#include "phycas/phycas.h"
#if defined(ALL_BIND_USING_CPPS_IN_ONE_FILE)
#	define INCLUDED_FROM_OTHER_BIND_USING_FILE
#	if defined(_MSC_VER)
//#warning not allowed in VC7
#		include "ncl/characters/nxs_characters_block.cpp"
#		include "ncl/command/nxs_command_output.cpp"
#	else
#		warning using macro to include nxs_charcters_block.cpp TEMPORARY HACK!
#		include "ncl/characters/nxs_characters_block.cpp"
#		warning using macro to include nxs_command_output.cpp TEMPORARY HACK!
#		include "ncl/command/nxs_command_output.cpp"
#	endif
#endif


#include "phycas/modules/scm/scm.hpp"
#include "cipres_services/tree_merge/tree_merge_i.hpp"
#if ! defined(NDEBUG)
#	include <iostream>
	using std::cout;
	using std::endl;
#endif
using std::string;


::CipresIDL_api1::Tree * CipresIDL_api1_TreeMerge_i::mergeTrees (const CipresIDL_api1::TreeSeq & trees)
  ACE_THROW_SPEC ((CORBA::SystemException))
	{
	typedef std::set<CORBA::Long> SetCorbaLong;
	SetCorbaLong indices;
	VecString strVec;
	const UInt nTrees = trees.length();
	strVec.reserve(nTrees);
	for (UInt i = 0; i < nTrees; ++i)
		{
		const CipresIDL_api1::Tree & treeI = trees[i];
		string tree_i(treeI.m_newick.in());
		strVec.push_back(tree_i); //shouldn't need to copy strings here
		const UInt nLeaves =  treeI.m_leafSet.length();
		for (UInt j = 0; j < nLeaves; ++j)
			indices.insert(treeI.m_leafSet[j]);
#		if ! defined(NDEBUG)
			cout << "Tree " << i << ' '<<  tree_i << endl;
#		endif
		}
	
	const std::string & s = NewickSCM(strVec);
	
	CipresIDL_api1::Tree_var t = new CipresIDL_api1::Tree;
	t->m_newick = CORBA::string_dup(s.c_str());
	t->m_name = CORBA::string_dup("MergedTree");
	t->m_score.noScore(0.0);
	t->m_leafSet.length(indices.size());
	SetCorbaLong::const_iterator indIt = indices.begin();
	for (UInt k = 0; indIt != indices.end(); ++k, ++indIt)
		t->m_leafSet[k] = *indIt;
	return t._retn();
	}

char * CipresIDL_api1_TreeMerge_i::getUIXml()
  ACE_THROW_SPEC ((CORBA::SystemException))
	{
	return CORBA::string_dup("");
	}

CORBA::Boolean CipresIDL_api1_TreeMerge_i::execute (const char * command, CORBA::String_out display)
  ACE_THROW_SPEC ((CORBA::SystemException))
	{
	return CORBA::Boolean(true);
	}

// -*- C++ -*-
//
// $Id: tree_merge_i.cpp,v 1.2 2005/06/22 20:31:30 mholder Exp $

// ****  Code generated by the The ACE ORB (TAO) IDL Compiler ****
// TAO and the TAO IDL Compiler have been developed by:
//       Center for Distributed Object Computing
//       Washington University
//       St. Louis, MO
//       USA
//       http://www.cs.wustl.edu/~schmidt/doc-center.html
// and
//       Distributed Object Computing Laboratory
//       University of California at Irvine
//       Irvine, CA
//       USA
//       http://doc.ece.uci.edu/
// and
//       Institute for Software Integrated Systems
//       Vanderbilt University
//       Nashville, TN
//       USA
//       http://www.isis.vanderbilt.edu/
//
// Information about TAO is available at:
//     http://www.cs.wustl.edu/~schmidt/TAO.html