Clustal Omega
1.0.3
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Go to the source code of this file.
Functions | |
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 |
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.
[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 |
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