Author: mes
Date: 2010-10-20 21:09:29 -0700 (Wed, 20 Oct 2010)
New Revision: 22325
Removed:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyFunction.java
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetwork.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetworkFactory.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTable.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableEntry.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableFactory.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableManager.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableUtil.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/Identifiable.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/SUIDFactory.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AboutToRemoveEdgeEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AboutToRemoveNodeEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractColumnEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractEdgeEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractEdgeListEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractNodeEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractNodeListEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AddedEdgeEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/ColumnDeletedEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/SelectedEdgesEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/SelectedNodesEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/UnselectedEdgesEvent.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/UnselectedNodesEvent.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/CyRootNetworkFactory.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CySubNetwork.java
Log:
many javadoc updates
Deleted: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyFunction.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyFunction.java
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyFunction.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -1,74 +0,0 @@
-
-/*
- Copyright (c) 2008, 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;
-
-/**
- * A {...@link CyRow} in a {...@link CyTable} may contain either
- * values of the base types (see {...@link CyTable}) or a
- * CyFunction. CyFunctions are evaluated when the value for the
- * row is accessed and return the newly created value. These
- * can be used as references to rows in other columns or CyDataTables.
- */
-public interface CyFunction<T> {
-/**
- * @return The type of the value returned by the function.
- */
- Class<T> getBaseType();
-
- /**
- * This method will evaluate the function when it is called.
- *
- * @return The value returned by this function.
- */
- T getValue();
-
- /**
- *
- DOCUMENT ME!
- *
- * @return The string that defines the function.
- */
- String getFunction();
-
- /**
- *
- DOCUMENT ME!
- *
- * @param functionDesc A string describing the function.
- */
- void setFunction(String functionDesc);
-}
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
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetwork.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -37,9 +37,7 @@
package org.cytoscape.model;
import java.util.List;
-import java.util.Map;
-
/**
* CyNetwork is the primary interface for representing a network (graph) data
structure.
* All algorithms should take a
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetworkFactory.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetworkFactory.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyNetworkFactory.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,9 +36,15 @@
/**
- *
- */
+ * A singleton factory object used for instantiating CyNetwork
+ * objects. The CyNetworkFactory should be available as an
+ * OSGi service.
+ */
public interface CyNetworkFactory {
-
+
+ /**
+ * Returns a new, empty {...@link CyNetwork} object.
+ * @return A new, empty {...@link CyNetwork} object.
+ */
CyNetwork getInstance();
}
Modified: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -44,38 +44,43 @@
*/
public interface CyRow {
/**
+ * Returns the value found for this row in the specified column
+ * with the specified type.
* @param columnName The name identifying the attribute.
* @param type The type of the column.
- *
* @return the value found for this row in the specified column
*/
<T> T get(String columnName, Class<?extends T> type);
/**
+ * Set the specified column for this row to the specified value.
* @param columnName The name identifying the attribute.
* @param value The value to assign the specified column in this row
*/
<T> void set(String columnName, T value);
/**
+ * Returns the Class object that is defined for this column.
* @param columnName The name of the column to check.
* @return The Class object that is defined for this column. Will
* return null if the column has not been defined. Will always return
- * a base type. If the value is actually a {...@link CyFunction} the
- * function will be evaluated and the function must evaluate to the
- * type of the column.
+ * a base type.
*/
Class<?> contains(String columnName);
/**
+ * Indicates whether the column of the specified type contains
+ * a non-null value.
* @param columnName The name identifying the attribute.
* @param type The type of the column.
* @return true if the value specified in this row at this column
- * is not null?
+ * of the specified type is not null.
*/
<T> boolean contains(String columnName, Class<?extends T> type);
/**
+ * Returns a map of column names to Objects that contain the values
+ * contained in this Row.
* @return A map of column names to Objects that contain the values
* contained in this Row.
*/
@@ -84,11 +89,13 @@
/**
* Don't use this! This is a hack for the VizMapper and will go away
* once the VizMapper is refactored.
+ * @return The row Object that represents the value in a column.
*/
Object getRaw(String columnName);
/**
* Returns the {...@link CyTable} that this row belongs to.
+ * @return the {...@link CyTable} that this row belongs to.
