JWS-112 Bumping version of ClustalO (src, binaries and windows) to version 1.2.4.

[jabaws.git] / binaries / src / clustalo / src / clustal / hhalign_wrapper.h

diff --git a/binaries/src/clustalo/src/clustal/hhalign_wrapper.h b/binaries/src/clustalo/src/clustal/hhalign_wrapper.h
index 385a7ec..0d88e5b 100644 (file)
--- a/binaries/src/clustalo/src/clustal/hhalign_wrapper.h
+++ b/binaries/src/clustalo/src/clustal/hhalign_wrapper.h
@@ -13,12 +13,22 @@
  ********************************************************************/
 
 /*
- *  RCS $Id: hhalign_wrapper.h 241 2011-05-04 14:37:17Z fabian $
+ *  RCS $Id: hhalign_wrapper.h 289 2013-09-17 10:09:37Z fabian $
  */
 
+extern void
+SetDefaultHhalignPara(hhalign_para *prHhalignPara);
+
+extern int
+PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
+
+extern double 
+PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
 
 extern double
 HHalignWrapper(mseq_t *mseq, int *piOrderLR,
                double *pdSeqWeights, int iNodeCount,
                hmm_light *prHMMList, int iHMMCount,
                int iProfProfSeparator, hhalign_para rHhalignPara);
+void
+SanitiseUnknown(mseq_t *mseq);