Author: mes
Date: 2012-04-20 17:07:45 -0700 (Fri, 20 Apr 2012)
New Revision: 28941
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutContext.java
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutTask.java
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractPartitionLayoutTask.java
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/LayoutPoint.java
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/WeightTypes.java
Log:
updated javadoc
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutContext.java
===================================================================
---
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutContext.java
2012-04-21 00:03:12 UTC (rev 28940)
+++
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutContext.java
2012-04-21 00:07:45 UTC (rev 28941)
@@ -3,13 +3,19 @@
import org.cytoscape.work.Tunable;
import org.cytoscape.work.util.ListSingleSelection;
+/**
+ * The tunable context used to configure the layout algorithm.
+ */
public class AbstractLayoutContext implements CyLayoutContext {
private static final String ALL_NODES = "All Nodes";
private static final String SELECTED_NODES = "Selected Nodes";
private boolean useOnlySelectedNodes = false;
-
+
+ /**
+ * A method used internally only.
+ */
@Tunable(description = "Apply to")
public final ListSingleSelection<String> getSubmenuOptions() {
final ListSingleSelection<String> options = new
ListSingleSelection<String>(ALL_NODES, SELECTED_NODES);
@@ -17,6 +23,9 @@
return options;
}
+ /**
+ * A method used internally only. DO NOT USE!
+ */
public final void setSubmenuOptions(ListSingleSelection<String>
options) {
useOnlySelectedNodes =
SELECTED_NODES.equals(options.getSelectedValue());
}
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutTask.java
===================================================================
---
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutTask.java
2012-04-21 00:03:12 UTC (rev 28940)
+++
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutTask.java
2012-04-21 00:07:45 UTC (rev 28941)
@@ -112,15 +112,19 @@
/**
* Constructor.
+ * @param name The name of the layout algorithm.
* @param networkView The network view that the layout algorithm will
be applied to.
- * @param name The name of the algorithm. Used for setting attributes
associated with
- * this layout.
- * @param selectedOnly Indicates whether the layout should be applied
to the selected nodes
- * or not.
- * @param staticNodes The list of nodes whose positions are meant to be
locked and
- * not changed.
+ * @param nodesToLayOut The set of nodes to be laid out.
+ * @param supportedNodeAttributeTypes The set of supported node
attribute types.
+ * @param supportedEdgeAttributeTypes The set of supported edge
attribute types.
+ * @param initialAttributes The list of initial attribute column names.
*/
- public AbstractLayoutTask(String name, CyNetworkView networkView,
Set<View<CyNode>> nodesToLayOut, Set<Class<?>> supportedNodeAttributeTypes,
Set<Class<?>> supportedEdgeAttributeTypes, List<String> initialAttributes) {
+ public AbstractLayoutTask(String name,
+ CyNetworkView networkView,
+ Set<View<CyNode>> nodesToLayOut,
+ Set<Class<?>> supportedNodeAttributeTypes,
+ Set<Class<?>> supportedEdgeAttributeTypes,
+ List<String> initialAttributes) {
super();
this.networkView = networkView;
@@ -136,6 +140,9 @@
this.initialAttributes = initialAttributes;
}
+ /**
+ * {@inheritDoc}
+ */
@Override
public final void run(final TaskMonitor taskMonitor) {
final long start = System.currentTimeMillis();
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractPartitionLayoutTask.java
===================================================================
---
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractPartitionLayoutTask.java
2012-04-21 00:03:12 UTC (rev 28940)
+++
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/AbstractPartitionLayoutTask.java
2012-04-21 00:07:45 UTC (rev 28941)
@@ -66,19 +66,24 @@
/**
* Creates a new AbstractPartitionLayoutTask object.
- * @param networkView the CyNetworkView being partitioned.
* @param name The name of the layout algorithm.
* @param singlePartition Whether this layout algorithm should execute
on a
* single partition instead of multiple partitions.
- * @param supportedNodeAttributeTypes
- * @param supportedEdgeAttributeTypes
- * @param selectedOnly Whether the this layout algorithm should execute
on
- * just the nodes currently selected.
- * @param staticNodes A set of nodes that should NOT be moved by the
- * layout algorithm.
+ * @param networkView the CyNetworkView being partitioned.
+ * @param nodesToLayOut the set of nodes to layout.
+ * @param supportedNodeAttributeTypes The types of node attributes
supported by this algorithm.
+ * @param supportedEdgeAttributeTypes The types of edge attributes
supported by this algorithm.
+ * @param initialAttributes A list of attribute column names supported
by this layout.
