ExtensionSpacesDistance/TestWholeCode.java at main · MariaAVC/ExtensionSpacesDistance · GitHub

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import java.util.*;
import distanceAlg1.*;
import BHVExtMinDistance.*;

import static polyAlg.PolyMain.getGeodesic;

public class TestWholeCode{
    private static PhyloTree StartingTree;
    private static PhyloTree EndingTree;
    private static Vector<String> completeLeafSet;

    public static void main(String[] args){
        PhyloNicePrinter nicePrint = new PhyloNicePrinter();
        StartingTree = new PhyloTree("(L7:7.8,(L1:4.3,L6:4.8):5,(L2:5.2,(L3:5,(L4:4.3,L5:5.3):7.2):4.9):0)",false);
        EndingTree = new PhyloTree("(L7:7.8,L1:3.9,(L4:4.3,(L3:5,(L6:7.1,(L2:4.4,L5:5.3):0):3.55):3.55):0)",false);

        System.out.println("Starting Tree: "+ nicePrint.toString(StartingTree));

        System.out.println("\n Ending Tree: "+ nicePrint.toString(EndingTree));

        Geodesic tempGeode = getGeodesic(StartingTree, EndingTree, null);

        Geodesic tempGeode2 = parPolyMain.getGeodesic(StartingTree, EndingTree);

        System.out.println("Classic Geodesic: "+ nicePrint.toString(tempGeode, StartingTree.getLeaf2NumMap()));

        System.out.println("My Geodesic: "+ nicePrint.toString(tempGeode2, StartingTree.getLeaf2NumMap()));


        //StartingTree = new PhyloTree("(A:2,E:9,((D:14,(H:8,G:10):31):5,(F:11,C:14):15):21)",false);
        /*StartingTree = new PhyloTree("(A:1,B:1,(E:1,(C:1,D:1):3):5)",false);

        System.out.println("Starting Tree: "+ nicePrint.toString(StartingTree));

        //EndingTree = new PhyloTree("(A:5,B:3,(G:15,((D:10,F:20):24,(E:10,(H:14,I:12):26):30):16):12)",false);
        EndingTree = new PhyloTree("(A:2,D:2,((E:2,F:1):3,(B:2,C:2):4):4)",false);

        System.out.println("Ending Tree: "+ nicePrint.toString(EndingTree));

        completeLeafSet = new Vector<String>();
        completeLeafSet.add("A");
        completeLeafSet.add("B");
        completeLeafSet.add("C");
        completeLeafSet.add("D");
        completeLeafSet.add("E");
        completeLeafSet.add("F");
        //completeLeafSet.add("G");
        //completeLeafSet.add("H");
        //completeLeafSet.add("I");

        ExtensionSpace startES = new ExtensionSpace(StartingTree, completeLeafSet);

        ExtensionSpace endES = new ExtensionSpace(EndingTree, completeLeafSet);

        endES.PrintSummary(true);
        System.out.println("\n \n");

        ExtensionSpaceDistance testDistance = new ExtensionSpaceDistance(startES, endES);


        System.out.println("");
        System.out.println("");
        System.out.println("Orthants in the Starting Extension Space: ");
        startES.PrintOrthants();
        System.out.println("");
        System.out.println("");
        System.out.println("Orthants in the Ending Extension Space: ");
        endES.PrintOrthants();
        System.out.println("");
        System.out.println("");

        if (args.length>0){
            testDistance.PrintSummary(false, args[0]);
        } else{
            System.out.println("And the distances are: ");
            testDistance.PrintSummary(true);
        }

        Map<Integer, List<Integer>> TestJointNNImap = testDistance.JointNNI(startES, endES);

        System.out.println("The joint NNI map: ");

        for (int i = 0; i < TestJointNNImap.size(); i++){
            System.out.println("   "+i+": "+TestJointNNImap.get(i));
        }*/
    }
}