*/
CyTable getDataTable();
}
Modified: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTable.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTable.java
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTable.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -41,9 +41,11 @@
/**
- *
+ * A simple representation of a table object consisting of rows
+ * and columns. Columns have names and specific types and rows
+ * contain the data for a specific index.
*/
-public interface CyTable {
+public interface CyTable extends Identifiable {
/**
* By default all {...@link CyRow}s created have a primary key column
of type {...@link Integer}
* that gets created at initialization which is identified by this
string. If the
@@ -62,47 +64,48 @@
boolean isPublic();
/**
- * @return The session unique identifier.
+ * Returns a human readable name for the CyTable.
+ * @return A human readable name for the CyTable.
*/
- long getSUID();
+ String getTitle();
/**
- * @return A human readable name for the CyTable.
+ * Allows the title of the table to be set. The title is meant to be
+ * human readable and suitable for use in a user interface.
+ * @param title The human readable title for the CyTable suitable for
use in a user
+ * interface.
*/
- String getTitle();
+ void setTitle(String title);
/**
+ * Returns the name of the primary key column for this table.
* @return The name of the primary key column for this table.
*/
String getPrimaryKey();
/**
+ * Returns the class type of the primary key column for this table.
* @return The class type of the primary key column for this table.
*/
Class<?> getPrimaryKeyType();
/**
- *
- * @param title The human readable title for the CyTable suitable for
use in a user
- * interface.
- */
- void setTitle(String title);
-
- /**
* The keySet of this map defines all columns in the CyTable and the
* the values of this map define the types of the columns.
- *
* @return A map of column names to the {...@link Class} objects that
defines
* the column type.
*/
Map<String, Class<?>> getColumnTypeMap();
/**
+ * Will delete the column of the specified name.
* @param columnName The name identifying the attribute.
*/
void deleteColumn(String columnName);
/**
+ * Create a column of the specified name with the specified type
+ * and uniqueness.
* @param columnName The name identifying the attribute.
* @param type The type of the column.
* @param unique Whether the values contained in the column must be
unique
@@ -110,16 +113,18 @@
<T> void createColumn(String columnName, Class<?extends T> type,
boolean unique);
/**
- * Unique columns can be used to map the values from one CyTable to
another.
+ * Returns a list of column names where the values within the column are
+ * guaranteed to be unique. Unique columns can be used to map the values
+ * from one CyTable to another.
* @return A list of column names where the values within the column are
* guaranteed to be unique.
*/
List<String> getUniqueColumns();
/**
+ * Returns the list of all values contained in the specified column.
* @param columnName The name identifying the attribute.
* @param type The type of the column.
- *
* @return the list of all values contained in the specified column.
*/
<T> List<T> getColumnValues(String columnName, Class<?extends T> type);
@@ -128,16 +133,15 @@
* Returns the row specified by the primary key object and if a row
* for the specified key does not yet exist in the table, a new row
* will be created and the new row will be returned.
- *
* @param primaryKey The primary key index of the row to return.
- *
* @return The {...@link CyRow} identified by the specified key or a new
* row identified by the key if one did not already exist.
*/
CyRow getRow(Object primaryKey);
/**
- * Return a list of all the rows stored in this data table
+ * Return a list of all the rows stored in this data table.
+ * @return a list of all the rows stored in this data table.
*/
List<CyRow> getAllRows();
}
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
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableEntry.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -37,11 +37,13 @@
package org.cytoscape.model;
/**
- * DOCUMENT ME!
- */
+ * CyTableEntry is an interface that indicates that the implementing
+ * object can be considered a key into a table. In general, table
+ * entries will be things like nodes, edges, and networks..
+ */
public interface CyTableEntry extends Identifiable {
- /*
+ /* 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.
*/
@@ -58,7 +60,18 @@
*/
String NETWORK = "NETWORK";
- CyRow getCyRow(String namespace);
+ /**
+ * Returns the row for the specified table name for this object.
+ * @param tableName the name of the table from which to extract the
row..
+ * @return the row in the table of the specified name for this object.
+ */
+ CyRow getCyRow(String tableName);
+ /**
+ * A convenience method that returns the row in the default table
+ * for this object. This method is equivalent to calling
+ * getCyRow("default").
