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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embAlignPrintLocal

Print a local alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignPrintLocal (
      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
);

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 local alignment Nucleotides or proteins as needed.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embAlignUnused

Calls unused functions to avoid warning messages

Synopsis

Prototype

void embAlignUnused (
      void
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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 width
);

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
width:(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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embAlignPrintProfile

Print a profile alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignPrintProfile (
      AjPFile outf,
      const char* a,
      const char* b,
      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
);

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
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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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,
      const AjPMatrixf matrix,
      ajint offset1,
      ajint offset2
);

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
matrix:(Input)Floating point matrix
offset1:(Input)first sequence offset
offset2:(Input)second sequence offset

Input & Output

align:(Modify)Alignment object

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

See Also

See other functions in this section

Availability

In release 3.0.0

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,
      const AjPMatrixf matrix,
      ajint offset1,
      ajint offset2
);

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
matrix:(Input)Floating point matrix
offset1:(Input)first sequence offset
offset2:(Input)second sequence offset

Input & Output

align:(Modify)Alignment object

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embAlignReportProfile

Print a profile alignment Nucleotides or proteins as needed.

Synopsis

Prototype

void embAlignReportProfile (
      AjPAlign thys,
      const AjPSeqset seqset,
      const char* a,
      const char* b,
      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
);

Input

seqset:(Input)Aligned sequence set
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
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

thys:(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

See Also

See other functions in this section

Availability

In release 3.0.0