embaln.c

Function embAlignPathCalc

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

Prototype

float 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
`float`		RETURN	Maximum score

From EMBOSS 1.0.0

Function embAlignPathCalcWithEndGapPenalties

Create path matrix for Needleman-Wunsch alignment of two sequences. Nucleotides or proteins as needed. Supports end gap penalties.

Prototype

float embAlignPathCalcWithEndGapPenalties (
      const char* a,
      const char* b,
      ajint lena,
      ajint lenb,
      float gapopen,
      float gapextend,
      float endgapopen,
      float endgapextend,
      ajint* start1,
      ajint* start2,
      float* const* sub,
      const AjPSeqCvt cvt,
      float* m,
      float* ix,
      float* iy,
      ajint* compass,
      AjBool show,
      AjBool endweight
);

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 endgapopen Input end gap opening penalty

float endgapextend Input end gap extension penalty

ajint* start1 Output start of alignment in first sequence

ajint* start2 Output start of alignment in second sequence

float* const* sub Input substitution matrix from AjPMatrixf

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

float* m Output Match scores array, m(i,j) is the best score up to (i,j) given that a(i) is aligned to b(j)

float* ix Output Gap scores array, ix(i,j) is the best score given that a(i) is aligned to a gap (in an insertion with respect to b)

float* iy Output Gap scores array, iy(i,j) is the best score given that b(i) is in an insertion with respect to a

ajint* compass Output Path direction pointer array

AjBool show Input Display path matrix

AjBool endweight Input Use end gap weights

float RETURN Score

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`	`endgapopen`	Input	end gap opening penalty
`float`	`endgapextend`	Input	end gap extension penalty
`ajint*`	`start1`	Output	start of alignment in first sequence
`ajint*`	`start2`	Output	start of alignment in second sequence
`float* const*`	`sub`	Input	substitution matrix from AjPMatrixf
`const AjPSeqCvt`	`cvt`	Input	Conversion array for AjPMatrixf
`float*`	`m`	Output	Match scores array, m(i,j) is the best score up to (i,j) given that a(i) is aligned to b(j)
`float*`	`ix`	Output	Gap scores array, ix(i,j) is the best score given that a(i) is aligned to a gap (in an insertion with respect to b)
`float*`	`iy`	Output	Gap scores array, iy(i,j) is the best score given that b(i) is in an insertion with respect to a
`ajint*`	`compass`	Output	Path direction pointer array
`AjBool`	`show`	Input	Display path matrix
`AjBool`	`endweight`	Input	Use end gap weights
`float`		RETURN	Score

From EMBOSS 6.2.0

Function embAlignPathCalcSW

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

Prototype

float 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
`float`		RETURN	Maximum score

From EMBOSS 2.8.0

Function embAlignWalkSWMatrix

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

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,
      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

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
`ajint*`	`start1`	Output	start of alignment in first sequence
`ajint*`	`start2`	Output	start of alignment in second sequence
`void`		RETURN

From EMBOSS 1.0.0

Function embAlignWalkNWMatrix

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

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 ajint* compass
);

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 ajint* compass Input Path direction pointer array

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 ajint*`	`compass`	Input	Path direction pointer array
`void`		RETURN

From EMBOSS 1.0.0

Function embAlignWalkNWMatrixUsingCompass

Walk down a matrix for Needleman Wunsch which was constructed using end gap penalties. Form aligned strings. Nucleotides or proteins as needed.

Prototype

void embAlignWalkNWMatrixUsingCompass (
      const char* p,
      const char* q,
      AjPStr* m,
      AjPStr* n,
      ajuint lena,
      ajuint lenb,
      ajint* start1,
      ajint* start2,
      ajint const* compass
);

Type Name Read/Write Description

const char* p Input first sequence

const char* q Input second sequence

AjPStr* m Output alignment for first sequence

AjPStr* n Output alignment for second sequence

ajuint lena Input length of first sequence

ajuint lenb Input length of second sequence

ajint* start1 Output start of alignment in first sequence

ajint* start2 Output start of alignment in second sequence

ajint const* compass Input Path direction pointer array

void RETURN

Type	Name	Read/Write	Description
`const char*`	`p`	Input	first sequence
`const char*`	`q`	Input	second sequence
`AjPStr*`	`m`	Output	alignment for first sequence
`AjPStr*`	`n`	Output	alignment for second sequence
`ajuint`	`lena`	Input	length of first sequence
`ajuint`	`lenb`	Input	length of second sequence
`ajint*`	`start1`	Output	start of alignment in first sequence
`ajint*`	`start2`	Output	start of alignment in second sequence
`ajint const*`	`compass`	Input	Path direction pointer array
`void`		RETURN

From EMBOSS 6.2.0

Function embAlignPrintGlobal

Print a global alignment Nucleotides or proteins as needed.

