Author: mes
Date: 2011-04-29 15:43:55 -0700 (Fri, 29 Apr 2011)
New Revision: 24862
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
Log:
initial layout api cleanup
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -85,7 +85,7 @@
* Creates a new GroupAttributesLayout object.
*/
public GroupAttributesLayout(UndoSupport undoSupport, CyTableManager
tableMgr) {
- super(undoSupport);
+ super(undoSupport, "attributes-layout", "Group Attributes
Layout");
this.tableMgr = tableMgr;
}
@@ -98,22 +98,4 @@
public boolean tunablesAreValid(final Appendable errMsg) {
return true;
}
-
-
- /**
- * Overrides for CyLayoutAlgorithm support
- */
- public String getName() {
- return "attributes-layout";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- return "Group Attributes Layout";
- }
-
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -68,29 +68,11 @@
* @param nodes DOCUMENT ME!
*/
public StackedNodeLayout(UndoSupport undoSupport) {
- super(undoSupport);
+ super(undoSupport, "stacked-node-layout", "Stacked Node
Layout");
}
public TaskIterator getTaskIterator() {
return new TaskIterator(new StackedNodeLayoutTask(networkView,
getName(), selectedOnly, staticNodes,
x_position, y_start_position));
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName() {
- return "Stacked Node Layout";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- return getName();
- }
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -115,14 +115,14 @@
@Tunable(description="Don't partition graph before layout",
groups="Standard settings")
public boolean singlePartition;
- boolean supportWeights = true;
+ final boolean supportWeights;
/**
* This is the constructor for the bioLayout algorithm.
*/
public BioLayoutFRAlgorithm(UndoSupport undoSupport, boolean
supportEdgeWeights) {
- super(undoSupport);
+ super(undoSupport, "fruchterman-rheingold", (supportEdgeWeights
? "Edge-weighted Force directed (BioLayout)" : "Force directed (BioLayout)"));
supportWeights = supportEdgeWeights;
@@ -141,31 +141,4 @@
public boolean tunablesAreValid(final Appendable errMsg) {
return true;
}
-
- /**
- * Return the "name" of this algorithm. This is meant
- * to be used by programs for deciding which algorithm to
- * use. toString() should be used for the human-readable
- * name.
- *
- * @return the algorithm name
- */
- public String getName() {
- return "fruchterman-rheingold";
- }
-
- /**
- * Return the "title" of this algorithm. This is meant
- * to be used for titles and labels that represent this
- * algorithm.
- *
- * @return the human-readable algorithm name
- */
- public String toString() {
- if (supportWeights)
- return "Edge-weighted Force directed (BioLayout)";
- else
-
- return "Force directed (BioLayout)";
- }
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -75,13 +75,14 @@
public double m_disconnectedNodeDistanceSpringRestLength=2000.0;
@Tunable(description="Strength to apply to avoid collisions",
groups="Algorithm settings")
public double m_anticollisionSpringStrength;
- @Tunable(description="Don't partition graph before layout",
groups="Standard settings")
+ @Tunable(description="Don't partition graph before layout",
groups="Standard settings")
public boolean singlePartition;
- private boolean supportWeights = true;
+ private final boolean supportWeights;
public BioLayoutKKAlgorithm(UndoSupport un, boolean supportEdgeWeights)
{
- super(un);
+ super(un, (supportEdgeWeights ? "kamada-kawai" :
"kamada-kawai-noweight"),
+ (supportEdgeWeights ? "Edge-weighted Spring
Embedded" : "Spring Embedded") );
supportWeights = supportEdgeWeights;
}
@@ -100,28 +101,4 @@
public boolean tunablesAreValid(final Appendable errMsg) {
return true;
}
-
- /**
- * Overrides for LayoutAlgorithm support
- */
- public String getName() {
- if (supportWeights)
- return "kamada-kawai-noweight";
- else
-
- return "kamada-kawai";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- if (supportWeights)
- return "Edge-weighted Spring Embedded";
- else
-
- return "Spring Embedded";
- }
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -31,12 +31,11 @@
* Creates a new Layout object.
*/
public CircularLayoutAlgorithm(UndoSupport un) {
- super(un);
+ super(un, "circular", "Circular Layout");
}
//TODO how to validate these values?
public boolean tunablesAreValid(final Appendable errMsg) {
-
return true;
}
@@ -56,25 +55,4 @@
public boolean supportsSelectedOnly() {
return false;
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName() {
- return "circular";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- return "Circular Layout";
- }
-
-
-
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -67,7 +67,8 @@
*/
public AttributeCircleLayout(final UndoSupport undoSupport, final
boolean supportNodeAttributes)
{
- super(undoSupport);
+ super(undoSupport, (supportNodeAttributes ? "attribute-circle":
"circle"),
+ (supportNodeAttributes ? "Attribute Circle
Layout" : "Circle Layout") );
this.supportNodeAttributes = supportNodeAttributes;
}
@@ -75,8 +76,7 @@
* Creates a new AttributeCircleLayout object.
*/
public AttributeCircleLayout(final UndoSupport undoSupport) {
- super(undoSupport);
- this.supportNodeAttributes = true;
+ this(undoSupport,true);
}
@Override
@@ -137,31 +137,4 @@
return attList;
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- if (!supportNodeAttributes) {
- return "Circle Layout";
- } else {
- return "Attribute Circle Layout";
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName() {
- if (!supportNodeAttributes)
- return "circle";
- else
-
- return "attribute-circle";
- }
-
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -23,14 +23,15 @@
public class DegreeSortedCircleLayout extends AbstractLayout implements
TunableValidator {
private static final String DEGREE_ATTR_NAME = "degree";
private CyTableManager tableMgr;
- @Tunable(description="Don't partition graph before layout",
groups="Standard settings")
+
+ @Tunable(description="Don't partition graph before layout",
groups="Standard settings")
public boolean singlePartition;
/**
* Creates a new DegreeSortedCircleLayout object.
*/
public DegreeSortedCircleLayout(UndoSupport undoSupport, CyTableManager
tableMgr) {
- super(undoSupport);
+ super(undoSupport, "degree-circle", "Degree Sorted Circle
Layout");
this.tableMgr = tableMgr;
}
@@ -45,22 +46,4 @@
staticNodes,
DEGREE_ATTR_NAME,
tableMgr,
singlePartition));
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- return "Degree Sorted Circle Layout";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName() {
- return "degree-circle";
- }
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -39,7 +39,7 @@
* Creates a new ISOMLayout object.
*/
public ISOMLayout(UndoSupport undoSupport) {
- super(undoSupport);
+ super(undoSupport,"isom", "Inverted Self-Organizing Map
Layout");
}
// TODO
@@ -59,24 +59,6 @@
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- return "Inverted Self-Organizing Map Layout";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName() {
- return "isom";
- }
-
- /**
* We do support selected only
*
* @return true
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2011-04-29 22:43:31 UTC (rev 24861)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2011-04-29 22:43:55 UTC (rev 24862)
@@ -92,7 +92,7 @@
* Creates a new HierarchicalLayoutAlgorithm object.
*/
public HierarchicalLayoutAlgorithm(UndoSupport undoSupport) {
- super(undoSupport);
+ super(undoSupport, "hierarchical", "Hierarchical Layout");
}
// TODO
@@ -113,21 +113,4 @@
public boolean supportsSelectedOnly() {
return true;
}
-
- /**
- * Overrides for LayoutAlgorithm support
- */
- public String getName() {
- return "hierarchical";
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toString() {
- return "Hierarchical Layout";
- }
-
}
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