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
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