+ * @return the row in the default table for this object.
+ */
CyRow attrs();
}
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableFactory.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableFactory.java
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableFactory.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -46,17 +46,20 @@
*/
public interface CyTableFactory {
/**
+ * Creates a CyTable object with the specified name, primary key, and
visibility.
* @param title The name of the CyTable.
* @param primaryKey The name primaryKey column for this table.
* @param primaryKeyType The type of the primaryKey column for this
table.
* @param pub Whether or not the CyTable should be public.
- *
* @return A new {...@link CyTable} with the specified name that is
either public or not (see
* {...@link CyTable#isPublic}.
*/
CyTable createTable(String title, String primaryKey, Class<?>
primaryKeyType, boolean pub);
+ // TODO move these into table manager!
+
/**
+ * Returns a list of all table SUIDs with the specified visibility.
* @param includePrivate Whether to include private CyDataTables
* in the list (i.e. all possible CyDataTables) or not.
* @return A list containing CyTable SUIDs either
@@ -66,9 +69,8 @@
List<Long> getAllTableSUIDs(boolean includePrivate);
/**
- *
+ * Returns the table with teh specified SUID.
* @param suid The SUID identifying the CyTable.
- *
* @return The CyTable identified by the suid. Will return null if a
CyTable doesn't
* exist for the specified SUID.
*/
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
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableManager.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -40,14 +40,27 @@
/**
- *
+ * A singleton object that provides access to the available
+ * tables in the system. Should be provided as an OSGi service.
*/
public interface CyTableManager {
/**
- * @return The table containing network attributes for the specified
network.
+ * Returns a map of table names to tables, which contain the attributes
+ * for the specified network.
+ * @param type The type of map to retrieve: NODE, EDGE, or NETWORK.
+ * @param network The network associated with the map.
+ * @return a map of table names to tables, which contain the attributes
+ * 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);
}
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableUtil.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableUtil.java
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyTableUtil.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -41,7 +41,8 @@
/**
- *
+ * A collection of stateless, static utility methods provided to
+ * simplify querying of table objects.
*/
public class CyTableUtil {
private CyTableUtil() {}
@@ -51,6 +52,12 @@
* in the CyNetwork.DEFAULT_ATTRS namespace specified by columnName and
are in
* the specified state. If the attribute doesn't exist or is not of
type
* Boolean an IllegalArgumentException will be thrown.
+ * @param net The network to be queried.
+ * @param columnName The name of the column to be tested.
+ * @param state The state being queried.
+ * @return a list of nodes that have a boolean attribute in the
+ * CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in
+ * the specified state.
*/
public static List<CyNode> getNodesInState(final CyNetwork net, final
String columnName, final boolean state) {
if ( net == null )
@@ -67,6 +74,12 @@
* in the CyNetwork.DEFAULT_ATTRS namespace specified by columnName and
are in
* the specified state. If the attribute doesn't exist or is not of
type
* Boolean an IllegalArgumentException will be thrown.
+ * @param net The network to be queried.
+ * @param columnName The name of the column to be tested.
+ * @param state The state being queried.
+ * @return a list of edges that have a boolean attribute in the
+ * CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in
+ * the specified state.
*/
public static List<CyEdge> getEdgesInState(final CyNetwork net, final
String columnName, final boolean state) {
if ( net == null )
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/Identifiable.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/Identifiable.java
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/Identifiable.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -39,8 +39,13 @@
/**
* Any object that implements this interface shall return a session unique
* identifier that shall be unique among all instances of objects that
- * implement this interface. The identifier should be greater than 0.
+ * implement this interface. The identifier shall be greater than 0.
*/
public interface Identifiable {
+
+ /**
+ * Returns the SUID of the implementing object.
+ * @return the SUID of the implementing object.
+ */
long getSUID();
}
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/SUIDFactory.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/SUIDFactory.java
2010-10-21 00:12:09 UTC (rev 22324)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/SUIDFactory.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -41,11 +41,14 @@
*/
public abstract class SUIDFactory {
- private SUIDFactory() {
- }
+ private SUIDFactory() { }
private static long count = 1;
+ /**
+ * Returns the next available SUID.
+ * @return the next available SUID.
