********************************************************************/
/*
- * RCS $Id: hhalign.h 241 2011-05-04 14:37:17Z fabian $
+ * RCS $Id: hhalign.h 296 2014-10-07 12:15:41Z fabian $
*/
extern int
hhalign(char **ppcFirstProf, int iFirstCnt, double *pdWeightsL,
char **ppcSecndProf, int iSecndCnt, double *pdWeightsR,
- double *dScore_p, hmm_light *prHMM,
+ double *dScore_p, hmm_light *prHMM, hmm_light *prHMM2,
char *pcPrealigned1, char *pcRepresent1,
char *pcPrealigned2, char *pcRepresent2,
- hhalign_para rHhalignPara,
- int iFlag,
+ hhalign_para rHhalignPara, hhalign_scores *rHHscores,
+ int iFlag, int iVerbosity,
char zcAux[], char zcError[]);