embaln.c

Function embAlignPathCalc

Create path matrix for Needleman-Wunsch Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignPathCalc (
      const char* a,
      const char* b,
      ajint lena,
      ajint lenb,
      float gapopen,
      float gapextend,
      float* path,
      float* const* sub,
      const AjPSeqCvt cvt,
      ajint* compass,
      AjBool show
);

Type Name Read/Write Description

const char* a Input first sequence

const char* b Input second sequence

ajint lena Input length of first sequence

ajint lenb Input length of second sequence

float gapopen Input gap opening penalty

float gapextend Input gap extension penalty

float* path Output path matrix

float* const* sub Input substitution matrix from AjPMatrixf

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

ajint* compass Output Path direction pointer array

AjBool show Input Display path matrix Optimised to keep a maximum value to avoid looping down or left to find the maximum. (il 29/07/99)

void RETURN

Type	Name	Read/Write	Description
const char*	a	Input	first sequence
const char*	b	Input	second sequence
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
float	gapopen	Input	gap opening penalty
float	gapextend	Input	gap extension penalty
float*	path	Output	path matrix
float* const*	sub	Input	substitution matrix from AjPMatrixf
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
ajint*	compass	Output	Path direction pointer array
AjBool	show	Input	Display path matrix Optimised to keep a maximum value to avoid looping down or left to find the maximum. (il 29/07/99)
void		RETURN

Input

a:	(Input)	first sequence
b:	(Input)	second sequence
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
gapopen:	(Input)	gap opening penalty
gapextend:	(Input)	gap extension penalty
sub:	(Input)	substitution matrix from AjPMatrixf
cvt:	(Input)	Conversion array for AjPMatrixf
show:	(Input)	Display path matrix Optimised to keep a maximum value to avoid looping down or left to find the maximum. (il 29/07/99)

Output

path:	(Output)	path matrix
compass:	(Output)	Path direction pointer array

Returns

void:

No return value

Description

Create path matrix for Needleman-Wunsch Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignPathCalcSW

Create path matrix for Smith-Waterman Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignPathCalcSW (
      const char* a,
      const char* b,
      ajint lena,
      ajint lenb,
      float gapopen,
      float gapextend,
      float* path,
      float* const* sub,
      const AjPSeqCvt cvt,
      ajint* compass,
      AjBool show
);

Type	Name	Read/Write	Description
const char*	a	Input	first sequence
const char*	b	Input	second sequence
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
float	gapopen	Input	gap opening penalty
float	gapextend	Input	gap extension penalty
float*	path	Output	path matrix
float* const*	sub	Input	substitution matrix from AjPMatrixf
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
ajint*	compass	Output	Path direction pointer array
AjBool	show	Input	Display path matrix Optimised to keep a maximum value to avoid looping down or left to find the maximum. (il 29/07/99)
void		RETURN

Input

a:	(Input)	first sequence
b:	(Input)	second sequence
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
gapopen:	(Input)	gap opening penalty
gapextend:	(Input)	gap extension penalty
sub:	(Input)	substitution matrix from AjPMatrixf
cvt:	(Input)	Conversion array for AjPMatrixf
show:	(Input)	Display path matrix Optimised to keep a maximum value to avoid looping down or left to find the maximum. (il 29/07/99)

Output

path:	(Output)	path matrix
compass:	(Output)	Path direction pointer array

Returns

void:

No return value

Description

Create path matrix for Smith-Waterman Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignScoreNWMatrix

Score a matrix for Needleman Wunsch. Nucleotides or proteins as needed.

Synopsis

Prototype

float embAlignScoreNWMatrix (
      const float* path,
      const AjPSeq a,
      const AjPSeq b,
      float* const* fmatrix,
      const AjPSeqCvt cvt,
      ajint lena,
      ajint lenb,
      float gapopen,
      const ajint* compass,
      float gapextend,
      ajint* start1,
      ajint* start2
);

Type Name Read/Write Description

const float* path Input path matrix

const AjPSeq a Input first sequence

const AjPSeq b Input second sequence

float* const* fmatrix Input substitution matrix from AjPMatrixf

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

ajint lena Input length of first sequence

ajint lenb Input length of second sequence

float gapopen Input gap opening coefficient

const ajint* compass Input Path direction pointer array

float gapextend Input gap extension coefficient

ajint* start1 Output start of alignment in first sequence

ajint* start2 Output start of alignment in second sequence

float RETURN Maximum path axis score

Type	Name	Read/Write	Description
const float*	path	Input	path matrix
const AjPSeq	a	Input	first sequence
const AjPSeq	b	Input	second sequence
float* const*	fmatrix	Input	substitution matrix from AjPMatrixf
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
float	gapopen	Input	gap opening coefficient
const ajint*	compass	Input	Path direction pointer array
float	gapextend	Input	gap extension coefficient
ajint*	start1	Output	start of alignment in first sequence
ajint*	start2	Output	start of alignment in second sequence
float		RETURN	Maximum path axis score

