Author: mes
Date: 2011-10-20 13:24:30 -0700 (Thu, 20 Oct 2011)
New Revision: 27248
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/MapNetworkAttrTask.java
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/CyNetworkReader.java
core3/api/trunk/session-api/src/main/java/org/cytoscape/session/events/SessionAboutToBeSavedEvent.java
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/VisualProperty.java
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/DefaultViewEditor.java
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/editor/VisualPropertyEditor.java
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTask.java
Log:
javadoc updates and minor tweak to MapNetworkAttrTask
Modified:
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/MapNetworkAttrTask.java
===================================================================
---
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/MapNetworkAttrTask.java
2011-10-20 20:23:22 UTC (rev 27247)
+++
core3/api/trunk/core-task-api/src/main/java/org/cytoscape/task/MapNetworkAttrTask.java
2011-10-20 20:24:30 UTC (rev 27248)
@@ -16,7 +16,11 @@
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
-/** #ASKMIKE */
+/**
+ * This is a simple {@link Task} that will take a loaded table and ask whether
+ * the columns in the new table should become virtual columns in the node or
+ * edge table of the current network, all networks, or no networks.
+ */
public final class MapNetworkAttrTask extends AbstractTask {
@Tunable(description="Map to current network only")
public boolean currentNetworkOnly = true;
@@ -24,27 +28,26 @@
private final Class<? extends CyTableEntry> type; // Must be node or
edge!
private final CyTable newGlobalTable;
private final CyNetworkManager networkManager;
- final private CyApplicationManager applicationManager;
- private String key = null;
- private String mappingKey = null;
-
- public MapNetworkAttrTask(final Class<? extends CyTableEntry> type,
final CyTable newGlobalTable,
- String key, String mappingKey,
- final CyNetworkManager networkManager,
- final CyApplicationManager applicationManager)
- {
- this(type,newGlobalTable,networkManager, applicationManager);
- this.key = key;
- this.mappingKey = mappingKey;
- }
+ private final CyApplicationManager applicationManager;
+ private String mappingKey;
-
- public MapNetworkAttrTask(final Class<? extends CyTableEntry> type,
final CyTable newGlobalTable,
- final CyNetworkManager networkManager,
- final CyApplicationManager applicationManager)
+ /**
+ * Constructor.
+ * @param type The type of table to map to, either CyNode.class or
CyEdge.class.
+ * @param newGlobalTable The table to be mapped.
+ * @param mappingKey The column name in the existing table used to join
with the primary key in the new table.
+ * @param networkManager The network manager used to access the list of
all networks.
+ * @param applicationManager The application manager used to access the
current network.
+ */
+ public MapNetworkAttrTask(final Class<? extends CyTableEntry> type,
+ final CyTable newGlobalTable,
+ String mappingKey,
+ final CyNetworkManager networkManager,
+ final CyApplicationManager applicationManager)
{
this.type = type;
this.newGlobalTable = newGlobalTable;
+ this.mappingKey = mappingKey;
this.networkManager = networkManager;
this.applicationManager = applicationManager;
@@ -53,6 +56,29 @@
}
+ /**
+ * Constructor. Will attempt to map existing tables based on the {@link
CyTableEntry.NAME}
+ * column.
+ * @param type The type of table to map to, either CyNode.class or
CyEdge.class.
+ * @param newGlobalTable The table to be mapped.
+ * @param networkManager The network manager used to access the list of
all networks.
+ * @param applicationManager The application manager used to access the
current network.
+ */
+ public MapNetworkAttrTask(final Class<? extends CyTableEntry> type,
+ final CyTable newGlobalTable,
+ final CyNetworkManager networkManager,
+ final CyApplicationManager applicationManager)
+ {
+ this(type,newGlobalTable,CyTableEntry.NAME,networkManager,
applicationManager);
+ }
+
+
+ /**
+ * Executes the task.
+ * @param taskMonitor The TaskMonitor used to track the state of the
task execution.
+ * @throws Exception All Exceptions throw will be caught and handled by
the
+ * {@link org.cytoscape.work.TaskManager} executing the task.
