Week 6 with GSoC

The sixth week was mainly focused on improving the code structure as well as implementation of the LayoutContext for fCoSE layout algorithm in the plugin.

TODOs

• Generate a layout context for the fCoSE layout algorithm.
• Implement TunableValidator for the layout context.
• Get the parameters for the layout from the user using Tunable.
• Dynamically generate the layout request using the parameters from the user.

Experiments with code

• Implement TunableValidator for the layout context to validate the parameters for the layout.

package org.cytoscape.sample.internal;

import java.io.IOException;

import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;

public class CustomLayoutContext  implements TunableValidator {

	@Tunable(description="Randomize")
	public boolean randomize = true; // Default value
	@Tunable(description="Node Dimensions Include Labels")
	public boolean nodeDimensionsIncludeLabels= true;// Default value
	@Tunable(description="Uniform Node Dimensions")
	public boolean uniformNodeDimensions= false;// Default value
	@Tunable(description="Pack Components")
	public boolean packComponents= true;// Default value
	@Tunable(description="Tile")
	public boolean tile= true;// Default value

	@Tunable(description="Padding")
	public int padding= 30;// Default value
	@Tunable(description="Node Repulsion")
	public int nodeRepulsion= 4500;// Default value
	@Tunable(description="Ideal Edge Length")
	public int idealEdgeLength= 50;// Default value
	@Tunable(description="Edge Elasticity")
	public double edgeElasticity= 0.45;// Default value
	@Tunable(description="Nesting Factor")
	public double nestingFactor= 0.1;// Default value
	@Tunable(description="Number of Iterations")
	public int numIter= 2500;// Default value
	@Tunable(description="Tiling Padding Vertical")
	public int tilingPaddingVertical= 10;// Default value
	@Tunable(description="Tiling Padding Horizontal")
	public int tilingPaddingHorizontal= 10;// Default value
	@Tunable(description="Gravity")
	public double gravity= 0.25;// Default value
	@Tunable(description="Gravity Range")
	public double gravityRange= 3.8;// Default value
	@Tunable(description="Gravity Compound")
	public double gravityCompound= 1;// Default value
	@Tunable(description="Gravity Range Compound")
	public double gravityRangeCompound= 1.5;// Default value
	@Tunable(description="Initial Energy On Incremental")
	public double initialEnergyOnIncremental= 0.3;// Default value


	public ValidationState getValidationState(final Appendable errMsg) {
		return ValidationState.OK;
	}
}

Learnings

• The TunableValidator interface is used to validate the parameters for the layout.
• The Tunable annotation is used to get the parameters from the user.
• The LayoutContext is used to get and set the parameters for the layout from the user.
• The layout context along with the tunable parameters generate a GUI for the user to input the parameters in a user friendly way.

Milestones

Successful implementation of the layout context for the fCoSE layout algorithm in the plugin to get the user entered parameters.

JSONObject layoutOptions = new JSONObject();
layoutOptions.put("name", "fcose");
layoutOptions.put("randomize", myContext.randomize);
layoutOptions.put("padding", myContext.padding);
layoutOptions.put("nodeDimensionsIncludeLabels", myContext.nodeDimensionsIncludeLabels);
layoutOptions.put("uniformNodeDimensions", myContext.uniformNodeDimensions);
layoutOptions.put("packComponents", myContext.packComponents);
layoutOptions.put("nodeRepulsion", myContext.nodeRepulsion);
layoutOptions.put("idealEdgeLength", myContext.idealEdgeLength);
layoutOptions.put("edgeElasticity", myContext.edgeElasticity);
layoutOptions.put("nestingFactor", myContext.nestingFactor);
layoutOptions.put("numIter", myContext.numIter);
layoutOptions.put("tile", myContext.tile);
layoutOptions.put("tilingPaddingVertical", myContext.tilingPaddingVertical);
layoutOptions.put("tilingPaddingHorizontal", myContext.tilingPaddingHorizontal);
layoutOptions.put("gravity", myContext.gravity);
layoutOptions.put("gravityRange", myContext.gravityRange);
layoutOptions.put("gravityCompound", myContext.gravityCompound);
layoutOptions.put("gravityRangeCompound", myContext.gravityRangeCompound);
layoutOptions.put("initialEnergyOnIncremental", myContext.initialEnergyOnIncremental);