Input

path:	(Input)	path matrix
a:	(Input)	first sequence
b:	(Input)	second sequence
fmatrix:	(Input)	substitution matrix from AjPMatrixf
cvt:	(Input)	Conversion array for AjPMatrixf
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
gapopen:	(Input)	gap opening coefficient
compass:	(Input)	Path direction pointer array
gapextend:	(Input)	gap extension coefficient

Output

start1:	(Output)	start of alignment in first sequence
start2:	(Output)	start of alignment in second sequence

Returns

float:

Maximum path axis score

Description

Score a matrix for Needleman Wunsch. Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignScoreSWMatrix

Walk down a matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Synopsis

Prototype

float embAlignScoreSWMatrix (
      const float* path,
      const ajint* compass,
      float gapopen,
      float gapextend,
      const AjPSeq a,
      const AjPSeq b,
      ajint lena,
      ajint lenb,
      float* const* sub,
      const AjPSeqCvt cvt,
      ajint* start1,
      ajint* start2
);

Type Name Read/Write Description

const float* path Input path matrix

const ajint* compass Input Path direction pointer array

float gapopen Input gap opening penalty

float gapextend Input gap extension penalty

const AjPSeq a Input first sequence

const AjPSeq b Input second sequence

ajint lena Input length of first sequence

ajint lenb Input length of second sequence

float* const* sub Input substitution matrix from AjPMatrixf

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

ajint* start1 Output start of alignment in first sequence

ajint* start2 Output start of alignment in second sequence

float RETURN Score of best matching segment

Type	Name	Read/Write	Description
const float*	path	Input	path matrix
const ajint*	compass	Input	Path direction pointer array
float	gapopen	Input	gap opening penalty
float	gapextend	Input	gap extension penalty
const AjPSeq	a	Input	first sequence
const AjPSeq	b	Input	second sequence
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
float* const*	sub	Input	substitution matrix from AjPMatrixf
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
ajint*	start1	Output	start of alignment in first sequence
ajint*	start2	Output	start of alignment in second sequence
float		RETURN	Score of best matching segment

Input

path:	(Input)	path matrix
compass:	(Input)	Path direction pointer array
gapopen:	(Input)	gap opening penalty
gapextend:	(Input)	gap extension penalty
a:	(Input)	first sequence
b:	(Input)	second sequence
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
sub:	(Input)	substitution matrix from AjPMatrixf
cvt:	(Input)	Conversion array for AjPMatrixf

Output

start1:	(Output)	start of alignment in first sequence
start2:	(Output)	start of alignment in second sequence

Returns

float:

Score of best matching segment

Description

Walk down a matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignWalkSWMatrix

Walk down a matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignWalkSWMatrix (
      const float* path,
      const ajint* compass,
      float gapopen,
      float gapextend,
      const AjPSeq a,
      const AjPSeq b,
      AjPStr* m,
      AjPStr* n,
      ajint lena,
      ajint lenb,
      float* const* sub,
      const AjPSeqCvt cvt,
      ajint* start1,
      ajint* start2
);

Type Name Read/Write Description

const float* path Input path matrix

const ajint* compass Input Path direction pointer array

float gapopen Input gap opening penalty

float gapextend Input gap extension penalty

const AjPSeq a Input first sequence

const AjPSeq b Input second sequence

AjPStr* m Output alignment for first sequence

AjPStr* n Output alignment for second sequence

ajint lena Input length of first sequence

ajint lenb Input length of second sequence

float* const* sub Input substitution matrix from AjPMatrixf

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

ajint* start1 Output start of alignment in first sequence

ajint* start2 Output start of alignment in second sequence

void RETURN

Type	Name	Read/Write	Description
const float*	path	Input	path matrix
const ajint*	compass	Input	Path direction pointer array
float	gapopen	Input	gap opening penalty
float	gapextend	Input	gap extension penalty
const AjPSeq	a	Input	first sequence
const AjPSeq	b	Input	second sequence
AjPStr*	m	Output	alignment for first sequence
AjPStr*	n	Output	alignment for second sequence
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
float* const*	sub	Input	substitution matrix from AjPMatrixf
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
ajint*	start1	Output	start of alignment in first sequence
ajint*	start2	Output	start of alignment in second sequence
void		RETURN

