Author: mes
Date: 2012-04-17 14:45:54 -0700 (Tue, 17 Apr 2012)
New Revision: 28866
Added:
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/package-info.java
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/package-info.java
Modified:
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/GroupChangedEvent.java
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/package-info.java
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/Aggregator.java
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/AttributeHandlingType.java
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/CyGroupAggregationManager.java
Log:
fixes #789 updated all javdoc, added package-info and fixed all warnings
Modified:
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
2012-04-17 21:45:36 UTC (rev 28865)
+++
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/CyGroupManager.java
2012-04-17 21:45:54 UTC (rev 28866)
@@ -52,7 +52,7 @@
* the network is null, then return only those
* groups that have been designated as
* "global" (no referenced network)
- * for this {@link CyRootNetwork}
+ * for this {@link
org.cytoscape.model.subnetwork.CyRootNetwork}
* @return the complete set of all the currently known groups
* in a Cytoscape network
*/
@@ -110,9 +110,9 @@
/**
* Registers a group with the group manager. Does nothing
* if the group is already known to the group manager.
+ * Fires GroupAddedEvent.
*
* @param group a non-null {@link CyGroup}
- * @fires GroupAddedEvent
*/
public void addGroup(final CyGroup group);
Modified:
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupChangedEvent.java
===================================================================
---
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupChangedEvent.java
2012-04-17 21:45:36 UTC (rev 28865)
+++
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/GroupChangedEvent.java
2012-04-17 21:45:54 UTC (rev 28866)
@@ -15,9 +15,24 @@
* @CyAPI.Final.Class
*/
public final class GroupChangedEvent extends AbstractCyEvent<CyGroup> {
+ /**
+ * An enum describing the type of change that happened to the group.
+ */
public enum ChangeType {
- NODE_ADDED, INTERNAL_EDGE_ADDED, EXTERNAL_EDGE_ADDED,
- NODES_ADDED, NODES_REMOVED, EDGES_ADDED, EDGES_REMOVED }
+ /** A single node was added. */
+ NODE_ADDED,
+ /** A single internal edge was added. */
+ INTERNAL_EDGE_ADDED,
+ /** A single external edge was added. */
+ EXTERNAL_EDGE_ADDED,
+ /** Mulitple nodes were added. */
+ NODES_ADDED,
+ /** One or more nodes were removed. */
+ NODES_REMOVED,
+ /** Multiple edges were added. */
+ EDGES_ADDED,
+ /** One or more edges were removed. */
+ EDGES_REMOVED }
private CyIdentifiable whatChanged;
private List<CyNode> nodeList;
@@ -26,7 +41,7 @@
/**
* Constructs event.
* @param source the {@link CyGroup} that has been changed.
- * @param whatChanged the {@link CyNode} or {@link CyEdge} or list of
{@link CyNodes} that were added or removed.
+ * @param whatChanged the {@link CyNode} or {@link CyEdge} or list of
{@link CyNode}s that were added or removed.
*/
@SuppressWarnings({ "rawtypes", "unchecked" })
public GroupChangedEvent(final CyGroup source, final Object
whatChanged, ChangeType change) {
Added:
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/package-info.java
===================================================================
---
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/package-info.java
(rev 0)
+++
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/events/package-info.java
2012-04-17 21:45:54 UTC (rev 28866)
@@ -0,0 +1,5 @@
+/**
+ * This package contains the various events and listeners
+ * related to group management, creation, and destruction.
+ */
+package org.cytoscape.group.events;
Modified:
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/package-info.java
===================================================================
---
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/package-info.java
2012-04-17 21:45:36 UTC (rev 28865)
+++
core3/api/trunk/group-api/src/main/java/org/cytoscape/group/package-info.java
2012-04-17 21:45:54 UTC (rev 28866)
@@ -1,15 +1,15 @@
/**
* This package provides an API for creating and managing
- * groups in Cytoscape. A {@link CyGroup} is a collection
+ * groups in Cytoscape. A {@link org.cytoscape.group.CyGroup} is a collection
* of nodes and associated edges represented by a node in a
* network. It is stored internally as a
* network and a list of external edges (edges that connect
* from nodes within the group to nodes outside of the group.
* Groups may contain nodes which represent groups, which allows
* for the creation of explicit hierarchies of groups. To create
- * a group, use one of the {@link CyGroupFactory} methods. A
- * {@link CyGroupManager} service is provided that tracks which
- * groups apply in which networks and which {@link CyNode}s
- * actually represent {@link CyGroups}.
