Author: scooter Date: 2012-01-23 16:28:27 -0800 (Mon, 23 Jan 2012) New Revision: 28080
Added: core3/api/trunk/group-api/ core3/api/trunk/group-api/pom.xml core3/api/trunk/group-api/src/ core3/api/trunk/group-api/src/main/ core3/api/trunk/group-api/src/main/java/ core3/api/trunk/group-api/src/main/java/org/ core3/api/trunk/group-api/src/main/java/org/cytoscape/ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroup.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupFactory.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupManager.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/AbstractGroupEvent.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/AbstractGroupManagerEvent.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeDestroyedEvent.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeDestroyedListener.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeRemovedEvent.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeRemovedListener.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedEvent.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedListener.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedToNetworkEvent.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedToNetworkListener.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupCollapsedEvent.java core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupCollapsedListener.java core3/api/trunk/group-api/src/test/ core3/api/trunk/group-api/src/test/java/ core3/api/trunk/group-api/src/test/java/org/ core3/api/trunk/group-api/src/test/java/org/cytoscape/ core3/api/trunk/group-api/src/test/java/org/cytoscape/group/ core3/api/trunk/group-api/src/test/java/org/cytoscape/group/AbstractCyGroupTest.java core3/api/trunk/group-api/src/test/java/org/cytoscape/group/events/ Log: First landing of group api Added: core3/api/trunk/group-api/pom.xml =================================================================== --- core3/api/trunk/group-api/pom.xml (rev 0) +++ core3/api/trunk/group-api/pom.xml 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,113 @@ +<?xml version="1.0" encoding="UTF-8"?> +<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> + + <parent> + <artifactId>api-parent</artifactId> + <groupId>org.cytoscape</groupId> + <version>3.0.0-alpha8-SNAPSHOT</version> + </parent> + + <properties> + <bundle.symbolicName>org.cytoscape.group-api</bundle.symbolicName> + <bundle.namespace>org.cytoscape.group</bundle.namespace> + </properties> + + <modelVersion>4.0.0</modelVersion> + <groupId>org.cytoscape</groupId> + <artifactId>group-api</artifactId> + + <name>${bundle.symbolicName} [${bundle.namespace}]</name> + + <packaging>bundle</packaging> + + <repositories> + <!-- bootstrap for cytoscape dependencies, namely the parent POM snapshots --> + <repository> + <id>cytoscape_snapshots</id> + <snapshots> + <enabled>true</enabled> + </snapshots> + <releases> + <enabled>false</enabled> + </releases> + <name>Cytoscape Snapshots</name> + <url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url> + </repository> + <!-- bootstrap for cytoscape dependencies, namely the parent POM releases --> + <repository> + <id>cytoscape_releases</id> + <snapshots> + <enabled>false</enabled> + </snapshots> + <releases> + <enabled>true</enabled> + </releases> + <name>Cytoscape Releases</name> + <url>http://code.cytoscape.org/nexus/content/repositories/releases/</url> + </repository> + </repositories> + + <build> + <plugins> + <plugin> + <groupId>org.apache.felix</groupId> + <artifactId>maven-bundle-plugin</artifactId> + <version>${maven-bundle-plugin.version}</version> + <extensions>true</extensions> + <configuration> + <instructions> + <Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName> + <Bundle-Version>${project.version}</Bundle-Version> + <Export-Package>!${bundle.namespace}.internal.*,${bundle.namespace}.*;version="${project.version}"</Export-Package> + <Private-Package>${bundle.namespace}.internal.*</Private-Package> + </instructions> + </configuration> + </plugin> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-jar-plugin</artifactId> + <version>${maven-jar-plugin.version}</version> + <executions> + <execution> + <goals> + <goal>test-jar</goal> + </goals> + </execution> + </executions> + </plugin> + </plugins> + </build> + + <dependencies> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>event-api</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>model-api</artifactId> + <version>${project.version}</version> + </dependency> + + <dependency> + <groupId>junit</groupId> + <artifactId>junit</artifactId> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.mockito</groupId> + <artifactId>mockito-all</artifactId> + <scope>test</scope> + </dependency> + <dependency> + <groupId>org.cytoscape</groupId> + <artifactId>event-api</artifactId> + <version>${project.version}</version> + <type>test-jar</type> + <scope>test</scope> + </dependency> + + </dependencies> + +</project> Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroup.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroup.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroup.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,198 @@ +/* + Copyright (c) 2008, 2010, The Cytoscape Consortium (www.cytoscape.org) + + 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.group; + +import org.cytoscape.model.CyEdge; +import org.cytoscape.model.CyNetwork; +import org.cytoscape.model.CyNode; +import org.cytoscape.model.subnetwork.CyRootNetwork; + +import java.util.Collection; +import java.util.List; +import java.util.Set; + + +/** + * An object that represents a group of nodes and edges. Groups at the model + * layer are a simple extension of a CyNode that creates a subnetwork for every + * for every group. Groups may be added to networks in the same way that nodes + * are. To determine if a node in a network is a group, use the instanceof keyword + * to check for CyGroup: if (node instanceof CyGroup). + * + * @CyAPI.Api.Interface + */ +public interface CyGroup { + /** + * Return the {@link CyNode} that represents this group + * in the network. + * + * @return the {@link CyNode} for this group + */ + CyNode getGroupNode(); + + /** + * Returns the list of nodes contained within this group. + * + * @return A list of CyNodes + * returns null otherwise. + */ + List<CyNode> getNodeList(); + + /** + * Returns the list of edges contained within this group. + * + * @return A list of CyEdges + */ + List<CyEdge> getInteriorEdgeList(); + + /** + * Returns the list of exterior edges connected to the + * nodes within this group. + * + * @return A list of CyEdges + */ + Set<CyEdge> getExteriorEdgeList(); + + /** + * Returns the network referenced by this group. All + * groups will point to a network, although the network + * might not have any nodes or edges. This is the internal + * network representation of the group, not the networks that + * the group is a member of. + * + * @return A reference to a CyNetwork + */ + CyNetwork getGroupNetwork(); + + /** + * Add a node to a group + * + * @param node the node to add + */ + void addNode(CyNode node); + + /** + * Add an internal edge to a group. Both the source and destination + * nodes must already be added. + * + * @param edge the edge to add + */ + void addInternalEdge(CyEdge edge); + + /** + * Add an external edge to a group. One of the source and destination + * nodes must already be added. + * + * @param edge the edge to add + */ + void addExternalEdge(CyEdge edge); + + /** + * Add a list of nodes and their edges + * + * @param nodes the list of nodes to add + */ + void addNodes(List<CyNode> nodes); + + /** + * Remove a set of nodes from a group + * + * @param nodes the nodes to remove + */ + void removeNodes(Collection<CyNode> nodes); + + /** + * Return the root network for this group. A group can only + * exist within one root network, and all nodes and edges + * that are part of the group must exist within that root network + * also. + * + * @return the root network for this group + */ + CyRootNetwork getRootNetwork(); // Should this return a CyNetwork instead? + + /** + * Add a group to an additional network. When groups are created, they are created in + * a particular network. The can also be shown in other networks, as long as all of + * the networks are in the same {@link CyRootNetwork} + * + * @param network the {@link CyNetwork} to add the group to + */ + public void addGroupToNetwork(CyNetwork network); + + /** + * Remove a group from a network. + * + * @param network the {@link CyNetwork} to remove the group from + */ + public void removeGroupFromNetwork(CyNetwork network); + + /** + * Return the list of {@link CyNetwork}s this group is in. + * + * @return the set of {@link CyNetwork}s that contain this group + */ + public Set<CyNetwork> getNetworkSet(); + + /** + * Check to see if this group is defined in a particular network. + * + * @param network the {@link CyNetwork} to test + * @return true if the group is in that network + */ + public boolean isInNetwork(CyNetwork network); + + /** + * Collapse this group in the designated network. Note that this is a "model-level" + * collapse, which removes all of the member nodes and edges and replaces them + * with the node that represents the group in the network. This does not imply + * a specific visual