*/
- public AbstractPartitionLayoutTask(final String name, final boolean
singlePartition, CyNetworkView networkView, Set<View<CyNode>> nodesToLayOut,
Set<Class<?>> supportedNodeAttributeTypes, Set<Class<?>>
supportedEdgeAttributeTypes, List<String> initialAttributes) {
- super(name, networkView, nodesToLayOut,
supportedNodeAttributeTypes, supportedEdgeAttributeTypes, initialAttributes);
+ public AbstractPartitionLayoutTask(final String name,
+ final boolean singlePartition,
+ CyNetworkView networkView,
+ Set<View<CyNode>> nodesToLayOut,
+ Set<Class<?>>
supportedNodeAttributeTypes,
+ Set<Class<?>>
supportedEdgeAttributeTypes,
+ List<String> initialAttributes) {
+ super(name, networkView, nodesToLayOut,
supportedNodeAttributeTypes,
+ supportedEdgeAttributeTypes, initialAttributes);
this.singlePartition = singlePartition;
}
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
===================================================================
---
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
2012-04-21 00:03:12 UTC (rev 28940)
+++
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
2012-04-21 00:07:45 UTC (rev 28941)
@@ -46,42 +46,38 @@
public interface CyLayoutAlgorithm<T extends CyLayoutContext> {
/**
- *
- * @param networkView
- * @param layoutContext
- * @param nodesToLayOut
- *
+ * Creates a task iterator containing the layout tasks.
+ * @param networkView The network view that the layout algorithm should
be applied to.
+ * @param layoutContext The layout context for this layout algorithm.
+ * @param nodesToLayOut The set of node views to layout.
* @return taskIterator contains layout tasks.
*/
TaskIterator createTaskIterator(CyNetworkView networkView, T
layoutContext, Set<View<CyNode>> nodesToLayOut);
/**
- *
- * @param networkView
- * @param layoutContext
- * @param nodesToLayOut
- *
- * @return
+ * Returns true if the task factory is ready to produce a task iterator.
+ * @param networkView The network view that the layout algorithm should
be applied to.
+ * @param layoutContext The layout context for this layout algorithm.
+ * @param nodesToLayOut The set of node views to layout.
+ * @return true if the task factory is ready to produce a task iterator.
*/
boolean isReady(CyNetworkView networkView, T layoutContext,
Set<View<CyNode>> nodesToLayOut);
/**
- *
- * @return
+ * Returns the layout context object.
+ * @return The layout context object.
*/
T createLayoutContext();
/**
* Tests to see if this layout supports doing a layout based on node
attributes.
- *
* @return types of allowable attribute types.
*/
Set<Class<?>> getSupportedNodeAttributeTypes();
/**
* Tests to see if this layout supports doing a layout based on edge
attributes.
- *
* @return types of allowable attribute types.
*/
Set<Class<?>> getSupportedEdgeAttributeTypes();
@@ -94,7 +90,6 @@
* to allow the user to perform an unweighted layout. Note that this
value
* will be set using setLayoutAttribute() just like other attributes,
so the
* layout algorithm will need to check for it.
- *
* @return List of column names (i.e. attributes) used for
attribute-based layouts.
*/
List<String> getInitialAttributeList();
@@ -102,7 +97,6 @@
/**
* Returns the computer-readable name of the layout. To get
* a human readable name, use toString().
- *
* @return The computer-readable name of the layout.
*/
String getName();
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/LayoutPoint.java
===================================================================
---
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/LayoutPoint.java
2012-04-21 00:03:12 UTC (rev 28940)
+++
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/LayoutPoint.java
2012-04-21 00:07:45 UTC (rev 28941)
@@ -3,22 +3,34 @@
/**
* Simple immutable object which represents a point (x, y).
- *
*/
public final class LayoutPoint {
private final double x;
private final double y;
+ /**
+ * Constructor.
+ * @param x The X location of the point.
+ * @param y The Y location of the point.
+ */
public LayoutPoint(final double x, final double y) {
this.x = x;
this.y = y;
}
+ /**
+ * Returns the X location of the point.
+ * @return the X location of the point.
+ */
public double getX() {
return x;
}
+ /**
+ * Returns the Y location of the point.
+ * @return the Y location of the point.
+ */
public double getY() {
return y;
}
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/WeightTypes.java
===================================================================
---
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/WeightTypes.java
2012-04-21 00:03:12 UTC (rev 28940)
+++
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/WeightTypes.java
2012-04-21 00:07:45 UTC (rev 28941)
@@ -5,9 +5,13 @@
* @CyAPI.Enum.Class
*/
public enum WeightTypes {
+ /** Use a heuristic to guess. */
GUESS("Heuristic"),
+ /** Use the negative log value. */
LOG("-Log(value)"),
+ /** Use 1 minus the normalized value. */
DISTANCE("1 - normalized value"),
+ /** Use the normalized value. */
WEIGHT("normalized value");
private String name;
@@ -18,4 +22,4 @@
* @return the name of the weighting type.
*/
public String toString() { return name; }
-}
\ No newline at end of file
+}
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