@Test public void simpleTest() { String[] taxa = new String[]{"1", "2", "3", "4", "5", "6", "7"}; double[][] distances = new double[][]{ {0, 2, 5, 5, 5, 5, 3}, {2, 0, 5, 5, 5, 5, 3}, {5, 5, 0, 2, 4, 4, 4}, {5, 5, 2, 0, 4, 4, 4}, {5, 5, 4, 4, 0, 2, 4}, {5, 5, 4, 4, 2, 0, 4}, {3, 3, 4, 4, 4, 4, 0} }; DistanceMatrix distanceMatrix = new FlexibleDistanceMatrix(new IdentifierList(taxa), distances); IdentifierList circularOrdering = new IdentifierList(new int[]{7, 2, 1, 3, 4, 5, 6}); NetMEResult result = new NetME().execute(distanceMatrix, circularOrdering); }
public NetMEResult execute(DistanceMatrix distanceMatrix, IdentifierList circularOrdering) { return new MinimumEvolutionCalculator().calcMinEvoTree(distanceMatrix, circularOrdering); }
NetME extends RunnableTool { public NetMEResult execute(DistanceMatrix distanceMatrix, IdentifierList circularOrdering) { return new MinimumEvolutionCalculator().calcMinEvoTree(distanceMatrix, circularOrdering); } }
NetME extends RunnableTool { public NetMEResult execute(DistanceMatrix distanceMatrix, IdentifierList circularOrdering) { return new MinimumEvolutionCalculator().calcMinEvoTree(distanceMatrix, circularOrdering); } NetME();  NetME(NetMEOptions options);  NetME(NetMEOptions options, StatusTracker statusTracker); }
NetME extends RunnableTool { public NetMEResult execute(DistanceMatrix distanceMatrix, IdentifierList circularOrdering) { return new MinimumEvolutionCalculator().calcMinEvoTree(distanceMatrix, circularOrdering); } NetME();  NetME(NetMEOptions options);  NetME(NetMEOptions options, StatusTracker statusTracker); NetMEOptions getOptions(); void setOptions(NetMEOptions options); NetMEResult execute(DistanceMatrix distanceMatrix, IdentifierList circularOrdering); @Override void run(); }
NetME extends RunnableTool { public NetMEResult execute(DistanceMatrix distanceMatrix, IdentifierList circularOrdering) { return new MinimumEvolutionCalculator().calcMinEvoTree(distanceMatrix, circularOrdering); } NetME();  NetME(NetMEOptions options);  NetME(NetMEOptions options, StatusTracker statusTracker); NetMEOptions getOptions(); void setOptions(NetMEOptions options); NetMEResult execute(DistanceMatrix distanceMatrix, IdentifierList circularOrdering); @Override void run();  }