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
);

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

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
);

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

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
);

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

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
);

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

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
);

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

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
);

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

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
);

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

From EMBOSS 1.0.0


Function embAlignUnused

Calls unused functions to avoid warning messages

Prototype

void embAlignUnused (
      void
);

TypeNameRead/WriteDescription
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
);

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

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
);

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

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
);

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

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
);

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

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
);

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

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
);

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

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
);

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

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
);

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

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
);

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

From EMBOSS 2.3.0