/usr/include/clustalo/clustal/hhalign_wrapper.h is in libclustalo-dev 1.2.1-1.
This file is owned by root:root, with mode 0o644.
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* 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_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);
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