ajseqtype.c

Function ajSeqTypeCheckS

Tests the type of a sequence is compatible with a defined type. If the type can have gaps, also tests for gap characters. Used for input validation - writes error message if the type check fails

Prototype

AjBool ajSeqTypeCheckS (
      AjPStr* pthys,
      const AjPStr type_name
);

Type Name Read/Write Description

AjPStr* pthys Modify Sequence string

const AjPStr type_name Input Sequence type

AjBool RETURN ajTrue if compatible.

Type	Name	Read/Write	Description
`AjPStr*`	`pthys`	Modify	Sequence string
`const AjPStr`	`type_name`	Input	Sequence type
`AjBool`		RETURN	ajTrue if compatible.

From EMBOSS 2.7.0

Function ajSeqTypeCheckIn

Tests the type of a sequence is compatible with a defined type. If the type can have gaps, also tests for gap characters. Used for input validation - writes error message if the type check fails

Prototype

AjBool ajSeqTypeCheckIn (
      AjPSeq thys,
      const AjPSeqin seqin
);

Type Name Read/Write Description

AjPSeq thys Modify Sequence object

const AjPSeqin seqin Input Sequence input object

AjBool RETURN ajTrue if compatible.

Type	Name	Read/Write	Description
`AjPSeq`	`thys`	Modify	Sequence object
`const AjPSeqin`	`seqin`	Input	Sequence input object
`AjBool`		RETURN	ajTrue if compatible.

From EMBOSS 2.7.0

Function ajSeqTypeNucS

Checks sequence type for nucleotide without gaps.

Prototype

char ajSeqTypeNucS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Function ajSeqTypeDnaS

Checks sequence type for DNA without gaps.

Prototype

char ajSeqTypeDnaS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Function ajSeqTypeRnaS

Checks sequence type for RNA without gaps

Prototype

char ajSeqTypeRnaS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Prototype

char ajSeqTypeGapdnaS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Prototype

char ajSeqTypeGaprnaS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Function ajSeqTypeGapnucS

Checks sequence type for nucleotide with gaps.

Prototype

char ajSeqTypeGapnucS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Function ajSeqTypeAnyprotS

Checks sequence type for anything that can be in a protein sequence

Prototype

char ajSeqTypeAnyprotS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Function ajSeqTypeProtS

Checks sequence type for anything that can be in a protein sequence

Prototype

char ajSeqTypeProtS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Function ajSeqTypeGapanyS

Checks sequence type for any sequence with gaps.

Prototype

char ajSeqTypeGapanyS (
      const AjPStr thys
);

Type Name Read/Write Description

const AjPStr thys Input Sequence string (unchanged at present)

char RETURN invalid character if any.

Type	Name	Read/Write	Description
`const AjPStr`	`thys`	Input	Sequence string (unchanged at present)
`char`		RETURN	invalid character if any.

From EMBOSS 2.7.0

Function ajSeqGap

Sets non-sequence characters to valid gap characters, and pads with extra gaps if necessary to a specified length

Prototype

void ajSeqGap (
      AjPSeq thys,
      char gapc,
      char padc
);

Type Name Read/Write Description

AjPSeq thys Modify Sequence

char gapc Input Standard gap character

char padc Input Gap character for ends of sequence

void RETURN

Type	Name	Read/Write	Description
`AjPSeq`	`thys`	Modify	Sequence
`char`	`gapc`	Input	Standard gap character
`char`	`padc`	Input	Gap character for ends of sequence
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqGapLen

Sets non-sequence characters to valid gap characters, and pads with extra gaps if necessary to a specified length

Prototype

void ajSeqGapLen (
      AjPSeq thys,
      char gapc,
      char padc,
      ajint ilen
);

Type Name Read/Write Description

AjPSeq thys Modify Sequence

char gapc Input Standard gap character

char padc Input Gap character for ends of sequence

ajint ilen Input Sequence length. Expanded if longer than current length

void RETURN

Type	Name	Read/Write	Description
`AjPSeq`	`thys`	Modify	Sequence
`char`	`gapc`	Input	Standard gap character
`char`	`padc`	Input	Gap character for ends of sequence
`ajint`	`ilen`	Input	Sequence length. Expanded if longer than current length
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqGapS

Sets non-sequence characters to valid gap characters, and pads with extra gaps if necessary to a specified length

Prototype

void ajSeqGapS (
      AjPStr* seq,
      char gapc
);

Type Name Read/Write Description

AjPStr* seq Modify Sequence

char gapc Input Standard gap character

void RETURN

Type	Name	Read/Write	Description
`AjPStr*`	`seq`	Modify	Sequence
`char`	`gapc`	Input	Standard gap character
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqSetNuc

Sets a sequence type to "nucleotide"

Prototype

void ajSeqSetNuc (
      AjPSeq thys
);