Input

path:	(Input)	path matrix
compass:	(Input)	Path direction pointer array
gapopen:	(Input)	gap opening penalty
gapextend:	(Input)	gap extension penalty
a:	(Input)	first sequence
b:	(Input)	second sequence
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
sub:	(Input)	substitution matrix from AjPMatrixf
cvt:	(Input)	Conversion array for AjPMatrixf

Output

m:	(Output)	alignment for first sequence
n:	(Output)	alignment for second sequence
start1:	(Output)	start of alignment in first sequence
start2:	(Output)	start of alignment in second sequence

Returns

void:

No return value

Description

Walk down a matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignWalkNWMatrix

Walk down a matrix for Needleman Wunsch. Form aligned strings. Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignWalkNWMatrix (
      const float* path,
      const AjPSeq a,
      const AjPSeq b,
      AjPStr* m,
      AjPStr* n,
      ajint lena,
      ajint lenb,
      ajint* start1,
      ajint* start2,
      float gapopen,
      float gapextend,
      const AjPSeqCvt cvt,
      const ajint* compass,
      float* const* sub
);

Type Name Read/Write Description

const float* path Input path matrix

const AjPSeq a Input first sequence

const AjPSeq b Input second sequence

AjPStr* m Output alignment for first sequence

AjPStr* n Output alignment for second sequence

ajint lena Input length of first sequence

ajint lenb Input length of second sequence

ajint* start1 Output start of alignment in first sequence

ajint* start2 Output start of alignment in second sequence

float gapopen Input gap open penalty

float gapextend Input gap extension penalty

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

const ajint* compass Input Path direction pointer array

float* const* sub Input substitution matrix from AjPMatrixf

void RETURN

Type	Name	Read/Write	Description
const float*	path	Input	path matrix
const AjPSeq	a	Input	first sequence
const AjPSeq	b	Input	second sequence
AjPStr*	m	Output	alignment for first sequence
AjPStr*	n	Output	alignment for second sequence
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
ajint*	start1	Output	start of alignment in first sequence
ajint*	start2	Output	start of alignment in second sequence
float	gapopen	Input	gap open penalty
float	gapextend	Input	gap extension penalty
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
const ajint*	compass	Input	Path direction pointer array
float* const*	sub	Input	substitution matrix from AjPMatrixf
void		RETURN

Input

path:	(Input)	path matrix
a:	(Input)	first sequence
b:	(Input)	second sequence
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
gapopen:	(Input)	gap open penalty
gapextend:	(Input)	gap extension penalty
cvt:	(Input)	Conversion array for AjPMatrixf
compass:	(Input)	Path direction pointer array
sub:	(Input)	substitution matrix from AjPMatrixf

Output

m:	(Output)	alignment for first sequence
n:	(Output)	alignment for second sequence
start1:	(Output)	start of alignment in first sequence
start2:	(Output)	start of alignment in second sequence

Returns

void:

No return value

Description

Walk down a matrix for Needleman Wunsch. Form aligned strings. Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignPrintGlobal

Print a global alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignPrintGlobal (
      AjPFile outf,
      const char* a,
      const char* b,
      const AjPStr m,
      const AjPStr n,
      ajint start1,
      ajint start2,
      float score,
      AjBool mark,
      float* const* sub,
      const AjPSeqCvt cvt,
      const char* namea,
      const char* nameb,
      ajint begina,
      ajint beginb
);

Type Name Read/Write Description

AjPFile outf Modify output stream

const char* a Input complete first sequence

const char* b Input complete second sequence

const AjPStr m Input Walk alignment for first sequence

const AjPStr n Input Walk alignment for second sequence

ajint start1 Input start of alignment in first sequence

ajint start2 Input start of alignment in second sequence

float score Input alignment score from AlignScoreX

AjBool mark Input mark matches and conservatives

float* const* sub Input substitution matrix

const AjPSeqCvt cvt Input conversion table for matrix

const char* namea Input name of first sequence

const char* nameb Input name of second sequence

ajint begina Input first sequence offset

ajint beginb Input second sequence offset

void RETURN

Type	Name	Read/Write	Description
AjPFile	outf	Modify	output stream
const char*	a	Input	complete first sequence
const char*	b	Input	complete second sequence
const AjPStr	m	Input	Walk alignment for first sequence
const AjPStr	n	Input	Walk alignment for second sequence
ajint	start1	Input	start of alignment in first sequence
ajint	start2	Input	start of alignment in second sequence
float	score	Input	alignment score from AlignScoreX
AjBool	mark	Input	mark matches and conservatives
float* const*	sub	Input	substitution matrix
const AjPSeqCvt	cvt	Input	conversion table for matrix
const char*	namea	Input	name of first sequence
const char*	nameb	Input	name of second sequence
ajint	begina	Input	first sequence offset
ajint	beginb	Input	second sequence offset
void		RETURN

