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

module CipresIDL_api1
{
	interface Advisor: Scriptable, LifeCycle 
	{
	  /*
	    should be able to input and output raw sequences
	  */
		void setUnalignedDataMatrix (in DataMatrix matrix)
		  raises (BadArgException);
	  /* 
	     don't really want to expose aligned test matrix really
	     let user refer to MatrixAlign module for that
	     MTH to Kevin: should this getUnalignedDataMatrix be deprecated?
	  */

		DataMatrix getUnalignedDataMatrix ();

	  /* only other interesting operation is suggestion step
	     produces a string of recommended parameter settings
	  */
	  string getSuggestions();

	  /*
	    later need to export each DCM parameter suggestion out 
	    individually (or as package) since this module needs to
	    interface with CIPRES main Rec-i-DCM3 module - it will just
	    suggest default settings for the Rec-i-DCM3 analysis based
	    on raw sequence inputs

	    create a new datatype for this - package a set of suggestions for a set of parameters
	  */


	  
	};
};