Clustal Omega  1.2.4
hhalign_wrapper.h
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1 /*********************************************************************
2  * Clustal Omega - Multiple sequence alignment
3  *
4  * Copyright (C) 2010 University College Dublin
5  *
6  * Clustal-Omega is free software; you can redistribute it and/or
7  * modify it under the terms of the GNU General Public License as
8  * published by the Free Software Foundation; either version 2 of the
9  * License, or (at your option) any later version.
10  *
11  * This file is part of Clustal-Omega.
12  *
13  ********************************************************************/
14 
15 /*
16  * RCS $Id: hhalign_wrapper.h 289 2013-09-17 10:09:37Z fabian $
17  */
18 
19 extern void
20 SetDefaultHhalignPara(hhalign_para *prHhalignPara);
21 
22 extern int
23 PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
24 
25 extern double
26 PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
27 
28 extern double
29 HHalignWrapper(mseq_t *mseq, int *piOrderLR,
30  double *pdSeqWeights, int iNodeCount,
31  hmm_light *prHMMList, int iHMMCount,
32  int iProfProfSeparator, hhalign_para rHhalignPara);
33 void
34 SanitiseUnknown(mseq_t *mseq);
int PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile)
PosteriorProbabilities() calculates posterior probabilities of aligning a single sequences on-to an a...
Definition: hhalign_wrapper.c:503
void SetDefaultHhalignPara(hhalign_para *prHhalignPara)
FIXME.
Definition: hhalign_wrapper.c:51
double HHalignWrapper(mseq_t *mseq, int *piOrderLR, double *pdSeqWeights, int iNodeCount, hmm_light *prHMMList, int iHMMCount, int iProfProfSeparator, hhalign_para rHhalignPara)
wrapper for hhalign. This is a frontend function to the ported hhalign code.
Definition: hhalign_wrapper.c:868
structure for storing multiple sequences
Definition: seq.h:47
double PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize)
sequentially align (chain) sequences
Definition: hhalign_wrapper.c:617
void SanitiseUnknown(mseq_t *mseq)
get rid of unknown residues
Definition: hhalign_wrapper.c:99