+ */
public void run(final TaskMonitor taskMonitor) throws Exception {
taskMonitor.setTitle("Mapping virtual columns");
@@ -84,15 +110,7 @@
for (final CyTable targetTable : targetTables) {
if (cancelled)
return;
- if (mappingKey == null){
- // use primary key to do table join
- targetTable.addVirtualColumns(newGlobalTable,
sourceTableJoinColumn,
- CyTableEntry.NAME, false);
- }
- else {
- // use alternative key
- targetTable.addVirtualColumns(newGlobalTable,
sourceTableJoinColumn, mappingKey, false);
- }
+ targetTable.addVirtualColumns(newGlobalTable,
sourceTableJoinColumn, mappingKey, false);
}
}
-}
\ No newline at end of file
+}
Modified:
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/CyNetworkReader.java
===================================================================
---
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/CyNetworkReader.java
2011-10-20 20:23:22 UTC (rev 27247)
+++
core3/api/trunk/io-api/src/main/java/org/cytoscape/io/read/CyNetworkReader.java
2011-10-20 20:24:30 UTC (rev 27248)
@@ -4,11 +4,12 @@
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.Task;
-/** #ASKMIKE
+/**
* An extension of the Task interface that returns an array of
- * {@link org.cytoscape.view.model.CyNetworkView} objects as well as optional
- * {@link org.cytoscape.view.vizmap.VisualStyle} objects that are read as part
- * of the Task. Instances of this interface are created by
+ * {@link org.cytoscape.model.CyNetwork} objects that are read as part
+ * of the Task. An additional method provides an option for readers
+ * to create {@link CyNetworkView}s from the networks it has read as
+ * well. Instances of this interface are created by
* InputStreamTaskFactory objects registered as OSGi services, which are in
turn
* processed by associated reader manager objects that distinguish
* InputStreamTaskFactories based on the DataCategory associated with the
@@ -16,8 +17,17 @@
*/
public interface CyNetworkReader extends Task {
+ /**
+ * Returns an array of networks read after executing the run() method
of {@link Task}.
+ * @return an array of networks read after executing the run() method
of {@link Task}.
+ */
CyNetwork[] getCyNetworks();
+ /**
+ * A method to build a {@link CyNetworkView} from one of the networks
just read.
+ * @param network A network just read by the task and part of the
getCyNetworks() array.
+ * @return A {@link CyNetworkView} created by the reader for the
network specified.
+ */
CyNetworkView buildCyNetworkView(final CyNetwork network);
}
Modified:
core3/api/trunk/session-api/src/main/java/org/cytoscape/session/events/SessionAboutToBeSavedEvent.java
===================================================================
---
core3/api/trunk/session-api/src/main/java/org/cytoscape/session/events/SessionAboutToBeSavedEvent.java
2011-10-20 20:23:22 UTC (rev 27247)
+++
core3/api/trunk/session-api/src/main/java/org/cytoscape/session/events/SessionAboutToBeSavedEvent.java
2011-10-20 20:24:30 UTC (rev 27248)
@@ -88,7 +88,7 @@
/**
* A method that allows plugins to specify desktop-related data to be
* stored in the session.
- * @param desktop
+ * @param desktop Setting the {@link Desktop} object associated with
this event.
*/
public void setDesktop(Desktop desktop) {
this.desktop = desktop;
@@ -107,8 +107,8 @@
/**
* A method that allows plugins to add Cytopanel-related information to
be
* stored in the session.
- * @param cytopanel
- * @throws Exception #ASKMIKE Shouldn't this be nullptrexcept?
+ * @param cytopanel The CytoPanel to be added.
+ * @throws NullPointerException If the cytopanel to be added is null.
*/
public void addCytopanel(Cytopanel cytopanel) throws Exception {
if (cytopanel == null)
@@ -116,5 +116,4 @@
cytopanels.add(cytopanel);
}
-
}
Modified:
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/VisualProperty.java
===================================================================
---
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/VisualProperty.java
2011-10-20 20:23:22 UTC (rev 27247)
+++
core3/api/trunk/viewmodel-api/src/main/java/org/cytoscape/view/model/VisualProperty.java
2011-10-20 20:24:30 UTC (rev 27248)
@@ -54,8 +54,7 @@
/**
* The default value of this property. This value is immutable.
- *
- * @return DOCUMENT ME!
+ * @return The default value of this property.
*/
T getDefault();
@@ -63,8 +62,7 @@
/**
* A short string used to identify this visual property and suitable for
* serializing to XML and other text formats.
- *
- * @return DOCUMENT ME!
+ * @return A short string used to identify this visual property and
suitable for serialization.
*/
String getIdString();
@@ -72,8 +70,7 @@
/**
* A short string suitable for presentation to humans. Should not be
used
* for serialization.
- *
- * @return DOCUMENT ME!
+ * @return A short string suitable for presentation to humans.
*/
String getDisplayName();
@@ -102,15 +99,14 @@
/**
* In some cases, default value from visual style is not suitable, such
as x, y, z location of nodes.
* If this flag is on, it will be ignored and it will be controlled by
mapping only.
- * #ASKMIKE
- * @return
+ * @return true if the default value should be ignored (as with x,y,z
locations) and false otherwise.
