ajseqabi.c


Function ajSeqABITest

Test file type is ABI format - look for 'ABIF' flag (which may be in one of 2 places).

Prototype

AjBool ajSeqABITest (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
AjBool RETURNajTrue on success

From EMBOSS 1.8.0


Function ajSeqABIReadConfid

Read in confidence values from an ABI trace file.

Prototype

AjBool ajSeqABIReadConfid (
      AjPFile fp,
      ajlong pconO,
      ajlong numBases,
      float* Pqual
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format input file
ajlongpconOInputPCON offset in an ABI file
ajlongnumBasesInputnumber of bases
float*PqualOutputarray of confidence values
AjBool RETURNajTrue on success

From EMBOSS 6.3.0


Function ajSeqABIReadSeq

Read in a sequence from an ABI trace file.

Prototype

AjBool ajSeqABIReadSeq (
      AjPFile fp,
      ajlong baseO,
      ajlong numBases,
      AjPStr* nseq
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format input file
ajlongbaseOInputPBAS offset in an ABI file
ajlongnumBasesInputnumber of bases
AjPStr*nseqOutputread sequence
AjBool RETURNajTrue on success

From EMBOSS 1.8.0


Function ajSeqABIMachineName

Get the name of the machine used to obtain an ABI trace file.

Prototype

AjBool ajSeqABIMachineName (
      AjPFile fp,
      AjPStr* machine
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
AjPStr*machineOutputmachine name
AjBool RETURNajTrue on success

From EMBOSS 1.8.0


Function ajSeqABIGetNData

Find 'DATA' tag and get the number of data points.

Prototype

ajint ajSeqABIGetNData (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNNumber of data points in file

From EMBOSS 1.8.0


Function ajSeqABIGetNBase

Find the 'PBAS' tag in an ABI trace file and get the number of bases.

Prototype

ajint ajSeqABIGetNBase (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNNumber of bases in file

From EMBOSS 1.8.0


Function ajSeqABIGetData

Read in the processed trace data from an ABI file.

Prototype

void ajSeqABIGetData (
      AjPFile fp,
      const ajlong* Offset,
      ajlong numPoints,
      AjPInt2d trace
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
const ajlong*OffsetInputdata offset in ABI file
ajlongnumPointsInputnumber of data points
AjPInt2dtraceOutput(4xnumPoints) array of trace data
void RETURN

From EMBOSS 1.8.0


Function ajSeqABIGetBasePosition

Read in the base positions from an ABI file.

Prototype

void ajSeqABIGetBasePosition (
      AjPFile fp,
      ajlong numBases,
      AjPShort* basePositions
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajlongnumBasesInputnumber of bases to be read
AjPShort*basePositionsOutputbase positions output
void RETURN

From EMBOSS 1.8.0


Function ajSeqABIGetSignal

Read in the signal strength information from an ABI file.

Prototype

void ajSeqABIGetSignal (
      AjPFile fp,
      ajlong fwo_,
      ajshort* sigC,
      ajshort* sigA,
      ajshort* sigG,
      ajshort* sigT
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajlongfwo_Inputfield order
ajshort*sigCOutputaverage signal strength for C
ajshort*sigAOutputaverage signal strength for A
ajshort*sigGOutputaverage signal strength for G
ajshort*sigTOutputaverage signal strength for T
void RETURN

From EMBOSS 1.8.0


Function ajSeqABIGetBaseSpace

Read in the base spacing from an ABI file.

Prototype

float ajSeqABIGetBaseSpace (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
float RETURNbase spacing

From EMBOSS 1.8.0


Function ajSeqABIGetBaseOffset

Routine to get the 'PBAS' tag offset in an ABI file.

Prototype

ajint ajSeqABIGetBaseOffset (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURN'PBAS' tag offset in an ABI file

From EMBOSS 1.8.0


Function ajSeqABIGetBasePosOffset

Routine to get the 'PLOC', base position, tag offset in an ABI file

Prototype

ajint ajSeqABIGetBasePosOffset (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNbase position offset in an ABI file

From EMBOSS 1.8.0


Function ajSeqABIGetConfidOffset

Routine to get the 'PCON' confidence tag offset in an ABI file.

Prototype

ajint ajSeqABIGetConfidOffset (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURN'PCON' tag offset in an ABI file

From EMBOSS 6.3.0


Function ajSeqABIGetFWO

Routine to get the "FWO" tag, field order ("GATC"), tag.

Prototype

ajint ajSeqABIGetFWO (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNfield order

From EMBOSS 1.8.0


Function ajSeqABIGetPrimerOffset

Routine to get the primer offset in an ABI file.

Prototype

ajint ajSeqABIGetPrimerOffset (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNprimer offset

From EMBOSS 1.8.0


Function ajSeqABIGetPrimerPosition

Routine to get the primer position in an ABI file.

Prototype

ajint ajSeqABIGetPrimerPosition (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNprimer position

From EMBOSS 1.8.0


Function ajSeqABIGetTraceOffset

Get the processed trace data ('DATA' tag) offset in an ABI file.

Prototype

AjBool ajSeqABIGetTraceOffset (
      AjPFile fp,
      ajlong* Offset
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajlong*OffsetOutputtrace data offset, used in ajSeqABIGetData
AjBool RETURNajTrue on success

From EMBOSS 1.8.0


Function ajSeqABISampleName

Get the sample name from an ABI trace file.

Prototype

AjBool ajSeqABISampleName (
      AjPFile fp,
      AjPStr* sample
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
AjPStr*sampleOutputsample name
AjBool RETURNtrue if read successfully

From EMBOSS 2.0.0