for every CyTableEntry that
+ * holds the selection state of the entry.
+ */
+ String SELECTED = "selected";
+
/* TODO RESOLVE THIS!!!!
* The following strings have been moved from Visual Property.
* We use String instead of enum in case we need to extend it later.
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableManager.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableManager.java
2010-10-22 23:44:46 UTC (rev 22349)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableManager.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -54,13 +54,4 @@
* for the specified network.
*/
Map<String,CyTable> getTableMap(String type, CyNetwork network);
-
-
- /**
- * Sets the map of table names to tables for the specified network.
- * @param type The type of map: NODE, EDGE, or NETWORK.
- * @param network The network associated with the map.
- * @param map The map of table names to tables.
- */
- void setTableMap(String type, CyNetwork network, Map<String,CyTable>
map);
}
Added:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/package-info.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/package-info.java
(rev 0)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/package-info.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -0,0 +1,5 @@
+/**
+ * This package contains the event interfaces necessary for communicating
+ * with the classes in org.cytoscape.model.
+ */
+package org.cytoscape.model.events;
Added: core3/model-api/trunk/src/main/java/org/cytoscape/model/package-info.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/package-info.java
(rev 0)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/package-info.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -0,0 +1,5 @@
+/**
+ * This package contains the core interfaces that define the basic network and
+ * table data types that constitute the foundation of Cytoscape.
+ */
+package org.cytoscape.model;
Added:
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/package-info.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/package-info.java
(rev 0)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/package-info.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -0,0 +1,6 @@
+/**
+ * This package contains rootnetwork and subnetwork extensions to the
+ * CyNetwork interface that provide a more complex meta-network
+ * data model.
+ */
+package org.cytoscape.model.subnetwork;
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
2010-10-22 23:44:46 UTC (rev 22349)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -59,7 +59,6 @@
public abstract class AbstractCyNodeTest extends TestCase {
protected CyNetwork net;
-
/**
* DOCUMENT ME!
*/
@@ -70,343 +69,6 @@
assertTrue("index >= 0", n2.getIndex() >= 0);
}
- /**
- * DOCUMENT ME!
- */
- public void testBasicGetNeighborList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
- CyNode n4 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, false);
- CyEdge e2 = net.addEdge(n2, n3, false);
-
- // one neighbor
- List<CyNode> l = n1.getNeighborList(CyEdge.Type.ANY);
- assertEquals("one neighbor", 1, l.size());
- assertTrue("contains node 2", l.contains(n2));
-
- // two neighbors
- l = n2.getNeighborList(CyEdge.Type.ANY);
- assertEquals("two neighbors", 2, l.size());
- assertTrue("contains node 1", l.contains(n1));
- assertTrue("contains node 3", l.contains(n3));
- assertFalse("contains node 4", l.contains(n4));
-
- // no neighbors
- l = n4.getNeighborList(CyEdge.Type.ANY);
- assertEquals("no neighbors", 0, l.size());
-
- // whoa! what about self edges?
- // TODO
- CyEdge e3 = net.addEdge(n4, n4, false);
- l = n4.getNeighborList(CyEdge.Type.ANY);
- assertEquals("one neighbor?", 1, l.size());
-
- CyEdge e4 = net.addEdge(n4, n4, true);
- l = n4.getNeighborList(CyEdge.Type.ANY);
- assertEquals("two neighbors", 2, l.size());
- }
-
- /**
- * DOCUMENT ME!
- */
- public void testUndirectedGetNeighborList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
- CyNode n4 = net.addNode();
- CyNode n5 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, false);
- CyEdge e2 = net.addEdge(n2, n3, false);
- CyEdge e3 = net.addEdge(n4, n2, false);
- CyEdge e4 = net.addEdge(n4, n1, false);
-
- List<CyNode> l = n1.getNeighborList(CyEdge.Type.UNDIRECTED);
- assertEquals("node 1 neighbors", 2, l.size());
- assertTrue("contains node 2", l.contains(n2));
- assertTrue("contains node 4", l.contains(n4));
-
- l = n2.getNeighborList(CyEdge.Type.UNDIRECTED);
- assertEquals("node 2 neighbors", 3, l.size());
- assertTrue("contains node 1", l.contains(n1));
- assertTrue("contains node 3", l.contains(n3));
- assertTrue("contains node 4", l.contains(n4));
-
- l = n2.getNeighborList(CyEdge.Type.ANY);
- assertEquals("node 2 neighbors", 3, l.size());
- assertTrue("contains node 1", l.contains(n1));
- assertTrue("contains node 3", l.contains(n3));
- assertTrue("contains node 4", l.contains(n4));
-
- l = n2.getNeighborList(CyEdge.Type.INCOMING);
- assertEquals("node 2 neighbors", 0, l.size());
-
- l = n2.getNeighborList(CyEdge.Type.OUTGOING);
- assertEquals("node 2 neighbors", 0, l.size());
-
- l = n2.getNeighborList(CyEdge.Type.DIRECTED);
- assertEquals("node 2 neighbors", 0, l.size());
- }
-
- /**
- * DOCUMENT ME!