Input

a:	(Input)	complete first sequence
b:	(Input)	complete second sequence
m:	(Input)	Walk alignment for first sequence
n:	(Input)	Walk alignment for second sequence
start1:	(Input)	start of alignment in first sequence
start2:	(Input)	start of alignment in second sequence
score:	(Input)	alignment score from AlignScoreX
mark:	(Input)	mark matches and conservatives
sub:	(Input)	substitution matrix
cvt:	(Input)	conversion table for matrix
namea:	(Input)	name of first sequence
nameb:	(Input)	name of second sequence
begina:	(Input)	first sequence offset
beginb:	(Input)	second sequence offset

Input & Output

outf:

(Modify)

output stream

Returns

void:

No return value

Description

Print a global alignment Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignPrintLocal

Print a local alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignPrintLocal (
      AjPFile outf,
      const AjPStr m,
      const AjPStr n,
      ajint start1,
      ajint start2,
      float score,
      AjBool mark,
      float* const* sub,
      const AjPSeqCvt cvt,
      const char* namea,
      const char* nameb,
      ajint begina,
      ajint beginb
);

Type Name Read/Write Description

AjPFile outf Modify output stream

const AjPStr m Input Walk alignment for first sequence

const AjPStr n Input Walk alignment for second sequence

ajint start1 Input start of alignment in first sequence

ajint start2 Input start of alignment in second sequence

float score Input alignment score from AlignScoreX

AjBool mark Input mark matches and conservatives

float* const* sub Input substitution matrix

const AjPSeqCvt cvt Input conversion table for matrix

const char* namea Input name of first sequence

const char* nameb Input name of second sequence

ajint begina Input first sequence offset

ajint beginb Input second sequence offset

void RETURN

Type	Name	Read/Write	Description
AjPFile	outf	Modify	output stream
const AjPStr	m	Input	Walk alignment for first sequence
const AjPStr	n	Input	Walk alignment for second sequence
ajint	start1	Input	start of alignment in first sequence
ajint	start2	Input	start of alignment in second sequence
float	score	Input	alignment score from AlignScoreX
AjBool	mark	Input	mark matches and conservatives
float* const*	sub	Input	substitution matrix
const AjPSeqCvt	cvt	Input	conversion table for matrix
const char*	namea	Input	name of first sequence
const char*	nameb	Input	name of second sequence
ajint	begina	Input	first sequence offset
ajint	beginb	Input	second sequence offset
void		RETURN

Input

m:	(Input)	Walk alignment for first sequence
n:	(Input)	Walk alignment for second sequence
start1:	(Input)	start of alignment in first sequence
start2:	(Input)	start of alignment in second sequence
score:	(Input)	alignment score from AlignScoreX
mark:	(Input)	mark matches and conservatives
sub:	(Input)	substitution matrix
cvt:	(Input)	conversion table for matrix
namea:	(Input)	name of first sequence
nameb:	(Input)	name of second sequence
begina:	(Input)	first sequence offset
beginb:	(Input)	second sequence offset

Input & Output

outf:

(Modify)

output stream

Returns

void:

No return value

Description

Print a local alignment Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignUnused

Calls unused functions to avoid warning messages

Synopsis

Prototype

void embAlignUnused (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
void		RETURN

Returns

void:

No return value

Description

Calls unused functions to avoid warning messages

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignPathCalcFast

Create path matrix for Smith-Waterman and Needleman-Wunsch Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignPathCalcFast (
      const char* a,
      const char* b,
      ajint lena,
      ajint lenb,
      float gapopen,
      float gapextend,
      float* path,
      float* const* sub,
      const AjPSeqCvt cvt,
      ajint* compass,
      AjBool show,
      ajint pathwidth
);

Type Name Read/Write Description

const char* a Input first sequence

const char* b Input second sequence

ajint lena Input length of first sequence

ajint lenb Input length of second sequence

float gapopen Input gap opening penalty

float gapextend Input gap extension penalty

float* path Output path matrix

float* const* sub Input substitution matrix from AjPMatrixf

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

ajint* compass Output Path direction pointer array

AjBool show Input Display path matrix

ajint pathwidth Input width of path matrix Optimised to keep a maximum value to avoid looping down or left to find the maximum. (il 29/07/99) Further speeded up by using only width calculations instead of lena.