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

From EMBOSS 1.0.0

Function embAlignUnused

Calls unused functions to avoid warning messages

Prototype

void embAlignUnused (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 2.0.0

Function embAlignPathCalcSWFast

Create path matrix for Needleman-Wunsch with limited width around main diagonal.

Prototype

float embAlignPathCalcSWFast (
      const char* a,
      const char* b,
      ajint lena,
      ajint lenb,
      ajint offset,
      ajint pathwidth,
      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

ajint offset Input Diagonal offset. Zero is start of a and b. Negative is position in a. Positive is position in b.

ajint pathwidth Input width of path matrix

float gapopen Input gap opening penalty

float gapextend Input gap extension penalty

float* path Output path matrix of size (minlength*pathwidth + (pathwidth/2)*pathwidth) current value: (pathwidth*(lena+1)), lena==lenb

float* const* sub Input substitution matrix from AjPMatrixf

const AjPSeqCvt cvt Input Conversion array for AjPMatrixf

ajint* compass Output Path direction pointer array or same dimensions as path

AjBool show Input Display path matrix

float RETURN Maximum score

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
`ajint`	`offset`	Input	Diagonal offset. Zero is start of a and b. Negative is position in a. Positive is position in b.
`ajint`	`pathwidth`	Input	width of path matrix
`float`	`gapopen`	Input	gap opening penalty
`float`	`gapextend`	Input	gap extension penalty
`float*`	`path`	Output	path matrix of size (minlengthpathwidth + (pathwidth/2)pathwidth) current value: (pathwidth*(lena+1)), lena==lenb
`float* const*`	`sub`	Input	substitution matrix from AjPMatrixf
`const AjPSeqCvt`	`cvt`	Input	Conversion array for AjPMatrixf
`ajint*`	`compass`	Output	Path direction pointer array or same dimensions as path
`AjBool`	`show`	Input	Display path matrix
`float`		RETURN	Maximum score

From EMBOSS 6.0.0

Function embAlignWalkSWMatrixFast

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

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,
      ajint offset,
      ajint width,
      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

ajint offset Input Diagonal offset. Zero is start of a and b. Negative is position in a. Positive is position in b.

ajint width Input width of path matrix

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
`ajint`	`offset`	Input	Diagonal offset. Zero is start of a and b. Negative is position in a. Positive is position in b.
`ajint`	`width`	Input	width of path matrix
`ajint*`	`start1`	Output	start of alignment in first sequence
`ajint*`	`start2`	Output	start of alignment in second sequence
`void`		RETURN

From EMBOSS 1.0.0

Function embAlignProfilePathCalc

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

Prototype

float embAlignProfilePathCalc (
      const char* a,
      ajint proflen,
      ajint seqlen,
      float gapopen,
      float gapextend,
      float* path,
      float* const* pmatrix,
      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* pmatrix Input profile matrix

ajint* compass Output Path direction pointer array

AjBool show Input Display path matrix

float RETURN Maximum score

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*`	`pmatrix`	Input	profile matrix
`ajint*`	`compass`	Output	Path direction pointer array
`AjBool`	`show`	Input	Display path matrix
`float`		RETURN	Maximum score

From EMBOSS 1.0.0

Function embAlignWalkProfileMatrix

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

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* pmatrix,
      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* pmatrix Input profile

ajint* start1 Output start of alignment in consensus sequence

ajint* start2 Output start of alignment in test 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 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*`	`pmatrix`	Input	profile
`ajint*`	`start1`	Output	start of alignment in consensus sequence
`ajint*`	`start2`	Output	start of alignment in test sequence
`void`		RETURN

From EMBOSS 1.0.0

Function embAlignPrintProfile

Print a profile alignment Nucleotides or proteins as needed.

Prototype

void embAlignPrintProfile (
      AjPFile outf,
      const AjPStr m,
      const AjPStr n,
      ajint start1,
      ajint start2,
      float score,
      AjBool mark,
      float* const* pmatrix,
      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* pmatrix 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

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*`	`pmatrix`	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

From EMBOSS 1.0.0

Function embAlignCalcSimilarity

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

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

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

From EMBOSS 1.6.3

Function embAlignReportGlobal

Print a global alignment Nucleotides or proteins as needed.

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

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

From EMBOSS 2.1.0

Function embAlignReportLocal

Print a local alignment Nucleotides or proteins as needed.

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

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

From EMBOSS 2.1.0

Function embAlignReportProfile

Print a profile alignment Nucleotides or proteins as needed.

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

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

From EMBOSS 2.3.0