src/clustal/hhalign_wrapper.c File Reference

#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <ctype.h>
#include <stdbool.h>
#include "seq.h"
#include "squid/squid.h"
#include <limits.h>
#include <strings.h>
#include <stdarg.h>
#include <stdio.h>
#include "util.h"
#include "seq.h"
#include "squid/stopwatch.h"
#include "hhalign/general.h"
#include "hhalign/hhfunc.h"
#include "hhalign/hhalign.h"

Include dependency graph for hhalign_wrapper.c:

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Defines
#define	APPLY_BG_HMM_UP_TO_TREE_DEPTH 10
#define	TIMING 0
#define	TRACE 0
#define	NOTX 'N'
Functions
void	SetDefaultHhalignPara (hhalign_para *prHhalignPara)
	FIXME.
void	SanitiseUnknown (mseq_t *mseq)
	get rid of unknown residues
void	TranslateUnknown2Ambiguity (mseq_t *mseq)
	translate unknown residues back to ambiguity codes; hhalign translates ambiguity codes (B,Z) into unknown residue (X). we still have the original (un-aligned) residue information, by iterating along the original and aligned sequences we can reconstruct where codes have been changed and restore them to their original value
void	ReAttachLeadingGaps (mseq_t *prMSeq, int iProfProfSeparator)
	re-attach leading and trailing gaps to alignment
void	PrepareAlignment (mseq_t mseq, char ppcProfile1, char ppcProfile2, double pdWeightsL, double pdWeightsR, double pdSeqWeights, int iLeafCountL, int piLeafListL, int iLeafCountR, int piLeafListR)
	reallocate enough memory for alignment and attach sequence pointers to profiles
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.

Define Documentation

#define APPLY_BG_HMM_UP_TO_TREE_DEPTH 10

#define NOTX 'N'

#define TIMING 0

#define TRACE 0

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 PrepareAlignment	(	mseq_t *	mseq,
		char **	ppcProfile1,
		char **	ppcProfile2,
		double *	pdWeightsL,
		double *	pdWeightsR,
		double *	pdSeqWeights,
		int	iLeafCountL,
		int *	piLeafListL,
		int	iLeafCountR,
		int *	piLeafListR
	)

reallocate enough memory for alignment and attach sequence pointers to profiles

Parameters:

`[in,out]`	mseq	sequence/profile data, increase memory for sequences in profiles
`[out]`	ppcProfile1	pointers to sequencese in 1st profile
`[out]`	ppcProfile2	pointers to sequencese in 2nd profile
`[out]`	pdWeightsL	weights (normalised to 1.0) for sequences in left profile
`[out]`	pdWeightsR	weights (normalised to 1.0) for sequences in right profile
`[in]`	pdSeqWeights	weights for _all_ sequences in alignment
`[in]`	iLeafCountL	number of sequences in 1st profile
`[in]`	piLeafListL	array of integer IDs of sequences in 1st profile
`[in]`	iLeafCountR	number of sequences in 2nd profile
`[in]`	piLeafListR	array of integer IDs of sequences in 2nd profile

void ReAttachLeadingGaps	(	mseq_t *	prMSeq,
		int	iProfProfSeparator
	)

re-attach leading and trailing gaps to alignment

Parameters:

`[in,out]`	prMSeq	alignment structure (at this stage there should be no un-aligned sequences)
`[in]`	iProfProfSeparator	gives sizes of input profiles, -1 if no input-profiles but un-aligned sequences

Note:: leading and tailing profile columns that only contain gaps have no effect on the alignment and are removed during the alignment. if they are encountered a warning message is printed to screen. some users like to preserve these gap columns FS, r213->214

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

void TranslateUnknown2Ambiguity ( mseq_t * mseq )

translate unknown residues back to ambiguity codes; hhalign translates ambiguity codes (B,Z) into unknown residue (X). we still have the original (un-aligned) residue information, by iterating along the original and aligned sequences we can reconstruct where codes have been changed and restore them to their original value

Parameters:

[in,out] mseq sequence/profile data, mseq->seq [in,out] is changed to conform with mseq->orig_seq [in]

src/clustal/hhalign_wrapper.c File Reference

Defines

Functions

Define Documentation

Function Documentation