X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fclustalo%2Fsrc%2Fhhalign%2Fhhalign.h;h=1942ea5a841ddefc3785cdc9dda407485226276d;hb=1eab6cadc31107fabe7ef060de1ae91eeb4a025b;hp=34ac78e05c6d36350d6a42d3db9243a0f45a5ec9;hpb=b222b987978b6b2d4b6fb1b4a3a2a0ea87a19c3d;p=jabaws.git

diff --git a/binaries/src/clustalo/src/hhalign/hhalign.h b/binaries/src/clustalo/src/hhalign/hhalign.h
index 34ac78e..1942ea5 100644
--- a/binaries/src/clustalo/src/hhalign/hhalign.h
+++ b/binaries/src/clustalo/src/hhalign/hhalign.h
@@ -15,16 +15,16 @@
  ********************************************************************/
 
 /*
- * 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[]);