representation. + * + * @param network the {@link CyNetwork} that this group should be collapsed in + */ + void collapse(CyNetwork network); + + /** + * Expand this group in the designated network. Note that this is a "model-level" + * expansion, which removes the node that represents the group from the network + * and adds all of the member nodes and edges. This does not imply + * a specific visual representation. + * + * @param network the {@link CyNetwork} that this group should be expanded in + */ + void expand(CyNetwork network); + + /** + * Return whether this group is expanded or collapsed in the designated network. + * + * @param network the {@link CyNetwork} we're interested in + * @return true if the group is collapsed in that network. + */ + boolean isCollapsed(CyNetwork network); + +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupFactory.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupFactory.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupFactory.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,76 @@ +/* + Copyright (c) 2008, 2010, The Cytoscape Consortium (www.cytoscape.org) + + 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.group; + +import org.cytoscape.group.CyGroup; +import org.cytoscape.model.CyEdge; +import org.cytoscape.model.CyNetwork; +import org.cytoscape.model.CyNode; + +import java.util.List; + + +/** + * An interface describing a factory used for creating + * {@link CyGroup} objects. This factory will be + * provided as a service through Spring/OSGi. + * @CyAPI.Api.Interface + */ +public interface CyGroupFactory { + /** + * Creates a CyGroup object in the referenced network. + * + * @param network the {@link CyNetwork} this group is part of + * @return A new {@link CyGroup} as part of the designated network. + */ + public CyGroup createGroup(CyNetwork network); + + /** + * Creates a CyGroup object in the referenced network initially populated with + * the supplied nodes. + * + * @param network the {@link CyNetwork} this group is part of + * @param nodes the {@link CyNode}s that are part of this group. + * @param edges the {@link CyEdge}s that are part of this group. If this is null, the edges + * are determined based on the node connectivity. + * @return A new {@link CyGroup} as part of the designated network. + */ + public CyGroup createGroup(CyNetwork network, List<CyNode> nodes, List<CyEdge> edges); + + /** + * Creates a CyGroup object in the referenced network from an existing {@link CyNode}. + * + * @param network the {@link CyNetwork} this group is part of + * @param node the {@link CyNode} to convert into a group + * @param nodes the {@link CyNode}s that are part of this group. + * @param edges the {@link CyEdge}s that are part of this group. If this is null, the edges + * are determined based on the node connectivity. + * @return A new {@link CyGroup} as part of the designated network. + */ + public CyGroup createGroup(CyNetwork network, CyNode node, List<CyNode>nodes, List<CyEdge> edges); +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupManager.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupManager.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupManager.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,92 @@ +/* + File: CyGroupManager.java + + Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org) + + 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.group; + + +import java.util.List; +import java.util.Set; + +import org.cytoscape.group.CyGroup; +import org.cytoscape.model.CyNetwork; +import org.cytoscape.model.CyNode; + + +/** + * Basic access to groups in an instance of Cytoscape. + * @CyAPI.Api.Interface + */ +public interface CyGroupManager { + /** + * Provides the set of all the groups known to the groups manager in a particular network. + * + * @param network the network to get the groups from. If the network is null, then + * return only those groups that have been designated as "global" (no referenced network) + * for this {@link CyRootNetwork} + * @return the complete set of all the currently known groups in a Cytoscape network + */ + public Set<CyGroup> getGroupSet(CyNetwork network); + + /** + * Return the list of {@link CyGroup}s this node is in. + * + * @param node the {@link CyNode} we want get the groups for + * @return the list of {@link CyGroup}s the node is in + * null if it is not in any groups + */ + public List<CyGroup> getGroupsForNode(CyNode node); + + /** + * Test to see if this node represents a {@link CyGroup} in + * a particular {@link CyNetwork}. + * + * @param node the {@link CyNode} to test + * @param network the {@link CyNetwork} to test + * @return true if this node represents a group + */ + public boolean isGroup(CyNode node, CyNetwork network); + + /** + * Destroy a group. + * + * @param group the {@link CyGroup} to remove. + **/ + public void destroyGroup(CyGroup group); + + /** + * Registers a group with the group manager. Does nothing if the group is already + * known to the group manager. + * + * @param group a non-null {@link CyGroup} + */ + public void addGroup(final CyGroup group); + + /** Releases all currently held references and resources. */ + public void reset(); +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/AbstractGroupEvent.