embaln.c


Function embAlignPathCalc

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

Synopsis

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
);

TypeNameRead/WriteDescription
const char*aInputfirst sequence
const char*bInputsecond sequence
ajintlenaInputlength of first sequence
ajintlenbInputlength of second sequence
floatgapopenInputgap opening penalty
floatgapextendInputgap extension penalty
float*pathOutputpath matrix
float* const*subInputsubstitution matrix from AjPMatrixf
const AjPSeqCvtcvtInputConversion array for AjPMatrixf
ajint*compassOutputPath direction pointer array
AjBoolshowInputDisplay path matrix
float RETURNMaximum score

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
Output
path:(Output)path matrix
compass:(Output)Path direction pointer array
Returns
float:Maximum score

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 6.4.0

Function embAlignPathCalcWithEndGapPenalties

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

Synopsis

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
);

TypeNameRead/WriteDescription
const char*aInputfirst sequence
const char*bInputsecond sequence
ajintlenaInputlength of first sequence
ajintlenbInputlength of second sequence
floatgapopenInputgap opening penalty
floatgapextendInputgap extension penalty
floatendgapopenInputend gap opening penalty
floatendgapextendInputend gap extension penalty
ajint*start1Outputstart of alignment in first sequence
ajint*start2Outputstart of alignment in second sequence
float* const*subInputsubstitution matrix from AjPMatrixf
const AjPSeqCvtcvtInputConversion array for AjPMatrixf
float*mOutputMatch scores array, m(i,j) is the best score up to (i,j) given that a(i) is aligned to b(j)
float*ixOutputGap 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*iyOutputGap scores array, iy(i,j) is the best score given that b(i) is in an insertion with respect to a
ajint*compassOutputPath direction pointer array
AjBoolshowInputDisplay path matrix
AjBoolendweightInputUse end gap weights
float RETURNScore

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

Description

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

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 6.4.0

Function embAlignPathCalcSW

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

Synopsis

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
);

TypeNameRead/WriteDescription
const char*aInputfirst sequence
const char*bInputsecond sequence
ajintlenaInputlength of first sequence
ajintlenbInputlength of second sequence
floatgapopenInputgap opening penalty
floatgapextendInputgap extension penalty
float*pathOutputpath matrix
float* const*subInputsubstitution matrix from AjPMatrixf
const AjPSeqCvtcvtInputConversion array for AjPMatrixf
ajint*compassOutputPath direction pointer array
AjBoolshowInputDisplay path matrix
float RETURNMaximum score

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
Output
path:(Output)path matrix
compass:(Output)Path direction pointer array
Returns
float:Maximum score

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 6.4.0

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,
      ajint* start1,
      ajint* start2
);

TypeNameRead/WriteDescription
const float*pathInputpath matrix
const ajint*compassInputPath direction pointer array
floatgapopenInputgap opening penalty
floatgapextendInputgap extension penalty
const AjPSeqaInputfirst sequence
const AjPSeqbInputsecond sequence
AjPStr*mOutputalignment for first sequence
AjPStr*nOutputalignment for second sequence
ajintlenaInputlength of first sequence
ajintlenbInputlength of second sequence
ajint*start1Outputstart of alignment in first sequence
ajint*start2Outputstart 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
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 6.4.0

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 ajint* compass
);

TypeNameRead/WriteDescription
const float*pathInputpath matrix
const AjPSeqaInputfirst sequence
const AjPSeqbInputsecond sequence
AjPStr*mOutputalignment for first sequence
AjPStr*nOutputalignment for second sequence
ajintlenaInputlength of first sequence
ajintlenbInputlength of second sequence
ajint*start1Outputstart of alignment in first sequence
ajint*start2Outputstart of alignment in second sequence
floatgapopenInputgap open penalty
floatgapextendInputgap extension penalty
const ajint*compassInputPath direction pointer array
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
compass:(Input)Path direction pointer array
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 6.4.0

