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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`AjBool`		RETURN	ajTrue 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format input file

ajlong pconO Input PCON offset in an ABI file

ajlong numBases Input number of bases

float* Pqual Output array of confidence values

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format input file
`ajlong`	`pconO`	Input	PCON offset in an ABI file
`ajlong`	`numBases`	Input	number of bases
`float*`	`Pqual`	Output	array of confidence values
`AjBool`		RETURN	ajTrue 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format input file

ajlong baseO Input PBAS offset in an ABI file

ajlong numBases Input number of bases

AjPStr* nseq Output read sequence

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format input file
`ajlong`	`baseO`	Input	PBAS offset in an ABI file
`ajlong`	`numBases`	Input	number of bases
`AjPStr*`	`nseq`	Output	read sequence
`AjBool`		RETURN	ajTrue 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

AjPStr* machine Output machine name

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`AjPStr*`	`machine`	Output	machine name
`AjBool`		RETURN	ajTrue on success

From EMBOSS 1.8.0

Function ajSeqABIGetNData

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

Prototype

ajint ajSeqABIGetNData (
      AjPFile fp
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajint RETURN Number of data points in file

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajint`		RETURN	Number 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajint RETURN Number of bases in file

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajint`		RETURN	Number 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

const ajlong* Offset Input data offset in ABI file

ajlong numPoints Input number of data points

AjPInt2d trace Output (4xnumPoints) array of trace data

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`const ajlong*`	`Offset`	Input	data offset in ABI file
`ajlong`	`numPoints`	Input	number of data points
`AjPInt2d`	`trace`	Output	(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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajlong numBases Input number of bases to be read

AjPShort* basePositions Output base positions output

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajlong`	`numBases`	Input	number of bases to be read
`AjPShort*`	`basePositions`	Output	base 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajlong fwo_ Input field order

ajshort* sigC Output average signal strength for C

ajshort* sigA Output average signal strength for A

ajshort* sigG Output average signal strength for G

ajshort* sigT Output average signal strength for T

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajlong`	`fwo_`	Input	field order
`ajshort*`	`sigC`	Output	average signal strength for C
`ajshort*`	`sigA`	Output	average signal strength for A
`ajshort*`	`sigG`	Output	average signal strength for G
`ajshort*`	`sigT`	Output	average 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

float RETURN base spacing

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`float`		RETURN	base spacing

From EMBOSS 1.8.0

Function ajSeqABIGetBaseOffset

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

Prototype

ajint ajSeqABIGetBaseOffset (
      AjPFile fp
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajint RETURN 'PBAS' tag offset in an ABI file

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajint RETURN base position offset in an ABI file

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajint`		RETURN	base 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajint RETURN 'PCON' tag offset in an ABI file

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajint RETURN field order

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajint`		RETURN	field order

From EMBOSS 1.8.0

Function ajSeqABIGetPrimerOffset

Routine to get the primer offset in an ABI file.

Prototype

ajint ajSeqABIGetPrimerOffset (
      AjPFile fp
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajint RETURN primer offset

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajint`		RETURN	primer offset

From EMBOSS 1.8.0

Function ajSeqABIGetPrimerPosition

Routine to get the primer position in an ABI file.

Prototype

ajint ajSeqABIGetPrimerPosition (
      AjPFile fp
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajint RETURN primer position

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajint`		RETURN	primer 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

ajlong* Offset Output trace data offset, used in ajSeqABIGetData

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`ajlong*`	`Offset`	Output	trace data offset, used in ajSeqABIGetData
`AjBool`		RETURN	ajTrue 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
);

Type Name Read/Write Description

AjPFile fp Modify ABI format file

AjPStr* sample Output sample name

AjBool RETURN true if read successfully

Type	Name	Read/Write	Description
`AjPFile`	`fp`	Modify	ABI format file
`AjPStr*`	`sample`	Output	sample name
`AjBool`		RETURN	true if read successfully

From EMBOSS 2.0.0