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/AbstractGroupEvent.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/AbstractGroupEvent.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,27 @@ +package org.cytoscape.group.events; + + +import org.cytoscape.event.AbstractCyEvent; +import org.cytoscape.group.CyGroup; +import org.cytoscape.group.CyGroupManager; +import org.cytoscape.model.CyNetwork; + + +/** + * Base class for all derived concrete event classes classes in this package that require a CyNetwork. + */ +class AbstractGroupEvent extends AbstractCyEvent<CyGroup> { + private final CyNetwork net; + + AbstractGroupEvent(final CyGroup source, final Class<?> listenerClass, final CyNetwork network) { + super(source, listenerClass); + + if (network == null) + throw new NullPointerException("the \"network\" parameter must never be null!"); + this.net = network; + } + + public final CyNetwork getNetwork() { + return net; + } +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/AbstractGroupManagerEvent.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/AbstractGroupManagerEvent.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/AbstractGroupManagerEvent.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,26 @@ +package org.cytoscape.group.events; + + +import org.cytoscape.event.AbstractCyEvent; +import org.cytoscape.group.CyGroup; +import org.cytoscape.group.CyGroupManager; + + +/** + * Base class for all derived concrete event classes classes in this package that require a CyNetwork. + */ +class AbstractGroupManagerEvent extends AbstractCyEvent<CyGroupManager> { + private final CyGroup group; + + AbstractGroupManagerEvent(final CyGroupManager source, final Class<?> listenerClass, final CyGroup group) { + super(source, listenerClass); + + if (group == null) + throw new NullPointerException("the \"group\" parameter must never be null!"); + this.group = group; + } + + public final CyGroup getGroup() { + return group; + } +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeDestroyedEvent.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeDestroyedEvent.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeDestroyedEvent.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,21 @@ +package org.cytoscape.group.events; + + +import org.cytoscape.group.CyGroupManager; +import org.cytoscape.group.CyGroup; + + +/** + * This event signals that a group is about to be destroyed. + * @CyAPI.Final.Class + */ +public final class GroupAboutToBeDestroyedEvent extends AbstractGroupManagerEvent { + /** + * Constructs event. + * @param source the {@link CyGroupManager} of the group about to be destroyed. + * @param group the {@link CyGroup} about to be destroyed. + */ + public GroupAboutToBeDestroyedEvent(final CyGroupManager source, final CyGroup group) { + super(source, GroupAboutToBeDestroyedListener.class, group); + } +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeDestroyedListener.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeDestroyedListener.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeDestroyedListener.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,16 @@ +package org.cytoscape.group.events; + + +import org.cytoscape.event.CyListener; + +/** + * Listener for {@link GroupAboutToBeDestroyedEvent} + * @CyAPI.Spi.Interface + */ +public interface GroupAboutToBeDestroyedListener extends CyListener { + /** + * The method that should handle the specified event. + * @param e The event to be handled. + */ + public void handleEvent(GroupAboutToBeDestroyedEvent e); +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeRemovedEvent.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeRemovedEvent.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeRemovedEvent.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,22 @@ +package org.cytoscape.group.events; + + +import org.cytoscape.group.CyGroupManager; +import org.cytoscape.group.CyGroup; +import org.cytoscape.model.CyNetwork; + + +/** + * This event signals that a network has been added. + * @CyAPI.Final.Class + */ +public final class GroupAboutToBeRemovedEvent extends AbstractGroupEvent { + /** + * Constructs event. + * @param source the {@link CyGroup} that is about to be removed. + * @param network the {@link CyNetwork} the group is about to be removed from + */ + public GroupAboutToBeRemovedEvent(final CyGroup source, final CyNetwork network) { + super(source, GroupAboutToBeRemovedListener.class, network); + } +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeRemovedListener.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeRemovedListener.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAboutToBeRemovedListener.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,16 @@ +package org.cytoscape.group.events; + +import org.cytoscape.event.CyListener; + + +/** + * Listener for {@link GroupAboutToBeRemovedEvent} + * @CyAPI.Spi.Interface + */ +public interface GroupAboutToBeRemovedListener extends CyListener { + /** + * The method that should handle the specified event. + * @param e The event to be handled. + */ + public void handleEvent(GroupAboutToBeRemovedEvent e); +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedEvent.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedEvent.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedEvent.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,21 @@ +package org.cytoscape.group.events; + + +import org.cytoscape.group.CyGroupManager; +import org.cytoscape.group.CyGroup; + + +/** + * This event signals that a network has been added. + * @CyAPI.Final.Class + */ +public final class GroupAddedEvent extends AbstractGroupManagerEvent { + /** + * Constructs event. + * @param source the {@link CyGroupManager} the group has been added to. + * @param group the {@link CyGroup} that has been added. + */ + public GroupAddedEvent(final CyGroupManager source, final CyGroup group) { + super(source, GroupAddedListener.class, group); + } +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedListener.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedListener.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedListener.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,16 @@ +package org.cytoscape.group.events; + +import org.cytoscape.event.CyListener; + + +/** + * Listener for {@link GroupAddedEvent} + * @CyAPI.Spi.Interface + */ +public interface GroupAddedListener extends CyListener { + /** + * The method that should handle the specified event. + * @param e The event to be handled. + */ + public void handleEvent(GroupAddedEvent e); +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedToNetworkEvent.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedToNetworkEvent.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedToNetworkEvent.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,22 @@ +package org.cytoscape.group.events; + + +import org.cytoscape.group.CyGroupManager; +import org.cytoscape.group.CyGroup; +import org.cytoscape.model.CyNetwork; + + +/** + * This event signals that a network has been added. + * @CyAPI.Final.Class + */ +public final class GroupAddedToNetworkEvent extends AbstractGroupEvent { + /** + * Constructs event. + * @param source the {@link CyGroup} that has been added. + * @param network the {@link CyNetwork} the group has been added to. + */ + public GroupAddedToNetworkEvent(final CyGroup source, final CyNetwork network) { + super(source, GroupAddedToNetworkListener.class, network); + } +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedToNetworkListener.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedToNetworkListener.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupAddedToNetworkListener.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,16 @@ +package org.cytoscape.group.events; + +import org.cytoscape.event.CyListener; + + +/** + * Listener for {@link GroupAddedToNetworkEvent} + * @CyAPI.Spi.Interface + */ +public interface GroupAddedToNetworkListener extends CyListener { + /** + * The method that should handle the specified event. + * @param e The event to be handled. + */ + public void handleEvent(GroupAddedToNetworkEvent e); +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupCollapsedEvent.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupCollapsedEvent.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupCollapsedEvent.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,35 @@ +package org.cytoscape.group.events; + + +import org.cytoscape.group.CyGroupManager; +import org.cytoscape.group.CyGroup; + +import org.cytoscape.model.CyNetwork; + + +/** + * This event signals that a network has been added. + * @CyAPI.Final.Class + */ +public final class GroupCollapsedEvent extends AbstractGroupEvent { + private boolean collapsed; + + /** + * Constructs event. + * @param source the {@link CyGroup} that has been changed. + * @param network the {@link CyNetwork} the group has been changed in. + */ + public GroupCollapsedEvent(final CyGroup source, final CyNetwork network, boolean collapsed) { + super(source, GroupCollapsedListener.class, network); + this.collapsed = collapsed; + } + + /** + * Is the group collapsed or expanded? + * + * @return true if the group was collapsed + */ + public boolean collapsed() { + return collapsed; + } +} Added: core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupCollapsedListener.java =================================================================== --- core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupCollapsedListener.java (rev 0) +++ core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupCollapsedListener.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,16 @@ +package org.cytoscape.group.events; + +import org.cytoscape.event.CyListener; + + +/** + * Listener for {@link GroupCollapsedEvent} + * @CyAPI.Spi.Interface + */ +public interface GroupCollapsedListener extends CyListener { + /** + * The method that should handle the specified event. + * @param e The event to be handled. + */ + public void handleEvent(GroupCollapsedEvent e); +} Added: core3/api/trunk/group-api/src/test/java/org/cytoscape/group/AbstractCyGroupTest.java =================================================================== --- core3/api/trunk/group-api/src/test/java/org/cytoscape/group/AbstractCyGroupTest.java (rev 0) +++ core3/api/trunk/group-api/src/test/java/org/cytoscape/group/AbstractCyGroupTest.java 2012-01-24 00:28:27 UTC (rev 28080) @@ -0,0 +1,124 @@ +/* + Copyright (c) 2008, 2010-2011, The Cytoscape Consortium (www.cytoscape.org) + + 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.group; + + +import static org.junit.Assert.*; +import java.util.ArrayList; +import java.util.List; + +import org.cytoscape.group.CyGroup; +import org.cytoscape.model.CyEdge; +import org.cytoscape.model.CyNetwork; +import org.cytoscape.model.CyNode; + +import org.junit.Before; +import org.junit.Test; + + +public abstract class AbstractCyGroupTest { + + protected CyNetwork net; + protected CyGroupFactory groupFactory; + + private CyGroup group; + private CyEdge edge1; + private CyEdge edge2; + private CyEdge edge3; + private CyEdge edge4; + private CyEdge edge5; + + protected void defaultSetUp() { + CyNode node1 = net.addNode(); + CyNode node2 = net.addNode(); + CyNode node3 = net.addNode(); + CyNode node4 = net.addNode(); + CyNode node5 = net.addNode(); + List<CyNode> groupNodes = new ArrayList<CyNode>(); + groupNodes.add(node1); + groupNodes.add(node2); + groupNodes.add(node3); + + edge1 = net.addEdge(node1, node2, false); + edge2 = net.addEdge(node2, node3, false); + edge3 = net.addEdge(node2, node4, false); + edge4 = net.addEdge(node2, node5, false); + edge5 = net.addEdge(node3, node5, false); + + List<CyEdge> groupEdges = new ArrayList<CyEdge>(); + groupEdges.add(edge1); + groupEdges.add(edge2); + groupEdges.add(edge3); + groupEdges.add(edge4); + + // Create a group + group = groupFactory.createGroup(net, groupNodes, groupEdges); + } + + @Test + public void testNetworkCreation() { + assertTrue("net has 5 nodes", net.getNodeCount() == 5); + assertTrue("net has 5 edges", net.getEdgeCount() == 5); + } + + @Test + public void testGroupCreated() { + assertTrue("group node count = 3", group.getNodeList().size() == 3); + assertTrue("group internal edge count = 2", group.getInteriorEdgeList().size() == 2); + assertTrue("group external edge count = 2", group.getExteriorEdgeList().size() == 2); + } + + @Test + public void testAddExternalEdge() { + group.addExternalEdge(edge5); + assertTrue("group external edge count = 3", group.getExteriorEdgeList().size() == 3); + } + + @Test + public void testCollapse() { + assertTrue("group is not collapsed", !group.isCollapsed(net)); + + group.collapse(net); + assertTrue("group is collapsed", group.isCollapsed(net)); + + assertTrue("net has 3 nodes", net.getNodeCount() == 3); + + assertTrue("net has group node", net.containsNode(group.getGroupNode())); + } + + @Test + public void testExpand() { + group.expand(net); + assertTrue("group is expanded", !group.isCollapsed(net)); + + assertTrue("net has 5 nodes", net.getNodeCount() == 5); + + assertTrue("net does not have group node", !net.containsNode(group.getGroupNode())); + } + +} -- You received this message because you are subscribed to the Google Groups "cytoscape-cvs" group. 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