- */
- public void testDirectedGetNeighborList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
- CyNode n4 = net.addNode();
- CyNode n5 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, true);
- CyEdge e2 = net.addEdge(n2, n3, true);
- CyEdge e3 = net.addEdge(n4, n2, true);
- CyEdge e4 = net.addEdge(n4, n1, true);
- CyEdge e5 = net.addEdge(n5, n2, false);
-
- List<CyNode> l = n1.getNeighborList(CyEdge.Type.DIRECTED);
- assertEquals("node 1 neighbors directed", 2, l.size());
- assertTrue("contains node 2", l.contains(n2));
- assertTrue("contains node 4", l.contains(n4));
-
- l = n1.getNeighborList(CyEdge.Type.INCOMING);
- assertEquals("node 1 neighbors incoming", 1, l.size());
- assertTrue("contains node 4", l.contains(n4));
-
- l = n1.getNeighborList(CyEdge.Type.OUTGOING);
- assertEquals("node 1 neighbors outgoing", 1, l.size());
- assertTrue("contains node 2", l.contains(n2));
-
- l = n2.getNeighborList(CyEdge.Type.UNDIRECTED);
- assertEquals("node 2 neighbors undirected", 1, l.size());
- assertTrue("contains node 5", l.contains(n5));
-
- l = n2.getNeighborList(CyEdge.Type.DIRECTED);
- assertEquals("node 2 neighbors directed", 3, l.size());
- assertTrue("contains node 1", l.contains(n1));
- assertTrue("contains node 3", l.contains(n3));
- assertTrue("contains node 4", l.contains(n4));
-
- l = n2.getNeighborList(CyEdge.Type.INCOMING);
- assertEquals("node 2 neighbors incoming", 2, l.size());
- assertTrue("contains node 1", l.contains(n1));
- assertTrue("contains node 4", l.contains(n4));
-
- l = n2.getNeighborList(CyEdge.Type.OUTGOING);
- assertEquals("node 2 neighbors outgoing", 1, l.size());
- assertTrue("contains node 3", l.contains(n3));
- }
-
- /**
- * DOCUMENT ME!
- */
- public void testBasicGetAdjacentEdgeList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
- CyNode n4 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, false);
- CyEdge e2 = net.addEdge(n2, n3, false);
-
- // one edge
- List<CyEdge> l = n1.getAdjacentEdgeList(CyEdge.Type.ANY);
- assertEquals("one adjacent edge", 1, l.size());
- assertTrue("contains edge 1", l.contains(e1));
-
- // two edge
- l = n2.getAdjacentEdgeList(CyEdge.Type.ANY);
- assertEquals("two adjacent edges", 2, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 2", l.contains(e2));
-
- // no adjacent edges
- l = n4.getAdjacentEdgeList(CyEdge.Type.ANY);
- assertEquals("no edges", 0, l.size());
-
- // whoa! what about self edges?
- // TODO
- CyEdge e3 = net.addEdge(n4, n4, false);
- l = n4.getAdjacentEdgeList(CyEdge.Type.ANY);
- assertEquals("one adjacent edge?", 1, l.size());
- }
-
- /**
- * DOCUMENT ME!
- */
- public void testUndirectedGetAdjacentEdgeList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
- CyNode n4 = net.addNode();
- CyNode n5 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, false);
- CyEdge e2 = net.addEdge(n2, n3, false);
- CyEdge e3 = net.addEdge(n4, n2, false);
- CyEdge e4 = net.addEdge(n4, n1, false);
-
- List<CyEdge> l = n1.getAdjacentEdgeList(CyEdge.Type.UNDIRECTED);
- assertEquals("node 1 adjacent edges", 2, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 4", l.contains(e4));
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.UNDIRECTED);
- assertEquals("node 2 adjacent edges", 3, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 2", l.contains(e2));
- assertTrue("contains edge 3", l.contains(e3));
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.ANY);
- assertEquals("node 2 adjacent edges", 3, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 2", l.contains(e2));
- assertTrue("contains edge 3", l.contains(e3));
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.INCOMING);
- assertEquals("node 2 adjacent edges", 0, l.size());
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.OUTGOING);
- assertEquals("node 2 adjacent edges", 0, l.size());
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.DIRECTED);
- assertEquals("node 2 adjacent edges", 0, l.size());
- }
-
- /**
- * DOCUMENT ME!
