#36 improved performance; starting to implement 'Algorithm' class

though the version that's using the Algorithm object doesn't work, yet

src/main/java/org/fujaba/graphengine/PatternEngine.java

@@ -9,6 +9,8 @@
 
 import javax.naming.spi.DirStateFactory.Result;
 
+import org.fujaba.graphengine.algorithm.Algorithm;
+import org.fujaba.graphengine.algorithm.Application;
 import org.fujaba.graphengine.graph.Graph;
 import org.fujaba.graphengine.graph.Node;
 import org.fujaba.graphengine.isomorphismtools.IsomorphismHandlerCSPLowHeuristics;

src/main/java/org/fujaba/graphengine/algorithm/Algorithm.java

@@ -0,0 +1,104 @@
+package org.fujaba.graphengine.algorithm;
+
+import java.util.ArrayList;
+
+import org.fujaba.graphengine.Match;
+import org.fujaba.graphengine.PatternEngine;
+import org.fujaba.graphengine.graph.Graph;
+import org.fujaba.graphengine.pattern.PatternGraph;
+
+public class Algorithm {
+
+	private String name;
+	private ArrayList<Algorithm> algorithmSteps;
+	private PatternGraph atomicAlgorithm;
+	private boolean repeating;
+
+	public Algorithm(String name) {
+		this.name = name;
+		this.algorithmSteps = new ArrayList<Algorithm>();
+		this.atomicAlgorithm = null;
+		this.repeating = true;
+	}
+
+	public Application process(Graph input) {
+		Graph output = input;
+		if (atomicAlgorithm != null) {
+			while (true) {
+				ArrayList<Match> matches = PatternEngine.matchPattern(output, atomicAlgorithm, true);
+				if (matches.size() > 0) {
+					output = PatternEngine.applyMatch(matches.get(0));
+//					System.err.println("\n" + atomicAlgorithm.getName());
+//					System.err.println(output);
+					if (!repeating) {
+						break;
+					}
+				} else {
+					break;
+				}
+			}
+		} else {
+			for (Algorithm algo: algorithmSteps) {
+				while (true) {
+					Graph subAlgorithmInput = output;
+					Application subAlgorithmApplication = algo.process(subAlgorithmInput);
+					if (subAlgorithmInput != subAlgorithmApplication.getOutput()) {
+						output = subAlgorithmApplication.getOutput();
+						System.err.println("\n" + subAlgorithmApplication.getAlgorithm().getName());
+						System.err.println(output);
+						if (!repeating) {
+							break;
+						}
+					} else {
+						break;
+					}
+				}
+			}
+		}
+		return new Application(this, input, output);
+	}
+
+	public String getName() {
+		return name;
+	}
+	public Algorithm setName(String name) {
+		this.name = name;
+		return this;
+	}
+	public ArrayList<Algorithm> getAlgorithmSteps() {
+		return algorithmSteps;
+	}
+	public Algorithm setAlgorithmSteps(ArrayList<Algorithm> algorithmSteps) {
+		this.algorithmSteps = algorithmSteps;
+		return this;
+	}
+	public Algorithm addAlgorithmStep(Algorithm step) {
+		this.algorithmSteps.add(step);
+		return this;
+	}
+	public Algorithm addAlgorithmStep(PatternGraph step) {
+		return addAlgorithmStep(step, true);
+	}
+	public Algorithm addAlgorithmStep(PatternGraph step, boolean repeating) {
+		Algorithm newStep = new Algorithm(step.getName());
+		newStep.setAtomicAlgorithm(step);
+		newStep.setRepeating(repeating);
+		this.algorithmSteps.add(newStep);
+		return this;
+	}
+	public PatternGraph getAtomicAlgorithm() {
+		return atomicAlgorithm;
+	}
+	public Algorithm setAtomicAlgorithm(PatternGraph atomicAlgorithm) {
+		this.atomicAlgorithm = atomicAlgorithm;
+		return this;
+	}
+	public boolean isRepeating() {
+		return repeating;
+	}
+	public Algorithm setRepeating(boolean repeat) {
+		this.repeating = repeat;
+		return this;
+	}
+
+}

src/main/java/org/fujaba/graphengine/algorithm/Application.java

@@ -0,0 +1,39 @@
+package org.fujaba.graphengine.algorithm;
+
+import org.fujaba.graphengine.graph.Graph;
+
+public class Application {
+
+	private Algorithm algorithm;
+	private Graph input;
+	private Graph output;
+
+	public Application(Algorithm algorithm, Graph input, Graph output) {
+		this.algorithm = algorithm;
+		this.input = input;
+		this.output = output;
+	}
+
+	public Algorithm getAlgorithm() {
+		return algorithm;
+	}
+	public Application setAlgorithm(Algorithm algorithm) {
+		this.algorithm = algorithm;
+		return this;
+	}
+	public Graph getInput() {
+		return input;
+	}
+	public Application setInput(Graph input) {
+		this.input = input;
+		return this;
+	}
+	public Graph getOutput() {
+		return output;
+	}
+	public Application setOutput(Graph output) {
+		this.output = output;
+		return this;
+	}
+
+}