#include "api1/Cipres.idl"
#include <CosEventChannelAdmin.idl>

module CipresIDL_api1
{
	/*
		Todo: add method for adding new sequences to an alignment. 
		Todo: add an observer to getAlignedMatrix().

		Usage: 
			- first call Scriptable.execute() if you need to "configure" the service
			- then call setTaxa &  setInputMatrix
			- optionally, call setGuideTree
			- call getAlignedMatrix() to do the alignment
			- after getAlignedMatrix() returns you can call getScore and getGuideTree().
	*/
	interface MatrixAlign: Scriptable, LifeCycle 
	{
		void setTaxa(in TaxonInfoSeq taxa) raises(BadArgException, ApplicationException);
		void setInputMatrix(in DataMatrix characters) raises(BadArgException, ApplicationException);	
		void setGuideTree(in Tree guideTree) raises(BadArgException, ApplicationException);

		//TaxonInfoSeq getTaxa() raises(ApplicationException);
		DataMatrix getAlignedMatrix() raises(ApplicationException);
		Tree getGuideTree() raises(ApplicationException);
		double getScore() raises(ApplicationException);
	};
};