GmlFormat.java

package nl.helixsoft.graph;

import java.io.OutputStream;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Map;

import nl.helixsoft.util.AttributesTable;

import org.apache.commons.collections15.BidiMap;

import edu.uci.ics.jung.algorithms.util.Indexer;
import edu.uci.ics.jung.graph.DirectedGraph;

/**
 * Note that the node attribute "label" will be used as the node identifier during GML import in Cytoscape.
 * The Node id itself will be converted to an integer.
 * The formatter will warn if you try to supply label as an attribute. 
 */
public final class GmlFormat 
{
	/** tool class should never be instantiated */
	private GmlFormat() {}
	
	/** same as other writeGml, but sorts nodes and edges, for stable output. */
	public static <V, E> void writeGml(OutputStream fos, final DirectedGraph<V, E> graph, AttributesTable<V> nodeAttr, AttributesTable<E> edgeAttr, Comparator<V> comp)
	{
		List<V> sortedV = new ArrayList<V>(graph.getVertices());
		Collections.sort (sortedV, comp);

		// GML uses integers as node ids, so start by creating integer inex.
		final BidiMap<V, Integer> idx = Indexer.create(sortedV);
		
		GmlEmitter gml = new GmlEmitter(fos);
		gml.startList("graph");

		writeNodes (nodeAttr, idx, gml, sortedV);

		List<E> sortedE = new ArrayList<E>(graph.getEdges());
		Collections.sort (sortedE, new Comparator<E>() {
			
				@Override	
				public int compare (E e1, E e2)
				{
					int i1 = idx.get(graph.getSource(e1));
					int i2 = idx.get(graph.getSource(e2));
					
					if (i1 < i2) return -1;
					if (i1 > i2) return 1;
					
					int j1 = idx.get(graph.getDest(e1));
					int j2 = idx.get(graph.getDest(e2));
					
					if (j1 < j2) return -1;
					if (j1 > j2) return 1;
					return 0;
				}
			}
		);
		
		writeEdges(graph, edgeAttr, idx, gml, sortedE);

		gml.closeList();
		gml.close();
	}

	private static <V, E> void writeEdges(final DirectedGraph<V, E> graph,
			AttributesTable<E> edgeAttr, final BidiMap<V, Integer> idx,
			GmlEmitter gml, Collection<E> edges) 
	{
		for (E e : edges)
		{
			V s = graph.getSource(e);
			V t = graph.getDest(e);
			gml.startList("edge");
			gml.intLiteral("source", idx.get(s));
			gml.intLiteral("target", idx.get(t));
			
			gml.stringLiteral ("interaction", e.toString());
			
			for (Map.Entry<String, Object> entry : edgeAttr.getAttributes(e))
			{
				if ("interaction".equals (entry.getKey()))
				{
					System.err.println ("WARNING, ignoring reserved attribute " + entry.getKey() + " from attribute table");
					continue;
				}
				
				Object val = entry.getValue();
				if (val instanceof Number)
				{
					gml.numberLiteral(entry.getKey(), (Number)val);
				}
				else
				{
					gml.stringLiteral(entry.getKey(), "" + val);
				}
			}
			gml.closeList();
		}
	}
	
	public static <V, E> void writeGml(OutputStream fos, DirectedGraph<V, E> graph, AttributesTable<V> nodeAttr, AttributesTable<E> edgeAttr)
	{
		// GML uses integers as node ids, so start by creating integer inex.
		final BidiMap<V, Integer> idx = Indexer.create(graph.getVertices());
		
		GmlEmitter gml = new GmlEmitter(fos);
		gml.startList("graph");

		writeNodes(nodeAttr, idx, gml, graph.getVertices());
		writeEdges(graph, edgeAttr, idx, gml, graph.getEdges());
		gml.closeList();
		gml.close();
	}

	private static <V> void writeNodes(AttributesTable<V> nodeAttr,
			final BidiMap<V, Integer> idx, GmlEmitter gml, Collection<V> nodes) 
	{
		for (V v : nodes)
		{
			gml.startList("node");
			gml.intLiteral("id", idx.get(v));
			
			// label will be used as ID during import in Cytoscape.  
			gml.stringLiteral ("label", v.toString());
			
			for (Map.Entry<String, Object> entry : nodeAttr.getAttributes(v))
			{
				if ("label".equals(entry.getKey()) || "id".equals (entry.getKey()))
				{
					System.err.println ("WARNING, ignoring reserved attribute " + entry.getKey() + " from attribute table");
					continue;
				}
				
				Object val = entry.getValue();
				if (val instanceof Number)
				{
					gml.numberLiteral(entry.getKey(), (Number)val);
				}
				else
				{
					gml.stringLiteral(entry.getKey(), "" + val);
				}
			}
			gml.closeList();
		}
	};
}