+ * a group, use one of the {@link org.cytoscape.group.CyGroupFactory} methods.
A
+ * {@link org.cytoscape.group.CyGroupManager} service is provided that tracks
which
+ * groups apply in which networks and which {@link
org.cytoscape.model.CyNode}s
+ * actually represent {@link org.cytoscape.group.CyGroup}s.
*/
package org.cytoscape.group;
Modified:
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/Aggregator.java
===================================================================
---
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/Aggregator.java
2012-04-17 21:45:36 UTC (rev 28865)
+++
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/Aggregator.java
2012-04-17 21:45:54 UTC (rev 28866)
@@ -3,7 +3,12 @@
import org.cytoscape.group.CyGroup;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyTable;
-
+
+/**
+ * The Aggregator interface acts as a service interface for
+ * different methods of aggregating attribute data for the
+ * nodes in a {@link CyGroup}.
+ */
public interface Aggregator<T> {
/**
* Return the Class this aggregator supports
Modified:
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/AttributeHandlingType.java
===================================================================
---
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/AttributeHandlingType.java
2012-04-17 21:45:36 UTC (rev 28865)
+++
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/AttributeHandlingType.java
2012-04-17 21:45:54 UTC (rev 28866)
@@ -40,22 +40,40 @@
* AttributeHandlingType arrays defined below.
*/
public enum AttributeHandlingType {
+ /** No aggregation. */
NONE("None"),
+ /** Aggregated as comma-separated values. */
CSV("Comma-separated Values"),
+ /** Aggregated as tab-separated values. */
TSV("Tab-separated Values"),
+ /** Aggregated as most common value. */
MCV("Most Common Value"),
+ /** Aggregated as the sum of all values. */
SUM("Sum"),
+ /** Aggregated as the average of all values. */
AVG("Average"),
+ /** Aggregated as the minimum value. */
MIN("Minimum value"),
+ /** Aggregated as the maximum value. */
MAX("Maximum value"),
+ /** Aggregated as the median value. */
MEDIAN("Median value"),
+ /** Aggregated as a concatenation of all values. */
CONCAT("Concatenate"),
+ /** Aggregated as unique values. */
UNIQUE("Unique Values"),
+ /** Aggregated as a logical AND of all values. */
AND("Logical AND"),
+ /** Aggregated as a logical OR of all values. */
OR("Logical OR"),
+ /** Default, no aggregation. */
DEFAULT("(no override)");
private String name;
private AttributeHandlingType(String s) { name = s; }
+ /**
+ * Returns a human readable name for this enum value.
+ * @return a human readable name for this enum value.
+ */
public String toString() { return name; }
}
Modified:
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/CyGroupAggregationManager.java
===================================================================
---
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/CyGroupAggregationManager.java
2012-04-17 21:45:36 UTC (rev 28865)
+++
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/CyGroupAggregationManager.java
2012-04-17 21:45:54 UTC (rev 28866)
@@ -18,16 +18,16 @@
* provide a specific aggregation algorithm for a specific CyColumn
* type.
*
- * @param aggregator the {@Link Aggregator}
+ * @param aggregator the {@link Aggregator}
*/
- public void addAggregator(Aggregator aggregator);
+ void addAggregator(Aggregator aggregator);
/**
* Remove an aggregator from the available aggregators.
*
- * @param aggregator the {@Link Aggregator} to remove
+ * @param aggregator the {@link Aggregator} to remove
*/
- public void removeAggregator(Aggregator aggregator);
+ void removeAggregator(Aggregator aggregator);
/**
* Get the list of aggregators for a particular Class.
@@ -35,19 +35,19 @@
* @param type the {@link Class} to get aggregators for
* @return the list of aggregators
*/
- public List<Aggregator> getAggregators(Class type);
+ List<Aggregator> getAggregators(Class type);
/**
* Get the list of aggregators.
*
* @return the list of aggregators
*/
- public List<Aggregator> getAggregators();
+ List<Aggregator> getAggregators();
/**
* Get the list of classes for which have aggregators.
*
* @return the list of classes we're aggregating
*/
- public List<Class> getSupportedClasses();
+ List<Class> getSupportedClasses();
}
Added:
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/package-info.java
===================================================================
---
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/package-info.java
(rev 0)
+++
core3/api/trunk/group-data-api/src/main/java/org/cytoscape/group/data/package-info.java
2012-04-17 21:45:54 UTC (rev 28866)
@@ -0,0 +1,5 @@
+
+/**
+ * An api for configuring {@link org.cytoscape.group.CyGroup}s.
+ */
+package org.cytoscape.group.data;
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