#include "TreeRefineC.h"
#include "CipresHelper.h"
#include "CipresRegistry.h"
#include "orbsvcs/CosNamingC.h"
#include <iostream>
#include <fstream>
using namespace std;


/*
	If first arg is "-ns" uses naming service.  
		Next arg is the name of the object we want (eg. "TreeRefine")
		Subsequent args identify the Naming Service: 
			eg. -ORBInitRef NameService=corbaloc:iiop:10.0.1.5:1050/NameService  
	Otherwise first arg is an ior file name.
*/
int main(int argc, char *argv[])
{
	try
	{
		CORBA::ORB_var orb = CORBA::ORB_init(argc, argv, "orb1");

		if (argc < 2)
		{
			cerr << "usage: " << argv[0] << " iorFileName" << endl;
			return 1;
		}

		CORBA::Object_var object;
		if (strcmp(argv[1], "-ns") == 0)
		{
			// todo: check for right number of arguments before accessing argv
			CipresRegistry registry(orb.in());
			object = registry.nsFind(argv[2]);
		} else
		{
			fstream f(argv[1], ios::in);
			CORBA::String_var iorstring;
			f >> iorstring;
			cout << "ior is: " << iorstring << endl;
			object = orb->string_to_object(iorstring);
		}
		if (CORBA::is_nil(object.in()))
		{
			cerr << "Nil object ref" << endl;
			throw 0;
		}
		CipresIDL_api1::TreeRefine_var tr_var = CipresIDL_api1::TreeRefine::_narrow(object.in());
		if (CORBA::is_nil(tr_var.in()))
		{
			cerr << "Object ref is not of type TreeImprove" << endl;
			throw 0;
		}

		CipresIDL_api1::DataMatrix chars;
		chars.m_symbols= "ACGT";
		chars.m_numStates = 4;
		chars.m_stride = 1;
		chars.m_numCharacters = 4;

		chars.m_matrix.length(4);
		chars.m_matrix[0].length(3);
		chars.m_matrix[0][0] = 1;
		chars.m_matrix[0][1] = 2; 
		chars.m_matrix[0][2] = 3;

		chars.m_matrix[1].length(3);
		chars.m_matrix[1][0] = 3;
		chars.m_matrix[1][1] = 2;
		chars.m_matrix[1][2] = 1;

		chars.m_matrix[2].length(3);
		chars.m_matrix[2][0] = 3;
		chars.m_matrix[2][1] = 3;
		chars.m_matrix[2][2] = 3;

		chars.m_matrix[3].length(3);
		chars.m_matrix[3][0] = 3;
		chars.m_matrix[3][1] = 3;
		chars.m_matrix[3][2] = 1;

		cout << "setting matrix:" << endl;
		cout << chars << endl;

		cout << "calling setMatrix" << endl;
		tr_var->setMatrix(chars);

		CipresIDL_api1::Tree tree;
		tree.m_score = 0;

		// paup requires a semicolon at the end of the newick string
		tree.m_newick = CORBA::string_dup("((1,2,3),4);");
		tree.m_leafSet.length(4);
		for (int i = 0; i < 4; i++)
		{
			tree.m_leafSet[i] = i + 1;
		}

		cout << "calling setTree: " << tree.m_newick << endl;
		tr_var->setTree(tree);

		cout << "calling refineTree" << endl;
		CipresIDL_api1::Tree_var resultTree  = tr_var->refineTree();
		cout << "got tree: " << resultTree->m_newick << endl;


		orb->destroy();
	}
	catch(CORBA::Exception &ex)
	{
		cerr << "CORBA Exception raised: " << ex << endl;
		return 1;
	}
	return 0;
}