+ */
public static synchronized long getNextSUID() {
return count++;
}
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AboutToRemoveEdgeEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AboutToRemoveEdgeEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AboutToRemoveEdgeEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,8 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
-
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AboutToRemoveNodeEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AboutToRemoveNodeEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AboutToRemoveNodeEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,8 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
-
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractColumnEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractColumnEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractColumnEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,7 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
import org.cytoscape.event.AbstractCyEvent;
import org.cytoscape.model.CyTable;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractEdgeEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractEdgeEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractEdgeEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,7 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
import org.cytoscape.event.AbstractCyEvent;
import org.cytoscape.model.CyEdge;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractEdgeListEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractEdgeListEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractEdgeListEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,7 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
import org.cytoscape.event.AbstractCyEvent;
import org.cytoscape.model.CyEdge;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractNodeEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractNodeEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractNodeEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,7 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
import org.cytoscape.event.AbstractCyEvent;
import org.cytoscape.model.CyNetwork;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractNodeListEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractNodeListEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AbstractNodeListEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,7 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
import org.cytoscape.event.AbstractCyEvent;
import org.cytoscape.model.CyNode;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AddedEdgeEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AddedEdgeEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/AddedEdgeEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,7 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/ColumnDeletedEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/ColumnDeletedEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/ColumnDeletedEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -36,7 +36,6 @@
package org.cytoscape.model.events;
-import org.cytoscape.event.CyEvent;
import org.cytoscape.model.CyTable;
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/SelectedEdgesEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/SelectedEdgesEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/SelectedEdgesEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -4,7 +4,6 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.event.CyEvent;
import java.util.List;
public final class SelectedEdgesEvent extends AbstractEdgeListEvent {
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/SelectedNodesEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/SelectedNodesEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/SelectedNodesEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -4,7 +4,6 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.event.CyEvent;
import java.util.List;
public final class SelectedNodesEvent extends AbstractNodeListEvent {
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/UnselectedEdgesEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/UnselectedEdgesEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/UnselectedEdgesEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -4,7 +4,6 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.event.CyEvent;
import java.util.List;
public final class UnselectedEdgesEvent extends AbstractEdgeListEvent {
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/UnselectedNodesEvent.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/UnselectedNodesEvent.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/events/UnselectedNodesEvent.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -4,7 +4,6 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.event.CyEvent;
import java.util.List;
public final class UnselectedNodesEvent extends AbstractNodeListEvent {
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
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CyRootNetwork.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -57,28 +57,16 @@
* <ul><li>A <b>CyRootNetwork</b> is a {...@link CyNetwork} that
* adds methods for maintaining the meta-network.
* All {...@link CyNode}s and {...@link CyEdge}s in all {...@link
CySubNetwork}s
- * that are part of this CyRootNetwork, including all {...@link CyMetaNode}s.
- * <li>A {...@link CySubNetwork} is a group of nodes and edges
- * that are a sub-network of a {...@link CyRootNetwork}. The
- * {...@link CySubNetwork} can be represented within another {...@link
CySubNetwork}
- * by a {...@link CyMetaNode}. A {...@link CySubNetwork} may be thought
- * of as a projection of the graph implemented by the <b>CyRootNetwork</b>.
- * <li>A {...@link CyMetaNode} is a {...@link CyNode} that represents
- * a {...@link CySubNetwork} in a {...@link CyNetwork}.
- * </ul>
- * These three additional interfaces can be used to create and
- * maintain a complex graph structure. In order to avoid requiring
- * all plugins and other uses of this package to test for
- * and support the presence of a meta-network, Cytoscape provides
- * a {...@link CyNetwork} that is a "flattened" version of the
- * meta-network (essentially all {...@link CyNode}s and {...@link CyEdge}s
- * except {...@link CyMetaNode}s and their associated {...@link CyEdge}s.
+ * that are part of this CyRootNetwork.
+ * <li>A {...@link CySubNetwork} is a set of nodes and edges
+ * that comprise a sub-network of a {...@link CyRootNetwork}.
+ * A {...@link CySubNetwork} may be thought of as a projection of
+ * the graph implemented by the <b>CyRootNetwork</b>.
*/
public interface CyRootNetwork extends CyNetwork {
/**
* Create an empty {...@link CySubNetwork}.