Type Name Read/Write Description

AjPSeq thys Modify Sequence object

void RETURN

Type	Name	Read/Write	Description
`AjPSeq`	`thys`	Modify	Sequence object
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqSetProt

Sets a sequence type to "protein"

Prototype

void ajSeqSetProt (
      AjPSeq thys
);

Type Name Read/Write Description

AjPSeq thys Modify Sequence object

void RETURN

Type	Name	Read/Write	Description
`AjPSeq`	`thys`	Modify	Sequence object
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqsetSetNuc

Sets a sequence set type to "nucleotide"

Prototype

void ajSeqsetSetNuc (
      AjPSeqset thys
);

Type Name Read/Write Description

AjPSeqset thys Modify Sequence set object

void RETURN

Type	Name	Read/Write	Description
`AjPSeqset`	`thys`	Modify	Sequence set object
`void`		RETURN

From EMBOSS 2.8.0

Function ajSeqsetSetProt

Sets a sequence set type to "protein"

Prototype

void ajSeqsetSetProt (
      AjPSeqset thys
);

Type Name Read/Write Description

AjPSeqset thys Modify Sequence set object

void RETURN

Type	Name	Read/Write	Description
`AjPSeqset`	`thys`	Modify	Sequence set object
`void`		RETURN

From EMBOSS 2.8.0

Function ajSeqType

Sets the type of a sequence if it has not yet been defined.

Prototype

void ajSeqType (
      AjPSeq thys
);

Type Name Read/Write Description

AjPSeq thys Modify Sequence object

void RETURN

Type	Name	Read/Write	Description
`AjPSeq`	`thys`	Modify	Sequence object
`void`		RETURN

From EMBOSS 1.0.0

Function ajSeqPrintType

Prints the seqType definitions. For EMBOSS entrails output

Prototype

void ajSeqPrintType (
      AjPFile outf,
      AjBool full
);

Type Name Read/Write Description

AjPFile outf Modify Output file

AjBool full Input Full output

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file
`AjBool`	`full`	Input	Full output
`void`		RETURN

From EMBOSS 2.5.0

Function ajSeqTypeIsProt

Returns ajTrue is sequence type can be a protein (or 'any')

Prototype

AjBool ajSeqTypeIsProt (
      const AjPStr type_name
);

Type Name Read/Write Description

const AjPStr type_name Input Sequence type

AjBool RETURN ajTrue if sequence can be protein

Type	Name	Read/Write	Description
`const AjPStr`	`type_name`	Input	Sequence type
`AjBool`		RETURN	ajTrue if sequence can be protein

From EMBOSS 2.7.0

Function ajSeqTypeIsNuc

Returns ajTrue is sequence type can be a nucleotide (or 'any')

Prototype

AjBool ajSeqTypeIsNuc (
      const AjPStr type_name
);

Type Name Read/Write Description

const AjPStr type_name Input Sequence type

AjBool RETURN ajTrue if sequence can be nucleotide

Type	Name	Read/Write	Description
`const AjPStr`	`type_name`	Input	Sequence type
`AjBool`		RETURN	ajTrue if sequence can be nucleotide

From EMBOSS 2.7.0

Function ajSeqTypeIsAny

Returns ajTrue is sequence type can be a protein or nucleotide

Prototype

AjBool ajSeqTypeIsAny (
      const AjPStr type_name
);

Type Name Read/Write Description

const AjPStr type_name Input Sequence type

AjBool RETURN ajTrue if sequence can be protein or nucleotide

Type	Name	Read/Write	Description
`const AjPStr`	`type_name`	Input	Sequence type
`AjBool`		RETURN	ajTrue if sequence can be protein or nucleotide

From EMBOSS 2.7.0

Function ajSeqTypeSummary

Returns ajTrue is sequence type can be a protein or nucleotide

Prototype

AjBool ajSeqTypeSummary (
      const AjPStr type_name,
      AjPStr* Ptype,
      AjBool* gaps
);

Type Name Read/Write Description

const AjPStr type_name Input Sequence type

AjPStr* Ptype Output Sequence type 'protein' 'nucleotide' or 'any'

AjBool* gaps Output True if gap characters are preserved

AjBool RETURN ajTrue if sequence can be protein or nucleotide

Type	Name	Read/Write	Description
`const AjPStr`	`type_name`	Input	Sequence type
`AjPStr*`	`Ptype`	Output	Sequence type 'protein' 'nucleotide' or 'any'
`AjBool*`	`gaps`	Output	True if gap characters are preserved
`AjBool`		RETURN	ajTrue if sequence can be protein or nucleotide

From EMBOSS 4.0.0

Function ajSeqTypeExit

Cleans up sequence type processing internal memory

Prototype

void ajSeqTypeExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 4.0.0

Function ajSeqTypeUnused

Dummy function to catch all unused functions defined in the ajseqtype source file.

Prototype

void ajSeqTypeUnused (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 4.1.0