- */
- public void testDirectedGetAdjacentEdgeList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
- CyNode n4 = net.addNode();
- CyNode n5 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, true);
- CyEdge e2 = net.addEdge(n2, n3, true);
- CyEdge e3 = net.addEdge(n4, n2, true);
- CyEdge e4 = net.addEdge(n4, n1, true);
- CyEdge e5 = net.addEdge(n5, n2, false);
-
- List<CyEdge> l = n1.getAdjacentEdgeList(CyEdge.Type.DIRECTED);
- assertEquals("node 1 adjacent edges directed", 2, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 4", l.contains(e4));
-
- l = n1.getAdjacentEdgeList(CyEdge.Type.INCOMING);
- assertEquals("node 1 adjacent edges incoming", 1, l.size());
- assertTrue("contains edge 4", l.contains(e4));
-
- l = n1.getAdjacentEdgeList(CyEdge.Type.OUTGOING);
- assertEquals("node 1 adjacent edges outgoing", 1, l.size());
- assertTrue("contains edge 1", l.contains(e1));
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.UNDIRECTED);
- assertEquals("node 2 adjacent edges undirected", 1, l.size());
- assertTrue("contains edge 5", l.contains(e5));
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.DIRECTED);
- assertEquals("node 2 adjacent edges directed", 3, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 2", l.contains(e2));
- assertTrue("contains edge 3", l.contains(e3));
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.INCOMING);
- assertEquals("node 2 adjacent edges incoming", 2, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 3", l.contains(e3));
-
- l = n2.getAdjacentEdgeList(CyEdge.Type.OUTGOING);
- assertEquals("node 2 adjacent edges outgoing", 1, l.size());
- assertTrue("contains edge 2", l.contains(e2));
- }
-
- /**
- * DOCUMENT ME!
- */
- public void testBasicGetConnectingEdgeList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, false);
- CyEdge e2 = net.addEdge(n2, n3, false);
- CyEdge e3 = net.addEdge(n1, n2, false);
- CyEdge e4 = net.addEdge(n1, n2, false);
-
- // between node 1 and 2
- List<CyEdge> l = n1.getConnectingEdgeList(n2, CyEdge.Type.ANY);
- assertEquals("connecting edges", 3, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 3", l.contains(e1));
- assertTrue("contains edge 4", l.contains(e4));
-
- // between node 2 and 3
- l = n3.getConnectingEdgeList(n2, CyEdge.Type.ANY);
- assertEquals("connecting edges", 1, l.size());
- assertTrue("contains edge 2", l.contains(e2));
-
- // between node 2 and 3 after adding an edge
- CyEdge e5 = net.addEdge(n3, n2, false);
- l = n2.getConnectingEdgeList(n3, CyEdge.Type.ANY);
- assertEquals("connecting edges", 2, l.size());
- assertTrue("contains edge 2", l.contains(e2));
- assertTrue("contains edge 5", l.contains(e5));
-
- // between node 2 and 3 after deleting an edge
- boolean rem5 = net.removeEdge(e5);
- assertTrue("removed successfully", rem5);
- l = n2.getConnectingEdgeList(n3, CyEdge.Type.ANY);
- assertEquals("connecting edges", 1, l.size());
- assertTrue("contains edge 2", l.contains(e2));
- }
-
- /**
- * DOCUMENT ME!
- */
- public void testUndirectedBasicGetConnectingEdgeList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, false);
- CyEdge e2 = net.addEdge(n2, n3, false);
- CyEdge e3 = net.addEdge(n1, n2, false);
- CyEdge e4 = net.addEdge(n1, n2, true);
-
- // between node 1 and 2
- List<CyEdge> l = n1.getConnectingEdgeList(n2,
CyEdge.Type.UNDIRECTED);
- assertEquals("connecting edges", 2, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 3", l.contains(e3));
- }
-
- /**
- * DOCUMENT ME!
- */
- public void testDirectedBasicGetConnectingEdgeList() {
- CyNode n1 = net.addNode();
- CyNode n2 = net.addNode();
- CyNode n3 = net.addNode();
-
- CyEdge e1 = net.addEdge(n1, n2, true);
- CyEdge e2 = net.addEdge(n2, n3, true);
- CyEdge e3 = net.addEdge(n1, n2, true);
- CyEdge e4 = net.addEdge(n2, n1, true);
- CyEdge e5 = net.addEdge(n2, n1, false);
-
- // between node 1 and 2
- List<CyEdge> l = n1.getConnectingEdgeList(n2,
CyEdge.Type.DIRECTED);
- assertEquals("connecting edges", 3, l.size());
- assertTrue("contains edge 1", l.contains(e1));
- assertTrue("contains edge 3", l.contains(e3));
- assertTrue("contains edge 4", l.contains(e4));
- }
-
public void testDefaultAttributes() {
CyNode n1 = net.addNode();
assertEquals( String.class, n1.attrs().contains("name"));
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableManagerTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableManagerTest.java
2010-10-22 23:44:46 UTC (rev 22349)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableManagerTest.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -49,67 +49,39 @@
import static org.mockito.Mockito.*;
-/**
- * DOCUMENT ME!