void RETURN

Type	Name	Read/Write	Description
const char*	a	Input	first sequence
const char*	b	Input	second sequence
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
float	gapopen	Input	gap opening penalty
float	gapextend	Input	gap extension penalty
float*	path	Output	path matrix
float* const*	sub	Input	substitution matrix from AjPMatrixf
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
ajint*	compass	Output	Path direction pointer array
AjBool	show	Input	Display path matrix
ajint	pathwidth	Input	width of path matrix Optimised to keep a maximum value to avoid looping down or left to find the maximum. (il 29/07/99) Further speeded up by using only width calculations instead of lena.
void		RETURN

Input

a:	(Input)	first sequence
b:	(Input)	second sequence
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
gapopen:	(Input)	gap opening penalty
gapextend:	(Input)	gap extension penalty
sub:	(Input)	substitution matrix from AjPMatrixf
cvt:	(Input)	Conversion array for AjPMatrixf
show:	(Input)	Display path matrix
pathwidth:	(Input)	width of path matrix Optimised to keep a maximum value to avoid looping down or left to find the maximum. (il 29/07/99) Further speeded up by using only width calculations instead of lena.

Output

path:	(Output)	path matrix
compass:	(Output)	Path direction pointer array

Returns

void:

No return value

Description

Create path matrix for Smith-Waterman and Needleman-Wunsch Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignScoreSWMatrixFast

Walk down a matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Synopsis

Prototype

float embAlignScoreSWMatrixFast (
      const float* path,
      const ajint* compass,
      float gapopen,
      float gapextend,
      const AjPSeq a,
      const AjPSeq b,
      ajint lena,
      ajint lenb,
      float* const* sub,
      const AjPSeqCvt cvt,
      ajint* start1,
      ajint* start2,
      ajint pathwidth
);

Type	Name	Read/Write	Description
const float*	path	Input	path matrix
const ajint*	compass	Input	Path direction pointer array
float	gapopen	Input	gap opening penalty
float	gapextend	Input	gap extension penalty
const AjPSeq	a	Input	first sequence
const AjPSeq	b	Input	second sequence
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
float* const*	sub	Input	substitution matrix from AjPMatrixf
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
ajint*	start1	Output	start of alignment in first sequence
ajint*	start2	Output	start of alignment in second sequence
ajint	pathwidth	Input	width of path matrix
float		RETURN	Score of best matching segment

Input

path:	(Input)	path matrix
compass:	(Input)	Path direction pointer array
gapopen:	(Input)	gap opening penalty
gapextend:	(Input)	gap extension penalty
a:	(Input)	first sequence
b:	(Input)	second sequence
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
sub:	(Input)	substitution matrix from AjPMatrixf
cvt:	(Input)	Conversion array for AjPMatrixf
pathwidth:	(Input)	width of path matrix

Output

start1:	(Output)	start of alignment in first sequence
start2:	(Output)	start of alignment in second sequence

Returns

float:

Score of best matching segment

Description

Walk down a matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignWalkSWMatrixFast

Walk down a matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignWalkSWMatrixFast (
      const float* path,
      const ajint* compass,
      float gapopen,
      float gapextend,
      const AjPSeq a,
      const AjPSeq b,
      AjPStr* m,
      AjPStr* n,
      ajint lena,
      ajint lenb,
      float* const* sub,
      const AjPSeqCvt cvt,
      ajint* start1,
      ajint* start2,
      ajint pathwidth
);

Type Name Read/Write Description

const float* path Input path matrix

const ajint* compass Input Path direction pointer array

float gapopen Input gap opening penalty

float gapextend Input gap extension penalty

const AjPSeq a Input first sequence

const AjPSeq b Input second sequence

AjPStr* m Output alignment for first sequence

AjPStr* n Output alignment for second sequence

ajint lena Input length of first sequence

ajint lenb Input length of second sequence

float* const* sub Input substitution matrix from AjPMatrixf

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

ajint* start1 Output start of alignment in first sequence

ajint* start2 Output start of alignment in second sequence

ajint pathwidth Input width of path matrix

void RETURN

Type	Name	Read/Write	Description
const float*	path	Input	path matrix
const ajint*	compass	Input	Path direction pointer array
float	gapopen	Input	gap opening penalty
float	gapextend	Input	gap extension penalty
const AjPSeq	a	Input	first sequence
const AjPSeq	b	Input	second sequence
AjPStr*	m	Output	alignment for first sequence
AjPStr*	n	Output	alignment for second sequence
ajint	lena	Input	length of first sequence
ajint	lenb	Input	length of second sequence
float* const*	sub	Input	substitution matrix from AjPMatrixf
const AjPSeqCvt	cvt	Input	Conversion array for AjPMatrixf
ajint*	start1	Output	start of alignment in first sequence
ajint*	start2	Output	start of alignment in second sequence
ajint	pathwidth	Input	width of path matrix
void		RETURN

