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

Synopsis

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.

Input

type_name:

(Input)

Sequence type

Input & Output

pthys:

(Modify)

Sequence string

Returns

AjBool:

ajTrue if compatible.

Description

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

Availability

In release 6.4.0

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

Synopsis

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.

Input

seqin:

(Input)

Sequence input object

Input & Output

thys:

(Modify)

Sequence object

Returns

AjBool:

ajTrue if compatible.

Description

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

Availability

In release 6.4.0

Function ajSeqTypeNucS

Checks sequence type for nucleotide without gaps.

RNA and DNA codes are accepted as is.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

Checks sequence type for nucleotide without gaps.

RNA and DNA codes are accepted as is.

Availability

In release 6.4.0

Function ajSeqTypeDnaS

Checks sequence type for DNA without gaps.

RNA and DNA codes are accepted as is.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

Checks sequence type for DNA without gaps.

RNA and DNA codes are accepted as is.

Availability

In release 6.4.0

Function ajSeqTypeRnaS

Checks sequence type for RNA without gaps

RNA codes are accepted as is.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

Checks sequence type for RNA without gaps

RNA codes are accepted as is.

Availability

In release 6.4.0

Function ajSeqTypeGapdnaS

Checks sequence type for Dna with gaps

DNA codes are accepted as is.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

Checks sequence type for Dna with gaps

DNA codes are accepted as is.

Availability

In release 6.4.0

Function ajSeqTypeGaprnaS

Checks sequence type for RNA with gaps

RNA codes are accepted as is.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

Checks sequence type for RNA with gaps

RNA codes are accepted as is.

Availability

In release 6.4.0

Function ajSeqTypeGapnucS

Checks sequence type for nucleotide with gaps.

RNA and DNA codes are accepted as is.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

Checks sequence type for nucleotide with gaps.

RNA and DNA codes are accepted as is.

Availability

In release 6.4.0

Function ajSeqTypeAnyprotS

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

Stop codes are replaced with gaps.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

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

Stop codes are replaced with gaps.

Availability

In release 6.4.0

Function ajSeqTypeProtS

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

Stop codes are replaced with gaps.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

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

Stop codes are replaced with gaps.

Availability

In release 6.4.0

Function ajSeqTypeGapanyS

Checks sequence type for any sequence with gaps.

Stops ('*') are allowed so this could be a 3 frame translation of DNA.

Synopsis

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.

Input

thys:

(Input)

Sequence string (unchanged at present)

Returns

char:

invalid character if any.

Description

Checks sequence type for any sequence with gaps.

Stops ('*') are allowed so this could be a 3 frame translation of DNA.

Availability

In release 6.4.0

Function ajSeqGap

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

Synopsis

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

Input

gapc:	(Input)	Standard gap character
padc:	(Input)	Gap character for ends of sequence

Input & Output

thys:

(Modify)

Sequence

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Function ajSeqGapLen

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

Synopsis

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

Input

gapc:	(Input)	Standard gap character
padc:	(Input)	Gap character for ends of sequence
ilen:	(Input)	Sequence length. Expanded if longer than current length

Input & Output

thys:

(Modify)

Sequence

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Function ajSeqGapS

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

Synopsis

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

Input

gapc:

(Input)

Standard gap character

Input & Output

seq:

(Modify)

Sequence

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Function ajSeqSetNuc

Sets a sequence type to "nucleotide"

Synopsis

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

Input & Output

thys:

(Modify)

Sequence object

Returns

void:

No return value

Description

Sets a sequence type to "nucleotide"

Availability

In release 6.4.0

Function ajSeqSetProt

Sets a sequence type to "protein"

Synopsis

Prototype

void ajSeqSetProt (
      AjPSeq thys
);

Type Name Read/Write Description

AjPSeq thys Modify Sequence object

void RETURN

Input & Output

thys:

(Modify)

Sequence object

Returns

void:

No return value

Description

Sets a sequence type to "protein"

Availability

In release 6.4.0

Function ajSeqsetSetNuc

Sets a sequence set type to "nucleotide"

Synopsis

Prototype

void ajSeqsetSetNuc (
      AjPSeqset thys
);

Type Name Read/Write Description

AjPSeqset thys Modify Sequence set object

void RETURN

Input & Output

thys:

(Modify)

Sequence set object

Returns

void:

No return value

Description

Sets a sequence set type to "nucleotide"

Availability

In release 6.4.0

Function ajSeqsetSetProt

Sets a sequence set type to "protein"

Synopsis

Prototype

void ajSeqsetSetProt (
      AjPSeqset thys
);

Type Name Read/Write Description

AjPSeqset thys Modify Sequence set object

void RETURN

Input & Output

thys:

(Modify)

Sequence set object

Returns

void:

No return value

Description

Sets a sequence set type to "protein"

Availability

In release 6.4.0

Function ajSeqType

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

Synopsis

Prototype

void ajSeqType (
      AjPSeq thys
);

Type Name Read/Write Description

AjPSeq thys Modify Sequence object

void RETURN

Input & Output

thys:

(Modify)

Sequence object

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

Function ajSeqPrintType

Prints the seqType definitions. For EMBOSS entrails output

Synopsis

Prototype

void ajSeqPrintType (
      AjPFile outf,
      AjBool full
);

Type Name Read/Write Description

AjPFile outf Modify Output file

AjBool full Input Full output

void RETURN

Input

full:

(Input)

Full output

Input & Output

outf:

(Modify)

Output file

Returns

void:

No return value

Description

Prints the seqType definitions. For EMBOSS entrails output

Availability

In release 6.4.0

Function ajSeqTypeIsProt

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

Synopsis

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

Input

type_name:

(Input)

Sequence type

Returns

AjBool:

ajTrue if sequence can be protein

Description

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

Availability

In release 6.4.0

Function ajSeqTypeIsNuc

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

Synopsis

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

Input

type_name:

(Input)

Sequence type

Returns

AjBool:

ajTrue if sequence can be nucleotide

Description

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

Availability

In release 6.4.0

Function ajSeqTypeIsAny

Returns ajTrue is sequence type can be a protein or nucleotide

Synopsis

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

Input

type_name:

(Input)

Sequence type

Returns

AjBool:

ajTrue if sequence can be protein or nucleotide

Description

Returns ajTrue is sequence type can be a protein or nucleotide

Availability

In release 6.4.0

Function ajSeqTypeSummary

Returns ajTrue is sequence type can be a protein or nucleotide

Synopsis

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

Input

type_name:

(Input)

Sequence type

Output

Ptype:	(Output)	Sequence type 'protein' 'nucleotide' or 'any'
gaps:	(Output)	True if gap characters are preserved

Returns

AjBool:

ajTrue if sequence can be protein or nucleotide

Description

Returns ajTrue is sequence type can be a protein or nucleotide

Availability

In release 6.4.0

Function ajSeqTypeExit

Cleans up sequence type processing internal memory

Synopsis

Prototype

void ajSeqTypeExit (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

Cleans up sequence type processing internal memory

Availability

In release 6.4.0

Function ajSeqTypeUnused

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

Synopsis

Prototype

void ajSeqTypeUnused (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

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

Availability

In release 6.4.0

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

ajseqtype.c

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