/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
 
 /*********************************************************************
  * Clustal Omega - Multiple sequence alignment
  *
  * Copyright (C) 2010 University College Dublin
  *
  * Clustal-Omega is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License as
  * published by the Free Software Foundation; either version 2 of the
  * License, or (at your option) any later version.
  *
  * This file is part of Clustal-Omega.
  *
  ********************************************************************/
 
 /*
  * RCS $Id: hhalign.h 284 2013-06-12 10:10:11Z fabian $
  */
 
 
 extern int 
 hhalign(char **ppcFirstProf, int iFirstCnt, double *pdWeightsL, 
         char **ppcSecndProf, int iSecndCnt, double *pdWeightsR, 
         double *dScore_p, hmm_light *prHMM, 
         char *pcPrealigned1, char *pcRepresent1,
         char *pcPrealigned2, char *pcRepresent2,
         hhalign_para rHhalignPara, hhalign_scores *rHHscores, 
         int iFlag, int iVerbosity,
         char zcAux[], char zcError[]);