ajseqabi.c

Function ajSeqABITest

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

Synopsis

Prototype
AjBool ajSeqABITest (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
AjBool RETURNajTrue on success

Input & Output
fp:(Modify)ABI format file
Returns
AjBool:ajTrue on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIReadConfid

Read in confidence values from an ABI trace file.

Synopsis

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

Input
pconO:(Input)PCON offset in an ABI file
numBases:(Input)number of bases
Output
Pqual:(Output)array of confidence values
Input & Output
fp:(Modify)ABI format input file
Returns
AjBool:ajTrue on success

Description

Read in confidence values from an ABI trace file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIReadSeq

Read in a sequence from an ABI trace file.

Synopsis

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

Input
baseO:(Input)PBAS offset in an ABI file
numBases:(Input)number of bases
Output
nseq:(Output)read sequence
Input & Output
fp:(Modify)ABI format input file
Returns
AjBool:ajTrue on success

Description

Read in a sequence from an ABI trace file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIMachineName

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

Synopsis

Prototype
AjBool ajSeqABIMachineName (
      AjPFile fp,
      AjPStr* machine
);

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

Output
machine:(Output)machine name
Input & Output
fp:(Modify)ABI format file
Returns
AjBool:ajTrue on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetNData

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

Synopsis

Prototype
ajint ajSeqABIGetNData (
      AjPFile fp
);

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

Input & Output
fp:(Modify)ABI format file
Returns
ajint:Number of data points in file

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetNBase

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

Synopsis

Prototype
ajint ajSeqABIGetNBase (
      AjPFile fp
);

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

Input & Output
fp:(Modify)ABI format file
Returns
ajint:Number of bases in file

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetData

Read in the processed trace data from an ABI file.

Synopsis

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

Input
Offset:(Input)data offset in ABI file
numPoints:(Input)number of data points
Output
trace:(Output)(4xnumPoints) array of trace data
Input & Output
fp:(Modify)ABI format file
Returns
void:No return value

Description

Read in the processed trace data from an ABI file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetBasePosition

Read in the base positions from an ABI file.

Synopsis

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

Input
numBases:(Input)number of bases to be read
Output
basePositions:(Output)base positions output
Input & Output
fp:(Modify)ABI format file
Returns
void:No return value

Description

Read in the base positions from an ABI file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetSignal

Read in the signal strength information from an ABI file.

Synopsis

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

Input
fwo_:(Input)field order
Output
sigC:(Output)average signal strength for C
sigA:(Output)average signal strength for A
sigG:(Output)average signal strength for G
sigT:(Output)average signal strength for T
Input & Output
fp:(Modify)ABI format file
Returns
void:No return value

Description

Read in the signal strength information from an ABI file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetBaseSpace

Read in the base spacing from an ABI file.

Synopsis

Prototype
float ajSeqABIGetBaseSpace (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
float RETURNbase spacing

Input & Output
fp:(Modify)ABI format file
Returns
float:base spacing

Description

Read in the base spacing from an ABI file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetBaseOffset

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

Synopsis

Prototype
ajint ajSeqABIGetBaseOffset (
      AjPFile fp
);

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

Input & Output
fp:(Modify)ABI format file
Returns
ajint:'PBAS' tag offset in an ABI file

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetBasePosOffset

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

Synopsis

Prototype
ajint ajSeqABIGetBasePosOffset (
      AjPFile fp
);

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

Input & Output
fp:(Modify)ABI format file
Returns
ajint:base position offset in an ABI file

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetConfidOffset

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

Synopsis

Prototype
ajint ajSeqABIGetConfidOffset (
      AjPFile fp
);

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

Input & Output
fp:(Modify)ABI format file
Returns
ajint:'PCON' tag offset in an ABI file

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetFWO

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

Synopsis

Prototype
ajint ajSeqABIGetFWO (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNfield order

Input & Output
fp:(Modify)ABI format file
Returns
ajint:field order

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetPrimerOffset

Routine to get the primer offset in an ABI file.

Synopsis

Prototype
ajint ajSeqABIGetPrimerOffset (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNprimer offset

Input & Output
fp:(Modify)ABI format file
Returns
ajint:primer offset

Description

Routine to get the primer offset in an ABI file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetPrimerPosition

Routine to get the primer position in an ABI file.

Synopsis

Prototype
ajint ajSeqABIGetPrimerPosition (
      AjPFile fp
);

TypeNameRead/WriteDescription
AjPFilefpModifyABI format file
ajint RETURNprimer position

Input & Output
fp:(Modify)ABI format file
Returns
ajint:primer position

Description

Routine to get the primer position in an ABI file.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABIGetTraceOffset

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

Synopsis

Prototype
AjBool ajSeqABIGetTraceOffset (
      AjPFile fp,
      ajlong* Offset
);

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

Output
Offset:(Output)trace data offset, used in ajSeqABIGetData
Input & Output
fp:(Modify)ABI format file
Returns
AjBool:ajTrue on success

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajSeqABISampleName

Get the sample name from an ABI trace file.

Synopsis

Prototype
AjBool ajSeqABISampleName (
      AjPFile fp,
      AjPStr* sample
);

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

Output
sample:(Output)sample name
Input & Output
fp:(Modify)ABI format file
Returns
AjBool:true if read successfully

Description

Get the sample name from an ABI trace file.

See Also

See other functions in this section

Availability

In release 6.4.0