Input

path:	(Input)	path matrix
compass:	(Input)	Path direction pointer array
gapopen:	(Input)	gap opening penalty
gapextend:	(Input)	gap extension penalty
a:	(Input)	first sequence
b:	(Input)	second sequence
lena:	(Input)	length of first sequence
lenb:	(Input)	length of second sequence
sub:	(Input)	substitution matrix from AjPMatrixf
cvt:	(Input)	Conversion array for AjPMatrixf
pathwidth:	(Input)	width of path matrix

Output

m:	(Output)	alignment for first sequence
n:	(Output)	alignment for second sequence
start1:	(Output)	start of alignment in first sequence
start2:	(Output)	start of alignment in second sequence

Returns

void:

No return value

Description

Walk down a matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignProfilePathCalc

Create path matrix for a profile Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignProfilePathCalc (
      const char* a,
      ajint proflen,
      ajint seqlen,
      float gapopen,
      float gapextend,
      float* path,
      float* const* fmatrix,
      ajint* compass,
      AjBool show
);

Type Name Read/Write Description

const char* a Input sequence

ajint proflen Input length of profile

ajint seqlen Input length of sequence

float gapopen Input gap opening coefficient

float gapextend Input gap extension coefficient

float* path Output path matrix

float* const* fmatrix Input profile matrix

ajint* compass Output Path direction pointer array

AjBool show Input Display path matrix

void RETURN

Type	Name	Read/Write	Description
const char*	a	Input	sequence
ajint	proflen	Input	length of profile
ajint	seqlen	Input	length of sequence
float	gapopen	Input	gap opening coefficient
float	gapextend	Input	gap extension coefficient
float*	path	Output	path matrix
float* const*	fmatrix	Input	profile matrix
ajint*	compass	Output	Path direction pointer array
AjBool	show	Input	Display path matrix
void		RETURN

Input

a:	(Input)	sequence
proflen:	(Input)	length of profile
seqlen:	(Input)	length of sequence
gapopen:	(Input)	gap opening coefficient
gapextend:	(Input)	gap extension coefficient
fmatrix:	(Input)	profile matrix
show:	(Input)	Display path matrix

Output

path:	(Output)	path matrix
compass:	(Output)	Path direction pointer array

Returns

void:

No return value

Description

Create path matrix for a profile Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignWalkProfileMatrix

Walk down a profile path matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignWalkProfileMatrix (
      const float* path,
      const ajint* compass,
      float gapopen,
      float gapextend,
      const AjPStr cons,
      const AjPStr seq,
      AjPStr* m,
      AjPStr* n,
      ajint proflen,
      ajint seqlen,
      float* const* fmatrix,
      ajint* start1,
      ajint* start2
);

Type Name Read/Write Description

const float* path Input path matrix

const ajint* compass Input Path direction pointer array

float gapopen Input gap opening coeff

float gapextend Input gap extension coeff

const AjPStr cons Input consensus sequence

const AjPStr seq Input second sequence

AjPStr* m Output alignment for consensus sequence

AjPStr* n Output alignment for second sequence

ajint proflen Input length of consensus sequence

ajint seqlen Input length of test sequence

float* const* fmatrix Input profile

ajint* start1 Output start of alignment in consensus sequence

ajint* start2 Output start of alignment in test sequence

void RETURN

Input

path:	(Input)	path matrix
compass:	(Input)	Path direction pointer array
gapopen:	(Input)	gap opening coeff
gapextend:	(Input)	gap extension coeff
cons:	(Input)	consensus sequence
seq:	(Input)	second sequence
proflen:	(Input)	length of consensus sequence
seqlen:	(Input)	length of test sequence
fmatrix:	(Input)	profile

Output

m:	(Output)	alignment for consensus sequence
n:	(Output)	alignment for second sequence
start1:	(Output)	start of alignment in consensus sequence
start2:	(Output)	start of alignment in test sequence

Returns

void:

No return value

Description

Walk down a profile path matrix for Smith Waterman. Form aligned strings. Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignPrintProfile

Print a profile alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignPrintProfile (
      AjPFile outf,
      const AjPStr m,
      const AjPStr n,
      ajint start1,
      ajint start2,
      float score,
      AjBool mark,
      float* const* fmatrix,
      const char* namea,
      const char* nameb,
      ajint begina,
      ajint beginb
);