Function embAlignWalkNWMatrixUsingCompass

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

Synopsis

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

TypeNameRead/WriteDescription
const char*pInputfirst sequence
const char*qInputsecond sequence
AjPStr*mOutputalignment for first sequence
AjPStr*nOutputalignment for second sequence
ajuintlenaInputlength of first sequence
ajuintlenbInputlength of second sequence
ajint*start1Outputstart of alignment in first sequence
ajint*start2Outputstart of alignment in second sequence
ajint const*compassInputPath direction pointer array
void RETURN

Input
p:(Input)first sequence
q:(Input)second sequence
lena:(Input)length of first sequence
lenb:(Input)length of second sequence
compass:(Input)Path direction pointer array
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 which was constructed using end gap penalties. 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 6.4.0

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
);

TypeNameRead/WriteDescription
AjPFileoutfModifyoutput stream
const char*aInputcomplete first sequence
const char*bInputcomplete second sequence
const AjPStrmInputWalk alignment for first sequence
const AjPStrnInputWalk alignment for second sequence
ajintstart1Inputstart of alignment in first sequence
ajintstart2Inputstart of alignment in second sequence
floatscoreInputalignment score from AlignScoreX
AjBoolmarkInputmark matches and conservatives
float* const*subInputsubstitution matrix
const AjPSeqCvtcvtInputconversion table for matrix
const char*nameaInputname of first sequence
const char*namebInputname of second sequence
ajintbeginaInputfirst sequence offset
ajintbeginbInputsecond 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embAlignUnused

Calls unused functions to avoid warning messages

Synopsis

Prototype
void embAlignUnused (
      void
);

TypeNameRead/WriteDescription
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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embAlignPathCalcSWFast

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

Nucleotides or proteins as needed.

Synopsis

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
);

TypeNameRead/WriteDescription
const char*aInputfirst sequence
const char*bInputsecond sequence
ajintlenaInputlength of first sequence
ajintlenbInputlength of second sequence
ajintoffsetInputDiagonal offset. Zero is start of a and b. Negative is position in a. Positive is position in b.
ajintpathwidthInputwidth of path matrix
floatgapopenInputgap opening penalty
floatgapextendInputgap extension penalty
float*pathOutputpath matrix of size (minlength*pathwidth + (pathwidth/2)*pathwidth) current value: (pathwidth*(lena+1)), lena==lenb
float* const*subInputsubstitution matrix from AjPMatrixf
const AjPSeqCvtcvtInputConversion array for AjPMatrixf
ajint*compassOutputPath direction pointer array or same dimensions as path
AjBoolshowInputDisplay path matrix
float RETURNMaximum score

Input
a:(Input)first sequence
b:(Input)second sequence
lena:(Input)length of first sequence
lenb:(Input)length of second sequence
offset:(Input)Diagonal offset. Zero is start of a and b. Negative is position in a. Positive is position in b.
pathwidth:(Input)width of path matrix
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
Output
path:(Output)path matrix of size (minlength*pathwidth + (pathwidth/2)*pathwidth) current value: (pathwidth*(lena+1)), lena==lenb
compass:(Output)Path direction pointer array or same dimensions as path
Returns
float:Maximum score

Description

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

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 6.4.0

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,
      ajint offset,
      ajint width,
      ajint* start1,
      ajint* start2
);

TypeNameRead/WriteDescription
const float*pathInputpath matrix
const ajint*compassInputPath direction pointer array
floatgapopenInputgap opening penalty
floatgapextendInputgap extension penalty
const AjPSeqaInputfirst sequence
const AjPSeqbInputsecond sequence
AjPStr*mOutputalignment for first sequence
AjPStr*nOutputalignment for second sequence
ajintlenaInputlength of first sequence
ajintlenbInputlength of second sequence
ajintoffsetInputDiagonal offset. Zero is start of a and b. Negative is position in a. Positive is position in b.
ajintwidthInputwidth of path matrix
ajint*start1Outputstart of alignment in first sequence
ajint*start2Outputstart 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
offset:(Input)Diagonal offset. Zero is start of a and b. Negative is position in a. Positive is position in b.
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 6.4.0

Function embAlignProfilePathCalc

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

Synopsis

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

TypeNameRead/WriteDescription
const char*aInputsequence
ajintproflenInputlength of profile
ajintseqlenInputlength of sequence
floatgapopenInputgap opening coefficient
floatgapextendInputgap extension coefficient
float*pathOutputpath matrix
float* const*pmatrixInputprofile matrix
ajint*compassOutputPath direction pointer array
AjBoolshowInputDisplay path matrix
float RETURNMaximum score