- */
public abstract class AbstractCyTableManagerTest extends TestCase {
+ /**
+ * Must be supplied by implementer.
+ */
protected CyTableManager mgr;
- private CyNetwork n;
- public void setUp() {
- n = mock(CyNetwork.class);
- }
+ /**
+ * Must be supplied by implementer.
+ */
+ protected CyNetwork goodNetwork;
- // we want to return null if a table map has not been set
- public void testGetEmptyTableMap() {
- assertNull( mgr.getTableMap("NETWORK",n) );
- assertNull( mgr.getTableMap("NODE",n) );
- assertNull( mgr.getTableMap("EDGE",n) );
- }
+ private CyNetwork badNetwork;
- public void testGetSetTableMap() {
- assertNotNull(n);
- checkGetSet("NETWORK");
- checkGetSet("NODE");
- checkGetSet("EDGE");
+ public void setUp() {
+ badNetwork = mock(CyNetwork.class);
}
- private void checkGetSet(String type) {
- assertNotNull(n);
- Map<String, CyTable> map = new HashMap<String,CyTable>();
-
- mgr.setTableMap(type, n, map);
-
- assertNotNull(mgr.getTableMap(type, n));
- assertEquals(map,mgr.getTableMap(type, n));
+ public void testGoodNetwork() {
+ assertNotNull(
mgr.getTableMap(CyTableEntry.NETWORK,goodNetwork) );
+ assertNotNull( mgr.getTableMap(CyTableEntry.NODE,goodNetwork) );
+ assertNotNull( mgr.getTableMap(CyTableEntry.EDGE,goodNetwork) );
}
- // to clean up a table map
- public void testSetNullTableMap() {
- Map<String, CyTable> map = new HashMap<String,CyTable>();
-
- mgr.setTableMap("NETWORK", n, map);
-
- assertNotNull(mgr.getTableMap("NETWORK", n));
- assertEquals(map,mgr.getTableMap("NETWORK", n));
-
- mgr.setTableMap("NETWORK", n, null);
-
- assertNull(mgr.getTableMap("NETWORK", n));
+ public void testBadNetwork() {
+ assertNull( mgr.getTableMap(CyTableEntry.NETWORK,badNetwork) );
+ assertNull( mgr.getTableMap(CyTableEntry.NODE,badNetwork) );
+ assertNull( mgr.getTableMap(CyTableEntry.EDGE,badNetwork) );
}
- public void testNullGetTableMap() {
- assertNull(mgr.getTableMap("NETWORK", null));
+ public void testNullNetwork() {
+ assertNull( mgr.getTableMap(CyTableEntry.NETWORK,null) );
+ assertNull( mgr.getTableMap(CyTableEntry.NODE,null) );
+ assertNull( mgr.getTableMap(CyTableEntry.EDGE,null) );
}
-
- public void testSetNullGraphObjectTableMap() {
- Map<String, CyTable> map = new HashMap<String,CyTable>();
- try {
- mgr.setTableMap("NETWORK", null, map);
- } catch (NullPointerException npe) {
- return;
- }
- fail("did not catch expected exception");
- }
}
Deleted:
core3/model-api/trunk/src/test/java/org/cytoscape/model/StubTableManager.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/StubTableManager.java
2010-10-22 23:44:46 UTC (rev 22349)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/StubTableManager.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -1,49 +0,0 @@
-
-/*
- Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-
-package org.cytoscape.model;
-
-import java.util.Map;
-import java.util.HashMap;
-
-public class StubTableManager implements CyTableManager {
-
- public Map<String,CyTable> getTableMap(String type, CyNetwork network) {
- return new HashMap<String,CyTable>();
- }
-
- public void setTableMap(String type, CyNetwork network,
Map<String,CyTable> map) { }
-}
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
2010-10-22 23:44:46 UTC (rev 22349)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/subnetwork/AbstractCySubNetworkTest.java
2010-10-25 16:58:58 UTC (rev 22350)
@@ -339,22 +339,6 @@
}
/**
- * Checks that getNeighbors works as expected for CyNode
- */
- public void testNodeAddedInSubnetworkNodeGetNeighbors() {
- defaultSetup();
-
- CyNode nz1 = sub.addNode();
- CyEdge ez1 = sub.addEdge(nz1,n1,true);
-
- List<CyNode> nzl = nz1.getNeighborList(CyEdge.Type.ANY);
- assertEquals(1,nzl.size());
-
- List<CyNode> nl = n1.getNeighborList(CyEdge.Type.ANY);
- assertEquals(3,nl.size());
- }
-
- /**
* Checks that getNeighbors works as expected for CySubNetwork
*/
public void testNodeAddedInSubnetworkSubGetNeighbors() {
--
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