Type Name Read/Write Description

AjPFile outf Modify output stream

const AjPStr m Input Walk alignment for first sequence

const AjPStr n Input Walk alignment for second sequence

ajint start1 Input start of alignment in first sequence

ajint start2 Input start of alignment in second sequence

float score Input alignment score from AlignScoreX

AjBool mark Input mark matches and conservatives

float* const* fmatrix Input profile

const char* namea Input name of first sequence

const char* nameb Input name of second sequence

ajint begina Input first sequence offset

ajint beginb Input second sequence offset

void RETURN

Input

m:	(Input)	Walk alignment for first sequence
n:	(Input)	Walk alignment for second sequence
start1:	(Input)	start of alignment in first sequence
start2:	(Input)	start of alignment in second sequence
score:	(Input)	alignment score from AlignScoreX
mark:	(Input)	mark matches and conservatives
fmatrix:	(Input)	profile
namea:	(Input)	name of first sequence
nameb:	(Input)	name of second sequence
begina:	(Input)	first sequence offset
beginb:	(Input)	second sequence offset

Input & Output

outf:

(Modify)

output stream

Returns

void:

No return value

Description

Print a profile alignment Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignCalcSimilarity

Calculate Similarity of two sequences (same length) Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignCalcSimilarity (
      const AjPStr m,
      const AjPStr n,
      float* const* sub,
      const AjPSeqCvt cvt,
      ajint lenm,
      ajint lenn,
      float* id,
      float* sim,
      float* idx,
      float* simx
);

Type Name Read/Write Description

const AjPStr m Input Walk alignment for first sequence

const AjPStr n Input Walk alignment for second sequence

float* const* sub Input substitution matrix

const AjPSeqCvt cvt Input conversion table for matrix

ajint lenm Input length of first sequence

ajint lenn Input length of second sequence

float* id Output % identity

float* sim Output % similarity

float* idx Output % identity wrt longest sequence

float* simx Output % similarity wrt longest sequence

void RETURN

Input

m:	(Input)	Walk alignment for first sequence
n:	(Input)	Walk alignment for second sequence
sub:	(Input)	substitution matrix
cvt:	(Input)	conversion table for matrix
lenm:	(Input)	length of first sequence
lenn:	(Input)	length of second sequence

Output

id:	(Output)	% identity
sim:	(Output)	% similarity
idx:	(Output)	% identity wrt longest sequence
simx:	(Output)	% similarity wrt longest sequence

Returns

void:

No return value

Description

Calculate Similarity of two sequences (same length) Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignScoreProfileMatrix

Score a profile path matrix for Smith Waterman. Nucleotides or proteins as needed.

Synopsis

Prototype

float embAlignScoreProfileMatrix (
      const float* path,
      const ajint* compass,
      float gapopen,
      float gapextend,
      const AjPStr seq,
      ajint proflen,
      ajint seqlen,
      float* const* fmatrix,
      ajint* start1,
      ajint* start2
);

Type Name Read/Write Description

const float* path Input path matrix

const ajint* compass Input Path direction pointer array

float gapopen Input gap opening coeff

float gapextend Input gap extension coeff

const AjPStr seq Input second sequence

ajint proflen Input length of consensus sequence

ajint seqlen Input length of test sequence

float* const* fmatrix Input profile

ajint* start1 Output start of alignment in consensus sequence

ajint* start2 Output start of alignment in test sequence

float RETURN profile alignment score

Input

path:	(Input)	path matrix
compass:	(Input)	Path direction pointer array
gapopen:	(Input)	gap opening coeff
gapextend:	(Input)	gap extension coeff
seq:	(Input)	second sequence
proflen:	(Input)	length of consensus sequence
seqlen:	(Input)	length of test sequence
fmatrix:	(Input)	profile

Output

start1:	(Output)	start of alignment in consensus sequence
start2:	(Output)	start of alignment in test sequence

Returns

float:

profile alignment score

Description

Score a profile path matrix for Smith Waterman. Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignReportGlobal

Print a global alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignReportGlobal (
      AjPAlign align,
      const AjPSeq seqa,
      const AjPSeq seqb,
      const AjPStr m,
      const AjPStr n,
      ajint start1,
      ajint start2,
      float gapopen,
      float gapextend,
      float score,
      AjPMatrixf matrix,
      ajint offset1,
      ajint offset2
);