*/
boolean shouldIgnoreDefault();
/**
* VisualProperty is always associated with a data type. For example,
EDGE_COLOR is associated with
- * {@link org.cytoscape.model.CyEdge} data object. In that case, this
returns Class<CyEdge>.
+ * {@link org.cytoscape.model.CyEdge} data object. In that case, this
returns Class<CyEdge>.
* For now, return data types are CyNode, CyEdge, and CyNetwork.
*
* @return target data type of this visual property. CyNode, CyEdge,
or CyNetwork.
Modified:
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/DefaultViewEditor.java
===================================================================
---
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/DefaultViewEditor.java
2011-10-20 20:23:22 UTC (rev 27247)
+++
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/DefaultViewEditor.java
2011-10-20 20:24:30 UTC (rev 27248)
@@ -7,22 +7,22 @@
/**
* Default View Editor is the component to display available visual properties
* and its default view for given Visual Style.
- *
* This component will be provided as a service.
- *
- * @author kono
- * @since Cytoscape 3.0
- *
*/
public interface DefaultViewEditor {
/**
- * For a given visual style name, returns a graphics of default.
+ * For a given visual style name, return a component containing
+ * a graphical view of the specified visual style.
*
* @param vs The {@link VisualStyle} to get the default view of.
- * @return the default graphics Component. #ASKMIKE
+ * @return a component containing a graphical view of the specified
visual style.
*/
- public Component getDefaultView(VisualStyle vs);
-
- public void showEditor(Component parent);
-}
\ No newline at end of file
+ Component getDefaultView(VisualStyle vs);
+
+ /**
+ * Show the default view editor in the specified parent component.
+ * @param parent The component in which the default view should be
shown.
+ */
+ void showEditor(Component parent);
+}
Modified:
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/editor/VisualPropertyEditor.java
===================================================================
---
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/editor/VisualPropertyEditor.java
2011-10-20 20:23:22 UTC (rev 27247)
+++
core3/api/trunk/vizmap-gui-api/src/main/java/org/cytoscape/view/vizmap/gui/editor/VisualPropertyEditor.java
2011-10-20 20:24:30 UTC (rev 27248)
@@ -45,8 +45,7 @@
* If plugin developer adds a custom visual property, they should implement
this
* in the presentation layer.
*
- * @param <T>
- * Type of object managed in the Visual Prop.
+ * @param <T> Type of object managed in the Visual Prop.
*
*/
public interface VisualPropertyEditor<T> {
@@ -59,7 +58,7 @@
/**
* Returns continuous mapping editor for the Visual Property. Return
value
- * is null is Continuous Editor does not exist. #ASKMIKE
+ * is null if Continuous Editor does not exist.
* @return a continuous mapping editor for the Visual Property.
*/
PropertyEditor getContinuousMappingEditor();
@@ -80,24 +79,26 @@
T showVisualPropertyValueEditor();
/**
- * Provide Cell renderer for JTable or JList. Developers can implement
- * custom cell renderers by using returned component.
+ * A custom cell renderer for Discrete table cells.
*
- * @return a TableCellRenderer for JTable or JList.
+ * @return a TableCellRenderer Discrete table cells.
*/
TableCellRenderer getDiscreteTableCellRenderer();
+ /**
+ * A custom cell renderer for Continuous table cells.
+ *
+ * @return a TableCellRenderer Continuous table cells.
+ */
TableCellRenderer getContinuousTableCellRenderer();
/**
* This is for default view editor.
*
- * @param width
- * DOCUMENT ME!
- * @param height
- * DOCUMENT ME!
+ * @param width The width of the desired Icon.
+ * @param height The height of the desired Icon.
*
- * @return DOCUMENT ME!
+ * @return An icon of the specified width and height.
*/
Icon getDefaultIcon(int width, int height);
}
Modified:
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTask.java
===================================================================
---
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTask.java
2011-10-20 20:23:22 UTC (rev 27247)
+++
core3/impl/trunk/table-import-impl/src/main/java/org/cytoscape/tableimport/internal/ui/ImportAttributeTableTask.java
2011-10-20 20:24:30 UTC (rev 27248)
@@ -88,7 +88,7 @@
CytoscapeServices.netMgr, CytoscapeServices.appMgr);
insertTasksAfterCurrentTask(task);
} else { /* Case 2: use an attribute as the key. */
- final MapNetworkAttrTask task = new
MapNetworkAttrTask(type, table, primaryKey, mappingKey,
+ final MapNetworkAttrTask task = new
MapNetworkAttrTask(type, table, mappingKey,
CytoscapeServices.netMgr,
CytoscapeServices.appMgr);
insertTasksAfterCurrentTask(task);
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
