src/clustal/hhalign_wrapper.h File Reference

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Functions
void	SetDefaultHhalignPara (hhalign_para *prHhalignPara)
	FIXME.
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.
void	SanitiseUnknown (mseq_t *mseq)
	get rid of unknown residues

---

Function Documentation

double HHalignWrapper	(	mseq_t *	prMSeq,
		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.

Parameters:

[in,out]	prMSeq	holds the unaligned sequences [in] and the final alignment [out]
[in]	piOrderLR	holds order in which sequences/profiles are to be aligned, even elements specify left nodes, odd elements right nodes, if even and odd are same then it is a leaf
[in]	pdSeqWeights	Weight per sequence. No weights used if NULL
[in]	iNodeCount	number of nodes in tree, piOrderLR has 2*iNodeCount elements
[in]	prHMMList	List of background HMMs (transition/emission probabilities)
[in]	iHMMCount	Number of input background HMMs
[in]	iProfProfSeparator	Gives the number of sequences in the first profile, if in profile/profile alignment mode (iNodeCount==3). That assumes mseqs holds the sequences of profile 1 and profile 2.
[in]	rHhalignPara	various parameters read from commandline

Returns:

score of the alignment FIXME what is this?

Note:

complex function. could use some simplification, more and documentation and a struct'uring of piOrderLR

HHalignWrapper can be entered in 2 different ways: (i) all sequences are un-aligned (ii) there are 2 (aligned) profiles. in the un-aligned case (i) the sequences come straight from Squid, that is, they have been sanitised, all non-alphabetic residues have been rendered as X's. In profile mode (ii) one profile may have been produced internally. In that case residues may have been translated back into their 'native' form, that is, they may contain un-sanitised residues. These will cause trouble during alignment

: introduced argument hhalign_para rHhalignPara; FS, r240 -> r241

: if hhalign() fails then try with Viterbi by setting MAC-RAM=0; FS, r241 -> r243

translate back ambiguity residues hhalign translates ambiguity codes (B,Z) into unknown residues (X). as we still have the original input we can substitute them back

void SanitiseUnknown

(

mseq_t *

mseq

)

get rid of unknown residues

Note:

HHalignWrapper can be entered in 2 different ways: (i) all sequences are un-aligned (ii) there are 2 (aligned) profiles. in the un-aligned case (i) the sequences come straight from Squid, that is, they have been sanitised, all non-alphabetic residues have been rendered as X's. In profile mode (ii) one profile may have been produced internally. In that case residues may have been translated back into their 'native' form, that is, they may contain un-sanitised residues. These will cause trouble during alignment FS, r213->214

void SetDefaultHhalignPara

(

hhalign_para *

prHhalignPara

)

FIXME.

Note:

prHalignPara has to point to an already allocated instance