Type Name Read/Write Description

AjPAlign align Modify Alignment object

const AjPSeq seqa Input Complete first sequence

const AjPSeq seqb Input Complete second sequence

const AjPStr m Input Walk alignment for first sequence

const AjPStr n Input Walk alignment for second sequence

ajint start1 Input start of alignment in first sequence

ajint start2 Input start of alignment in second sequence

float gapopen Input Gap open penalty to report

float gapextend Input Gap extend penalty to report

float score Input alignment score from AlignScoreX

AjPMatrixf matrix Modify Floating point matrix

ajint offset1 Input first sequence offset

ajint offset2 Input second sequence offset

void RETURN

Input

seqa:	(Input)	Complete first sequence
seqb:	(Input)	Complete second sequence
m:	(Input)	Walk alignment for first sequence
n:	(Input)	Walk alignment for second sequence
start1:	(Input)	start of alignment in first sequence
start2:	(Input)	start of alignment in second sequence
gapopen:	(Input)	Gap open penalty to report
gapextend:	(Input)	Gap extend penalty to report
score:	(Input)	alignment score from AlignScoreX
offset1:	(Input)	first sequence offset
offset2:	(Input)	second sequence offset

Input & Output

align:	(Modify)	Alignment object
matrix:	(Modify)	Floating point matrix

Returns

void:

No return value

Description

Print a global alignment Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignReportLocal

Print a local alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignReportLocal (
      AjPAlign align,
      const AjPSeq seqa,
      const AjPSeq seqb,
      const AjPStr m,
      const AjPStr n,
      ajint start1,
      ajint start2,
      float gapopen,
      float gapextend,
      float score,
      AjPMatrixf matrix,
      ajint offset1,
      ajint offset2
);

Type Name Read/Write Description

AjPAlign align Modify Alignment object

const AjPSeq seqa Input complete first sequence

const AjPSeq seqb Input complete second sequence

const AjPStr m Input Walk alignment for first sequence

const AjPStr n Input Walk alignment for second sequence

ajint start1 Input start of alignment in first sequence

ajint start2 Input start of alignment in second sequence

float gapopen Input Gap open penalty to report

float gapextend Input Gap extend penalty to report

float score Input alignment score from AlignScoreX

AjPMatrixf matrix Modify Floating point matrix

ajint offset1 Input first sequence offset

ajint offset2 Input second sequence offset

void RETURN

Input

seqa:	(Input)	complete first sequence
seqb:	(Input)	complete second sequence
m:	(Input)	Walk alignment for first sequence
n:	(Input)	Walk alignment for second sequence
start1:	(Input)	start of alignment in first sequence
start2:	(Input)	start of alignment in second sequence
gapopen:	(Input)	Gap open penalty to report
gapextend:	(Input)	Gap extend penalty to report
score:	(Input)	alignment score from AlignScoreX
offset1:	(Input)	first sequence offset
offset2:	(Input)	second sequence offset

Input & Output

align:	(Modify)	Alignment object
matrix:	(Modify)	Floating point matrix

Returns

void:

No return value

Description

Print a local alignment Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embAlignReportProfile

Print a profile alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignReportProfile (
      AjPAlign align,
      const AjPStr m,
      const AjPStr n,
      ajint start1,
      ajint start2,
      float score,
      const char* namea,
      const char* nameb
);

Type Name Read/Write Description

AjPAlign align Modify Alignment object

const AjPStr m Input Walk alignment for first sequence

const AjPStr n Input Walk alignment for second sequence

ajint start1 Input start of alignment in first sequence

ajint start2 Input start of alignment in second sequence

float score Input alignment score from AlignScoreX

const char* namea Input name of first sequence

const char* nameb Input name of second sequence

void RETURN

Input

m:	(Input)	Walk alignment for first sequence
n:	(Input)	Walk alignment for second sequence
start1:	(Input)	start of alignment in first sequence
start2:	(Input)	start of alignment in second sequence
score:	(Input)	alignment score from AlignScoreX
namea:	(Input)	name of first sequence
nameb:	(Input)	name of second sequence

Input & Output

align:

(Modify)

Alignment object

Returns

void:

No return value

Description

Print a profile alignment Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Type	Name	Read/Write	Description
AjPAlign	align	Modify	Alignment object
const AjPSeq	seqa	Input	Complete first sequence
const AjPSeq	seqb	Input	Complete second sequence
const AjPStr	m	Input	Walk alignment for first sequence
const AjPStr	n	Input	Walk alignment for second sequence
ajint	start1	Input	start of alignment in first sequence
ajint	start2	Input	start of alignment in second sequence
float	gapopen	Input	Gap open penalty to report
float	gapextend	Input	Gap extend penalty to report
float	score	Input	alignment score from AlignScoreX
AjPMatrixf	matrix	Modify	Floating point matrix
ajint	offset1	Input	first sequence offset
ajint	offset2	Input	second sequence offset
void		RETURN

embaln.c

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