PWPublicMethods.java

package org.phylowidget;

import java.util.List;

import org.andrewberman.ui.unsorted.Json;
import org.phylowidget.tree.PhyloNode;
import org.phylowidget.ui.JavascriptAccessibleMethods;

import processing.core.ExtendedPApplet;
import processing.core.PApplet;

public abstract class PWPublicMethods extends ExtendedPApplet implements JavascriptAccessibleMethods
{

	private PhyloTree getTree_obj()
	{
		return (PhyloTree) PWPlatform.getInstance().getThisAppContext().trees().getTree();
	}
	
	private PhyloNode getCurNode()
	{
		return getTree_obj().getHoveredNode();
	}
	
	public double getHoveredBranchLength()
	{
		return getTree_obj().getBranchLength(getCurNode());
	}

	public double getHoveredDepthToRoot()
	{
		return getTree_obj().getDepthToRoot(getCurNode());
	}
	
	public double getHoveredDistanceToRoot()
	{
		return getTree_obj().getHeightToRoot(getCurNode());
	}
	
	public int getHoveredLeafCount()
	{
		return getTree_obj().getNumEnclosedLeaves(getCurNode());
	}
	
	public double getHoveredMaxTreeLength()
	{
		return getTree_obj().getMaxHeightToLeaf(getCurNode());
	}
	
	public String getHoveredNode()
	{
		PhyloNode n = getTree_obj().getHoveredNode();
		if (n != null)
		{
			return n.getTree().getLabel(n);
		} else
		{
			return "";
		}
	}

	public int getHoveredNodeCount()
	{
		return getTree_obj().getAllNodes(getCurNode()).size();
	}

	public int getLeafCount()
	{
		return getTree_obj().getNumEnclosedLeaves(getTree_obj().getRoot());
	}
	public String[] getLeafNames()
	{
		List<PhyloNode> leaves = getTree_obj().getAllLeaves();
		String[] leafNames = new String[leaves.size()];
		for (int i=0; i < leaves.size(); i++)
		{
			leafNames[i] = getTree_obj().getLabel(leaves.get(i));
		}
		return leafNames;
	}

	public double getMaxTreeLength()
	{
		return getTree_obj().getMaxTreeLength();
	}
	public int getNodeCount()
	{
		return getTree_obj().getNodeCount();
	}

	public double getTotalTreeLength()
	{
		return getTree_obj().getTotalTreeLength();
	}

	public String getTree()
	{
		return getTreeNHX();
	}

	
	public String getTreeNewick()
	{
		return getTree_obj().getNewick();
	}
	
	public String getTreeNHX()
	{
		return getTree_obj().getNHX();
	}
	
	public String getTreeString()
	{
		return getTreeNHX();
	}
	
	public String getTreeNeXML()
	{
		return getTree_obj().getNeXML();
	}
	
	public String getNodeInfoJSON()
	{
		return Json.hashToJson(getCurNode().getNodeInfo());
	}
	
	public abstract String getUrlParameters();
	
	public abstract String getClipboardString(); // This is implemented in PhyloWidget.java
	
	public abstract void setClipboard(String clip); // This is implemented in PhyloWidget.java
	
	public abstract void setMessage(String message); // This is implemented in PhyloWidget.java
	
	public abstract void setTree(String tree); // This is implemented in PhyloWidget.java
	
	public abstract void setAnnotation(String nodeLabel, String key, String value); // This is implemented in PhyloWidget.java
	
	public abstract void setAnnotations(String nodeLabel, String annotationJson); // This is implemented in PhyloWidget.java
	
	public abstract void transformTree(String url); // Defined in PhyloWidget.java. Requires the "full" version of PhyloWidget.
	
}