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

void usage(const char *cmd)
{
	cerr << "Usage: " << 
		cmd << " [-CipresIOR <filename>]|[-CipresImpl <servicename>] [<-ORBxxx>]" << endl;
	cerr << "or " << cmd << " -ns <servicename> [<-ORBxxx>]" << endl;
	cerr << "servicename must be 'TreeImprove'" << endl;
}


/*
	If first arg is "-ns" uses naming service.  
		Next arg is the name of the object we want (eg. "TreeImprove")
		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[])
{
	CipresFacilitator * facilitator = NULL;
	try
	{
		facilitator = CipresFacilitator::getSingletonPtr();
		facilitator->initialize(argc, argv);

		CORBA::Object_var object;
		if (facilitator->lookupWithNameService() && facilitator->getImplName())
		{
			CipresNameService &ns = facilitator->getCipresNameService();
			object = ns.nsFind(facilitator->getImplName());
		} else if (facilitator->getIORFile())
		{
			object = facilitator->getObjectFromFile(facilitator->getIORFile());
		} else
		{
			usage(argv[0]);
			throw 0;
		}
		if (CORBA::is_nil(object.in()))
		{
			cerr << "Nil object ref" << endl;
			throw 0;
		}
		CipresIDL_api1::TreeImprove_var ti_var = CipresIDL_api1::TreeImprove::_narrow(object.in());
		if (CORBA::is_nil(ti_var.in()))
		{
			cerr << "Object ref is not of type TreeImprove" << endl;
			throw 0;
		}

#ifdef NOTDEF
		CipresIDL_api1::TaxonSeq taxonSeq;
		taxonSeq.length(4);
		taxonSeq[0] = CORBA::string_dup("fish");
		taxonSeq[1] = CORBA::string_dup("cat");
		taxonSeq[2] = CORBA::string_dup("dog");
		taxonSeq[3] = CORBA::string_dup("rabbit");
		cout << "calling setTaxa: " << taxonSeq << endl;
		ti_var->setTaxa(taxonSeq);
#endif

		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;
		ti_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;
		ti_var->setTree(tree);

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

		cout << "Calling remove() on the object ref.  Paup should exit." << endl;
		ti_var->remove();
	}
	catch(CORBA::Exception &ex)
	{
		cerr << "CORBA Exception raised: " << ex << endl;
	}
	catch (int)
	{
	}
	if (facilitator != NULL)
		facilitator->cleanup();
	return 0;
}