#include "TreeDecomposeC.h"
#include "CipresHelper.h"
#include "CipresRegistry.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. "TreeDecompose")
		Subsequent args identify the Naming Service: 
			eg. -ORBInitRef NameService=corbaloc:iiop:localhost: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");
		CORBA::Object_var object;

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

		CipresIDL_api1::TreeDecompose_var td_var = CipresIDL_api1::TreeDecompose::_narrow(object.in());
		if (CORBA::is_nil(td_var.in()))
		{
			cout << "Narrow to TreeDecompose type failed" << endl;
	 		return 1;
		}

		CipresIDL_api1::Tree tree;
		/*
		tree.m_newick = CORBA::string_dup(
			"((((a:.1,b:1):1,(t:3.2,g:1):2):1,(c:2,d:1):1):1,(((e:1,f:1):1,u:1):1,v:1.2,(x:0.2,y:1):1):1)");
		*/
		tree.m_newick = CORBA::string_dup(
			"((((2:.1,3:1):1,(1:3.2,10:1):2):1,(11:2,12:1):1):1,(((14:1,15:1):1,20:1):1,16:1.2,(30:0.2,31:1):1):1)");
		CipresIDL_api1::TaxonSeqSeq_var subsets = td_var->leafSetDecompose(tree);
		cout << "Decomposed tree: " << tree.m_newick.in() << endl;
		cout << "Into subsets: " << endl;
		cout << *subsets << endl;

		cout << "Sending bad tree - missing last ), expect an exception" << endl;
		try
		{
			tree.m_newick = CORBA::string_dup(
				"((((1:.1,2:1):1,(3:3.2,4:1):2):1,(5:2,6:1):1):1,(((7:1,8:1):1,9:1):1,10:1.2,(11:0.2,12:1):1):1");
			subsets = td_var->leafSetDecompose(tree);
			cout << "Decomposed tree: " << tree.m_newick.in() << endl;
			cout << "Into subsets: " << endl;
			cout << *subsets << endl;
		}
		catch(CipresIDL_api1::TreeParseException)
		{
			cout << "Caught TreeParseException" << endl;
		}

		cout << "Sending another good tree - a small one" << endl;
		tree.m_newick = CORBA::string_dup( "((((1:1,2:2):3.2,(3:5,4:1):7):3.6,(5:1.2,6):2):3.7,((7:5.5,8:3):2.2,9:4):10)");
		subsets = td_var->leafSetDecompose(tree);
		cout << "Decomposed tree: " << tree.m_newick.in() << endl;
		cout << "Into subsets: " << endl;
		cout << *subsets << endl;


#ifdef NOTDEF
		CORBA::Object_var object = orb->string_to_object(iorstring);
		CipresIDL_api1::TreeInfer_var ti_var = CipresIDL_api1::TreeInfer::_narrow(object.in());

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

		chars.m_matrix.length(2);
		chars.m_matrix[0].length(3);
		chars.m_matrix[0][0] = 0x01;
		chars.m_matrix[0][1] = 0x02; 
		chars.m_matrix[0][2] = 0xff;

		chars.m_matrix[1].length(3);
		chars.m_matrix[1][0] = 0x01;
		chars.m_matrix[1][1] = 0x03;
		chars.m_matrix[1][2] = 0x07;

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

		ti_var->setMatrix(chars);

#endif

		cout << "Shutting down dcm3" << endl;
		td_var->remove();
		orb->destroy();
	}
	catch(CORBA::Exception &ex)
	{
		cerr << "CORBA Exception raised: " << ex << endl;
		return 1;
	}
	return 0;
}