Input
a:(Input)sequence
proflen:(Input)length of profile
seqlen:(Input)length of sequence
gapopen:(Input)gap opening coefficient
gapextend:(Input)gap extension coefficient
pmatrix:(Input)profile matrix
show:(Input)Display path matrix
Output
path:(Output)path matrix
compass:(Output)Path direction pointer array
Returns
float:Maximum score

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 6.4.0

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* pmatrix,
      ajint* start1,
      ajint* start2
);

TypeNameRead/WriteDescription
const float*pathInputpath matrix
const ajint*compassInputPath direction pointer array
floatgapopenInputgap opening coeff
floatgapextendInputgap extension coeff
const AjPStrconsInputconsensus sequence
const AjPStrseqInputsecond sequence
AjPStr*mOutputalignment for consensus sequence
AjPStr*nOutputalignment for second sequence
ajintproflenInputlength of consensus sequence
ajintseqlenInputlength of test sequence
float* const*pmatrixInputprofile
ajint*start1Outputstart of alignment in consensus sequence
ajint*start2Outputstart 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
pmatrix:(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 6.4.0

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* pmatrix,
      const char* namea,
      const char* nameb,
      ajint begina,
      ajint beginb
);

TypeNameRead/WriteDescription
AjPFileoutfModifyoutput stream
const AjPStrmInputWalk alignment for first sequence
const AjPStrnInputWalk alignment for second sequence
ajintstart1Inputstart of alignment in first sequence
ajintstart2Inputstart of alignment in second sequence
floatscoreInputalignment score from AlignScoreX
AjBoolmarkInputmark matches and conservatives
float* const*pmatrixInputprofile
const char*nameaInputname of first sequence
const char*namebInputname of second sequence
ajintbeginaInputfirst sequence offset
ajintbeginbInputsecond 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
pmatrix:(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 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPStrmInputWalk alignment for first sequence
const AjPStrnInputWalk alignment for second sequence
float* const*subInputsubstitution matrix
const AjPSeqCvtcvtInputconversion table for matrix
ajintlenmInputlength of first sequence
ajintlennInputlength of second sequence
float*idOutput% identity
float*simOutput% similarity
float*idxOutput% identity wrt longest sequence
float*simxOutput% 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignalignModifyAlignment object
const AjPSeqseqaInputComplete first sequence
const AjPSeqseqbInputComplete second sequence
const AjPStrmInputWalk alignment for first sequence
const AjPStrnInputWalk alignment for second sequence
ajintstart1Inputstart of alignment in first sequence
ajintstart2Inputstart of alignment in second sequence
floatgapopenInputGap open penalty to report
floatgapextendInputGap extend penalty to report
floatscoreInputalignment score from AlignScoreX
AjPMatrixfmatrixModifyFloating point matrix
ajintoffset1Inputfirst sequence offset
ajintoffset2Inputsecond 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignalignModifyAlignment object
const AjPSeqseqaInputcomplete first sequence
const AjPSeqseqbInputcomplete second sequence
const AjPStrmInputWalk alignment for first sequence
const AjPStrnInputWalk alignment for second sequence
ajintstart1Inputstart of alignment in first sequence
ajintstart2Inputstart of alignment in second sequence
floatgapopenInputGap open penalty to report
floatgapextendInputGap extend penalty to report
floatscoreInputalignment score from AlignScoreX
AjPMatrixfmatrixModifyFloating point matrix
ajintoffset1Inputfirst sequence offset
ajintoffset2Inputsecond 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignalignModifyAlignment object
const AjPStrmInputWalk alignment for first sequence
const AjPStrnInputWalk alignment for second sequence
ajintstart1Inputstart of alignment in first sequence
ajintstart2Inputstart of alignment in second sequence
floatscoreInputalignment score from AlignScoreX
const char*nameaInputname of first sequence
const char*namebInputname 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

See Also

See other functions in this section

Availability

In release 6.4.0