- *
* @return The created {...@link CySubNetwork}.
*/
CySubNetwork addSubNetwork();
@@ -86,7 +74,6 @@
/**
* Removes the subnetwork from the root network, but not the nodes and
edges contained
* in the subnetwork.
- *
* @param sub the {...@link CySubNetwork} to remove.
*/
void removeSubNetwork(CySubNetwork sub);
Modified:
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CyRootNetworkFactory.java
===================================================================
---
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CyRootNetworkFactory.java
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CyRootNetworkFactory.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -38,11 +38,16 @@
import org.cytoscape.model.CyNetwork;
+/**
+ * A singleton object that provides access to the CyRootNetwork
+ * objects associated with CyNetwork objects.
+ */
public interface CyRootNetworkFactory {
/**
* Converts a CyNetwork to a CyRootNetwork
+ * @param n The CyNetwork for which to return the CyRootNework.
+ * @return The root network associated with the specified CyNetwork.
*/
CyRootNetwork convert(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
2010-10-21 00:12:09 UTC (rev 22324)
+++
core3/model-api/trunk/src/main/java/org/cytoscape/model/subnetwork/CySubNetwork.java
2010-10-21 04:09:29 UTC (rev 22325)
@@ -39,9 +39,7 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyEdge;
-import java.util.Set;
-
/**
* A CySubNetwork is a {...@link CyNetwork} that is contained within a parent
* {...@link CyNetwork}. See the description in {...@link CyRootNetwork} for
@@ -50,7 +48,6 @@
public interface CySubNetwork extends CyNetwork {
/**
* Return the {...@link CyRootNetwork} that contains this CySubNetwork.
- *
* @return the {...@link CyRootNetwork} that contains this
CySubNetowrk.
*/
CyRootNetwork getRootNetwork();
@@ -58,24 +55,24 @@
/**
* 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}.
- * This method also allows {...@link CyMetaNode} to be added to
subnetworks.
- *
* @param node CyNode to add to this subnetwork
+ * @return true if the node was successfully added to the subnetwork,
+ * false otherwise.
*/
boolean addNode(CyNode node);
/**
* 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}.
- *
* @param edge CyEdge to add to this subnetwork
+ * @return true if the edge was successfully added to the subnetwork,
+ * false otherwise.
*/
boolean addEdge(CyEdge edge);
/**
* A shortcut method that Creates a new {...@link CyNode} in both this
subnetwork
* <b>AND</b> in the {...@link CyRootNetwork}.
- *
* @return A new CyNode that exists in both this subnetwork and the
associated
* {...@link CyRootNetwork}.
*/
@@ -84,18 +81,23 @@
/**
* A shortcut method that Creates a new {...@link CyEdge} in both this
subnetwork
* <b>AND</b> in the {...@link CyRootNetwork}.
- *
+ * @param source The source node of the edge. The source node must exist
+ * in the root network.
+ * @param target The target node of the edge. The target node must exist
+ * in the root network.
+ * @param directed Whether the edge should be considered directed or
not.
* @return A new CyEdge that exists in both this subnetwork and the
associated
* {...@link CyRootNetwork}.
*/
- CyEdge addEdge(CyNode src, CyNode tgt, boolean directed);
+ CyEdge addEdge(CyNode source, CyNode target, boolean directed);
/**
* Removes a node from this {...@link CySubNetwork} but not from the
{...@link CyRootNetwork}.
* The node is removed from the CySubNetwork, but <i>not</i> deleted
* from the {...@link CyRootNetwork}.
- *
* @param node Node to remove from this subnetwork
+ * @return true if the node was successfully removed from the specified
subnetwork,
+ * false otherwise.
*/
boolean removeNode(CyNode node);
@@ -103,8 +105,9 @@
* Removes a edge from this {...@link CySubNetwork} but not from the
{...@link CyRootNetwork}.
* The edge is removed from the CySubNetwork, but <i>not</i> deleted
* from the {...@link CyRootNetwork}.
- *
* @param edge Edge to remove from this subnetwork
+ * @return true if the edge was successfully removed from the specified
subnetwork,
+ * false otherwise.
*/
boolean removeEdge(CyEdge edge);
}
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